[med-svn] [python-cobra] 02/10: Imported Upstream version 0.4.0b1
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jul 10 04:26:42 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-cobra.
commit 515cf06a2d8a118f4a25650056d2a0e05d1dd735
Author: عفيف الغراوي <afif at ghraoui.name>
Date: Thu Jul 9 18:05:38 2015 -0700
Imported Upstream version 0.4.0b1
---
.coveragerc | 54 +
.travis.yml | 7 +-
INSTALL.md | 31 +-
LICENSE | 1344 +-
README.md | 45 +-
appveyor.yml | 46 +
appveyor/install.ps1 | 85 +
appveyor/run_with_compiler.cmd | 47 +
cobra/VERSION | 2 +-
cobra/__init__.py | 2 +-
cobra/core/ArrayBasedModel.py | 4 +-
cobra/core/DictList.py | 10 +-
cobra/core/Gene.py | 143 +-
cobra/core/Metabolite.py | 183 +-
cobra/core/Model.py | 106 +-
cobra/core/Object.py | 2 +-
cobra/core/Reaction.py | 134 +-
cobra/core/Species.py | 46 +-
cobra/core/__init__.py | 1 -
cobra/external/__init__.py | 0
cobra/external/ppmap.py | 151 -
cobra/external/six.py | 747 -
cobra/flux_analysis/__init__.py | 12 +-
cobra/flux_analysis/deletion_worker.py | 2 +-
cobra/flux_analysis/double_deletion.py | 890 +-
cobra/flux_analysis/essentiality.py | 31 +-
cobra/flux_analysis/gapfilling.py | 165 +
cobra/flux_analysis/loopless.py | 2 +-
cobra/flux_analysis/moma.py | 353 +-
cobra/flux_analysis/objective.py | 45 -
cobra/flux_analysis/parsimonious.py | 2 -
cobra/flux_analysis/single_deletion.py | 416 +-
cobra/flux_analysis/variability.py | 60 +-
cobra/io/__init__.py | 4 +-
cobra/io/json.py | 8 +-
cobra/io/mat.py | 56 +-
cobra/io/sbml.py | 29 +-
cobra/io/sbml3.py | 429 +
cobra/manipulation/__init__.py | 4 +-
cobra/manipulation/delete.py | 124 +-
cobra/manipulation/modify.py | 47 +
cobra/mlab/__init__.py | 15 -
cobra/mlab/matlab_scripts/cell_to_string.m | 3 -
cobra/mlab/matlab_scripts/create_container.m | 2 -
cobra/mlab/matlab_scripts/load_mat.m | 3 -
cobra/mlab/matlab_scripts/save_from_python.m | 3 -
cobra/mlab/mlab.py | 405 -
cobra/oven/aliebrahim/gapAnalysis.py | 209 -
cobra/solvers/__init__.py | 4 +-
cobra/solvers/cglpk.pyx | 72 +-
cobra/solvers/coin.py | 136 +
cobra/solvers/cplex_solver.py | 20 +-
cobra/solvers/esolver.py | 2 +-
cobra/solvers/glpk.pxd | 11 +
cobra/solvers/gurobi_solver.py | 2 +-
cobra/solvers/mosek.py | 4 +-
cobra/test/__init__.py | 87 +-
cobra/test/data/iJO1366.json | 1 -
cobra/test/data/iJO1366.mat | Bin 1549400 -> 0 bytes
cobra/test/data/iJO1366.xml | 124980 ++++++------------
cobra/test/data/mini.json | 1 +
cobra/test/data/mini.mat | Bin 0 -> 14752 bytes
cobra/test/data/mini.pickle | Bin 0 -> 10952 bytes
cobra/test/data/mini_cobra.xml | 634 +
cobra/test/data/mini_fbc1.xml | 561 +
cobra/test/data/mini_fbc2.xml | 337 +
cobra/test/data/textbook.xml | 1562 +
cobra/test/data/update_pickles.py | 2 +-
cobra/test/flux_analysis.py | 361 +-
cobra/test/io_tests.py | 54 +-
cobra/test/solvers.py | 23 +-
cobra/test/unit_tests.py | 129 +-
cobra/topology/reporter_metabolites.py | 29 -
documentation_builder/autodoc.bat | 4 -
documentation_builder/autodoc.sh | 5 +-
documentation_builder/building_model.ipynb | 521 +-
documentation_builder/building_model.rst | 77 +-
documentation_builder/cobra.flux_analysis.rst | 16 +-
documentation_builder/cobra.io.rst | 8 +
documentation_builder/cobra.mlab.rst | 22 -
documentation_builder/cobra.rst | 2 -
documentation_builder/cobra.solvers.rst | 54 -
documentation_builder/conf.py | 16 +-
documentation_builder/deletions.ipynb | 1223 +-
documentation_builder/deletions.rst | 703 +-
documentation_builder/faq.ipynb | 634 +-
documentation_builder/faq.rst | 7 +
documentation_builder/gapfilling.ipynb | 185 +
documentation_builder/gapfilling.rst | 104 +
documentation_builder/getting_started.ipynb | 1715 +-
documentation_builder/getting_started.rst | 117 +-
documentation_builder/index.rst | 7 +
documentation_builder/io.ipynb | 592 +-
documentation_builder/io.rst | 146 +-
documentation_builder/loopless.ipynb | 521 +-
documentation_builder/loopless.rst | 23 +-
.../loopless_files/loopless_3_0.png | Bin 0 -> 10699 bytes
.../loopless_files/loopless_4_0.png | Bin 10776 -> 0 bytes
documentation_builder/milp.ipynb | 809 +-
documentation_builder/milp.rst | 25 +-
documentation_builder/phenotype_phase_plane.ipynb | 356 +-
documentation_builder/phenotype_phase_plane.rst | 56 +-
.../phenotype_phase_plane_3_0.png | Bin 0 -> 94579 bytes
.../phenotype_phase_plane_5_0.png | Bin 91579 -> 106030 bytes
.../phenotype_phase_plane_5_1.png | Bin 0 -> 97694 bytes
.../phenotype_phase_plane_7_0.png | Bin 101786 -> 68889 bytes
.../phenotype_phase_plane_7_1.png | Bin 93758 -> 0 bytes
.../phenotype_phase_plane_9_0.png | Bin 64219 -> 0 bytes
documentation_builder/pymatbridge.ipynb | 235 +
documentation_builder/pymatbridge.rst | 124 +
documentation_builder/pyscript.tpl | 29 -
documentation_builder/qp.ipynb | 586 +-
documentation_builder/qp.rst | 15 +-
documentation_builder/qp_files/qp_12_0.png | Bin 0 -> 14601 bytes
documentation_builder/qp_files/qp_14_0.png | Bin 16893 -> 0 bytes
documentation_builder/qp_files/qp_1_0.png | Bin 0 -> 18553 bytes
documentation_builder/qp_files/qp_3_0.png | Bin 21854 -> 0 bytes
documentation_builder/simulating.ipynb | 797 +-
documentation_builder/simulating.rst | 308 +-
documentation_builder/solvers.ipynb | 723 +
documentation_builder/solvers.rst | 451 +
examples/building_model.py | 126 -
examples/deletions.py | 92 -
examples/getting_started.py | 250 -
examples/io.py | 117 -
examples/loopless.py | 141 -
examples/milp.py | 217 -
examples/phenotype_phase_plane.py | 53 -
examples/qp.py | 133 -
examples/simulating.py | 81 -
ez_setup.py | 185 +-
setup.py | 97 +-
132 files changed, 53056 insertions(+), 95173 deletions(-)
diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..05ff111
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,54 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = cobra
+omit =
+ cobra/solvers/*
+ cobra/test/data/*
+ cobra/test_all.py
+ cobra/version.py
+ cobra/oven/*
+ # deprecated code
+ cobra/core/Formula.py
+ # can not be run with free solver
+ cobra/flux_analysis/moma.py
+
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+ # Have to re-enable the standard pragma
+ pragma: no cover
+
+ # Don't complain about missing debug-only code:
+ def __repr__
+ if self\.debug
+ print
+
+ # Don't complain about missing legacy code
+ _legacy
+
+ # Don't complain if tests don't hit defensive assertion code:
+ raise AssertionError
+ raise NotImplementedError
+
+ # Don't complain about code for importing
+ import
+ except ImportError
+
+ # Don't complain if non-runnable code isn't run:
+ if 0:
+ if __name__ == .__main__.:
+
+ # Don't complain about warnings
+ warn
+
+partial_branches:
+ pragma: no branch
+ # Don't complain about missing legacy code
+ _legacy
+
+ignore_errors = True
+
+[html]
+directory = coverage
diff --git a/.travis.yml b/.travis.yml
index 12a5f67..bda84cc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,12 +6,15 @@ python:
# command to install dependencies
before_install:
- export PIP_OPTS="-f https://opencobra.github.io/pypi_cobrapy_travis --no-index"
- - if [[ $TRAVIS_PYTHON_VERSION == 2* ]]; then pip install glpk $PIP_OPTS; fi
+ - if [[ $TRAVIS_PYTHON_VERSION == 2* ]]; then pip install glpk cylp $PIP_OPTS; fi
- pip install python-libsbml-experimental cython numpy scipy $PIP_OPTS
- wget https://opencobra.github.io/pypi_cobrapy_travis/travis_test_dependencies.zip # esolver, and glpk
- unzip travis_test_dependencies.zip
- export PATH=$PATH:$PWD
+ - pip install coveralls
install:
- python setup.py develop
# # command to run tests
-script: python setup.py test
+script: coverage run --source=cobra setup.py test
+after_success:
+ - coveralls
diff --git a/INSTALL.md b/INSTALL.md
index 5fbbda3..5c3f978 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -30,8 +30,10 @@ cobrapy, they are not explicitly supported at this time.
3. In a terminal, run ```sudo pip install cobra```
### Microsoft Windows
-Download and install the appropriate 32 bit or 64 bit installer,
-both of which can be downloaded from the [python package
+If you use pip in Windows, you can simply do ```pip install cobra```.
+
+To install without pip, you will need to download and use the appropriate
+installer for your version of python from the [python package
index](https://pypi.python.org/pypi/cobra/).
@@ -70,21 +72,22 @@ cobrapy. In addition, cobrapy currently supports these linear programming
solvers:
* ILOG/CPLEX (available with
- [Academic](https://www.ibm.com/developerworks/university/academicinitiative/)
- and
- [Commercial](http://www.ibm.com/software/integration/optimization/cplex-optimizer/)
- licenses).
+ [Academic](https://www.ibm.com/developerworks/university/academicinitiative/)
+ and
+ [Commercial](http://www.ibm.com/software/integration/optimization/cplex-optimizer/)
+ licenses).
* [gurobi](http://gurobi.com)
* [QSopt_ex esolver](http://www.dii.uchile.cl/~daespino/ESolver_doc/main.html)
* [MOSEK](http://www.mosek.com/)
-
-ILOG/CPLEX, MOSEK, and Gurobi are commercial software packages that currently
-provide free licenses for academics and support both linear and quadratic
-programming. GLPK is an opensource linear programming solver; however, it
-does not support quadratic programming and is not as robust as the
-commercial solvers when it comes to mixed-integer linear programming.
-QSopt_ex esolver is also open source, and can solve linear programs
-using rational operations, giving exact solutions.
+ * [coin-or clp and cbc](http://coin-or.org/) through
+ [cylp](https://github.com/coin-or/CyLP).
+
+ILOG/CPLEX, MOSEK, and Gurobi are commercial software packages that currently
+provide free licenses for academics and support both linear and quadratic
+programming. GLPK and clp are open source linear programming solvers; however,
+they may not be as robsut as the commercial solvers for mixed-integer and
+quadratic programming. QSopt_ex esolver is also open source, and can solve
+linear programs using rational operations, giving exact solutions.
# Testing your installation
diff --git a/LICENSE b/LICENSE
index 94a9ed0..99cec1b 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,674 +1,740 @@
GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
+ Version 2, June 1991
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
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-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
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- 12. No Surrender of Others' Freedom.
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+ 7. If, as a consequence of a court judgment or allegation of patent
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- 13. Use with the GNU Affero General Public License.
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+This section is intended to make thoroughly clear what is believed to
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+
+ 8. If the distribution and/or use of the Program is restricted in
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+original copyright holder who places the Program under this License
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+
+ 9. The Free Software Foundation may publish revised and/or new versions
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be similar in spirit to the present version, but may differ in detail to
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- Each version is given a distinguishing version number. If the
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- 15. Disclaimer of Warranty.
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- 16. Limitation of Liability.
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- 17. Interpretation of Sections 15 and 16.
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- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
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+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
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+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
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END OF TERMS AND CONDITIONS
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+----------------------------------------------------------------------------
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
-Also add information on how to contact you by electronic and paper mail.
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
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+ END OF TERMS AND CONDITIONS
diff --git a/README.md b/README.md
index dfe1848..b3575bd 100644
--- a/README.md
+++ b/README.md
@@ -1,28 +1,41 @@
cobrapy
=======
+COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used
+for genome-scale modeling of metabolic networks in both prokaryotes and
+eukaryotes. COBRApy is a constraint-based modeling package that is designed to
+accomodate the biological complexity of the next generation of COBRA models and
+provides access to commonly used COBRA methods, such as flux balance analysis,
+flux variability analysis, and gene deletion analyses.
+
To install, please follow the [instructions](INSTALL.md).
-The documentation is browseable online at [readthedocs](https://cobrapy.readthedocs.org/en/latest/)
-and can also be [downloaded](https://readthedocs.org/projects/cobrapy/downloads/).
+The documentation is browseable online at
+[readthedocs](https://cobrapy.readthedocs.org/en/latest/)
+and can also be
+[downloaded](https://readthedocs.org/projects/cobrapy/downloads/).
-Please use the [Google Group](http://groups.google.com/group/cobra-pie) for help. More information about
-opencobra is available at the [website](http://opencobra.github.io/).
+Please use the [Google Group](http://groups.google.com/group/cobra-pie) for
+help. More information about opencobra is available at the
+[website](http://opencobra.github.io/).
If you use cobrapy in a scientific publication, please cite
[doi:10.1186/1752-0509-7-74](http://dx.doi.org/doi:10.1186/1752-0509-7-74)
License
-------
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
+The cobrapy source is released under both the GPL and LGPL licenses. You may
+choose which license you choose to use the software under. However, please note
+that binary packages which include GLPK (such as the binary wheels for Windows
+and Mac OS X distributed at https://pypi.python.org/pypi/cobra) will be bound
+by its license as well.
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License or the Lesser GNU General Public
+License as published by the Free Software Foundation, either version 2 of the
+License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
diff --git a/appveyor.yml b/appveyor.yml
new file mode 100644
index 0000000..cf97d47
--- /dev/null
+++ b/appveyor.yml
@@ -0,0 +1,46 @@
+environment:
+
+ global:
+ # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
+ # /E:ON and /V:ON options are not enabled in the batch script intepreter
+ # See: http://stackoverflow.com/a/13751649/163740
+ WITH_COMPILER: "cmd /E:ON /V:ON /C .\\appveyor\\run_with_compiler.cmd"
+
+ matrix:
+ - PYTHON: "C:\\Python27"
+ PYTHON_VERSION: "2.7.8"
+ PYTHON_ARCH: "32"
+
+ - PYTHON: "C:\\Python27-x64"
+ PYTHON_VERSION: "2.7.8"
+ PYTHON_ARCH: "64"
+ WINDOWS_SDK_VERSION: "v7.0"
+
+ - PYTHON: "C:\\Python34-x64"
+ PYTHON_VERSION: "3.4.1"
+ PYTHON_ARCH: "64"
+ WINDOWS_SDK_VERSION: "v7.1"
+
+init:
+ - "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
+
+install:
+ - "powershell appveyor\\install.ps1"
+ # Download glpk.h and glpk.lib (separate files for 32/64 bit)
+ - ps: Start-FileDownload 'https://opencobra.github.io/pypi_cobrapy_travis/glpk.h'
+ - "appveyor DownloadFile https://opencobra.github.io/pypi_cobrapy_travis/glpk.lib%PYTHON_ARCH% -FileName glpk.lib"
+ - "%PYTHON%/python -m pip install Cython -f https://opencobra.github.io/pypi_cobrapy_travis/ --no-index"
+
+build: off
+
+test_script:
+ - "%WITH_COMPILER% %PYTHON%/python setup.py test"
+
+after_test:
+ - "%WITH_COMPILER% %PYTHON%/python setup.py bdist_wheel"
+
+artifacts:
+ - path: dist\*
+
+#on_success:
+# - TODO: upload the content of dist/*.whl to a public wheelhouse
diff --git a/appveyor/install.ps1 b/appveyor/install.ps1
new file mode 100644
index 0000000..3f05628
--- /dev/null
+++ b/appveyor/install.ps1
@@ -0,0 +1,85 @@
+# Sample script to install Python and pip under Windows
+# Authors: Olivier Grisel and Kyle Kastner
+# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+
+$BASE_URL = "https://www.python.org/ftp/python/"
+$GET_PIP_URL = "https://bootstrap.pypa.io/get-pip.py"
+$GET_PIP_PATH = "C:\get-pip.py"
+
+
+function DownloadPython ($python_version, $platform_suffix) {
+ $webclient = New-Object System.Net.WebClient
+ $filename = "python-" + $python_version + $platform_suffix + ".msi"
+ $url = $BASE_URL + $python_version + "/" + $filename
+
+ $basedir = $pwd.Path + "\"
+ $filepath = $basedir + $filename
+ if (Test-Path $filename) {
+ Write-Host "Reusing" $filepath
+ return $filepath
+ }
+
+ # Download and retry up to 5 times in case of network transient errors.
+ Write-Host "Downloading" $filename "from" $url
+ $retry_attempts = 3
+ for($i=0; $i -lt $retry_attempts; $i++){
+ try {
+ $webclient.DownloadFile($url, $filepath)
+ break
+ }
+ Catch [Exception]{
+ Start-Sleep 1
+ }
+ }
+ Write-Host "File saved at" $filepath
+ return $filepath
+}
+
+
+function InstallPython ($python_version, $architecture, $python_home) {
+ Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+ if (Test-Path $python_home) {
+ Write-Host $python_home "already exists, skipping."
+ return $false
+ }
+ if ($architecture -eq "32") {
+ $platform_suffix = ""
+ } else {
+ $platform_suffix = ".amd64"
+ }
+ $filepath = DownloadPython $python_version $platform_suffix
+ Write-Host "Installing" $filepath "to" $python_home
+ $args = "/qn /i $filepath TARGETDIR=$python_home"
+ Write-Host "msiexec.exe" $args
+ Start-Process -FilePath "msiexec.exe" -ArgumentList $args -Wait -Passthru
+ Write-Host "Python $python_version ($architecture) installation complete"
+ return $true
+}
+
+
+function InstallPip ($python_home) {
+ $pip_path = $python_home + "/Scripts/pip.exe"
+ $python_path = $python_home + "/python.exe"
+ if (-not(Test-Path $pip_path)) {
+ Write-Host "Installing pip..."
+ $webclient = New-Object System.Net.WebClient
+ $webclient.DownloadFile($GET_PIP_URL, $GET_PIP_PATH)
+ Write-Host "Executing:" $python_path $GET_PIP_PATH
+ Start-Process -FilePath "$python_path" -ArgumentList "$GET_PIP_PATH" -Wait -Passthru
+ } else {
+ Write-Host "pip already installed."
+ }
+}
+
+function InstallPackage ($python_home, $pkg) {
+ $pip_path = $python_home + "/Scripts/pip.exe"
+ & $pip_path install $pkg
+}
+
+function main () {
+ InstallPython $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
+ InstallPip $env:PYTHON
+ InstallPackage $env:PYTHON wheel
+}
+
+main
diff --git a/appveyor/run_with_compiler.cmd b/appveyor/run_with_compiler.cmd
new file mode 100644
index 0000000..3a472bc
--- /dev/null
+++ b/appveyor/run_with_compiler.cmd
@@ -0,0 +1,47 @@
+:: To build extensions for 64 bit Python 3, we need to configure environment
+:: variables to use the MSVC 2010 C++ compilers from GRMSDKX_EN_DVD.iso of:
+:: MS Windows SDK for Windows 7 and .NET Framework 4 (SDK v7.1)
+::
+:: To build extensions for 64 bit Python 2, we need to configure environment
+:: variables to use the MSVC 2008 C++ compilers from GRMSDKX_EN_DVD.iso of:
+:: MS Windows SDK for Windows 7 and .NET Framework 3.5 (SDK v7.0)
+::
+:: 32 bit builds do not require specific environment configurations.
+::
+:: Note: this script needs to be run with the /E:ON and /V:ON flags for the
+:: cmd interpreter, at least for (SDK v7.0)
+::
+:: More details at:
+:: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows
+:: http://stackoverflow.com/a/13751649/163740
+::
+:: Author: Olivier Grisel
+:: License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+ at ECHO OFF
+
+SET COMMAND_TO_RUN=%*
+SET WIN_SDK_ROOT=C:\Program Files\Microsoft SDKs\Windows
+
+SET MAJOR_PYTHON_VERSION="%PYTHON_VERSION:~0,1%"
+IF %MAJOR_PYTHON_VERSION% == "2" (
+ SET WINDOWS_SDK_VERSION="v7.0"
+) ELSE IF %MAJOR_PYTHON_VERSION% == "3" (
+ SET WINDOWS_SDK_VERSION="v7.1"
+) ELSE (
+ ECHO Unsupported Python version: "%MAJOR_PYTHON_VERSION%"
+ EXIT 1
+)
+
+IF "%PYTHON_ARCH%"=="64" (
+ ECHO Configuring Windows SDK %WINDOWS_SDK_VERSION% for Python %MAJOR_PYTHON_VERSION% on a 64 bit architecture
+ SET DISTUTILS_USE_SDK=1
+ SET MSSdk=1
+ "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Setup\WindowsSdkVer.exe" -q -version:%WINDOWS_SDK_VERSION%
+ "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Bin\SetEnv.cmd" /x64 /release
+ ECHO Executing: %COMMAND_TO_RUN%
+ call %COMMAND_TO_RUN% || EXIT 1
+) ELSE (
+ ECHO Using default MSVC build environment for 32 bit architecture
+ ECHO Executing: %COMMAND_TO_RUN%
+ call %COMMAND_TO_RUN% || EXIT 1
+)
diff --git a/cobra/VERSION b/cobra/VERSION
index d15723f..88b0e14 100644
--- a/cobra/VERSION
+++ b/cobra/VERSION
@@ -1 +1 @@
-0.3.2
+0.4.0b1
diff --git a/cobra/__init__.py b/cobra/__init__.py
index d63ad2e..4df31aa 100644
--- a/cobra/__init__.py
+++ b/cobra/__init__.py
@@ -18,7 +18,7 @@ _warnings.formatwarning = _warn_format
from .version import get_version
__version__ = get_version()
-from .core import Object, Formula, Metabolite, Gene, Reaction, Model, \
+from .core import Object, Metabolite, Gene, Reaction, Model, \
DictList, Species
from . import io, flux_analysis
diff --git a/cobra/core/ArrayBasedModel.py b/cobra/core/ArrayBasedModel.py
index 5822861..696b2bc 100644
--- a/cobra/core/ArrayBasedModel.py
+++ b/cobra/core/ArrayBasedModel.py
@@ -6,7 +6,7 @@ from numpy import array, hstack, ndarray
from scipy.sparse import lil_matrix, dok_matrix
from .Model import Model
-from ..external.six import iteritems
+from six import iteritems
class ArrayBasedModel(Model):
@@ -190,7 +190,7 @@ class ArrayBasedModel(Model):
self._update_matrices(reaction_list)
def remove_reactions(self, reactions, update_matrices=True, **kwargs):
- """remove reactions from teh model
+ """remove reactions from the model
See :func:`cobra.core.Model.Model.remove_reactions`
diff --git a/cobra/core/DictList.py b/cobra/core/DictList.py
index 20ab498..c61dc46 100644
--- a/cobra/core/DictList.py
+++ b/cobra/core/DictList.py
@@ -1,6 +1,6 @@
from copy import copy, deepcopy
import re
-from ..external.six import string_types, iteritems
+from six import string_types, iteritems
from itertools import islice
try:
@@ -47,7 +47,7 @@ class DictList(list):
def get_by_id(self, id):
"""return the element with a matching id"""
- return self[self._dict[id]]
+ return list.__getitem__(self, self._dict[id])
def list_attr(self, attribute):
"""return a list of the given attribute for every object
@@ -260,7 +260,7 @@ class DictList(list):
# If the pop occured from a location other than the end of the list,
# we will need to subtract 1 from every entry afterwards
if len(args) == 0 or args == [-1]: # removing from the end of the list
- return
+ return value
_dict = self._dict
for i, j in iteritems(_dict):
if j > index:
@@ -292,7 +292,9 @@ class DictList(list):
self._generate_index()
def __getitem__(self, i):
- if isinstance(i, slice):
+ if isinstance(i, int):
+ return list.__getitem__(self, i)
+ elif isinstance(i, slice):
selection = self.__class__()
selection._extend_nocheck(list.__getitem__(self, i))
return selection
diff --git a/cobra/core/Gene.py b/cobra/core/Gene.py
index 3396bf1..e7b4d84 100644
--- a/cobra/core/Gene.py
+++ b/cobra/core/Gene.py
@@ -1,48 +1,133 @@
import re
from warnings import warn
+from ast import parse as ast_parse, Name, And, Or, BitOr, BitAnd, BinOp, \
+ BoolOp, Attribute, Expression, NodeTransformer
+from keyword import kwlist
from .Species import Species
-class Gene(Species):
+keywords = list(kwlist)
+keywords.remove("and")
+keywords.remove("or")
+keywords.extend(("True", "False"))
+keyword_re = re.compile(r"(?=\b(%s)\b)" % "|".join(keywords))
+number_start_re = re.compile(r"(?=\b[0-9])")
+
+replacements = (
+ (".", "__COBRA_DOT__"),
+ ("'", "__COBRA_SQUOTE__"),
+ ('"', "__COBRA_DQUOTE__"),
+ (":", "__COBRA_COLON__"),
+ ("/", "__COBRA_FSLASH__"),
+ ("\\", "__COBRA_BSLASH"),
+ ("-", "__COBRA_DASH__"),
+ ("=", "__COBRA_EQ__")
+)
+
+
+# functions for gene reaction rules
+def ast2str(expr, level=0):
+ """convert compiled ast to gene_reaction_rule str"""
+ if isinstance(expr, Expression):
+ return ast2str(expr.body, 0) if hasattr(expr, "body") else ""
+ elif isinstance(expr, Name):
+ return expr.id
+ elif isinstance(expr, BoolOp):
+ op = expr.op
+ if isinstance(op, Or):
+ str_exp = " or ".join(ast2str(i, level + 1) for i in expr.values)
+ elif isinstance(op, And):
+ str_exp = " and ".join(ast2str(i, level + 1) for i in expr.values)
+ else:
+ raise TypeError("unsupported operation " + op.__class__.__name)
+ return "(" + str_exp + ")" if level else str_exp
+ elif expr is None:
+ return ""
+ else:
+ raise TypeError("unsupported operation " + repr(expr))
+
+
+def eval_gpr(expr, knockouts):
+ """evaluate compiled ast of gene_reaction_rule with knockouts"""
+ if isinstance(expr, Expression):
+ return eval_gpr(expr.body, knockouts)
+ elif isinstance(expr, Name):
+ return expr.id not in knockouts
+ elif isinstance(expr, BoolOp):
+ op = expr.op
+ if isinstance(op, Or):
+ return any(eval_gpr(i, knockouts) for i in expr.values)
+ elif isinstance(op, And):
+ return all(eval_gpr(i, knockouts) for i in expr.values)
+ else:
+ raise TypeError("unsupported operation " + op.__class__.__name__)
+ elif expr is None:
+ return True
+ else:
+ raise TypeError("unsupported operation " + repr(expr))
+
+
+class GPRCleaner(NodeTransformer):
+ """Parses compiled ast of a gene_reaction_rule and identifies genes
+
+ Parts of the tree are rewritten to allow periods in gene ID's and
+ bitwise boolean operations"""
+ def __init__(self):
+ NodeTransformer.__init__(self)
+ self.gene_set = set()
+
+ def visit_Name(self, node):
+ if node.id.startswith("__cobra_escape__"):
+ node.id = node.id[16:]
+ for replacement in replacements:
+ node.id = node.id.replace(replacement[1], replacement[0])
+ self.gene_set.add(node.id)
+ return node
+
+ def visit_BinOp(self, node):
+ self.generic_visit(node)
+ if isinstance(node.op, BitAnd):
+ return BoolOp(And(), (node.left, node.right))
+ elif isinstance(node.op, BitOr):
+ return BoolOp(Or(), (node.left, node.right))
+ else:
+ raise TypeError("unsupported operation '%s'" %
+ node.op.__class__.__name__)
+
+
+def parse_gpr(str_expr):
+ """parse gpr into AST
- """A Gene is a special class of metabolite.
+ returns: (ast_tree, {gene_ids})"""
+ str_expr = str_expr.strip()
+ if len(str_expr) == 0:
+ return None, set()
+ for replacement in replacements:
+ str_expr = str_expr.replace(replacement[0], replacement[1])
+ escaped_str = keyword_re.sub("__cobra_escape__", str_expr)
+ escaped_str = number_start_re.sub("__cobra_escape__", escaped_str)
+ tree = ast_parse(escaped_str, "<string>", "eval")
+ cleaner = GPRCleaner()
+ cleaner.visit(tree)
+ eval_gpr(tree, set()) # ensure the rule can be evaluated
+ return tree, cleaner.gene_set
- TODO: Make design decisions about TUs and such
- """
+class Gene(Species):
- def __init__(self, id, formula=None,
- name=None, compartment=None, strand='+',
- locus_start=0, locus_end=0, functional=True):
+ def __init__(self, id, name=None, functional=True):
"""
id: A string.
- formula: cobra.Formula or a chemical formula str. Defaults to None
- to save time in pickling and such.
-
name: String. A human readable name.
- compartment: None or a dictionary indicating the cellular location
- of the metabolite. Used when in a cobra.Reaction or Model
- object
-
- strand: '+' or '-' to indicate forward or reverse strand for DNA.
-
- locus_start: Int. The index of the starting base for the gene.
-
- locus_end: Int. The index of the last base for the gene.
-
functional: Boolean. Indicate whether the gene is functional. If it
is not functional then it cannot be used in an enzyme complex nor
can its products be used.
"""
- Species.__init__(self, id, formula=formula,
- name=name, compartment=compartment)
- self.locus_start = locus_start
- self.locus_end = locus_end
- self.strand = strand
+ Species.__init__(self, id, name=name)
self.functional = functional
def remove_from_model(self, model=None,
@@ -53,12 +138,14 @@ class Gene(Species):
the gene with 'False' in the gene association, else replace the gene
with 'True'
- .. note :: Simulating gene knockouts is much better handled by
- cobra.manipulation.delete_model_genes
+ .. deprecated :: 0.4
+ Use cobra.manipulation.delete_model_genes to simulate knockouts
+ and cobra.manipulation.remove_genes to remove genes from
+ the model.
"""
+ warn("Use cobra.manipulation.remove_genes instead")
if model is not None:
- warn("passing the model in is unnecessary and deprecated")
if model != self._model:
raise Exception("%s is a member of %s, not %s" %
(repr(self), repr(self._model), repr(model)))
diff --git a/cobra/core/Metabolite.py b/cobra/core/Metabolite.py
index 75093ec..d52094d 100644
--- a/cobra/core/Metabolite.py
+++ b/cobra/core/Metabolite.py
@@ -1,7 +1,13 @@
from warnings import warn
+import re
from .Species import Species
+# Numbers are not required because of the |(?=[A-Z])? block. See the
+# discussion in https://github.com/opencobra/cobrapy/issues/128 for
+# more details.
+element_re = re.compile("([A-Z][a-z]?)([0-9.]+[0-9.]?|(?=[A-Z])?)")
+
class Metabolite(Species):
"""Metabolite is a class for holding information regarding
@@ -14,7 +20,8 @@ class Metabolite(Species):
"""
id: str
- formula: cobra.Formula or String of a chemical formula.
+ formula: str
+ Chemical formula (i.e. H2O)
name: str
A human readable name.
@@ -24,11 +31,65 @@ class Metabolite(Species):
object
"""
- Species.__init__(self, id, formula, name, compartment)
+ Species.__init__(self, id, name)
+ self.formula = formula
+ # because in a Model a metabolite may participate in multiple Reactions
+ self.compartment = compartment
+ self.charge = None
+
self._constraint_sense = 'E'
self._bound = 0.
@property
+ def elements(self):
+ tmp_formula = self.formula
+ if tmp_formula is None:
+ return {}
+ # necessary for some old pickles which use the deprecated
+ # Formula class
+ tmp_formula = str(self.formula)
+ # commonly occuring characters in incorrectly constructed formulas
+ if "*" in tmp_formula:
+ warn("invalid character '*' found in formula '%s'" % self.formula)
+ tmp_formula = tmp_formula.replace("*", "")
+ if "(" in tmp_formula or ")" in tmp_formula:
+ warn("invalid formula (has parenthesis) in '%s'" % self.formula)
+ return None
+ composition = {}
+ parsed = element_re.findall(tmp_formula)
+ for (element, count) in parsed:
+ if count == '':
+ count = 1
+ else:
+ try:
+ count = float(count)
+ int_count = int(count)
+ if count == int_count:
+ count = int_count
+ else:
+ warn("%s is not an integer (in formula %s)" %
+ (count, self.formula))
+ except ValueError:
+ warn("failed to parse %s (in formula %s)" %
+ (count, self.formula))
+ return None
+ if element in composition:
+ composition[element] += count
+ else:
+ composition[element] = count
+ return composition
+
+ @property
+ def formula_weight(self):
+ """Calculate the formula weight"""
+ weight_dict = elements_and_molecular_weights
+ try:
+ return sum([count * elements_and_molecular_weights[element]
+ for element, count in self.elements.items()])
+ except KeyError as e:
+ warn("The element %s does not appear in the peridic table" % e)
+
+ @property
def y(self):
"""The shadow price for the metabolite in the most recent solution
@@ -75,3 +136,121 @@ class Metabolite(Species):
x.remove_from_model()
else:
raise Exception(method + " is not 'subtractive' or 'destructive'")
+
+
+elements_and_molecular_weights = {
+ 'H': 1.007940,
+ 'He': 4.002602,
+ 'Li': 6.941000,
+ 'Be': 9.012182,
+ 'B': 10.811000,
+ 'C': 12.010700,
+ 'N': 14.006700,
+ 'O': 15.999400,
+ 'F': 18.998403,
+ 'Ne': 20.179700,
+ 'Na': 22.989770,
+ 'Mg': 24.305000,
+ 'Al': 26.981538,
+ 'Si': 28.085500,
+ 'P': 30.973761,
+ 'S': 32.065000,
+ 'Cl': 35.453000,
+ 'Ar': 39.948000,
+ 'K': 39.098300,
+ 'Ca': 40.078000,
+ 'Sc': 44.955910,
+ 'Ti': 47.867000,
+ 'V': 50.941500,
+ 'Cr': 51.996100,
+ 'Mn': 54.938049,
+ 'Fe': 55.845000,
+ 'Co': 58.933200,
+ 'Ni': 58.693400,
+ 'Cu': 63.546000,
+ 'Zn': 65.409000,
+ 'Ga': 69.723000,
+ 'Ge': 72.640000,
+ 'As': 74.921600,
+ 'Se': 78.960000,
+ 'Br': 79.904000,
+ 'Kr': 83.798000,
+ 'Rb': 85.467800,
+ 'Sr': 87.620000,
+ 'Y': 88.905850,
+ 'Zr': 91.224000,
+ 'Nb': 92.906380,
+ 'Mo': 95.940000,
+ 'Tc': 98.000000,
+ 'Ru': 101.070000,
+ 'Rh': 102.905500,
+ 'Pd': 106.420000,
+ 'Ag': 107.868200,
+ 'Cd': 112.411000,
+ 'In': 114.818000,
+ 'Sn': 118.710000,
+ 'Sb': 121.760000,
+ 'Te': 127.600000,
+ 'I': 126.904470,
+ 'Xe': 131.293000,
+ 'Cs': 132.905450,
+ 'Ba': 137.327000,
+ 'La': 138.905500,
+ 'Ce': 140.116000,
+ 'Pr': 140.907650,
+ 'Nd': 144.240000,
+ 'Pm': 145.000000,
+ 'Sm': 150.360000,
+ 'Eu': 151.964000,
+ 'Gd': 157.250000,
+ 'Tb': 158.925340,
+ 'Dy': 162.500000,
+ 'Ho': 164.930320,
+ 'Er': 167.259000,
+ 'Tm': 168.934210,
+ 'Yb': 173.040000,
+ 'Lu': 174.967000,
+ 'Hf': 178.490000,
+ 'Ta': 180.947900,
+ 'W': 183.840000,
+ 'Re': 186.207000,
+ 'Os': 190.230000,
+ 'Ir': 192.217000,
+ 'Pt': 195.078000,
+ 'Au': 196.966550,
+ 'Hg': 200.590000,
+ 'Tl': 204.383300,
+ 'Pb': 207.200000,
+ 'Bi': 208.980380,
+ 'Po': 209.000000,
+ 'At': 210.000000,
+ 'Rn': 222.000000,
+ 'Fr': 223.000000,
+ 'Ra': 226.000000,
+ 'Ac': 227.000000,
+ 'Th': 232.038100,
+ 'Pa': 231.035880,
+ 'U': 238.028910,
+ 'Np': 237.000000,
+ 'Pu': 244.000000,
+ 'Am': 243.000000,
+ 'Cm': 247.000000,
+ 'Bk': 247.000000,
+ 'Cf': 251.000000,
+ 'Es': 252.000000,
+ 'Fm': 257.000000,
+ 'Md': 258.000000,
+ 'No': 259.000000,
+ 'Lr': 262.000000,
+ 'Rf': 261.000000,
+ 'Db': 262.000000,
+ 'Sg': 266.000000,
+ 'Bh': 264.000000,
+ 'Hs': 277.000000,
+ 'Mt': 268.000000,
+ 'Ds': 281.000000,
+ 'Rg': 272.000000,
+ 'Cn': 285.000000,
+ 'Uuq': 289.000000,
+ 'Uuh': 292.000000
+}
diff --git a/cobra/core/Model.py b/cobra/core/Model.py
index 72b0ec8..ef9d21e 100644
--- a/cobra/core/Model.py
+++ b/cobra/core/Model.py
@@ -1,10 +1,12 @@
from warnings import warn
from copy import deepcopy, copy
-from ..external.six import iteritems, string_types
+from six import iteritems, string_types
+
from ..solvers import optimize
from .Object import Object
from .Solution import Solution
+from .Reaction import Reaction
from .DictList import DictList
@@ -73,18 +75,11 @@ class Model(Object):
self.id = self.id + '_' + other_model.id
return self
- def guided_copy(self):
- """.. warning :: deprecated"""
- warn("deprecated")
- return self.copy()
-
- def copy(self, print_time=False):
+ def copy(self):
"""Provides a partial 'deepcopy' of the Model. All of the Metabolite,
Gene, and Reaction objects are created anew but in a faster fashion
than deepcopy
"""
- if print_time is not False:
- warn("print_time is a deprecated option")
new = self.__class__()
do_not_copy = {"metabolites", "reactions", "genes"}
for attr in self.__dict__:
@@ -148,22 +143,6 @@ class Model(Object):
x._model = self
self.metabolites += metabolite_list
- def _update_reaction(self, reaction):
- """.. warning :: deprecated"""
- warn("deprecated function")
- if not hasattr(reaction, '__iter__'):
- reaction = [reaction]
- for the_reaction in reaction:
- if the_reaction.id not in self.reactions:
- warn(the_reaction.id + ' is not in the model')
- continue
- reaction_index = self.reactions.index(the_reaction.id)
- self.reactions[reaction_index] = the_reaction
-
- def update(self):
- """.. warning :: removed"""
- raise Exception("Model.update is moved to ArrayBasedModel.")
-
def add_reaction(self, reaction):
"""Will add a cobra.Reaction object to the model, if
reaction.id is not in self.reactions.
@@ -247,9 +226,7 @@ class Model(Object):
from .ArrayBasedModel import ArrayBasedModel
return ArrayBasedModel(self, deepcopy_model=deepcopy_model, **kwargs)
- def optimize(self, objective_sense='maximize', solver=None,
- quadratic_component=None,
- **kwargs):
+ def optimize(self, objective_sense='maximize', **kwargs):
r"""Optimize model using flux balance analysis
objective_sense: 'maximize' or 'minimize'
@@ -273,18 +250,9 @@ class Model(Object):
specified with the appropriate keyword argument.
"""
- if "new_objective" in kwargs:
- warn("new_objective is deprecated. Use Model.change_objective")
- self.change_objective(kwargs.pop("new_objective"))
- if "error_reporting" in kwargs:
- warn("error_reporting deprecated")
- if quadratic_component is not None:
- kwargs["quadratic_component"] = quadratic_component
- the_solution = optimize(self, solver=solver,
- objective_sense=objective_sense,
- **kwargs)
- self.solution = the_solution
- return the_solution
+ solution = optimize(self, objective_sense=objective_sense, **kwargs)
+ self.solution = solution
+ return solution
def remove_reactions(self, reactions, delete=True,
remove_orphans=False):
@@ -341,43 +309,35 @@ class Model(Object):
return
def change_objective(self, objectives):
- """Change the objective in the cobrapy model.
+ """Change the model objective"""
+ self.objective = objectives
- objectives: A list or a dictionary. If a list then
- a list of reactions for which the coefficient in the
- linear objective is set as 1. If a dictionary then the
- key is the reaction and the value is the linear coefficient
- for the respective reaction.
+ @property
+ def objective(self):
+ return {reaction: reaction.objective_coefficient
+ for reaction in self.reactions
+ if reaction.objective_coefficient != 0}
- """
- # I did not want to refactor code just to rename the variable, but this
- # way the API uses the variable "objectives"
- the_objectives = objectives
+ @objective.setter
+ def objective(self, objectives):
# set all objective coefficients to 0 initially
for x in self.reactions:
x.objective_coefficient = 0.
- # update the objective coefficients if a dict is passed in
- if hasattr(the_objectives, "items"):
- for the_reaction, the_coefficient in iteritems(the_objectives):
- if isinstance(the_reaction, int):
- the_reaction = self.reactions[the_reaction]
- else:
- if hasattr(the_reaction, 'id'):
- the_reaction = the_reaction.id
- the_reaction = self.reactions.get_by_id(the_reaction)
- the_reaction.objective_coefficient = the_coefficient
- # If a list (or a single reaction is passed in), each reaction gets
- # 1 for the objective coefficent.
+ # case of a single reaction
+ if isinstance(objectives, string_types) or \
+ isinstance(objectives, Reaction):
+ self.reactions.get_by_id(str(objectives)).objective_coefficient = 1
+ elif isinstance(objectives, int):
+ self.reactions[objectives].objective_coefficient = 1
+
+ # case of an iterable
else:
- # Allow for objectives to be constructed from multiple reactions
- if not hasattr(the_objectives, "__iter__") or \
- isinstance(the_objectives, string_types):
- the_objectives = [the_objectives]
- for the_reaction in the_objectives:
- if isinstance(the_reaction, int):
- the_reaction = self.reactions[the_reaction]
+ for reaction_id in objectives:
+ if isinstance(reaction_id, int): # index in a list
+ reaction = self.reactions[reaction_id]
else:
- if hasattr(the_reaction, 'id'):
- the_reaction = the_reaction.id
- the_reaction = self.reactions.get_by_id(the_reaction)
- the_reaction.objective_coefficient = 1.
+ reaction = self.reactions.get_by_id(str(reaction_id))
+ # objective coefficient obtained from a dict, and is 1. if
+ # from a list.
+ reaction.objective_coefficient = objectives[reaction_id] \
+ if hasattr(objectives, "items") else 1.
diff --git a/cobra/core/Object.py b/cobra/core/Object.py
index 0b9eebb..5311b79 100644
--- a/cobra/core/Object.py
+++ b/cobra/core/Object.py
@@ -1,4 +1,4 @@
-from ..external.six import iteritems
+from six import iteritems
class Object(object):
diff --git a/cobra/core/Reaction.py b/cobra/core/Reaction.py
index cc07931..67103fd 100644
--- a/cobra/core/Reaction.py
+++ b/cobra/core/Reaction.py
@@ -5,10 +5,10 @@ import re
from copy import copy, deepcopy
from warnings import warn
-from ..external.six import string_types, iteritems
+from six import string_types, iteritems
from .Object import Object
-from .Gene import Gene
+from .Gene import Gene, parse_gpr
from .Metabolite import Metabolite
@@ -31,6 +31,7 @@ class Frozendict(dict):
# precompiled regular expressions
# Matches and/or in a gene reaction rule
and_or_search = re.compile(r'\(| and| or|\+|\)', re.IGNORECASE)
+gpr_clean = re.compile(' {2,}')
# This regular expression finds any single letter compartment enclosed in
# square brackets at the beginning of the string. For example [c] : foo --> bar
compartment_finder = re.compile("^\s*(\[[A-Za-z]\])\s*:*")
@@ -89,9 +90,14 @@ class Reaction(Object):
@gene_reaction_rule.setter
def gene_reaction_rule(self, new_rule):
- self._gene_reaction_rule = new_rule
- gene_names = set((re.compile(' {2,}').sub(
- ' ', and_or_search.sub('', self._gene_reaction_rule))).split(' '))
+ self._gene_reaction_rule = new_rule.strip()
+ try:
+ _, gene_names = parse_gpr(self._gene_reaction_rule)
+ except (SyntaxError, TypeError):
+ warn("malformed gene_reaction_rule '%s' for %s" %
+ (new_rule, repr(self)))
+ tmp_str = and_or_search.sub('', self._gene_reaction_rule)
+ gene_names = set((gpr_clean.sub(' ', tmp_str).split(' ')))
if '' in gene_names:
gene_names.remove('')
old_genes = self._genes
@@ -183,11 +189,6 @@ class Reaction(Object):
for x in self._genes:
x._reaction.add(self)
- def get_model(self):
- """.. deprecated :: 0.3.1 use model property instead"""
- warn("deprecated, use the model property instead")
- return self._model
-
def remove_from_model(self, model=None, remove_orphans=False):
"""Removes the reaction from the model while keeping it intact
@@ -296,26 +297,6 @@ class Reaction(Object):
# self._model = the_model
return new_reaction
- def guided_copy(self, the_model, metabolite_dict, gene_dict=None):
- """.. deprecated :: 0.3 use copy directly"""
- warn("deprecated")
- the_copy = Object.guided_copy(self)
- # Replace the complex items in a faster fashion
- the_copy._model = the_model
- if gene_dict:
- the_copy._genes = set([gene_dict[k.id]
- for k in self._genes])
- the_copy._metabolites = {metabolite_dict[k.id]: v
- for k, v in iteritems(self._metabolites)}
-
- # make the metabolites and genes aware of the reaction
- [k._reaction.add(the_copy)
- for k in the_copy._genes]
- [k._reaction.add(the_copy)
- for k in the_copy._metabolites.keys()]
-
- return(the_copy)
-
def pop(self, metabolite_id):
"""Remove a metabolite from the reaction and return the
stoichiometric coefficient.
@@ -399,42 +380,16 @@ class Reaction(Object):
self *= the_coefficient
return self
- def parse_gene_association(self, **kwargs):
- """.. deprecated :: 0.3 Set gene_reaction_rule directly"""
- warn("deprecated function")
- # trigger the update if that was the desired behavior for some reason
- self.gene_reaction_rule = self._gene_reaction_rule
-
- def add_gene_reaction_rule(self, the_rule):
- """.. deprecated :: 0.3 Set gene_reaction_rule directly"""
- self.gene_reaction_rule = the_rule
- warn("deprecated, assign to gene_reaction_rule directly")
-
- def get_reactants(self):
- """.. deprecated :: 0.3 use reactants property instead"""
- warn("deprecated, use the reactants property instead")
- return self.reactants
-
@property
def reactants(self):
"""Return a list of reactants for the reaction."""
return [k for k, v in self._metabolites.items() if v < 0]
- def get_products(self):
- """.. deprecated :: 0.3 use products property instead"""
- warn("depreacated, use the products property instead")
- return self.products
-
@property
def products(self):
"""Return a list of products for the reaction"""
return [k for k, v in self._metabolites.items() if v > 0]
- def get_gene(self):
- """.. deprecated :: 0.3 use genes property instead"""
- warn("deprecated, use the genes property instead")
- return list(self._genes)
-
def get_coefficient(self, metabolite_id):
"""Return the stoichiometric coefficient for a metabolite in
the reaction.
@@ -568,64 +523,21 @@ class Reaction(Object):
return reaction_string
def check_mass_balance(self):
- """Makes sure that the reaction is elementally-balanced."""
- reaction_element_dict = defaultdict(list)
- for the_metabolite, the_coefficient in self._metabolites.items():
- if the_metabolite.formula is not None:
- for k, v in the_metabolite.formula.elements.items():
- reaction_element_dict[k].append(the_coefficient * v)
- reaction_element_dict = {k: sum(v) for k, v
- in reaction_element_dict.items()}
- if sum(map(abs, reaction_element_dict.values())) != 0:
- return [self.id, reaction_element_dict]
- else:
- return []
-
- def print_values(self):
- """.. deprecated :: 0.3"""
- warn("deprecated")
- print("reaction:", self.id)
- print("subsystem", self.subsystem)
- print(self.reaction)
- print("bounds: (%.2f, %.2f)" % (self.lower_bound, self.upper_bound))
- print("objective_coefficient", self.objective_coefficient)
- print("gene reaction rule:", self.gene_reaction_rule)
+ """Makes sure that the reaction is elementally-balanced.
- def get_compartments(self):
+ returns a dict of {element: amount} for unbalanced elements.
+ This should be empty for balanced reactions.
"""
- """
- return(list(set([x.compartment for x in self._metabolites])))
+ reaction_element_dict = defaultdict(int)
+ for metabolite, coefficient in self._metabolites.items():
+ for element, amount in iteritems(metabolite.elements):
+ reaction_element_dict[element] += coefficient * amount
+ # filter out 0 values
+ return {k: v for k, v in iteritems(reaction_element_dict) if v != 0}
- def remove_gene(self, cobra_gene):
- """.. deprecated :: 0.3 update the gene_reaction_rule instead"""
- warn("deprecated: update the gene_reaction_rule instead")
- try:
- self._genes.remove(cobra_gene)
- cobra_gene._reaction.remove(self)
- except Exception as e:
- try:
- if hasattr(self._genes, 'keys'):
- self._genes = set(self._genes.keys())
- self.remove_gene(cobra_gene)
- except:
- raise Exception('Unable to remove %s from %s: %s' %
- (repr(cobra_gene), repr(self), e))
-
- def add_gene(self, cobra_gene):
- """.. deprecated :: 0.3 update the gene_reaction_rule instead"""
- warn("deprecated: update the gene_reaction_rule instead")
- try:
- self._genes.add(cobra_gene)
- cobra_gene._reaction.add(self)
- cobra_gene._model = self._model
- except Exception as e:
- try:
- if hasattr(self._genes, 'keys'):
- self._genes = set(self._genes.keys())
- self.add_gene(cobra_gene)
- except:
- raise Exception('Unable to add %s to %s: %s' %
- (repr(cobra_gene), repr(self), e))
+ def get_compartments(self):
+ """lists compartments the metabolites are in"""
+ return list({x.compartment for x in self._metabolites})
def _associate_gene(self, cobra_gene):
"""Associates a cobra.Gene object with a cobra.Reaction.
diff --git a/cobra/core/Species.py b/cobra/core/Species.py
index d167532..4dcc21e 100644
--- a/cobra/core/Species.py
+++ b/cobra/core/Species.py
@@ -1,6 +1,5 @@
from warnings import warn
from copy import deepcopy
-from .Formula import Formula
from .Object import Object
@@ -11,37 +10,18 @@ class Species(Object):
"""
- def __init__(self, id=None, formula=None,
- name=None, compartment=None, mnx_id=None):
+ def __init__(self, id=None, name=None):
"""
id: A string.
- formula: cobra.Formula or str of a chemical formula. Defaults to None
- to save time in pickling and such.
-
name: String. A human readable name.
- compartment: None or a dictionary indicating the cellular location
- of the metabolite. Used when in a cobra.Reaction or Model
- object
-
- mnx_id: None or a String of the MetaNetX.org ID for the object.
-
"""
- Object.__init__(self, id, mnx_id=mnx_id)
+ Object.__init__(self, id)
self.name = name
if not name:
self.name = self.id
- if isinstance(formula, str):
- formula = Formula(formula)
-
- self.formula = formula
- self.parse_composition()
- # because in a Model a metabolite may participate in multiple Reactions
- self.compartment = compartment
- # self.model is None or refers to the cobra.Model that
- # contains self
- self._model = self.charge = None
+ self._model = None
# references to reactions that operate on this species
self._reaction = set()
@@ -49,16 +29,6 @@ class Species(Object):
def reactions(self):
return frozenset(self._reaction)
- def parse_composition(self):
- """Breaks the chemical formula down by element.
- Useful for making sure Reactions are balanced.'
-
- """
- if isinstance(self.formula, Formula):
- self.formula.parse_composition()
- elif isinstance(self.formula, str):
- self.formula = Formula(self.formula)
-
def __getstate__(self):
"""Remove the references to container reactions when serializing to
avoid problems associated with recursion.
@@ -78,16 +48,6 @@ class Species(Object):
"""
return deepcopy(self)
- def guided_copy(self, the_model):
- """.. deprecated :: 0.3 Use copy directly"""
- warn("deprecated")
- the_copy = Object.guided_copy(self)
- # Copy the more complex objects in a faster fashion
- the_copy.formula = deepcopy(self.formula)
- the_copy._model = the_model
- the_copy._reaction = set()
- return(the_copy)
-
def get_reaction(self):
"""Returns a list of Reactions that contain this Species"""
warn("deprecated, used species.reactions instead")
diff --git a/cobra/core/__init__.py b/cobra/core/__init__.py
index abb3c3d..24e7859 100644
--- a/cobra/core/__init__.py
+++ b/cobra/core/__init__.py
@@ -1,6 +1,5 @@
from .DictList import DictList
from .Object import Object
-from .Formula import Formula
from .Gene import Gene
from .Metabolite import Metabolite
from .Reaction import Reaction
diff --git a/cobra/external/__init__.py b/cobra/external/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/cobra/external/ppmap.py b/cobra/external/ppmap.py
deleted file mode 100644
index 08d5ff3..0000000
--- a/cobra/external/ppmap.py
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/usr/bin/env python
-
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-#
-# * Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above
-# copyright notice, this list of conditions and the following
-# disclaimer in the documentation and/or other materials
-# provided with the distribution.
-#
-# * Neither the name of Kirk Strauser nor the names of other
-# contributors may be used to endorse or promote products
-# derived from this software without specific prior written
-# permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
-# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
-# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-
-"""
-Very basic parallel processing support
-
-Implements a work-alike of the builtin map() function that distributes
-work across many processes. As it uses Parallel Python to do the
-actual multi-processing, code using this must conform to the usual PP
-restrictions (arguments must be serializable, etc.)
-"""
-
-__author__ = "Kirk Strauser <kirk at strauser.com>"
-__version__ = "$Rev: 1139 $"
-__date__ = "$Date: 2008-04-16 $"
-
-import time
-import __builtin__
-
-try:
- import pp
-except:
- raise Exception('Could not import pp')
-__STATE = {'server': None}
-
-def ppmap(processes, function, sequence, *sequences):
- """Split the work of 'function' across the given number of
- processes. Set 'processes' to None to let Parallel Python
- autodetect the number of children to use.
-
- Although the calling semantics should be identical to
- __builtin__.map (even using __builtin__.map to process
- arguments), it differs in that it returns a generator instead of a
- list. This enables lazy evaluation of the results so that other
- work can be done while the subprocesses are still running.
-
- >>> def rangetotal(n): return n, sum(range(n))
- >>> list(map(rangetotal, range(1, 6)))
- [(1, 0), (2, 1), (3, 3), (4, 6), (5, 10)]
- >>> list(ppmap(1, rangetotal, range(1, 6)))
- [(1, 0), (2, 1), (3, 3), (4, 6), (5, 10)]
- """
-
- # Create a new server if one isn't already initialized
- if not __STATE['server']:
- __STATE['server'] = pp.Server()
-
- def submit(*args):
- """Send a job to the server"""
- return __STATE['server'].submit(function, args, globals=globals())
-
- # Merge all the passed-in argument lists together. This is done
- # that way because as with the map() function, at least one list
- # is required but the rest are optional.
- a = [sequence]
- a.extend(sequences)
- available_processes = sum( __STATE['server'].get_active_nodes().values())
- # Set the requested level of multi-processing
- if available_processes < processes:
- __STATE['server'].set_ncpus(processes-available_processes or 'autodetect')
-
- # First, submit all the jobs. Then harvest the results as they
- # come available.
- return (subproc() for subproc in __builtin__.map(submit, *a))
-
-if __name__ == '__main__':
- def add(x, y, z):
- """Add three values"""
- return x + y + z
-
- def busybeaver(x):
- """This can take a while"""
- for num in range(1000000):
- x = x + num
- return x
- # Immediate evaluation example
- start = time.time()
- results = ppmap(None, busybeaver, range(10))
- print 'Time to queue the jobs:', time.time() - start
- start = time.time()
- # Casting the ppmap generator to a list forces each result to be
- # evaluated. When done immediately after the jobs are submitted,
- # our program twiddles its thumbs while the work is finished.
- print list(results)
- print 'Time to get the results:', time.time() - start
-
- # Delayed evaluation example
- start = time.time()
- results = ppmap(None, busybeaver, range(10))
- print 'Time to queue the jobs:', time.time() - start
- # In contrast with the above example, this time we're submitting a
- # batch of jobs then going off to do more work while they're
- # processing. Maybe "time.sleep" isn't the most exciting example,
- # but it illustrates the point that our main program can do work
- # before ppmap() is finished. Imagine that you're submitting some
- # heavyweight image processing jobs at the beginning of your
- # program, going on to do other stuff like fetching more work to
- # do from a remote server, then coming back later to handle the
- # results.
- time.sleep(5)
- start = time.time()
- print list(results)
- print 'Time to get the first results:', time.time() - start
-
- # Built-in map example
- print map(add, [1, 2, 3], [4, 5, 6], [7, 8, 9])
-
- # Trivial ppmap tests
- for i in range(10):
- print '-' * 30
- start = time.time()
- print i, 'adders'
- print ppmap(i, add, [1, 2, 3], [4, 5, 6], [7, 8, 9])
- print 'Iteration time:', time.time() - start
-
- # Heavier ppmap tests
- for i in range(10):
- print '-' * 30
- start = time.time()
- print i, 'beavers'
- print ppmap(i, busybeaver, range(10))
- print 'Iteration time:', time.time() - start
diff --git a/cobra/external/six.py b/cobra/external/six.py
deleted file mode 100644
index f8f7d40..0000000
--- a/cobra/external/six.py
+++ /dev/null
@@ -1,747 +0,0 @@
-"""Utilities for writing code that runs on Python 2 and 3"""
-
-# Copyright (c) 2010-2014 Benjamin Peterson
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-
-import functools
-import operator
-import sys
-import types
-
-__author__ = "Benjamin Peterson <benjamin at python.org>"
-__version__ = "1.7.3"
-
-
-# Useful for very coarse version differentiation.
-PY2 = sys.version_info[0] == 2
-PY3 = sys.version_info[0] == 3
-
-if PY3:
- string_types = str,
- integer_types = int,
- class_types = type,
- text_type = str
- binary_type = bytes
-
- MAXSIZE = sys.maxsize
-else:
- string_types = basestring,
- integer_types = (int, long)
- class_types = (type, types.ClassType)
- text_type = unicode
- binary_type = str
-
- if sys.platform.startswith("java"):
- # Jython always uses 32 bits.
- MAXSIZE = int((1 << 31) - 1)
- else:
- # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
- class X(object):
- def __len__(self):
- return 1 << 31
- try:
- len(X())
- except OverflowError:
- # 32-bit
- MAXSIZE = int((1 << 31) - 1)
- else:
- # 64-bit
- MAXSIZE = int((1 << 63) - 1)
- del X
-
-
-def _add_doc(func, doc):
- """Add documentation to a function."""
- func.__doc__ = doc
-
-
-def _import_module(name):
- """Import module, returning the module after the last dot."""
- __import__(name)
- return sys.modules[name]
-
-
-class _LazyDescr(object):
-
- def __init__(self, name):
- self.name = name
-
- def __get__(self, obj, tp):
- result = self._resolve()
- setattr(obj, self.name, result) # Invokes __set__.
- # This is a bit ugly, but it avoids running this again.
- delattr(obj.__class__, self.name)
- return result
-
-
-class MovedModule(_LazyDescr):
-
- def __init__(self, name, old, new=None):
- super(MovedModule, self).__init__(name)
- if PY3:
- if new is None:
- new = name
- self.mod = new
- else:
- self.mod = old
-
- def _resolve(self):
- return _import_module(self.mod)
-
- def __getattr__(self, attr):
- _module = self._resolve()
- value = getattr(_module, attr)
- setattr(self, attr, value)
- return value
-
-
-class _LazyModule(types.ModuleType):
-
- def __init__(self, name):
- super(_LazyModule, self).__init__(name)
- self.__doc__ = self.__class__.__doc__
-
- def __dir__(self):
- attrs = ["__doc__", "__name__"]
- attrs += [attr.name for attr in self._moved_attributes]
- return attrs
-
- # Subclasses should override this
- _moved_attributes = []
-
-
-class MovedAttribute(_LazyDescr):
-
- def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None):
- super(MovedAttribute, self).__init__(name)
- if PY3:
- if new_mod is None:
- new_mod = name
- self.mod = new_mod
- if new_attr is None:
- if old_attr is None:
- new_attr = name
- else:
- new_attr = old_attr
- self.attr = new_attr
- else:
- self.mod = old_mod
- if old_attr is None:
- old_attr = name
- self.attr = old_attr
-
- def _resolve(self):
- module = _import_module(self.mod)
- return getattr(module, self.attr)
-
-
-class _SixMetaPathImporter(object):
- """
- A meta path importer to import six.moves and its submodules.
-
- This class implements a PEP302 finder and loader. It should be compatible
- with Python 2.5 and all existing versions of Python3
- """
- def __init__(self, six_module_name):
- self.name = six_module_name
- self.known_modules = {}
-
- def _add_module(self, mod, *fullnames):
- for fullname in fullnames:
- self.known_modules[self.name + "." + fullname] = mod
-
- def _get_module(self, fullname):
- return self.known_modules[self.name + "." + fullname]
-
- def find_module(self, fullname, path=None):
- if fullname in self.known_modules:
- return self
- return None
-
- def __get_module(self, fullname):
- try:
- return self.known_modules[fullname]
- except KeyError:
- raise ImportError("This loader does not know module " + fullname)
-
- def load_module(self, fullname):
- try:
- # in case of a reload
- return sys.modules[fullname]
- except KeyError:
- pass
- mod = self.__get_module(fullname)
- if isinstance(mod, MovedModule):
- mod = mod._resolve()
- else:
- mod.__loader__ = self
- sys.modules[fullname] = mod
- return mod
-
- def is_package(self, fullname):
- """
- Return true, if the named module is a package.
-
- We need this method to get correct spec objects with
- Python 3.4 (see PEP451)
- """
- return hasattr(self.__get_module(fullname), "__path__")
-
- def get_code(self, fullname):
- """Return None
-
- Required, if is_package is implemented"""
- self.__get_module(fullname) # eventually raises ImportError
- return None
- get_source = get_code # same as get_code
-
-_importer = _SixMetaPathImporter(__name__)
-
-
-class _MovedItems(_LazyModule):
- """Lazy loading of moved objects"""
- __path__ = [] # mark as package
-
-
-_moved_attributes = [
- MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
- MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
- MovedAttribute("filterfalse", "itertools", "itertools", "ifilterfalse", "filterfalse"),
- MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
- MovedAttribute("map", "itertools", "builtins", "imap", "map"),
- MovedAttribute("range", "__builtin__", "builtins", "xrange", "range"),
- MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
- MovedAttribute("reduce", "__builtin__", "functools"),
- MovedAttribute("StringIO", "StringIO", "io"),
- MovedAttribute("UserDict", "UserDict", "collections"),
- MovedAttribute("UserList", "UserList", "collections"),
- MovedAttribute("UserString", "UserString", "collections"),
- MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
- MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
- MovedAttribute("zip_longest", "itertools", "itertools", "izip_longest", "zip_longest"),
-
- MovedModule("builtins", "__builtin__"),
- MovedModule("configparser", "ConfigParser"),
- MovedModule("copyreg", "copy_reg"),
- MovedModule("dbm_gnu", "gdbm", "dbm.gnu"),
- MovedModule("_dummy_thread", "dummy_thread", "_dummy_thread"),
- MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
- MovedModule("http_cookies", "Cookie", "http.cookies"),
- MovedModule("html_entities", "htmlentitydefs", "html.entities"),
- MovedModule("html_parser", "HTMLParser", "html.parser"),
- MovedModule("http_client", "httplib", "http.client"),
- MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"),
- MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"),
- MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"),
- MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"),
- MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"),
- MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"),
- MovedModule("cPickle", "cPickle", "pickle"),
- MovedModule("queue", "Queue"),
- MovedModule("reprlib", "repr"),
- MovedModule("socketserver", "SocketServer"),
- MovedModule("_thread", "thread", "_thread"),
- MovedModule("tkinter", "Tkinter"),
- MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"),
- MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"),
- MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"),
- MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"),
- MovedModule("tkinter_tix", "Tix", "tkinter.tix"),
- MovedModule("tkinter_ttk", "ttk", "tkinter.ttk"),
- MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"),
- MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"),
- MovedModule("tkinter_colorchooser", "tkColorChooser",
- "tkinter.colorchooser"),
- MovedModule("tkinter_commondialog", "tkCommonDialog",
- "tkinter.commondialog"),
- MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"),
- MovedModule("tkinter_font", "tkFont", "tkinter.font"),
- MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"),
- MovedModule("tkinter_tksimpledialog", "tkSimpleDialog",
- "tkinter.simpledialog"),
- MovedModule("urllib_parse", __name__ + ".moves.urllib_parse", "urllib.parse"),
- MovedModule("urllib_error", __name__ + ".moves.urllib_error", "urllib.error"),
- MovedModule("urllib", __name__ + ".moves.urllib", __name__ + ".moves.urllib"),
- MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
- MovedModule("xmlrpc_client", "xmlrpclib", "xmlrpc.client"),
- MovedModule("xmlrpc_server", "SimpleXMLRPCServer", "xmlrpc.server"),
- MovedModule("winreg", "_winreg"),
-]
-for attr in _moved_attributes:
- setattr(_MovedItems, attr.name, attr)
- if isinstance(attr, MovedModule):
- _importer._add_module(attr, "moves." + attr.name)
-del attr
-
-_MovedItems._moved_attributes = _moved_attributes
-
-moves = _MovedItems(__name__ + ".moves")
-_importer._add_module(moves, "moves")
-
-
-class Module_six_moves_urllib_parse(_LazyModule):
- """Lazy loading of moved objects in six.moves.urllib_parse"""
-
-
-_urllib_parse_moved_attributes = [
- MovedAttribute("ParseResult", "urlparse", "urllib.parse"),
- MovedAttribute("SplitResult", "urlparse", "urllib.parse"),
- MovedAttribute("parse_qs", "urlparse", "urllib.parse"),
- MovedAttribute("parse_qsl", "urlparse", "urllib.parse"),
- MovedAttribute("urldefrag", "urlparse", "urllib.parse"),
- MovedAttribute("urljoin", "urlparse", "urllib.parse"),
- MovedAttribute("urlparse", "urlparse", "urllib.parse"),
- MovedAttribute("urlsplit", "urlparse", "urllib.parse"),
- MovedAttribute("urlunparse", "urlparse", "urllib.parse"),
- MovedAttribute("urlunsplit", "urlparse", "urllib.parse"),
- MovedAttribute("quote", "urllib", "urllib.parse"),
- MovedAttribute("quote_plus", "urllib", "urllib.parse"),
- MovedAttribute("unquote", "urllib", "urllib.parse"),
- MovedAttribute("unquote_plus", "urllib", "urllib.parse"),
- MovedAttribute("urlencode", "urllib", "urllib.parse"),
- MovedAttribute("splitquery", "urllib", "urllib.parse"),
-]
-for attr in _urllib_parse_moved_attributes:
- setattr(Module_six_moves_urllib_parse, attr.name, attr)
-del attr
-
-Module_six_moves_urllib_parse._moved_attributes = _urllib_parse_moved_attributes
-
-_importer._add_module(Module_six_moves_urllib_parse(__name__ + ".moves.urllib_parse"),
- "moves.urllib_parse", "moves.urllib.parse")
-
-
-class Module_six_moves_urllib_error(_LazyModule):
- """Lazy loading of moved objects in six.moves.urllib_error"""
-
-
-_urllib_error_moved_attributes = [
- MovedAttribute("URLError", "urllib2", "urllib.error"),
- MovedAttribute("HTTPError", "urllib2", "urllib.error"),
- MovedAttribute("ContentTooShortError", "urllib", "urllib.error"),
-]
-for attr in _urllib_error_moved_attributes:
- setattr(Module_six_moves_urllib_error, attr.name, attr)
-del attr
-
-Module_six_moves_urllib_error._moved_attributes = _urllib_error_moved_attributes
-
-_importer._add_module(Module_six_moves_urllib_error(__name__ + ".moves.urllib.error"),
- "moves.urllib_error", "moves.urllib.error")
-
-
-class Module_six_moves_urllib_request(_LazyModule):
- """Lazy loading of moved objects in six.moves.urllib_request"""
-
-
-_urllib_request_moved_attributes = [
- MovedAttribute("urlopen", "urllib2", "urllib.request"),
- MovedAttribute("install_opener", "urllib2", "urllib.request"),
- MovedAttribute("build_opener", "urllib2", "urllib.request"),
- MovedAttribute("pathname2url", "urllib", "urllib.request"),
- MovedAttribute("url2pathname", "urllib", "urllib.request"),
- MovedAttribute("getproxies", "urllib", "urllib.request"),
- MovedAttribute("Request", "urllib2", "urllib.request"),
- MovedAttribute("OpenerDirector", "urllib2", "urllib.request"),
- MovedAttribute("HTTPDefaultErrorHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPRedirectHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPCookieProcessor", "urllib2", "urllib.request"),
- MovedAttribute("ProxyHandler", "urllib2", "urllib.request"),
- MovedAttribute("BaseHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPPasswordMgr", "urllib2", "urllib.request"),
- MovedAttribute("HTTPPasswordMgrWithDefaultRealm", "urllib2", "urllib.request"),
- MovedAttribute("AbstractBasicAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPBasicAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("ProxyBasicAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("AbstractDigestAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPDigestAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("ProxyDigestAuthHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPSHandler", "urllib2", "urllib.request"),
- MovedAttribute("FileHandler", "urllib2", "urllib.request"),
- MovedAttribute("FTPHandler", "urllib2", "urllib.request"),
- MovedAttribute("CacheFTPHandler", "urllib2", "urllib.request"),
- MovedAttribute("UnknownHandler", "urllib2", "urllib.request"),
- MovedAttribute("HTTPErrorProcessor", "urllib2", "urllib.request"),
- MovedAttribute("urlretrieve", "urllib", "urllib.request"),
- MovedAttribute("urlcleanup", "urllib", "urllib.request"),
- MovedAttribute("URLopener", "urllib", "urllib.request"),
- MovedAttribute("FancyURLopener", "urllib", "urllib.request"),
- MovedAttribute("proxy_bypass", "urllib", "urllib.request"),
-]
-for attr in _urllib_request_moved_attributes:
- setattr(Module_six_moves_urllib_request, attr.name, attr)
-del attr
-
-Module_six_moves_urllib_request._moved_attributes = _urllib_request_moved_attributes
-
-_importer._add_module(Module_six_moves_urllib_request(__name__ + ".moves.urllib.request"),
- "moves.urllib_request", "moves.urllib.request")
-
-
-class Module_six_moves_urllib_response(_LazyModule):
- """Lazy loading of moved objects in six.moves.urllib_response"""
-
-
-_urllib_response_moved_attributes = [
- MovedAttribute("addbase", "urllib", "urllib.response"),
- MovedAttribute("addclosehook", "urllib", "urllib.response"),
- MovedAttribute("addinfo", "urllib", "urllib.response"),
- MovedAttribute("addinfourl", "urllib", "urllib.response"),
-]
-for attr in _urllib_response_moved_attributes:
- setattr(Module_six_moves_urllib_response, attr.name, attr)
-del attr
-
-Module_six_moves_urllib_response._moved_attributes = _urllib_response_moved_attributes
-
-_importer._add_module(Module_six_moves_urllib_response(__name__ + ".moves.urllib.response"),
- "moves.urllib_response", "moves.urllib.response")
-
-
-class Module_six_moves_urllib_robotparser(_LazyModule):
- """Lazy loading of moved objects in six.moves.urllib_robotparser"""
-
-
-_urllib_robotparser_moved_attributes = [
- MovedAttribute("RobotFileParser", "robotparser", "urllib.robotparser"),
-]
-for attr in _urllib_robotparser_moved_attributes:
- setattr(Module_six_moves_urllib_robotparser, attr.name, attr)
-del attr
-
-Module_six_moves_urllib_robotparser._moved_attributes = _urllib_robotparser_moved_attributes
-
-_importer._add_module(Module_six_moves_urllib_robotparser(__name__ + ".moves.urllib.robotparser"),
- "moves.urllib_robotparser", "moves.urllib.robotparser")
-
-
-class Module_six_moves_urllib(types.ModuleType):
- """Create a six.moves.urllib namespace that resembles the Python 3 namespace"""
- __path__ = [] # mark as package
- parse = _importer._get_module("moves.urllib_parse")
- error = _importer._get_module("moves.urllib_error")
- request = _importer._get_module("moves.urllib_request")
- response = _importer._get_module("moves.urllib_response")
- robotparser = _importer._get_module("moves.urllib_robotparser")
-
- def __dir__(self):
- return ['parse', 'error', 'request', 'response', 'robotparser']
-
-_importer._add_module(Module_six_moves_urllib(__name__ + ".moves.urllib"),
- "moves.urllib")
-
-
-def add_move(move):
- """Add an item to six.moves."""
- setattr(_MovedItems, move.name, move)
-
-
-def remove_move(name):
- """Remove item from six.moves."""
- try:
- delattr(_MovedItems, name)
- except AttributeError:
- try:
- del moves.__dict__[name]
- except KeyError:
- raise AttributeError("no such move, %r" % (name,))
-
-
-if PY3:
- _meth_func = "__func__"
- _meth_self = "__self__"
-
- _func_closure = "__closure__"
- _func_code = "__code__"
- _func_defaults = "__defaults__"
- _func_globals = "__globals__"
-else:
- _meth_func = "im_func"
- _meth_self = "im_self"
-
- _func_closure = "func_closure"
- _func_code = "func_code"
- _func_defaults = "func_defaults"
- _func_globals = "func_globals"
-
-
-try:
- advance_iterator = next
-except NameError:
- def advance_iterator(it):
- return it.next()
-next = advance_iterator
-
-
-try:
- callable = callable
-except NameError:
- def callable(obj):
- return any("__call__" in klass.__dict__ for klass in type(obj).__mro__)
-
-
-if PY3:
- def get_unbound_function(unbound):
- return unbound
-
- create_bound_method = types.MethodType
-
- Iterator = object
-else:
- def get_unbound_function(unbound):
- return unbound.im_func
-
- def create_bound_method(func, obj):
- return types.MethodType(func, obj, obj.__class__)
-
- class Iterator(object):
-
- def next(self):
- return type(self).__next__(self)
-
- callable = callable
-_add_doc(get_unbound_function,
- """Get the function out of a possibly unbound function""")
-
-
-get_method_function = operator.attrgetter(_meth_func)
-get_method_self = operator.attrgetter(_meth_self)
-get_function_closure = operator.attrgetter(_func_closure)
-get_function_code = operator.attrgetter(_func_code)
-get_function_defaults = operator.attrgetter(_func_defaults)
-get_function_globals = operator.attrgetter(_func_globals)
-
-
-if PY3:
- def iterkeys(d, **kw):
- return iter(d.keys(**kw))
-
- def itervalues(d, **kw):
- return iter(d.values(**kw))
-
- def iteritems(d, **kw):
- return iter(d.items(**kw))
-
- def iterlists(d, **kw):
- return iter(d.lists(**kw))
-else:
- def iterkeys(d, **kw):
- return iter(d.iterkeys(**kw))
-
- def itervalues(d, **kw):
- return iter(d.itervalues(**kw))
-
- def iteritems(d, **kw):
- return iter(d.iteritems(**kw))
-
- def iterlists(d, **kw):
- return iter(d.iterlists(**kw))
-
-_add_doc(iterkeys, "Return an iterator over the keys of a dictionary.")
-_add_doc(itervalues, "Return an iterator over the values of a dictionary.")
-_add_doc(iteritems,
- "Return an iterator over the (key, value) pairs of a dictionary.")
-_add_doc(iterlists,
- "Return an iterator over the (key, [values]) pairs of a dictionary.")
-
-
-if PY3:
- def b(s):
- return s.encode("latin-1")
- def u(s):
- return s
- unichr = chr
- if sys.version_info[1] <= 1:
- def int2byte(i):
- return bytes((i,))
- else:
- # This is about 2x faster than the implementation above on 3.2+
- int2byte = operator.methodcaller("to_bytes", 1, "big")
- byte2int = operator.itemgetter(0)
- indexbytes = operator.getitem
- iterbytes = iter
- import io
- StringIO = io.StringIO
- BytesIO = io.BytesIO
-else:
- def b(s):
- return s
- # Workaround for standalone backslash
- def u(s):
- return unicode(s.replace(r'\\', r'\\\\'), "unicode_escape")
- unichr = unichr
- int2byte = chr
- def byte2int(bs):
- return ord(bs[0])
- def indexbytes(buf, i):
- return ord(buf[i])
- def iterbytes(buf):
- return (ord(byte) for byte in buf)
- import StringIO
- StringIO = BytesIO = StringIO.StringIO
-_add_doc(b, """Byte literal""")
-_add_doc(u, """Text literal""")
-
-
-if PY3:
- exec_ = getattr(moves.builtins, "exec")
-
-
- def reraise(tp, value, tb=None):
- if value.__traceback__ is not tb:
- raise value.with_traceback(tb)
- raise value
-
-else:
- def exec_(_code_, _globs_=None, _locs_=None):
- """Execute code in a namespace."""
- if _globs_ is None:
- frame = sys._getframe(1)
- _globs_ = frame.f_globals
- if _locs_ is None:
- _locs_ = frame.f_locals
- del frame
- elif _locs_ is None:
- _locs_ = _globs_
- exec("""exec _code_ in _globs_, _locs_""")
-
-
- exec_("""def reraise(tp, value, tb=None):
- raise tp, value, tb
-""")
-
-
-print_ = getattr(moves.builtins, "print", None)
-if print_ is None:
- def print_(*args, **kwargs):
- """The new-style print function for Python 2.4 and 2.5."""
- fp = kwargs.pop("file", sys.stdout)
- if fp is None:
- return
- def write(data):
- if not isinstance(data, basestring):
- data = str(data)
- # If the file has an encoding, encode unicode with it.
- if (isinstance(fp, file) and
- isinstance(data, unicode) and
- fp.encoding is not None):
- errors = getattr(fp, "errors", None)
- if errors is None:
- errors = "strict"
- data = data.encode(fp.encoding, errors)
- fp.write(data)
- want_unicode = False
- sep = kwargs.pop("sep", None)
- if sep is not None:
- if isinstance(sep, unicode):
- want_unicode = True
- elif not isinstance(sep, str):
- raise TypeError("sep must be None or a string")
- end = kwargs.pop("end", None)
- if end is not None:
- if isinstance(end, unicode):
- want_unicode = True
- elif not isinstance(end, str):
- raise TypeError("end must be None or a string")
- if kwargs:
- raise TypeError("invalid keyword arguments to print()")
- if not want_unicode:
- for arg in args:
- if isinstance(arg, unicode):
- want_unicode = True
- break
- if want_unicode:
- newline = unicode("\n")
- space = unicode(" ")
- else:
- newline = "\n"
- space = " "
- if sep is None:
- sep = space
- if end is None:
- end = newline
- for i, arg in enumerate(args):
- if i:
- write(sep)
- write(arg)
- write(end)
-
-_add_doc(reraise, """Reraise an exception.""")
-
-if sys.version_info[0:2] < (3, 4):
- def wraps(wrapped):
- def wrapper(f):
- f = functools.wraps(wrapped)(f)
- f.__wrapped__ = wrapped
- return f
- return wrapper
-else:
- wraps = functools.wraps
-
-def with_metaclass(meta, *bases):
- """Create a base class with a metaclass."""
- # This requires a bit of explanation: the basic idea is to make a dummy
- # metaclass for one level of class instantiation that replaces itself with
- # the actual metaclass.
- class metaclass(meta):
- def __new__(cls, name, this_bases, d):
- return meta(name, bases, d)
- return type.__new__(metaclass, 'temporary_class', (), {})
-
-
-def add_metaclass(metaclass):
- """Class decorator for creating a class with a metaclass."""
- def wrapper(cls):
- orig_vars = cls.__dict__.copy()
- orig_vars.pop('__dict__', None)
- orig_vars.pop('__weakref__', None)
- slots = orig_vars.get('__slots__')
- if slots is not None:
- if isinstance(slots, str):
- slots = [slots]
- for slots_var in slots:
- orig_vars.pop(slots_var)
- return metaclass(cls.__name__, cls.__bases__, orig_vars)
- return wrapper
-
-# Complete the moves implementation.
-# This code is at the end of this module to speed up module loading.
-# Turn this module into a package.
-__path__ = [] # required for PEP 302 and PEP 451
-__package__ = __name__ # see PEP 366 @ReservedAssignment
-if globals().get("__spec__") is not None:
- __spec__.submodule_search_locations = [] # PEP 451 @UndefinedVariable
-# Remove other six meta path importers, since they cause problems. This can
-# happen if six is removed from sys.modules and then reloaded. (Setuptools does
-# this for some reason.)
-if sys.meta_path:
- for i, importer in enumerate(sys.meta_path):
- # Here's some real nastiness: Another "instance" of the six module might
- # be floating around. Therefore, we can't use isinstance() to check for
- # the six meta path importer, since the other six instance will have
- # inserted an importer with different class.
- if (type(importer).__name__ == "_SixMetaPathImporter" and
- importer.name == __name__):
- del sys.meta_path[i]
- break
- del i, importer
-# Finally, add the importer to the meta path import hook.
-sys.meta_path.append(_importer)
diff --git a/cobra/flux_analysis/__init__.py b/cobra/flux_analysis/__init__.py
index 9760f38..df132cd 100644
--- a/cobra/flux_analysis/__init__.py
+++ b/cobra/flux_analysis/__init__.py
@@ -4,13 +4,17 @@ except:
numpy = None
from .essentiality import assess_medium_component_essentiality
-from .variability import flux_variability_analysis
-from .single_deletion import single_deletion
+from .variability import flux_variability_analysis, find_blocked_reactions
+from .single_deletion import single_gene_deletion, single_reaction_deletion
+from .parsimonious import optimize_minimal_flux
+from .loopless import construct_loopless_model
+from .gapfilling import growMatch
if numpy:
- from .double_deletion import double_deletion
+ from .double_deletion import double_reaction_deletion, double_gene_deletion
+ from .phenotype_phase_plane import calculate_phenotype_phase_plane
else:
from warnings import warn
- warn("double_deletion requires numpy")
+ warn("double deletions and phase planes requires numpy")
del warn
del numpy
diff --git a/cobra/flux_analysis/deletion_worker.py b/cobra/flux_analysis/deletion_worker.py
index 2e6851e..68e7863 100644
--- a/cobra/flux_analysis/deletion_worker.py
+++ b/cobra/flux_analysis/deletion_worker.py
@@ -1,7 +1,7 @@
from multiprocessing import Queue, Process, cpu_count
from ..solvers import get_solver_name, solver_dict
-from ..external.six import iteritems
+from six import iteritems
def compute_fba_deletion_worker(cobra_model, solver, job_queue, output_queue,
diff --git a/cobra/flux_analysis/double_deletion.py b/cobra/flux_analysis/double_deletion.py
index 9a8aa17..012f9b5 100644
--- a/cobra/flux_analysis/double_deletion.py
+++ b/cobra/flux_analysis/double_deletion.py
@@ -1,80 +1,337 @@
-
-from __future__ import with_statement, print_function
-#cobra.flux_analysis.double_deletion.py
-#runs flux variablity analysis on a Model object.
-from copy import deepcopy
from warnings import warn
-from os import name as __name
-nan = float('nan')
-from sys import modules as __modules
-
from itertools import chain, product
+
+from six import iteritems, string_types
import numpy
from ..solvers import get_solver_name, solver_dict
-from ..external.six import iteritems, string_types
from ..manipulation.delete import find_gene_knockout_reactions, \
get_compiled_gene_reaction_rules
from .deletion_worker import CobraDeletionPool, CobraDeletionMockPool
try:
- from .moma import moma
-except:
- def moma(*args, **kwargs):
- raise Exception("moma dependencies missing")
+ import scipy
+except ImportError:
+ moma = None
+else:
+ from . import moma
try:
from pandas import DataFrame
except:
DataFrame = None
-def double_reaction_deletion_fba(cobra_model, reaction_list1=None,
- reaction_list2=None, solver=None,
- number_of_processes=None,
- return_frame=False, zero_cutoff=1e-15,
- **kwargs):
- """setting n_processes=1 explicitly disables multiprocessing"""
+
+# Utility functions
+def generate_matrix_indexes(ids1, ids2):
+ """map an identifier to an entry in the square result matrix"""
+ return {id: index for index, id in enumerate(set(chain(ids1, ids2)))}
+
+
+def yield_upper_tria_indexes(ids1, ids2, id_to_index):
+ """gives the necessary indexes in the upper triangle
+
+ ids1 and ids2 are lists of the identifiers i.e. gene id's or reaction
+ indexes to be knocked out. id_to_index maps each identifier to its index
+ in the result matrix.
+
+ Note that this does not return indexes for the diagonal. Those have
+ to be computed separately."""
+ # sets to check for inclusion in o(1)
+ id_set1 = set(ids1)
+ id_set2 = set(ids2)
+ for id1, id2 in product(ids1, ids2):
+ # indexes in the result matrix
+ index1 = id_to_index[id1]
+ index2 = id_to_index[id2]
+ # upper triangle
+ if index2 > index1:
+ yield ((index1, index2), (id1, id2))
+ # lower triangle but would be skipped, so return in upper triangle
+ elif id2 not in id_set1 or id1 not in id_set2:
+ yield((index2, index1), (id2, id1)) # note that order flipped
+
+
+def _format_upper_triangular_matrix(row_indexes, column_indexes, matrix):
+ """reformat the square upper-triangular result matrix
+
+ For example, results may look like this
+ [[ A B C D]
+ [ - - - -]
+ [ - - E F]
+ [ - - - G]]
+ In this case, the second row was skipped. This means we have
+ row_indexes [0, 2, 3] and column_indexes [0, 1, 2, 3]
+
+ First, it will reflect the upper triangle into the lower triangle
+ [[ A B C D]
+ [ B - - -]
+ [ C - E F]
+ [ D - F G]]
+
+ Finally, it will remove the missing rows and return
+ [[ A B C D]
+ [ C - E F]
+ [ D - F G]]
+ """
+ results = matrix.copy()
+ # Thse select the indexes for the upper triangle. However, switching
+ # the order selects the lower triangle.
+ triu1, triu2 = numpy.triu_indices(matrix.shape[0])
+ # This makes reflection pretty easy
+ results[triu2, triu1] = results[triu1, triu2]
+ # Remove the missing rows and return.
+ return results[row_indexes, :][:, column_indexes]
+
+
+def format_results_frame(row_ids, column_ids, matrix, return_frame=False):
+ """format results as a pandas.DataFrame if desired/possible
+
+ Otherwise returns a dict of
+ {"x": row_ids, "y": column_ids", "data": result_matrx}"""
+ if return_frame and DataFrame:
+ return DataFrame(data=matrix, index=row_ids, columns=column_ids)
+ elif return_frame and not DataFrame:
+ warn("could not import pandas.DataFrame")
+ return {"x": row_ids, "y": column_ids, "data": matrix}
+
+
+def double_deletion(cobra_model, element_list_1=None, element_list_2=None,
+ element_type='gene', **kwargs):
+ """Wrapper for double_gene_deletion and double_reaction_deletion
+
+ .. deprecated :: 0.4
+ Use double_reaction_deletion and double_gene_deletion
+ """
+ warn("deprecated - use single_reaction_deletion and single_gene_deletion")
+ if element_type == "reaction":
+ return double_reaction_deletion(cobra_model, element_list_1,
+ element_list_2, **kwargs)
+ elif element_type == "gene":
+ return double_gene_deletion(cobra_model, element_list_1,
+ element_list_2, **kwargs)
+ else:
+ raise Exception("unknown element type")
+
+
+def double_reaction_deletion(cobra_model,
+ reaction_list1=None, reaction_list2=None,
+ method="fba", return_frame=False,
+ solver=None, zero_cutoff=1e-12,
+ **kwargs):
+ """sequentially knocks out pairs of reactions in a model
+
+ cobra_model : :class:`~cobra.core.Model.Model`
+ cobra model in which to perform deletions
+
+ reaction_list1 : [:class:`~cobra.core.Reaction.Reaction`:] (or their id's)
+ Reactions to be deleted. These will be the rows in the result.
+ If not provided, all reactions will be used.
+
+ reaction_list2 : [:class:`~cobra.core.Reaction`:] (or their id's)
+ Reactions to be deleted. These will be the rows in the result.
+ If not provided, reaction_list1 will be used.
+
+ method: "fba" or "moma"
+ Procedure used to predict the growth rate
+
+ solver: str for solver name
+ This must be a QP-capable solver for MOMA. If left unspecified,
+ a suitable solver will be automatically chosen.
+
+ zero_cutoff: float
+ When checking to see if a value is 0, this threshold is used.
+
+ return_frame: bool
+ If true, formats the results as a pandas.Dataframe. Otherwise
+ returns a dict of the form:
+ {"x": row_labels, "y": column_labels", "data": 2D matrix}
+ """
+ # handle arguments which need to be passed on
if solver is None:
- solver = get_solver_name()
+ solver = get_solver_name(qp=(method == "moma"))
+ kwargs["solver"] = solver
+ kwargs["zero_cutoff"] = zero_cutoff
+
+ # generate other arguments
+
+ # identifiers for reactions are their indexes
if reaction_list1 is None:
reaction_indexes1 = range(len(cobra_model.reactions))
else:
- reaction_indexes1 = [cobra_model.reactions.index(r) for r in reaction_list1]
+ reaction_indexes1 = [cobra_model.reactions.index(r)
+ for r in reaction_list1]
if reaction_list2 is None:
reaction_indexes2 = reaction_indexes1
else:
- reaction_indexes2 = [cobra_model.reactions.index(r) for r in reaction_list2]
- # results are stored in a matrix. reaction_to_result maps a reaction index
- # to the index in the results matrix
- reaction_indexes = list(set(chain(reaction_indexes1, reaction_indexes2)))
- reaction_to_result = {reaction_index: result_index
- for result_index, reaction_index in enumerate(reaction_indexes)}
- row_indexes = [reaction_to_result[i] for i in reaction_indexes1]
- row_index_set = set(row_indexes)
- row_names = [cobra_model.reactions[i].id for i in reaction_indexes1]
- column_indexes = [reaction_to_result[i] for i in reaction_indexes2]
- column_index_set = set(column_indexes)
- column_names = [cobra_model.reactions[i].id for i in reaction_indexes2]
-
- n_results = len(reaction_to_result)
- results = numpy.empty((n_results, n_results))
- results.fill(numpy.nan)
+ reaction_indexes2 = [cobra_model.reactions.index(r)
+ for r in reaction_list2]
+ reaction_to_result = generate_matrix_indexes(reaction_indexes1,
+ reaction_indexes2)
+ # Determine 0 flux reactions. If an optimal solution passes no flux
+ # through the deleted reactions, then we know removing them will
+ # not change the solution.
wt_solution = solver_dict[solver].solve(cobra_model)
+ if wt_solution.status == "optimal":
+ kwargs["wt_growth_rate"] = wt_solution.f
+ kwargs["no_flux_reaction_indexes"] = \
+ {i for i, v in enumerate(wt_solution.x) if abs(v) < zero_cutoff}
+ else:
+ warn("wild-type solution status is '%s'" % wt_solution.status)
+
+ # call the computing functions
+ if method == "fba":
+ results = _double_reaction_deletion_fba(
+ cobra_model, reaction_indexes1, reaction_indexes2,
+ reaction_to_result, **kwargs)
+ elif method == "moma":
+ results = _double_reaction_deletion_moma(
+ cobra_model, reaction_indexes1, reaction_indexes2,
+ reaction_to_result, **kwargs)
+ else:
+ raise ValueError("Unknown deletion method '%s'" % method)
+
+ # convert upper triangular matrix to full matrix
+ full_result = _format_upper_triangular_matrix(
+ [reaction_to_result[i] for i in reaction_indexes1], # row indexes
+ [reaction_to_result[i] for i in reaction_indexes2], # col indexes
+ results)
+
+ # format appropriately with labels
+ row_ids = [cobra_model.reactions[i].id for i in reaction_indexes1]
+ column_ids = [cobra_model.reactions[i].id for i in reaction_indexes2]
+ return format_results_frame(row_ids, column_ids,
+ full_result, return_frame)
+
+
+def double_gene_deletion(cobra_model,
+ gene_list1=None, gene_list2=None,
+ method="fba", return_frame=False,
+ solver=None, zero_cutoff=1e-12,
+ **kwargs):
+ """sequentially knocks out pairs of genes in a model
+
+ cobra_model : :class:`~cobra.core.Model.Model`
+ cobra model in which to perform deletions
+
+ gene_list1 : [:class:`~cobra.core.Gene.Gene`:] (or their id's)
+ Genes to be deleted. These will be the rows in the result.
+ If not provided, all reactions will be used.
+
+ gene_list1 : [:class:`~cobra.core.Gene.Gene`:] (or their id's)
+ Genes to be deleted. These will be the rows in the result.
+ If not provided, reaction_list1 will be used.
+
+ method: "fba" or "moma"
+ Procedure used to predict the growth rate
+
+ solver: str for solver name
+ This must be a QP-capable solver for MOMA. If left unspecified,
+ a suitable solver will be automatically chosen.
+
+ zero_cutoff: float
+ When checking to see if a value is 0, this threshold is used.
+
+ number_of_processes: int for number of processes to use.
+ If unspecified, the number of parallel processes to use will be
+ automatically determined. Setting this to 1 explicitly disables used
+ of the multiprocessing library.
+
+ .. note:: multiprocessing is not supported with method=moma
+
+ return_frame: bool
+ If true, formats the results as a pandas.Dataframe. Otherwise
+ returns a dict of the form:
+ {"x": row_labels, "y": column_labels", "data": 2D matrix}
+ """
+ # handle arguments which need to be passed on
+ if solver is None:
+ solver = get_solver_name(qp=(method == "moma"))
+ kwargs["solver"] = solver
+ kwargs["zero_cutoff"] = zero_cutoff
+
+ # generate other arguments
+
+ # identifiers for genes
+ if gene_list1 is None:
+ gene_ids1 = cobra_model.genes.list_attr("id")
+ else:
+ gene_ids1 = [str(i) for i in gene_list1]
+ if gene_list2 is None:
+ gene_ids2 = gene_ids1
+ else:
+ gene_ids2 = [str(i) for i in gene_list2]
+
+ # The gene_id_to_result dict will map each gene id to the index
+ # in the result matrix.
+ gene_id_to_result = generate_matrix_indexes(gene_ids1, gene_ids2)
+
# Determine 0 flux reactions. If an optimal solution passes no flux
# through the deleted reactions, then we know removing them will
# not change the solution.
- wt_flux = wt_solution.f
- no_flux_reaction_indexes = {i for i, v in enumerate(wt_solution.x)
- if abs(v) < zero_cutoff}
+ wt_solution = solver_dict[solver].solve(cobra_model)
+ if wt_solution.status == "optimal":
+ kwargs["wt_growth_rate"] = wt_solution.f
+ kwargs["no_flux_reaction_indexes"] = \
+ {i for i, v in enumerate(wt_solution.x) if abs(v) < zero_cutoff}
+ else:
+ warn("wild-type solution status is '%s'" % wt_solution.status)
- if number_of_processes == 1: # explicitly disable multiprocessing
- PoolClass = CobraDeletionMockPool
+ if method == "fba":
+ result = _double_gene_deletion_fba(cobra_model, gene_ids1, gene_ids2,
+ gene_id_to_result, **kwargs)
+ elif method == "moma":
+ result = _double_gene_deletion_moma(cobra_model, gene_ids1, gene_ids2,
+ gene_id_to_result, **kwargs)
else:
- PoolClass = CobraDeletionPool
+ raise ValueError("Unknown deletion method '%s'" % method)
+
+ # convert upper triangular matrix to full matrix
+ full_result = _format_upper_triangular_matrix(
+ [gene_id_to_result[id] for id in gene_ids1], # row indexes
+ [gene_id_to_result[id] for id in gene_ids2], # col indexes,
+ result)
+
+ # format as a Dataframe if required
+ return format_results_frame(gene_ids1, gene_ids2,
+ full_result, return_frame)
+
+
+def _double_reaction_deletion_fba(cobra_model, reaction_indexes1,
+ reaction_indexes2, reaction_to_result,
+ solver, number_of_processes=None,
+ zero_cutoff=1e-15, wt_growth_rate=None,
+ no_flux_reaction_indexes=set(), **kwargs):
+ """compute double reaction deletions using fba
+
+ cobra_model: model
+
+ reaction_indexes1, reaction_indexes2: reaction indexes (used as unique
+ identifiers)
+
+ reaction_to_result: maps each reaction identifier to the entry in
+ the result matrix
+
+ no_flux_reaction_indexes: set of indexes for reactions in the model
+ which carry no flux in an optimal solution. For deletions only in
+ this set, the result will beset to wt_growth_rate.
+
+ returns an upper triangular square matrix
+ """
+ if solver is None:
+ solver = get_solver_name()
+
+ # generate the square result matrix
+ n_results = len(reaction_to_result)
+ results = numpy.empty((n_results, n_results))
+ results.fill(numpy.nan)
+
+ PoolClass = CobraDeletionMockPool if number_of_processes == 1 \
+ else CobraDeletionPool # explicitly disable multiprocessing
+
with PoolClass(cobra_model, n_processes=number_of_processes,
solver=solver, **kwargs) as pool:
- # submit jobs
# precompute all single deletions in the pool and store them along
# the diagonal
@@ -89,101 +346,55 @@ def double_reaction_deletion_fba(cobra_model, reaction_list1=None,
else: # only the diagonal needs to be set
results[result_index, result_index] = value
- for r1_index, r2_index in product(reaction_indexes1, reaction_indexes2):
- r1_result_index = reaction_to_result[r1_index]
- r2_result_index = reaction_to_result[r2_index]
- if r2_result_index > r1_result_index: # upper triangle only
- if results[r1_result_index, r1_result_index] == 0 or \
- results[r2_result_index, r2_result_index] == 0:
- continue
- # reactions removed carry no flux
- if r1_index in no_flux_reaction_indexes and \
- r2_index in no_flux_reaction_indexes:
- results[r1_result_index, r2_result_index] = wt_flux
- continue
- pool.submit((r1_index, r2_index),
- label=(r1_result_index, r2_result_index))
- # if it's a point only in the lower triangle, compute it
- # and put it in the upper triangle
- elif r1_result_index not in column_index_set or \
- r2_result_index not in row_index_set:
- pool.submit((r1_index, r2_index),
- label=(r2_result_index, r1_result_index))
-
+ # Run double knockouts in the upper triangle
+ index_selector = yield_upper_tria_indexes(
+ reaction_indexes1, reaction_indexes2, reaction_to_result)
+ for result_index, (r1_index, r2_index) in index_selector:
+ # skip if the result was already computed to be lethal
+ if results[result_index] == 0:
+ continue
+ # reactions removed carry no flux
+ if r1_index in no_flux_reaction_indexes and \
+ r2_index in no_flux_reaction_indexes:
+ results[result_index] = wt_growth_rate
+ continue
+ pool.submit((r1_index, r2_index), label=result_index)
# get results
for result in pool.receive_all():
results[result[0]] = result[1]
+ return results
- # reflect results
- triu1, triu2 = numpy.triu_indices(n_results)
- results[triu2, triu1] = results[triu1, triu2]
- results = results[row_indexes, :][:, column_indexes]
+def _double_gene_deletion_fba(cobra_model, gene_ids1, gene_ids2,
+ gene_id_to_result, solver,
+ number_of_processes=None, zero_cutoff=1e-12,
+ wt_growth_rate=None,
+ no_flux_reaction_indexes=set(), **kwargs):
+ """compute double gene deletions using fba
- if return_frame and DataFrame:
- return DataFrame(data=results, index=row_names, columns=column_names)
+ cobra_model: model
- elif return_frame and not DataFrame:
- warn("could not import pandas.DataFrame")
+ gene_ids1, gene_ids2: lists of id's to be knocked out
- return {"x": [cobra_model.reactions.get_by_id(i) for i in row_names],
- "y": [cobra_model.reactions.get_by_id(i) for i in column_names],
- "data": results}
+ gene_id_to_result: maps each gene identifier to the entry in
+ the result matrix
-def double_gene_deletion_fba(cobra_model, gene_list1=None, gene_list2=None,
- solver=None, number_of_processes=None,
- return_frame=False, zero_cutoff=1e-12, **kwargs):
- if solver is None:
- solver = get_solver_name()
- if gene_list1 is None:
- gene_list1 = cobra_model.genes
- else:
- gene_list1 = [cobra_model.genes.get_by_id(i)
- if isinstance(i, string_types) else i
- for i in gene_list1]
- if gene_list2 is None:
- gene_list2 = gene_list1
- else:
- gene_list2 = [cobra_model.genes.get_by_id(i)
- if isinstance(i, string_types) else i
- for i in gene_list2]
+ no_flux_reaction_indexes: set of indexes for reactions in the model
+ which carry no flux in an optimal solution. For deletions only in
+ this set, the result will beset to wt_growth_rate.
+
+ returns an upper triangular square matrix
+ """
# Because each gene reaction rule will be evaluated multiple times
# the reaction has multiple associated genes being deleted, compiling
# the gene reaction rules ahead of time increases efficiency greatly.
compiled_rules = get_compiled_gene_reaction_rules(cobra_model)
- # Store results in a matrix. The gene_id_to_result dict will map each
- # gene id to the index in the result matrix
- gene_ids1 = [i.id for i in gene_list1]
- gene_ids2 = [i.id for i in gene_list2]
- gene_id_to_result = {}
- n = 0
- for i in gene_ids1:
- if i not in gene_id_to_result:
- gene_id_to_result[i] = n
- n += 1
- for i in gene_ids2:
- if i not in gene_id_to_result:
- gene_id_to_result[i] = n
- n += 1
-
- row_indexes = [gene_id_to_result[id] for id in gene_ids1]
- row_index_set = set(row_indexes)
- column_indexes = [gene_id_to_result[id] for id in gene_ids2]
- column_index_set = set(column_indexes)
n_results = len(gene_id_to_result)
results = numpy.empty((n_results, n_results))
results.fill(numpy.nan)
- wt_solution = solver_dict[solver].solve(cobra_model)
- # Determine 0 flux reactions. If an optimal solution passes no flux
- # through the deleted reactions, then we know removing them will
- # not change the solution.
- wt_flux = wt_solution.f
- no_flux_reaction_indexes = {i for i, v in enumerate(wt_solution.x)
- if abs(v) < zero_cutoff}
-
if number_of_processes == 1: # explicitly disable multiprocessing
PoolClass = CobraDeletionMockPool
else:
@@ -205,35 +416,24 @@ def double_gene_deletion_fba(cobra_model, gene_list1=None, gene_list2=None,
results[:, result_index] = 0.
else: # only the diagonal needs to be set
results[result_index, result_index] = value
- # double deletions
- for gene1, gene2 in product(gene_list1, gene_list2):
- g1_result_index = gene_id_to_result[gene1.id]
- g2_result_index = gene_id_to_result[gene2.id]
- if g2_result_index > g1_result_index: # upper triangle only
- # if singly lethal the results have already been set
- if results[g1_result_index, g1_result_index] == 0 or \
- results[g2_result_index, g2_result_index] == 0:
- continue
- ko_reactions = find_gene_knockout_reactions(
- cobra_model, (gene1, gene2), compiled_rules)
- ko_indexes = [cobra_model.reactions.index(i)
- for i in ko_reactions]
- # if all removed gene indexes carry no flux
- if len(set(ko_indexes) - no_flux_reaction_indexes) == 0:
- results[g1_result_index, g2_result_index] = wt_flux
- continue
- pool.submit(ko_indexes,
- label=(g1_result_index, g2_result_index))
- # if it's a point only in the lower triangle, compute it
- # and put it in the upper triangle
- elif g1_result_index not in column_index_set or \
- g2_result_index not in row_index_set:
- ko_reactions = find_gene_knockout_reactions(
- cobra_model, (gene1, gene2), compiled_rules)
- ko_indexes = [cobra_model.reactions.index(i)
- for i in ko_reactions]
- pool.submit(ko_indexes,
- label=(g2_result_index, g1_result_index))
+
+ # Run double knockouts in the upper triangle
+ index_selector = yield_upper_tria_indexes(gene_ids1, gene_ids2,
+ gene_id_to_result)
+ for result_index, (gene1, gene2) in index_selector:
+
+ # if singly lethal the results have already been set
+ if results[result_index] == 0:
+ continue
+ ko_reactions = find_gene_knockout_reactions(
+ cobra_model, (gene1, gene2), compiled_rules)
+ ko_indexes = [cobra_model.reactions.index(i)
+ for i in ko_reactions]
+ # if all removed gene indexes carry no flux
+ if len(set(ko_indexes) - no_flux_reaction_indexes) == 0:
+ results[result_index] = wt_growth_rate
+ continue
+ pool.submit(ko_indexes, label=result_index)
for result in pool.receive_all():
value = result[1]
@@ -241,304 +441,140 @@ def double_gene_deletion_fba(cobra_model, gene_list1=None, gene_list2=None,
value = 0
results[result[0]] = value
- del pool
-
- # reflect results
- triu1, triu2 = numpy.triu_indices(n_results)
- results[triu2, triu1] = results[triu1, triu2]
+ return results
- results = results[row_indexes, :][:, column_indexes]
- if return_frame and DataFrame:
- return DataFrame(data=results, index=gene_ids1, columns=gene_ids2)
+def _double_reaction_deletion_moma(cobra_model, reaction_indexes1,
+ reaction_indexes2, reaction_to_result,
+ solver, number_of_processes=1,
+ zero_cutoff=1e-15, wt_growth_rate=None,
+ no_flux_reaction_indexes=set(), **kwargs):
+ """compute double reaction deletions using moma
- elif return_frame and not DataFrame:
- warn("could not import pandas.DataFrame")
+ cobra_model: model
- return {"x": [cobra_model.genes.get_by_id(i) for i in gene_ids1],
- "y": [cobra_model.genes.get_by_id(i) for i in gene_ids2],
- "data": results}
+ reaction_indexes1, reaction_indexes2: reaction indexes (used as unique
+ identifiers)
+ reaction_to_result: maps each reaction identifier to the entry in
+ the result matrix
-def double_deletion(cobra_model, element_list_1=None, element_list_2=None,
- method='fba', single_deletion_growth_dict=None,
- element_type='gene', solver=None,
- number_of_processes=None,
- return_frame=False, zero_cutoff=1e-12,
- **kwargs):
- """Run double gene or reaction deletions
+ no_flux_reaction_indexes: set of indexes for reactions in the model
+ which carry no flux in an optimal solution. For deletions only in
+ this set, the result will beset to wt_growth_rate.
- cobra_model: a cobra.Model object
+ number_of_processes: must be 1. Parallel MOMA not yet implmemented
- element_list_1: None or a list of elements (genes or reactions)
+ returns an upper triangular square matrix
+ """
+ if number_of_processes > 1:
+ raise NotImplementedError("parallel MOMA not implemented")
+ if moma is None:
+ raise RuntimeError("scipy required for MOMA")
- element_list_2: None or a list of elements (genes or reactions)
+ # generate the square result matrix
+ n_results = len(reaction_to_result)
+ results = numpy.empty((n_results, n_results))
+ results.fill(numpy.nan)
- method: 'fba' or 'moma'
- Whether to compute growth rates using flux balance analysis or
- minimization of metabolic adjustments.
+ # function to compute reaction knockouts with moma
+ moma_model, moma_obj = moma.create_euclidian_moma_model(cobra_model)
+
+ def run(indexes):
+ # If all the reactions carry no flux, deletion will have no effect.
+ if no_flux_reaction_indexes.issuperset(indexes):
+ return wt_growth_rate
+ return moma.moma_knockout(moma_model, moma_obj, indexes,
+ solver=solver, **kwargs).f
+
+ # precompute all single deletions and store them along the diagonal
+ for reaction_index, result_index in iteritems(reaction_to_result):
+ value = run((reaction_index,))
+ value = value if abs(value) > zero_cutoff else 0.
+ results[result_index, result_index] = value
+ # if singly lethal, the entire row and column are set to 0
+ if value == 0.:
+ results[result_index, :] = 0.
+ results[:, result_index] = 0.
+
+ # Run double knockouts in the upper triangle
+ index_selector = yield_upper_tria_indexes(
+ reaction_indexes1, reaction_indexes2, reaction_to_result)
+ for result_index, (r1_index, r2_index) in index_selector:
+ # skip if the result was already computed to be lethal
+ if results[result_index] == 0:
+ continue
+ else:
+ results[result_index] = run((r1_index, r2_index))
- number_of_processes: None or int
- The number of processor core to use. Setting 1 explicitly disables
- use of the multiprocessing library. By default, up to 4 cores will be
- used if available.
+ return results
- element_type: 'gene' or 'reaction'
- zero_cutoff: float
- For single deletions which are assumed to be lethal, any double
- deletion will also be assumed to be lethal. Additionally, removing only
- reactions with no flux will assume the result is the same as wild-type.
- This parameter sets the cutoff for the absolute value to determine if a
- flux is 0. To disable this optimization, set this to a negative value.
+def _double_gene_deletion_moma(cobra_model, gene_ids1, gene_ids2,
+ gene_id_to_result, solver,
+ number_of_processes=1,
+ zero_cutoff=1e-12, wt_growth_rate=None,
+ no_flux_reaction_indexes=set(), **kwargs):
+ """compute double gene deletions using moma
- solver: 'glpk', 'cglpk', 'gurobi', 'cplex' or None
+ cobra_model: model
- return_frame: bool
- If True, format data as a pandas Dataframe
+ gene_ids1, gene_ids2: lists of id's to be knocked out
- Returns a dictionary of the elements in the x dimension (x), the y
- dimension (y), and the growth simulation data (data).
+ gene_id_to_result: maps each gene identifier to the entry in
+ the result matrix
- """
+ number_of_processes: must be 1. Parallel MOMA not yet implemented
- if "error_reporting" in kwargs:
- warn("error_reporting option removed")
- kwargs.pop("error_reporting")
- if "single_deletion_growth_dict" in kwargs:
- warn("single_deletion_growth_dict option removed")
- kwargs.pop("single_deletion_growth_dict")
+ no_flux_reaction_indexes: set of indexes for reactions in the model
+ which carry no flux in an optimal solution. For deletions only in
+ this set, the result will beset to wt_growth_rate.
- if method == "fba":
- if element_type == "gene":
- return double_gene_deletion_fba(
- cobra_model,
- gene_list1=element_list_1,
- gene_list2=element_list_2,
- solver=solver,
- return_frame=return_frame,
- zero_cutoff=zero_cutoff,
- number_of_processes=number_of_processes,
- **kwargs)
- elif element_type == "reaction":
- return double_reaction_deletion_fba(
- cobra_model,
- reaction_list1=element_list_1,
- reaction_list2=element_list_2,
- solver=solver,
- zero_cutoff=zero_cutoff,
- return_frame=return_frame,
- number_of_processes=number_of_processes,
- **kwargs)
- else:
- raise ValueError("element_type %s not gene or reaction" %
- element_type)
+ returns an upper triangular square matrix
+ """
+ if number_of_processes > 1:
+ raise NotImplementedError("parallel MOMA not implemented")
+ if moma is None:
+ raise RuntimeError("scipy required for MOMA")
- if method != "moma":
- raise ValueError("method %s is not fba or moma" % method)
+ # Because each gene reaction rule will be evaluated multiple times
+ # the reaction has multiple associated genes being deleted, compiling
+ # the gene reaction rules ahead of time increases efficiency greatly.
+ compiled_rules = get_compiled_gene_reaction_rules(cobra_model)
- if solver is None:
- solver = get_solver_name()
+ # function to compute reaction knockouts with moma
+ moma_model, moma_obj = moma.create_euclidian_moma_model(cobra_model)
- if number_of_processes > 1:
- warn("parallel moma double deletion not implemented")
-
- if element_type == 'gene':
- return double_gene_deletion_moma(
- cobra_model, gene_list_1=element_list_1,
- gene_list_2=element_list_2, method=method,
- single_deletion_growth_dict=single_deletion_growth_dict,
- solver=solver,
- error_reporting=error_reporting)
- else:
- raise Exception("Double reaction deletion with moma not yet implemented")
-
-def double_gene_deletion_moma(cobra_model, gene_list_1=None, gene_list_2=None,
- method='moma', single_deletion_growth_dict=None,
- solver='glpk', growth_tolerance=1e-8,
- error_reporting=None):
- """This will disable reactions for all gene pairs from gene_list_1 and
- gene_list_2 and then run simulations to optimize for the objective
- function. The contribution of each reaction to the objective function
- is indicated in cobra_model.reactions[:].objective_coefficient vector.
-
- NOTE: We've assumed that there is no such thing as a synthetic rescue with
- this modeling framework.
-
- cobra_model: a cobra.Model object
-
- gene_list_1: Is None or a list of genes. If None then both gene_list_1
- and gene_list_2 are assumed to correspond to cobra_model.genes.
-
- gene_list_2: Is None or a list of genes. If None then gene_list_2 is
- assumed to correspond to gene_list_1.
-
- method: 'fba' or 'moma' to run flux balance analysis or minimization
- of metabolic adjustments.
-
- single_deletion_growth_dict: A dictionary that provides the growth
- rate information for single gene knock outs. This can speed up
- simulations because nonviable single deletion strains imply that all
- double deletion strains will also be nonviable.
-
- solver: 'glpk', 'gurobi', or 'cplex'.
-
- error_reporting: None or True
-
- growth_tolerance: float. The effective lower bound on the growth rate
- for a single deletion that is still considered capable of growth.
-
- Returns a dictionary of the gene ids in the x dimension (x) and the y
- dimension (y), and the growth simulation data (data).
-
- """
- #BUG: Since this might be called from ppmap, the modules need to
- #be imported. Modify ppmap to take depfuncs
- from numpy import zeros
- nan = float('nan')
- from cobra.flux_analysis.single_deletion import single_deletion
- from cobra.manipulation import delete_model_genes, undelete_model_genes
- ##TODO: Use keywords instead
- if isinstance(cobra_model, dict):
- tmp_dict = cobra_model
- cobra_model = tmp_dict['cobra_model']
- if 'gene_list_1' in tmp_dict:
- gene_list_1 = tmp_dict['gene_list_1']
- if 'gene_list_2' in tmp_dict:
- gene_list_2 = tmp_dict['gene_list_2']
- if 'method' in tmp_dict:
- method = tmp_dict['method']
- if 'single_deletion_growth_dict' in tmp_dict:
- single_deletion_growth_dict = tmp_dict['single_deletion_growth_dict']
- if 'solver' in tmp_dict:
- solver = tmp_dict['solver']
- if 'error_reporting' in tmp_dict:
- error_reporting = tmp_dict['error_reporting']
- else:
- cobra_model = cobra_model
- #this is a slow way to revert models.
- wt_model = cobra_model #NOTE: It may no longer be necessary to use a wt_model
- #due to undelete_model_genes
- if gene_list_1 is None:
- gene_list_1 = cobra_model.genes
- elif not hasattr(gene_list_1[0], 'id'):
- gene_list_1 = map(cobra_model.genes.get_by_id, gene_list_1)
- #Get default values to use if the deletions do not alter any reactions
- cobra_model.optimize(solver=solver)
- basal_f = cobra_model.solution.f
- if method.lower() == 'moma':
- wt_model = cobra_model.copy()
- combined_model = None
- single_gene_set = set(gene_list_1)
- if gene_list_2 is not None:
- if not hasattr(gene_list_2[0], 'id'):
- gene_list_2 = map(cobra_model.genes.get_by_id, gene_list_2)
- single_gene_set.update(gene_list_2)
- #Run the single deletion analysis to account for double deletions that
- #target the same gene and lethal deletions. We assume that there
- #aren't synthetic rescues.
- single_deletion_growth_dict = single_deletion(cobra_model,
- list(single_gene_set),
- method=method,
- solver=solver)[0]
- if gene_list_2 is None or gene_list_1 == gene_list_2:
- number_of_genes = len(gene_list_1)
- gene_list_2 = gene_list_1
- deletion_array = zeros([number_of_genes, number_of_genes])
- ##TODO: Speed up this triangular process
- #For the case where the contents of the lists are the same cut the work in half.
- #There might be a faster way to do this by using a triangular array function
- #in numpy
- #Populate the diagonal from the single deletion lists
- for i, the_gene in enumerate(gene_list_1):
- deletion_array[i, i] = single_deletion_growth_dict[the_gene.id]
- for i, gene_1 in enumerate(gene_list_1[:-1]):
- #TODO: Since there cannot be synthetic rescues we can assume
- #that the whole row for a lethal deletion
- #will be equal to that deletion.
- if single_deletion_growth_dict[gene_1.id] < growth_tolerance:
- tmp_solution = single_deletion_growth_dict[gene_1.id]
- for j in range(i+1, number_of_genes):
- deletion_array[j, i] = deletion_array[i, j] = tmp_solution
- else:
- for j, gene_2 in enumerate(gene_list_1[i+1:], i+1):
- if single_deletion_growth_dict[gene_2.id] < growth_tolerance:
- tmp_solution = single_deletion_growth_dict[gene_2.id]
- else:
- delete_model_genes(cobra_model, [gene_1, gene_2])
- if cobra_model._trimmed:
- if method.lower() == 'fba':
- #Assumes that the majority of perturbations don't change
- #reactions which is probably false
- cobra_model.optimize(solver=solver, error_reporting=error_reporting)
- the_status = cobra_model.solution.status
- tmp_solution = cobra_model.solution.f
- elif method.lower() == 'moma':
- try:
- moma_solution = moma(wt_model, cobra_model,
- combined_model=combined_model,
- solver=solver)
- tmp_solution = float(moma_solution.pop('objective_value'))
- the_status = moma_solution.pop('status')
- combined_model = moma_solution.pop('combined_model')
- del moma_solution
- except:
- tmp_solution = nan
- the_status = 'failed'
- if the_status not in ['opt', 'optimal'] and \
- error_reporting:
- print('%s / %s: %s status: %s'%(gene_1, gene_2, solver,
- the_status))
- #Reset the model to orginial form.
- undelete_model_genes(cobra_model)
- else:
- tmp_solution = basal_f
- deletion_array[j, i] = deletion_array[i, j] = tmp_solution
+ def run(gene_ids):
+ ko_reactions = find_gene_knockout_reactions(cobra_model, gene_ids)
+ ko_indexes = map(cobra_model.reactions.index, ko_reactions)
+ # If all the reactions carry no flux, deletion will have no effect.
+ if no_flux_reaction_indexes.issuperset(gene_ids):
+ return wt_growth_rate
+ return moma.moma_knockout(moma_model, moma_obj, ko_indexes,
+ solver=solver, **kwargs).f
- else:
- deletion_array = zeros([len(gene_list_1), len(gene_list_2)])
- #Now deal with the case where the gene lists are different
- for i, gene_1 in enumerate(gene_list_1):
- if single_deletion_growth_dict[gene_1.id] <= 0:
- for j in range(len(gene_list_2)):
- deletion_array[i, j] = 0.
- else:
- for j, gene_2 in enumerate(gene_list_2):
- #Assume no such thing as a synthetic rescue
- if single_deletion_growth_dict[gene_2.id] <= growth_tolerance:
- tmp_solution = single_deletion_growth_dict[gene_2.id]
- else:
- delete_model_genes(cobra_model, [gene_1, gene_2])
- if cobra_model._trimmed:
- if method.lower() == 'fba':
- cobra_model.optimize(solver=solver)
- tmp_solution = cobra_model.solution.f
- the_status = cobra_model.solution.status
- elif method.lower() == 'moma':
- try:
- moma_solution = moma(wt_model, cobra_model,
- combined_model=combined_model,
- solver=solver)
- tmp_solution = float(moma_solution.pop('objective_value'))
- the_status = moma_solution.pop('status')
- combined_model = moma_solution.pop('combined_model')
- del moma_solution
- except:
- tmp_solution = nan
- the_status = 'failed'
- if the_status not in ['opt', 'optimal'] and \
- error_reporting:
- print('%s / %s: %s status: %s'%(repr(gene_1), repr(gene_2), solver,
- cobra_model.solution.status))
- #Reset the model to wt form
- undelete_model_genes(cobra_model)
- else:
- tmp_solution = basal_f
- deletion_array[i, j] = tmp_solution
- if hasattr(gene_list_1, 'id'):
- gene_list_1 = [x.id for x in gene_list_1]
- if hasattr(gene_list_2, 'id'):
- gene_list_2 = [x.id for x in gene_list_2]
-
- return({'x': gene_list_1, 'y': gene_list_2, 'data': deletion_array})
+ n_results = len(gene_id_to_result)
+ results = numpy.empty((n_results, n_results))
+ results.fill(numpy.nan)
+ # precompute all single deletions and store them along the diagonal
+ for gene_id, result_index in iteritems(gene_id_to_result):
+ value = run((gene_id,))
+ value = value if abs(value) > zero_cutoff else 0.
+ results[result_index, result_index] = value
+ # If singly lethal, the entire row and column are set to 0.
+ if value == 0.:
+ results[result_index, :] = 0.
+ results[:, result_index] = 0.
+
+ # Run double knockouts in the upper triangle
+ index_selector = yield_upper_tria_indexes(gene_ids1, gene_ids2,
+ gene_id_to_result)
+ for result_index, (gene1, gene2) in index_selector:
+ # if singly lethal the results have already been set
+ if results[result_index] == 0:
+ continue
+ results[result_index] = run((gene1, gene2))
+
+ return results
diff --git a/cobra/flux_analysis/essentiality.py b/cobra/flux_analysis/essentiality.py
index 38cc06f..ee4435e 100644
--- a/cobra/flux_analysis/essentiality.py
+++ b/cobra/flux_analysis/essentiality.py
@@ -1,21 +1,8 @@
-from __future__ import with_statement
-#cobra.flux_analysis.essentiality.py
-#runs flux variablity analysis on a Model object.
-from os import name as __name
from warnings import warn
-if __name == 'java':
- warn("moma is not supported on %s"%__name)
- warn("flux_analysis.double_deletion is not supported on %s"%__name)
- def moma(a, **kwargs):
- raise Exception("moma is not supported on %s"%__name)
-
- def double_deletion(a, **kwargs):
- raise Exception("flux_analysis.double_deletion is not supported on %s"%__name)
-else:
- try:
- from cobra.flux_analysis.moma import moma
- except:
- warn("moma does not appear to be functional on your system")
+try:
+ from cobra.flux_analysis.moma import moma
+except:
+ warn("moma does not appear to be functional on your system")
from cobra.manipulation import initialize_growth_medium
def assess_medium_component_essentiality(cobra_model, the_components=None,
the_medium=None, medium_compartment='e', solver='glpk',
@@ -80,13 +67,3 @@ def assess_medium_component_essentiality(cobra_model, the_components=None,
the_reaction.lower_bound = original_lower_bound
return(essentiality_dict)
-
-def deletion_analysis(cobra_model, the_medium=None, deletion_type='single',
- work_directory=None, growth_cutoff=0.001,
- the_problem='return', number_of_processes=6, element_type='gene',
- solver='glpk', error_reporting=None, method='fba', element_list=None):
- """Performs single and/or double deletion analysis on all the genes in the model. Provides
- an interface to parallelize the deletion studies.
-
- """
- raise Exception("Deletion analysis has been dropped in favor of the single_deletion and double_deletion modules")
diff --git a/cobra/flux_analysis/gapfilling.py b/cobra/flux_analysis/gapfilling.py
new file mode 100644
index 0000000..d3d1602
--- /dev/null
+++ b/cobra/flux_analysis/gapfilling.py
@@ -0,0 +1,165 @@
+from __future__ import print_function
+
+from ..core import Model, Reaction, Metabolite
+from ..solvers import get_solver_name
+from ..manipulation import modify
+
+
+class SUXModelMILP(Model):
+ """Model with additional Universal and Exchange reactions.
+ Adds corresponding dummy reactions and dummy metabolites for each added
+ reaction which are used to impose MILP constraints to minimize the
+ total number of added reactions. See the figure for more
+ information on the structure of the matrix.
+ """
+ def __init__(self, model, Universal=None, threshold=.05,
+ penalties=None, dm_rxns=True, ex_rxns=False):
+ Model.__init__(self, "")
+ # store parameters
+ self.threshold = threshold
+ if penalties is None:
+ self.penalties = {"Universal": 1, "Exchange": 100, "Demand": 1}
+ else:
+ self.penalties = penalties
+ # want to only operate on a copy of Universal so as not to mess up
+ # is this necessary?
+ if Universal is None:
+ Universal = Model("Universal_Reactions")
+ else:
+ Universal = Universal.copy()
+
+ modify.convert_to_irreversible(Universal)
+
+ for rxn in Universal.reactions:
+ rxn.notes["gapfilling_type"] = "Universal"
+
+ # SUX += Exchange (when exchange generator has been written)
+ # For now, adding exchange reactions to Universal - could add to a new
+ # model called exchange and allow their addition or not....
+ if ex_rxns:
+ for m in model.metabolites:
+ rxn = Reaction('SMILEY_EX_' + m.id)
+ rxn.lower_bound = 0
+ rxn.upper_bound = 1000
+ rxn.add_metabolites({m: 1.0})
+ rxn.notes["gapfilling_type"] = "Exchange"
+ Universal.add_reaction(rxn)
+
+ if dm_rxns:
+ # ADD DEMAND REACTIONS FOR ALL METABOLITES TO UNIVERSAL MODEL
+ for m in model.metabolites:
+ rxn = Reaction('SMILEY_DM_' + m.id)
+ rxn.lower_bound = 0
+ rxn.upper_bound = 1000
+ rxn.add_metabolites({m: -1.0})
+ rxn.notes["gapfilling_type"] = "Demand"
+ Universal.add_reaction(rxn)
+
+ Model.add_reactions(self, model.copy().reactions)
+ Model.add_reactions(self, Universal.reactions)
+
+ # all reactions with an index < len(model.reactions) were original
+ self.original_reactions = self.reactions[:len(model.reactions)]
+ self.added_reactions = self.reactions[len(model.reactions):]
+
+ # Add MILP indicator reactions
+ indicators = []
+ for reaction in self.added_reactions:
+ dummy_metabolite = Metabolite("dummy_met_" + reaction.id)
+ dummy_metabolite._constraint_sense = "L"
+ reaction.add_metabolites({dummy_metabolite: 1})
+ indicator_reaction = Reaction("indicator_" + reaction.id)
+ indicator_reaction.add_metabolites(
+ {dummy_metabolite: -1 * reaction.upper_bound})
+ indicator_reaction.lower_bound = 0
+ indicator_reaction.upper_bound = 1
+ indicator_reaction.variable_kind = "integer"
+ indicator_reaction.objective_coefficient = \
+ self.penalties[reaction.notes["gapfilling_type"]]
+ indicators.append(indicator_reaction)
+ Model.add_reactions(self, indicators)
+
+ # original reaction objectives need to be set to lower bounds
+ self._update_objectives()
+
+ def _update_objectives(self, added=True):
+ """Update the metabolite which encodes the objective function
+ with the objective coefficients for the reaction, and impose
+ penalties for added reactions.
+ """
+ for reaction in self.original_reactions:
+ if reaction.objective_coefficient > 0:
+ reaction.lower_bound = max(
+ reaction.lower_bound,
+ reaction.objective_coefficient * self.threshold)
+ reaction.objective_coefficient = 0
+
+ def add_reactions(self, reactions):
+ Model.add_reactions(self, reactions)
+ self.original_reactions.extend(reactions)
+ self._update_objectives()
+
+ def solve(self, solver=None, iterations=1, debug=False, time_limit=100,
+ **solver_parameters):
+ """solve the MILP problem"""
+ if solver is None:
+ solver = get_solver_name(mip=True)
+ used_reactions = [None] * iterations
+ numeric_error_cutoff = 0.0001
+ self._update_objectives()
+ for i in range(iterations):
+ used_reactions[i] = []
+ self.optimize(objective_sense="minimize",
+ solver=solver, **solver_parameters)
+ if debug:
+ print("Iteration %d: Status is %s" % (i, self.solution.status))
+ for reaction in self.added_reactions:
+ # The dummy reaction should have a flux of either 0 or 1.
+ # If it is 1 (nonzero), then the reaction was used in
+ # the solution.
+ ind = self.reactions.get_by_id("indicator_" + reaction.id)
+ if ind.x > numeric_error_cutoff:
+ used_reactions[i].append(reaction)
+ ind.objective_coefficient += \
+ self.penalties[reaction.notes["gapfilling_type"]]
+ if debug:
+ print(' ', reaction, reaction.objective_coefficient)
+
+ return used_reactions
+
+
+def growMatch(model, Universal, dm_rxns=False, ex_rxns=False,
+ penalties=None, **solver_parameters):
+ """runs growMatch"""
+ SUX = SUXModelMILP(model, Universal, dm_rxns=dm_rxns, ex_rxns=ex_rxns,
+ penalties=penalties)
+ return SUX.solve(**solver_parameters)
+
+
+def SMILEY(model, metabolite_id, Universal,
+ dm_rxns=False, ex_rxns=False, panalties=None, **solver_parameters):
+ """
+ runs the SMILEY algorithm to determine which gaps should be
+ filled in order for the model to create the metabolite with the
+ given metabolite_id.
+
+ This function is good for running the algorithm once. For more fine-
+ grained control, create a SUXModelMILP object, add a demand reaction
+ for the given metabolite_id, and call the solve function on the
+ SUXModelMILP object.
+ """
+ SUX = SUXModelMILP(model, Universal, dm_rxns=dm_rxns, ex_rxns=ex_rxns,
+ penalties=penalties)
+ # change the objective to be the metabolite
+ for reaction in SUX.original_reactions:
+ reaction.objective_coefficient = 0
+ demand_name = "SMILEY_DM_" + metabolite_id
+ if demand_name not in SUX.reactions:
+ demand_reaction = Reaction(demand_name)
+ demand_reaction.add_metabolites(
+ {SUX.metabolites.get_by_id(metabolite_id): -1})
+ SUX.add_reaction(demand_reaction)
+ else:
+ demand_reaction = SUX.reactions.get_by_id(demand_name)
+ demand_reaction.lower_bound = SUX.threshold
+ return SUX.solve(**solver_parameters)
diff --git a/cobra/flux_analysis/loopless.py b/cobra/flux_analysis/loopless.py
index 9aad6df..f1ed6b6 100644
--- a/cobra/flux_analysis/loopless.py
+++ b/cobra/flux_analysis/loopless.py
@@ -1,6 +1,6 @@
from ..core import Reaction, Metabolite
from ..manipulation.modify import convert_to_irreversible
-from ..external.six import iteritems
+from six import iteritems
def construct_loopless_model(cobra_model):
diff --git a/cobra/flux_analysis/moma.py b/cobra/flux_analysis/moma.py
index 0f37177..11b7967 100644
--- a/cobra/flux_analysis/moma.py
+++ b/cobra/flux_analysis/moma.py
@@ -1,245 +1,112 @@
-from __future__ import print_function
-#cobra.flux_analysis.moma.py: Runs the minimization of metabolic
-#adjustment method described in Segre et al 2002 PNAS 99(23): 15112-7
-from os import name as __name
-from sys import modules as __modules
-from warnings import warn
-if __name == 'java':
- raise Exception("%s is not yet supported on jython"%__modules[__name__])
-from copy import deepcopy
-from time import time
-from math import ceil, floor
-
-#The next four imports need to be dealt with to obtain jython compatibilty
-from numpy import array, hstack, vstack, matrix, sum
-from scipy.sparse import eye, lil_matrix, dok_matrix
-from scipy.sparse import hstack as s_hstack
-from scipy.sparse import vstack as s_vstack
-
-from ..core import Reaction, Metabolite
-from ..manipulation import initialize_growth_medium, delete_model_genes
-from ..manipulation.modify import convert_to_irreversible
-from ..external.six import iteritems
-
-from warnings import warn
-
-def moma(wt_model, mutant_model, objective_sense='maximize', solver=None,
- tolerance_optimality=1e-8, tolerance_feasibility=1e-8,
- minimize_norm=False, the_problem='return', lp_method=0,
- combined_model=None, norm_type='euclidean'):
- """Runs the minimization of metabolic adjustment method described in
- Segre et al 2002 PNAS 99(23): 15112-7.
-
- wt_model: A cobra.Model object
-
- mutant_model: A cobra.Model object with different reaction bounds vs wt_model.
- To simulate deletions
-
- objective_sense: 'maximize' or 'minimize'
-
- solver: 'gurobi', 'cplex', or 'glpk'. Note: glpk cannot be used with
- norm_type 'euclidean'
-
- tolerance_optimality: Solver tolerance for optimality.
-
- tolerance_feasibility: Solver tolerance for feasibility.
-
- the_problem: None or a problem object for the specific solver that can be
- used to hot start the next solution.
-
- lp_method: The method to use for solving the problem. Depends on the solver. See
- the cobra.flux_analysis.solvers.py file for more info.
- For norm_type == 'euclidean':
- the primal simplex works best for the test model (gurobi: lp_method=0, cplex: lp_method=1)
-
- combined_model: an output from moma that represents the combined optimization
- to be solved. when this is not none. only assume that bounds have changed
- for the mutant or wild-type. This saves 0.2 seconds in stacking matrices.
-
-
- NOTE: Current function makes too many assumptions about the structures of the models
-
-
- """
- if solver is None:
- if norm_type == "euclidiean":
- solver = get_solver_name(qp=True)
- else:
- solver = get_solver_name() # linear is not even implemented yet
- if combined_model is not None or the_problem not in ['return']:
- warn("moma currently does not support reusing models or problems. " +\
- "continuing without them")
- combined_model = None
- the_problem = 'return'
- if solver.lower() == 'cplex' and lp_method == 0:
- #print 'for moma, solver method 0 is very slow for cplex. changing to method 1'
- lp_method = 1
- if solver.lower() == 'glpk' and norm_type == 'euclidean':
- try:
- from gurobipy import Model
- solver = 'gurobi'
- warn("GLPK can't solve quadratic problems like MOMA. Switched solver to %s"%solver)
- except:
- warn("GLPK can't solve quadratic problems like MOMA. Switching to linear MOMA")
-
- if norm_type == 'euclidean':
- #Reusing the basis can get the solver stuck.
- reuse_basis = False
- if combined_model and combined_model.norm_type != norm_type:
- print('Cannot use combined_model.norm_type = %s with user-specified norm type'%(combined_model.norm_type,
- norm_type))
- print('Defaulting to user-specified norm_type')
- combined_model = None
-
-
-
- number_of_reactions_in_common = len(set([x.id for x in wt_model.reactions]).intersection([x.id for x in mutant_model.reactions]))
- number_of_reactions = len(wt_model.reactions) + len(mutant_model.reactions)
-
- #Get the optimal wt objective value and adjust based on optimality tolerances
- wt_model.optimize(solver=solver)
- wt_optimal = deepcopy(wt_model.solution.f)
- if objective_sense == 'maximize':
- wt_optimal = floor(wt_optimal/tolerance_optimality)*tolerance_optimality
+from scipy.sparse import dok_matrix
+
+from ..solvers import get_solver_name, solver_dict
+
+
+def create_euclidian_moma_model(cobra_model, wt_model=None, **solver_args):
+ # make the wild type copy if none was supplied
+ if wt_model is None:
+ wt_model = cobra_model.copy()
else:
- wt_optimal = ceil(wt_optimal/tolerance_optimality)*tolerance_optimality
- if norm_type == 'linear':
- raise Exception('linear MOMA is not currently implmented')
- quadratic_component = None
- if minimize_norm:
- raise Exception('minimize_norm is not currently implemented')
- #just worry about the flux distribution and not the objective from the wt
- combined_model = mutant_model.copy()
- #implement this: combined_model.reactions[:].objective_coefficients = -wt_solution.x_dict
+ wt_model = wt_model.copy()
+ # ensure single objective
+ wt_obj = wt_model.reactions.query(lambda x: x > 0,
+ "objective_coefficient")
+ if len(wt_obj) != 1:
+ raise ValueError("wt_model must have exactly 1 objective, %d found"
+ % len(wt_obj))
+
+ obj = cobra_model.reactions.query(lambda x: x > 0, "objective_coefficient")
+ if len(obj) == 1:
+ objective_id = obj[0].id
else:
- #Construct a problem that attempts to maximize the objective in the WT model while
- #solving the quadratic problem. This new problem is constructed to try to find
- #a solution for the WT model that lies close to the mutant model. There are
- #often multiple equivalent solutions with M matrices and the one returned
- #by a simple cobra_model.optimize call may be too far from the mutant.
- #This only needs to be adjusted if we update mutant_model._S after deleting reactions
- if not combined_model:
- #Collect the set of wt reactions contributing to the objective.
- objective_reaction_coefficient_dict = dict([(x.id, x.objective_coefficient)
- for x in wt_model.reactions
- if x.objective_coefficient])
-
-
- combined_model = construct_difference_model(wt_model, mutant_model, norm_type)
- #Add in the virtual objective metabolite to constrain the wt_model to the space where
- #the objective was maximal
- objective_metabolite = Metabolite('wt_optimal')
- objective_metabolite._bound = wt_optimal
- if objective_sense == 'maximize':
- objective_metabolite._constraint_sense = 'G'
- else:
- objective_metabolite._constraint_sense = 'L'
-
- #TODO: this couples the wt_model objective reaction to the virtual metabolite
- #Currently, assumes a single objective reaction; however, this may be extended
- [combined_model.reactions.get_by_id(k).add_metabolites({objective_metabolite: v})
- for k, v in objective_reaction_coefficient_dict.items()]
-
-
-
-
-
-
- if norm_type == 'euclidean':
- #Makes assumptions about the structure of combined model
- quadratic_component = s_vstack((lil_matrix((number_of_reactions, number_of_reactions + number_of_reactions_in_common )),
- s_hstack((lil_matrix((number_of_reactions_in_common, number_of_reactions)),
- eye(number_of_reactions_in_common,number_of_reactions_in_common)))))
-
- elif norm_type == 'linear':
- quadratic_component = None
-
- combined_model.norm_type = norm_type
- cobra_model = combined_model
-
- the_problem = combined_model.optimize(objective_sense='minimize',
- quadratic_component=quadratic_component,
- solver=solver,
- tolerance_optimality=tolerance_optimality,
- tolerance_feasibility=tolerance_feasibility,
- lp_method=lp_method, reuse_basis=reuse_basis)
-
- if combined_model.solution.status != 'optimal':
- warn('optimal moma solution not found: solver status %s'%combined_model.solution.status +\
- ' returning the problem, the_combined model, and the quadratic component for trouble shooting')
- return(the_problem, combined_model, quadratic_component)
-
- solution = combined_model.solution
- mutant_dict = {}
- #Might be faster to quey based on mutant_model.reactions with the 'mutant_' prefix added
- _reaction_list = [x for x in combined_model.reactions if x.id.startswith('mutant_')]
- mutant_f = sum([mutant_model.reactions.get_by_id(x.id[len('mutant_'):]).objective_coefficient *
- x.x for x in _reaction_list])
- mutant_dict['objective_value'] = mutant_f
- wild_type_flux_total = sum([abs(solution.x_dict[x.id]) for x in wt_model.reactions])
- mutant_flux_total = sum(abs(x.x) for x in _reaction_list)
- #Need to use the new solution as there are multiple ways to achieve an optimal solution in
- #simulations with M matrices.
- mutant_dict['status'] = solution.status
- #TODO: Deal with maximize / minimize issues for a reversible model that's been converted to irreversible
- mutant_dict['flux_difference'] = flux_difference = sum([(solution.x_dict[x.id[len('mutant_'):]]
- - x.x)**2 for x in _reaction_list])
- mutant_dict['the_problem'] = the_problem
- mutant_dict['combined_model'] = combined_model
-
- del wt_model, mutant_model, quadratic_component, solution
- return(mutant_dict)
-
-
-def construct_difference_model(model_1, model_2, norm_type='euclidean'):
- """Combine two models into a larger model that is designed to calculate differences
- between the models
-
- """
- #Get index mappings
- common_dict = {}
- #Using copies of the models so things are modified above
- combined_model = model_1 = model_1.copy()
- model_2 = model_2.copy()
- for reaction_1 in model_1.reactions:
- try:
- reaction_2 = model_2.reactions.get_by_id(reaction_1.id)
- common_dict[reaction_1] = reaction_2
- except:
- continue
-
- #Add a prefix in front of the mutant_model metabolites and reactions to prevent
- #name collisions in DictList
- for the_dict_list in [model_2.metabolites,
- model_2.reactions]:
- [setattr(x, 'id', 'mutant_%s'%x.id)
- for x in the_dict_list]
- the_dict_list._generate_index() #Update the DictList.dicts
-
-
- combined_model.add_reactions(model_2.reactions)
- [setattr(x, 'objective_coefficient', 0.)
- for x in combined_model.reactions]
- #Add in the difference reactions. The mutant reactions and metabolites are already added.
- #This must be a list to maintain the correct order when adding the difference_metabolites
- difference_reactions = [] #Add the difference reactions at the end to speed things up
- difference_metabolites = []
- for reaction_1, reaction_2 in iteritems(common_dict):
- reaction_1._difference_partner = reaction_2
- reaction_2._difference_partner = reaction_1
- difference_reaction = Reaction('difference_%s'%reaction_1.id)
- difference_reactions.append(difference_reaction)
- difference_reaction.upper_bound = 100000
- difference_reaction.lower_bound = -1* difference_reaction.upper_bound
- difference_metabolite = Metabolite('difference_%s'%reaction_1.id)
- difference_metabolites.append(difference_metabolite)
- if norm_type == 'linear':
- difference_metabolite._constraint_sense = 'G'
- reaction_1.add_metabolites({difference_metabolite: -1.}, add_to_container_model=False)
- reaction_2.add_metabolites({difference_metabolite: 1.}, add_to_container_model=False)
- difference_reaction.add_metabolites({difference_metabolite: 1.}, add_to_container_model=False)
-
- combined_model.add_metabolites(difference_metabolites)
- combined_model.add_reactions(difference_reactions)
- return(combined_model)
-
+ raise ValueError("model must have exactly 1 objective, %d found" %
+ len(obj))
+
+ wt_model.optimize(**solver_args)
+ for reaction in wt_model.reactions:
+ # we don't want delete_model_gene to remove the wt reaction as well
+ reaction.gene_reaction_rule = ''
+ if reaction.objective_coefficient != 0:
+ reaction.objective_coefficient = 0
+ reaction.upper_bound = reaction.lower_bound = reaction.x
+ reaction.id = "MOMA_wt_" + reaction.id
+ for metabolite in wt_model.metabolites:
+ metabolite.id = "MOMA_wt_" + metabolite.id
+ wt_model.repair()
+
+ # make the moma model by combining both
+ moma_model = cobra_model.copy()
+ for reaction in moma_model.reactions:
+ reaction.objective_coefficient = 0
+ moma_model.add_reactions(wt_model.reactions)
+ return moma_model, objective_id
+
+
+def create_euclidian_distance_objective(n_moma_reactions):
+ """returns a matrix which will minimze the euclidian distance
+
+ This matrix has the structure
+ [ I -I]
+ [-I I]
+ where I is the identity matrix the same size as the number of
+ reactions in the original model.
+
+ n_moma_reactions: int
+ This is the number of reactions in the MOMA model, which should
+ be twice the number of reactions in the original model"""
+ if n_moma_reactions % 2 != 0:
+ raise ValueError("must be even")
+ n_reactions = n_moma_reactions // 2
+ Q = dok_matrix((n_reactions * 2, n_reactions * 2))
+ for i in range(2 * n_reactions):
+ Q[i, i] = 1
+ for i in range(n_reactions):
+ Q[i, n_reactions + i] = -1
+ Q[n_reactions + i, i] = -1
+ return Q
+
+
+def create_euclidian_distance_lp(moma_model, solver):
+ Q = create_euclidian_distance_objective(len(moma_model.reactions))
+ lp = solver.create_problem(moma_model, objective_sense="minimize",
+ quadratic_component=Q)
+ return lp
+
+
+def solve_moma_model(moma_model, objective_id, solver=None, **solver_args):
+ solver = solver_dict[solver if solver else get_solver_name(qp=True)]
+ lp = create_euclidian_distance_lp(moma_model, solver=solver)
+ solver.solve_problem(lp, **solver_args)
+ solution = solver.format_solution(lp, moma_model)
+ solution.f = 0. if solution.x_dict is None \
+ else solution.x_dict[objective_id]
+ moma_model.solution = solution
+ return solution
+
+
+def moma(wt_model, mutant_model, solver=None, **solver_args):
+ if "norm_type" in solver_args:
+ print("only euclidian norm type supported for moma")
+ solver_args.pop("norm_type")
+ moma_model, objective_id = create_euclidian_moma_model(mutant_model,
+ wt_model)
+ return solve_moma_model(moma_model, objective_id,
+ solver=solver, **solver_args)
+
+
+def moma_knockout(moma_model, moma_objective, reaction_indexes, **moma_args):
+ """computes result of reaction_knockouts using moma"""
+ n = len(moma_model.reactions) // 2
+ # knock out the reaction
+ for i in reaction_indexes:
+ mutant_reaction = moma_model.reactions[i]
+ mutant_reaction.lower_bound, mutant_reaction.upper_bound = (0., 0.)
+ result = solve_moma_model(moma_model, moma_objective, **moma_args)
+ # reset the knockouts
+ for i in reaction_indexes:
+ mutant_reaction = moma_model.reactions[i]
+ wt_reaction = moma_model.reactions[n + i]
+ mutant_reaction.lower_bound = wt_reaction.lower_bound
+ mutant_reaction.upper_bound = wt_reaction.upper_bound
+ return result
diff --git a/cobra/flux_analysis/objective.py b/cobra/flux_analysis/objective.py
deleted file mode 100644
index 7e92702..0000000
--- a/cobra/flux_analysis/objective.py
+++ /dev/null
@@ -1,45 +0,0 @@
-from warnings import warn
-warn("cobra.flux_analysis.objective is deprecated.")
-
-#cobra.flux_analysis.objective.py
-#functions for analyzing / creating objective functions
-from ..core.Reaction import Reaction
-from ..manipulation import initialize_growth_medium
-import sys
-if hasattr(sys, 'maxsize') and sys.maxsize > 2**32:
- try:
- from numpy import int64, int32
- except:
- int32 = int64 = int
-else:
- int32 = int
- int64 = int
-
-
-
-def assess_objective(model, objective=None,
- objective_cutoff=0.001, growth_medium=None):
- """DEPRECATED
- """
- from warnings import warn
- warn("cobra.flux_analysis.objective.assess_objective is deprecated. " +\
- "Please use cobra.flux_analysis.reaction.assess instead")
- return(False)
-
-
-
-
-def update_objective(cobra_model, the_objectives):
- """Revised to take advantage of the new Reaction classes.
-
- cobra_model: A cobra.Model
-
- the_objectives: A list or a dictionary. If a list then
- a list of reactions for which the coefficient in the
- linear objective is set as 1. If a dictionary then the
- key is the reaction and the value is the linear coefficient
- for the respective reaction.
-
- """
- return cobra_model.change_objective(the_objectives)
-
diff --git a/cobra/flux_analysis/parsimonious.py b/cobra/flux_analysis/parsimonious.py
index cb6ca49..921c81d 100644
--- a/cobra/flux_analysis/parsimonious.py
+++ b/cobra/flux_analysis/parsimonious.py
@@ -19,8 +19,6 @@ def optimize_minimal_flux(model, already_irreversible=False,
skipped.
"""
- if "new_objective" in optimize_kwargs:
- raise ValueError("Use objective coefficients, not new_objective")
if not already_irreversible:
modify.convert_to_irreversible(model)
model.optimize(**optimize_kwargs)
diff --git a/cobra/flux_analysis/single_deletion.py b/cobra/flux_analysis/single_deletion.py
index d5793a8..4ce985f 100644
--- a/cobra/flux_analysis/single_deletion.py
+++ b/cobra/flux_analysis/single_deletion.py
@@ -1,347 +1,181 @@
-from time import time
from warnings import warn
-from copy import deepcopy
-from ..external.six import string_types, iteritems
+from six import string_types, iteritems
from ..manipulation import delete_model_genes, undelete_model_genes
from ..manipulation.delete import find_gene_knockout_reactions
from ..solvers import solver_dict, get_solver_name
-
-
-nan = float('nan')
-
-
try:
- from .moma import moma
-except Exception as e:
- def moma(**kwargs):
- warn("moma is currently not functional")
+ import scipy
+except ImportError:
+ moma = None
+else:
+ from . import moma
def single_deletion(cobra_model, element_list=None,
- method='fba', element_type='gene', solver=None):
- """Wrapper for single_gene_deletion and the single_reaction_deletion
- functions
+ element_type='gene', **kwargs):
+ """Wrapper for single_gene_deletion and single_reaction_deletion
-
- cobra_model: a cobra.Model object
-
- element_list: Is None or a list of elements (genes or reactions) to
- delete.
+ .. deprecated :: 0.4
+ Use single_reaction_deletion and single_gene_deletion
+ """
+ warn("deprecated - use single_reaction_deletion and single_gene_deletion")
+ if element_type == "reaction":
+ return single_reaction_deletion(cobra_model, element_list, **kwargs)
+ elif element_type == "gene":
+ return single_gene_deletion(cobra_model, element_list, **kwargs)
+ else:
+ raise Exception("unknown element type")
- method: 'fba' or 'moma'
- the_problem: Is None, 'return', or an LP model object for the solver.
+def single_reaction_deletion(cobra_model, reaction_list=None, solver=None,
+ method="fba", **solver_args):
+ """sequentially knocks out each reaction in a model
- element_type: 'gene' or 'reaction'
+ reaction_list: list of reaction_ids or cobra.Reaction
- solver: 'glpk', 'gurobi', or 'cplex'.
+ method: "fba" or "moma"
- error_reporting: None or True to disable or enable printing errors encountered
- when trying to find the optimal solution.
+ returns ({reaction_id: growth_rate}, {reaction_id: status})"""
+ if reaction_list is None:
+ reaction_list = cobra_model.reactions
+ else:
+ reaction_list = [cobra_model.reactions.get_by_id(i)
+ if isinstance(i, string_types) else i
+ for i in reaction_list]
+ if method == "fba":
+ return single_reaction_deletion_fba(cobra_model, reaction_list,
+ solver=solver, **solver_args)
+ elif method == "moma":
+ return single_reaction_deletion_moma(cobra_model, reaction_list,
+ solver=solver, **solver_args)
+ else:
+ raise ValueError("Unknown deletion method '%s'" % method)
- discard_problems: Boolean. If True do not save problems. This will
- help with memory issues related to gurobi.
- .. warning:: This is deprecated.
- Returns a list of dictionaries: growth_rate_dict, solution_status_dict,
- problem_dict where the key corresponds to each element in element_list.
+def single_reaction_deletion_fba(cobra_model, reaction_list, solver=None,
+ **solver_args):
+ """sequentially knocks out each reaction in a model using FBA
- """
- if solver is None:
- solver = get_solver_name() if method == "fba" else get_solver_name(qp=True)
- # fast versions of functions
- if method == "fba":
- if element_type == "gene":
- return single_gene_deletion_fba(cobra_model, element_list,
- solver=solver)
- elif element_type == "reaction":
- return single_reaction_deletion_fba(cobra_model, element_list,
- solver=solver)
- if element_type == 'gene':
- the_solution = single_gene_deletion(cobra_model, element_list,
- method=method, solver=solver)
+ reaction_list: list of reaction_ids or cobra.Reaction
- else:
- the_solution = single_reaction_deletion(cobra_model, element_list,
- method=method, solver=solver)
- return the_solution
+ method: "fba" or "moma"
+ returns ({reaction_id: growth_rate}, {reaction_id: status})"""
-def single_reaction_deletion_fba(cobra_model, reaction_list=None, solver=None):
solver = solver_dict[get_solver_name() if solver is None else solver]
lp = solver.create_problem(cobra_model)
+
growth_rate_dict = {}
status_dict = {}
- if reaction_list is None:
- reaction_list = cobra_model.reactions
- else:
- reaction_list = [cobra_model.reactions.get_by_id(i) \
- if isinstance(i, string_types) else i \
- for i in reaction_list]
for reaction in reaction_list:
old_bounds = (reaction.lower_bound, reaction.upper_bound)
index = cobra_model.reactions.index(reaction)
solver.change_variable_bounds(lp, index, 0., 0.)
- solver.solve_problem(lp)
+ solver.solve_problem(lp, **solver_args)
+ # get the status and growth rate
status = solver.get_status(lp)
status_dict[reaction.id] = status
- growth_rate_dict[reaction.id] = solver.get_objective_value(lp) if status == "optimal" else 0.
+ growth_rate_dict[reaction.id] = solver.get_objective_value(lp) \
+ if status == "optimal" else 0.
# reset the problem
solver.change_variable_bounds(lp, index, old_bounds[0], old_bounds[1])
- return(growth_rate_dict, status_dict)
+ return (growth_rate_dict, status_dict)
+
+
+def single_reaction_deletion_moma(cobra_model, reaction_list, solver=None,
+ **solver_args):
+ """sequentially knocks out each reaction in a model using MOMA
+
+ reaction_list: list of reaction_ids or cobra.Reaction
+
+
+ returns ({reaction_id: growth_rate}, {reaction_id: status})"""
+ # The same function can not be used because MOMA can not re-use the
+ # same LP object. Problem re-use leads to incorrect solutions.
+ if moma is None:
+ raise RuntimeError("scipy required for moma")
+ solver = solver_dict[solver if solver else get_solver_name(qp=True)]
+ moma_model, moma_obj = moma.create_euclidian_moma_model(cobra_model)
-def single_gene_deletion_fba(cobra_model, gene_list=None, solver=None):
- solver = solver_dict[get_solver_name() if solver is None else solver]
- lp = solver.create_problem(cobra_model)
growth_rate_dict = {}
status_dict = {}
+ for reaction in reaction_list:
+ index = cobra_model.reactions.index(reaction)
+ solution = moma.moma_knockout(moma_model, moma_objective, (index,),
+ solver=solver, **solver_args)
+ status_dict[reaction.id] = solution.status
+ growth_rate_dict[reaction.id] = solution.f
+ return (growth_rate_dict, status_dict)
+
+
+def single_gene_deletion(cobra_model, gene_list=None, solver=None,
+ method="fba", **solver_args):
+ """sequentially knocks out each gene in a model
+
+ gene_list: list of gene_ids or cobra.Gene
+
+ method: "fba" or "moma"
+
+ returns ({gene_id: growth_rate}, {gene_id: status})"""
if gene_list is None:
gene_list = cobra_model.genes
else:
- gene_list = [cobra_model.genes.get_by_id(i) \
+ gene_list = [cobra_model.genes.get_by_id(i)
if isinstance(i, string_types) else i for i in gene_list]
+
+ if method == "fba":
+ return single_gene_deletion_fba(cobra_model, gene_list,
+ solver=solver, **solver_args)
+ elif method == "moma":
+ return single_gene_deletion_moma(cobra_model, gene_list,
+ solver=solver, **solver_args)
+ else:
+ raise ValueError("Unknown deletion method '%s'" % method)
+
+
+def single_gene_deletion_fba(cobra_model, gene_list, solver=None,
+ **solver_args):
+
+ solver = solver_dict[get_solver_name() if solver is None else solver]
+ lp = solver.create_problem(cobra_model)
+
+ growth_rate_dict = {}
+ status_dict = {}
for gene in gene_list:
old_bounds = {}
for reaction in find_gene_knockout_reactions(cobra_model, [gene]):
index = cobra_model.reactions.index(reaction)
old_bounds[index] = (reaction.lower_bound, reaction.upper_bound)
solver.change_variable_bounds(lp, index, 0., 0.)
- solver.solve_problem(lp)
+ solver.solve_problem(lp, **solver_args)
+ # get the status and growth rate
status = solver.get_status(lp)
status_dict[gene.id] = status
- growth_rate_dict[gene.id] = solver.get_objective_value(lp)# if status == "optimal" else 0.
+ growth_rate = solver.get_objective_value(lp) \
+ if status == "optimal" else 0.
+ growth_rate_dict[gene.id] = growth_rate
# reset the problem
for index, bounds in iteritems(old_bounds):
solver.change_variable_bounds(lp, index, bounds[0], bounds[1])
- return(growth_rate_dict, status_dict)
-
-def single_reaction_deletion(cobra_model, element_list=None,
- method='fba', the_problem='return',
- solver=None, error_reporting=None,
- discard_problems=True):
- """Performs optimization simulations to realize the objective defined
- from cobra_model.reactions[:].objective_coefficients after deleting each reaction
- from the model.
-
- cobra_model: a cobra.Model object
-
- element_list: Is None or a list of cobra.Reactions in cobra_model to disable.
- If None then disable each reaction in cobra_model.reactions and optimize for the
- objective function defined from cobra_model.reactions[:].objective_coefficients.
+ return (growth_rate_dict, status_dict)
- method: 'fba' is the only option at the moment.
- the_problem: Is None, 'reuse', or an LP model object for the solver.
-
- solver: 'glpk', 'gurobi', or 'cplex'.
-
- discard_problems: Boolean. If True do not save problems. This will
- help with memory issues related to gurobi.
-
- Returns a list of dictionaries: growth_rate_dict, solution_status_dict,
- problem_dict where the key corresponds to each reaction in reaction_list.
-
- """
- if solver is None:
- solver = get_solver_name() if method == "fba" else get_solver_name(qp=True)
- #element_list so we can merge single_reaction_deletion and single_gene_deletion
-
- wt_model = cobra_model.copy() #Original wild-type (wt) model.
- wt_model.id = 'Wild-Type'
- #MOMA constructs combined quadratic models thus we cannot reuse a model
- #generated by the cobra_model.optimize call
- if method.lower() == 'moma':
- the_problem = 'return'
- mutant_model = wt_model.copy() #Need a second model for moma
- else:
- mutant_model = cobra_model
- discard_problems = False
- if the_problem:
- the_problem = 'return'
- discard_problems = True
- the_problem = wt_model.optimize(the_problem=the_problem, solver=solver,
- error_reporting=error_reporting)
- wt_f = wt_model.solution.f
- wt_status = wt_model.solution.status
- wt_x = deepcopy(wt_model.solution.x)
- wt_x_dict = deepcopy(wt_model.solution.x_dict)
-
- wt_problem = the_problem
- if element_list is None:
- element_list = mutant_model.reactions
- elif not hasattr(element_list[0], 'id'):
- element_list = map(mutant_model.reactions.get_by_id, element_list)
- else:
- if mutant_model is not cobra_model:
- element_list = [x.id for x in element_list]
- element_list = map(mutant_model.genes.get_by_id, element_list)
+def single_gene_deletion_moma(cobra_model, gene_list, solver=None,
+ **solver_args):
+ if moma is None:
+ raise RuntimeError("scipy required for moma")
+ solver = solver if solver else get_solver_name(qp=True)
+ moma_model, moma_obj = moma.create_euclidian_moma_model(cobra_model)
growth_rate_dict = {}
- solution_status_dict = {}
- problem_dict = {}
- combined_model = None
- for the_element in element_list:
- #delete the gene
- #if the deletion alters the bounds then run simulation
- old_lower_bound, old_upper_bound = map(float, [the_element.lower_bound,
- the_element.upper_bound])
- mutant_model.id = the_element.id
- if old_lower_bound != 0 or old_upper_bound != 0:
- the_element.lower_bound = 0
- the_element.upper_bound = 0
- if method.lower() == 'fba':
- the_problem = mutant_model.optimize(the_problem=wt_problem,
- solver=solver,
- error_reporting=error_reporting)
- growth_rate_dict[the_element] = mutant_model.solution.f
- solution_status_dict[the_element] = mutant_model.solution.status
- elif method.lower() == 'moma':
- try:
- #TODO: Need to figure out why reusing the problem and the combined_model do not
- #speed things up here.
- moma_solution = moma(wt_model, mutant_model, solver=solver, the_problem=the_problem,
- combined_model=combined_model)
- the_problem = moma_solution.pop('the_problem')
- growth_rate_dict[the_element] = float(moma_solution.pop('objective_value'))
- solution_status_dict[the_element] = moma_solution.pop('status')
- combined_model = moma_solution.pop('combined_model')
- except:
- growth_rate_dict[the_element] = nan
- the_problem = None
- solution_status_dict[the_element] = 'failed'
-
- if discard_problems:
- problem_dict[the_element] = 'discarded'
- else:
- problem_dict[the_element] = the_problem
- if not the_problem:
- the_problem = wt_problem
- #reset the model
- the_element.lower_bound = old_lower_bound
- the_element.upper_bound = old_upper_bound
- #else just use the wt_f and x
- else:
- if discard_problems:
- problem_dict[the_element] = 'discarded'
- else:
- problem_dict[the_element] = wt_problem
- growth_rate_dict[the_element] = wt_f
- solution_status_dict[the_element] = wt_status
-
-
- return(growth_rate_dict, solution_status_dict, problem_dict)
-
-def single_gene_deletion(cobra_model, element_list=None,
- method='fba', the_problem='reuse', solver=None,
- error_reporting=None):
- """Performs optimization simulations to realize the objective defined
- from cobra_model.reactions[:].objective_coefficients after deleting each gene in
- gene_list from the model.
-
- cobra_model: a cobra.Model object
-
- element_list: Is None or a list of genes to delete. If None then
- disable each reaction associated with each gene in cobra_model.genes.
-
- method: 'fba' or 'moma'
-
- the_problem: Is None or 'reuse'.
-
- solver: 'glpk', 'gurobi', or 'cplex'.
-
- Returns a list of dictionaries: growth_rate_dict, solution_status_dict,
- problem_dict where the key corresponds to each reaction in reaction_list.
-
- TODO: Add in a section that allows copying and collection of problem for
- debugging purposes.
-
- """
- if solver is None:
- solver = get_solver_name() if method == "fba" else get_solver_name(qp=True)
- wt_model = cobra_model.copy() #Original wild-type (wt) model.
- wt_model.id = 'Wild-Type'
- #MOMA constructs combined quadratic models thus we cannot reuse a model
- #generated by the cobra_model.optimize call
- if method.lower() == 'moma':
- the_problem = 'return'
- mutant_model = wt_model.copy() #Need a second model for moma
- else:
- mutant_model = cobra_model
- discard_problems = False
- if the_problem:
- the_problem = 'return'
- discard_problems = True
-
- solver_object = solver_dict[solver]
- the_problem = solver_object.create_problem(wt_model)
- solver_object.solve_problem(the_problem)
- solution = solver_object.format_solution(the_problem, wt_model)
- wt_f = solution.f
- wt_status = solution.status
- wt_x = deepcopy(solution.x)
- wt_x_dict = deepcopy(solution.x_dict)
-
- if element_list is None:
- element_list = mutant_model.genes
- elif not hasattr(element_list[0], 'id'):
- element_list = map(mutant_model.genes.get_by_id, element_list)
- else:
- if mutant_model is not cobra_model:
- element_list = [x.id for x in element_list]
- element_list = map(mutant_model.genes.get_by_id, element_list)
- wt_problem = the_problem
-
- growth_rate_dict = {}
- solution_status_dict = {}
- problem_dict = {}
- combined_model = None
-
- for the_element in element_list:
- #delete the gene
- #if the deletion alters the bounds then run simulation
- delete_model_genes(mutant_model, the_element)
- mutant_model.id = the_element.id
- if mutant_model._trimmed:
- if method.lower() == 'fba':
- the_problem = mutant_model.optimize(the_problem=wt_problem,
- solver=solver,
- error_reporting=error_reporting)
- growth_rate_dict[the_element.id] = mutant_model.solution.f
- solution_status_dict[the_element.id] = mutant_model.solution.status
- elif method.lower() == 'moma':
- try:
- #TODO: Need to figure out why reusing the problem and the combined_model do not
- #speed things up here.
- moma_solution = moma(wt_model, mutant_model, solver=solver, the_problem=the_problem,
- combined_model=combined_model)
- the_problem = moma_solution.pop('the_problem')
- growth_rate_dict[the_element.id] = float(moma_solution.pop('objective_value'))
- solution_status_dict[the_element.id] = moma_solution.pop('status')
- combined_model = moma_solution.pop('combined_model')
- except:
- growth_rate_dict[the_element.id] = nan
- the_problem = None
- solution_status_dict[the_element.id] = 'failed'
-
- if discard_problems:
- problem_dict[the_element.id] = 'discarded'
- else:
- problem_dict[the_element.id] = the_problem
- if not the_problem:
- the_problem = wt_problem
- #reset the model
- undelete_model_genes(mutant_model)
- #else just use the wt_f and x
- else:
- if discard_problems:
- problem_dict[the_element.id] = 'discarded'
- else:
- problem_dict[the_element.id] = wt_problem
- growth_rate_dict[the_element.id] = wt_f
- solution_status_dict[the_element.id] = wt_status
-
-
- return(growth_rate_dict, solution_status_dict, problem_dict)
-
+ status_dict = {}
+ for gene in gene_list:
+ delete_model_genes(moma_model, [gene.id])
+ solution = moma.solve_moma_model(moma_model, moma_obj,
+ solver=solver, **solver_args)
+ status_dict[gene.id] = solution.status
+ growth_rate_dict[gene.id] = solution.f
+ undelete_model_genes(moma_model)
+ return (growth_rate_dict, status_dict)
diff --git a/cobra/flux_analysis/variability.py b/cobra/flux_analysis/variability.py
index 26c7d7e..e712199 100644
--- a/cobra/flux_analysis/variability.py
+++ b/cobra/flux_analysis/variability.py
@@ -1,6 +1,6 @@
from warnings import warn
-from ..external.six import iteritems, string_types
+from six import iteritems, string_types
from ..core.Metabolite import Metabolite
from ..solvers import solver_dict, get_solver_name
@@ -26,14 +26,9 @@ def flux_variability_analysis(cobra_model, reaction_list=None,
"""
if reaction_list is None and "the_reactions" in solver_args:
reaction_list = solver_args.pop("the_reactions")
- from warnings import warn
warn("the_reactions is deprecated. Please use reaction_list=")
if reaction_list is None:
reaction_list = cobra_model.reactions
- else:
- reaction_list = [cobra_model.reactions.get_by_id(i)
- if isinstance(i, string_types) else i
- for i in reaction_list]
solver = solver_dict[get_solver_name() if solver is None else solver]
lp = solver.create_problem(cobra_model)
solver.solve_problem(lp, objective_sense=objective_sense)
@@ -49,16 +44,23 @@ def flux_variability_analysis(cobra_model, reaction_list=None,
solver.change_variable_bounds(lp, i,
min(new_bounds), max(new_bounds))
solver.change_variable_objective(lp, i, 0.)
- # perform fva
+ return calculate_lp_variability(lp, solver, cobra_model, reaction_list,
+ **solver_args)
+
+
+def calculate_lp_variability(lp, solver, cobra_model, reaction_list,
+ **solver_args):
+ """calculate max and min of selected variables in an LP"""
fva_results = {}
for r in reaction_list:
- i = cobra_model.reactions.index(r)
- fva_results[r.id] = {}
+ r_id = str(r)
+ i = cobra_model.reactions.index(r_id)
+ fva_results[r_id] = {}
solver.change_variable_objective(lp, i, 1.)
solver.solve_problem(lp, objective_sense="maximize", **solver_args)
- fva_results[r.id]["maximum"] = solver.get_objective_value(lp)
+ fva_results[r_id]["maximum"] = solver.get_objective_value(lp)
solver.solve_problem(lp, objective_sense="minimize", **solver_args)
- fva_results[r.id]["minimum"] = solver.get_objective_value(lp)
+ fva_results[r_id]["minimum"] = solver.get_objective_value(lp)
# revert the problem to how it was before
solver.change_variable_objective(lp, i, 0.)
return fva_results
@@ -66,31 +68,31 @@ def flux_variability_analysis(cobra_model, reaction_list=None,
def find_blocked_reactions(cobra_model, reaction_list=None,
solver=None, zero_cutoff=1e-9,
- open_exchanges=False, **kwargs):
+ open_exchanges=False, **solver_args):
"""Finds reactions that cannot carry a flux with the current
exchange reaction settings for cobra_model, using flux variability
analysis.
"""
- from warnings import warn
if solver is None:
solver = get_solver_name()
- blocked_reactions = []
- if reaction_list is None and "the_reactions" in solver_args:
- reaction_list = solver_args.pop("the_reactions")
- warn("the_reactions is deprecated. Please use reaction_list=")
if open_exchanges:
- warn('DEPRECATED: Move to using the Reaction.boundary attribute')
- exchange_reactions = [x for x in cobra_model.reactions
- if x.startswith('EX')]
- for the_reaction in exchange_reactions:
- if the_reaction.lower_bound >= 0:
- the_reaction.lower_bound = -1000
- if the_reaction.upper_bound >= 0:
- the_reaction.upper_bound = 1000
+ # should not unnecessarily change model
+ cobra_model = cobra_model.copy()
+ for reaction in cobra_model.reactions:
+ if reaction.boundary:
+ reaction.lower_bound = min(reaction.lower_bound, -1000)
+ reaction.upper_bound = max(reaction.upper_bound, 1000)
+ if reaction_list is None:
+ reaction_list = cobra_model.reactions
+ # limit to reactions which are already 0. If the reactions alread
+ # carry flux in this solution, then they can not be blocked.
+ solution = solver_dict[solver].solve(cobra_model, **solver_args)
+ reaction_list = [i for i in reaction_list
+ if abs(solution.x_dict[i.id]) < zero_cutoff]
+ # run fva to find reactions where both max and min are 0
flux_span_dict = flux_variability_analysis(
cobra_model, fraction_of_optimum=0., reaction_list=reaction_list,
- solver=solver, **kwargs)
- blocked_reactions = [k for k, v in flux_span_dict.items()
- if max(map(abs, v.values())) < zero_cutoff]
- return blocked_reactions
+ solver=solver, **solver_args)
+ return [k for k, v in iteritems(flux_span_dict)
+ if max(map(abs, v.values())) < zero_cutoff]
diff --git a/cobra/io/__init__.py b/cobra/io/__init__.py
index b6c9bfc..8f26e92 100644
--- a/cobra/io/__init__.py
+++ b/cobra/io/__init__.py
@@ -10,9 +10,8 @@ except ImportError:
scipy = None
if libsbml:
- from .sbml import create_cobra_model_from_sbml_file as read_sbml_model
from .sbml import read_legacy_sbml
- from .sbml import write_cobra_model_to_sbml_file as write_sbml_model
+ from .sbml import write_cobra_model_to_sbml_file as write_legacy_sbml
else:
warn("cobra.io.sbml requires libsbml")
@@ -22,6 +21,7 @@ if scipy:
else:
warn("cobra.io.mat requires scipy")
+from .sbml3 import read_sbml_model, write_sbml_model
from .json import load_json_model
from .json import save_json_model, to_json
diff --git a/cobra/io/json.py b/cobra/io/json.py
index d4fe4c4..5344f83 100644
--- a/cobra/io/json.py
+++ b/cobra/io/json.py
@@ -3,8 +3,8 @@ from __future__ import absolute_import
import json
from warnings import warn
-from .. import Model, Metabolite, Reaction, Formula
-from ..external.six import iteritems, string_types
+from .. import Model, Metabolite, Reaction
+from six import iteritems, string_types
# Detect numpy types to replace them.
try:
@@ -37,7 +37,8 @@ def _fix_type(value):
return float(value)
if isinstance(value, bool_):
return bool(value)
- if isinstance(value, Formula):
+ # handle legacy Formula type
+ if value.__class__.__name__ == "Formula":
return str(value)
return value
@@ -53,7 +54,6 @@ def _from_dict(obj):
new_metabolite = Metabolite()
for k, v in iteritems(metabolite):
setattr(new_metabolite, k, v)
- new_metabolite.formula = Formula(new_metabolite.formula)
new_metabolites.append(new_metabolite)
model.add_metabolites(new_metabolites)
# add reactions
diff --git a/cobra/io/mat.py b/cobra/io/mat.py
index 7f29237..34e31b5 100644
--- a/cobra/io/mat.py
+++ b/cobra/io/mat.py
@@ -1,10 +1,12 @@
import re
+from uuid import uuid4
+from warnings import warn
from numpy import array, object as np_object
from scipy.io import loadmat, savemat
from scipy.sparse import coo_matrix
-from .. import Model, Metabolite, Reaction, Formula
+from .. import Model, Metabolite, Reaction
# try to use an ordered dict
try:
@@ -116,7 +118,7 @@ def create_mat_dict(model):
mat["ub"] = array(rxns.list_attr("upper_bound")) * 1.
mat["b"] = array(mets.list_attr("_bound")) * 1.
mat["c"] = array(rxns.list_attr("objective_coefficient")) * 1.
- mat["rev"] = array(rxns.list_attr("reversibility"))
+ mat["rev"] = array(rxns.list_attr("reversibility")) * 1
mat["description"] = str(model.description)
return mat
@@ -132,6 +134,11 @@ def from_mat_struct(mat_struct, model_id=None):
raise ValueError("not a valid mat struct")
if not set(["rxns", "mets", "S", "lb", "ub"]) <= set(m.dtype.names):
raise ValueError("not a valid mat struct")
+ if "c" in m.dtype.names:
+ c_vec = m["c"][0, 0]
+ else:
+ c_vec = None
+ warn("objective vector 'c' not found")
model = Model()
if "description" in m:
model.id = m["description"][0, 0][0]
@@ -149,8 +156,7 @@ def from_mat_struct(mat_struct, model_id=None):
except (IndexError, ValueError):
pass
try:
- new_metabolite.formula = \
- Formula(str(m["metFormulas"][0][0][i][0][0]))
+ new_metabolite.formula = str(m["metFormulas"][0][0][i][0][0])
except (IndexError, ValueError):
pass
model.add_metabolites([new_metabolite])
@@ -160,7 +166,8 @@ def from_mat_struct(mat_struct, model_id=None):
new_reaction.id = str(name[0][0])
new_reaction.lower_bound = float(m["lb"][0, 0][i][0])
new_reaction.upper_bound = float(m["ub"][0, 0][i][0])
- new_reaction.objective_coefficient = float(m["c"][0, 0][i][0])
+ if c_vec is not None:
+ new_reaction.objective_coefficient = float(c_vec[i][0])
try:
new_reaction.gene_reaction_rule = str(m['grRules'][0, 0][i][0][0])
except (IndexError, ValueError):
@@ -179,3 +186,42 @@ def from_mat_struct(mat_struct, model_id=None):
for i, j, v in zip(coo.row, coo.col, coo.data):
model.reactions[j].add_metabolites({model.metabolites[i]: v})
return model
+
+
+def _check(result):
+ """ensure success of a pymatbridge operation"""
+ if result["success"] is not True:
+ raise RuntimeError(result["content"]["stdout"])
+
+
+def model_to_pymatbridge(model, variable_name="model", matlab=None):
+ """send the model to a MATLAB workspace through pymatbridge
+
+ This model can then be manipulated through the COBRA toolbox
+
+ variable_name: str
+ The variable name to which the model will be assigned in the
+ MATLAB workspace
+
+ matlab: None or pymatbridge.Matlab instance
+ The MATLAB workspace to which the variable will be sent. If
+ this is None, then this will be sent to the same environment
+ used in IPython magics.
+
+ """
+ if matlab is None: # assumed to be running an IPython magic
+ from IPython import get_ipython
+ matlab = get_ipython().magics_manager.registry["MatlabMagics"].Matlab
+ model_info = create_mat_dict(model)
+ S = model_info["S"].todok()
+ model_info["S"] = 0
+ temp_S_name = "cobra_pymatbridge_temp_" + uuid4().hex
+ _check(matlab.set_variable(variable_name, model_info))
+ _check(matlab.set_variable(temp_S_name, S))
+ _check(matlab.run_code("%s.S = %s;" % (variable_name, temp_S_name)))
+ # all vectors need to be transposed
+ for i in model_info.keys():
+ if i == "S":
+ continue
+ _check(matlab.run_code("{0}.{1} = {0}.{1}';".format(variable_name, i)))
+ _check(matlab.run_code("clear %s;" % temp_S_name))
diff --git a/cobra/io/sbml.py b/cobra/io/sbml.py
index 821931b..0f960a3 100644
--- a/cobra/io/sbml.py
+++ b/cobra/io/sbml.py
@@ -1,7 +1,7 @@
#cobra/sbml.py: Tools for reading / writing SBML now contained in
#this module
#System modules
-from .. import Model, Reaction, Metabolite, Formula
+from .. import Model, Reaction, Metabolite
from os.path import isfile
from os import name as __name
from warnings import warn
@@ -160,7 +160,7 @@ def create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False, legacy_meta
if tmp_formula == '' and old_sbml:
tmp_formula = tmp_metabolite.name.split('_')[-1]
tmp_metabolite.name = tmp_metabolite.name[:-len(tmp_formula)-1]
- tmp_metabolite.formula = Formula(tmp_formula)
+ tmp_metabolite.formula = tmp_formula
metabolite_dict.update({metabolite_id: tmp_metabolite})
metabolites.append(tmp_metabolite)
cobra_model.add_metabolites(metabolites)
@@ -260,13 +260,14 @@ def create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False, legacy_meta
#TODO: READ IN OTHER NOTES AND GIVE THEM A reaction_ prefix.
#TODO: Make sure genes get added as objects
if 'GENE ASSOCIATION' in reaction_note_dict:
+ rule = reaction_note_dict['GENE ASSOCIATION'][0]
try:
- rule = reaction_note_dict['GENE ASSOCIATION'][0].encode('ascii')
- if rule.startswith(""") and rule.endswith("""):
- rule = rule[6:-6]
- reaction.gene_reaction_rule = str(rule)
- except:
- warn("gene_reaction_rule is not ascii compliant")
+ rule.encode('ascii')
+ except (UnicodeEncodeError, UnicodeDecodeError):
+ warn("gene_reaction_rule '%s' is not ascii compliant" % rule)
+ if rule.startswith(""") and rule.endswith("""):
+ rule = rule[6:-6]
+ reaction.gene_reaction_rule = rule
if 'GENE LIST' in reaction_note_dict:
reaction.systematic_names = reaction_note_dict['GENE LIST'][0]
elif 'GENES' in reaction_note_dict and \
@@ -410,7 +411,17 @@ def write_cobra_model_to_sbml_file(cobra_model, sbml_filename,
#Need to remove - for proper SBML. Replace with __
the_reaction_id = 'R_' + the_reaction.id.replace('-','__' )
sbml_reaction.setId(the_reaction_id)
- sbml_reaction.setReversible(the_reaction.reversibility)
+ # The reason we are not using the Reaction.reversibility property
+ # is because the SBML definition of reversibility does not quite
+ # match with the cobra definition. In cobra, reversibility implies
+ # that both positive and negative flux values are feasible. However,
+ # SBML requires negative-flux-only reactions to still be classified
+ # as reversible. To quote from the SBML Level 3 Version 1 Spec:
+ # > However, labeling a reaction as irreversible is interpreted as
+ # > an assertion that the rate expression will not have negative
+ # > values during a simulation.
+ # (Page 60 lines 44-45)
+ sbml_reaction.setReversible(the_reaction.lower_bound < 0)
if the_reaction.name:
sbml_reaction.setName(the_reaction.name)
else:
diff --git a/cobra/io/sbml3.py b/cobra/io/sbml3.py
new file mode 100644
index 0000000..0f85929
--- /dev/null
+++ b/cobra/io/sbml3.py
@@ -0,0 +1,429 @@
+from collections import defaultdict
+from warnings import warn
+from decimal import Decimal
+from ast import parse as ast_parse, Name, Or, And, BoolOp
+
+from six import iteritems
+
+from .. import Metabolite, Reaction, Gene, Model
+from ..core.Gene import parse_gpr
+
+
+try:
+ from xml.etree.cElementTree import parse, Element, SubElement, \
+ ElementTree, tostring, register_namespace
+except ImportError:
+ from xml.etree.ElementTree import parse, Element, SubElement, \
+ ElementTree, tostring, register_namespace
+
+# use sbml level 2 from sbml.py (which uses libsbml). Eventually, it would
+# be nice to use the libSBML converters directly instead.
+try:
+ import libsbml
+except ImportError:
+ libsbml = None
+else:
+ from .sbml import create_cobra_model_from_sbml_file as read_sbml2
+ from .sbml import write_cobra_model_to_sbml_file as write_sbml2
+
+try:
+ from sympy import Basic
+except:
+ class Basic:
+ pass
+
+
+# deal with namespaces
+namespaces = {"fbc": "http://www.sbml.org/sbml/level3/version1/fbc/version2",
+ "sbml": "http://www.sbml.org/sbml/level3/version1/core"}
+for key in namespaces:
+ register_namespace(key, namespaces[key])
+
+# XPATH query wrappers
+fbc_prefix = "{" + namespaces["fbc"] + "}"
+sbml_prefix = "{" + namespaces["sbml"] + "}"
+
+SBML_DOT = "__SBML_DOT__"
+# FBC TAGS
+OR_TAG = "fbc:or"
+AND_TAG = "fbc:and"
+GENEREF_TAG = "fbc:geneProductRef"
+GPR_TAG = "fbc:geneProductAssociation"
+GENELIST_TAG = "fbc:listOfGeneProducts"
+GENE_TAG = "fbc:geneProduct"
+# XPATHS
+BOUND_XPATH = "sbml:listOfParameters/sbml:parameter" # TODO only get constant
+COMPARTMENT_XPATH = "sbml:listOfCompartments/sbml:compartment"
+GENES_XPATH = GENELIST_TAG + "/" + GENE_TAG
+SPECIES_XPATH = "sbml:listOfSpecies/sbml:species[@boundaryCondition='%s']"
+OBJECTIVES_XPATH = ("fbc:objective[@fbc:id='%s']/"
+ "fbc:listOfFluxObjectives/"
+ "fbc:fluxObjective")
+
+
+def ns(query):
+ """replace prefixes with namespace"""
+ return query.replace("fbc:", fbc_prefix).replace("sbml:", sbml_prefix)
+
+
+def get_attrib(tag, attribute, type=lambda x: x, require=False):
+ value = tag.get(ns(attribute))
+ if require and value is None:
+ raise Exception("required attribute '%s' not found in tag '%s'" %
+ (attribute, tag.tag))
+ return type(value) if value is not None else None
+
+
+def set_attrib(xml, attribute_name, value):
+ if value is None or value == "":
+ return
+ xml.set(ns(attribute_name), str(value))
+
+
+# string utility functions
+def clip(string, prefix):
+ """clips a prefix from the beginning of a string if it exists
+
+ >>> clip("R_pgi", "R_")
+ "pgi"
+
+ """
+ return string[len(prefix):] if string.startswith(prefix) else string
+
+
+def strnum(number):
+ """Utility function to convert a number to a string"""
+ if isinstance(number, (Decimal, Basic, str)):
+ return str(number)
+ s = "%.15g" % number
+ return s.rstrip(".")
+
+
+def construct_gpr_xml(parent, expression):
+ """create gpr xml under parent node"""
+ if isinstance(expression, BoolOp):
+ op = expression.op
+ if isinstance(op, And):
+ new_parent = SubElement(parent, ns(AND_TAG))
+ elif isinstance(op, Or):
+ new_parent = SubElement(parent, ns(OR_TAG))
+ else:
+ raise Exception("unsupported operation " + op.__class__)
+ for arg in expression.values:
+ construct_gpr_xml(new_parent, arg)
+ elif isinstance(expression, Name):
+ gene_elem = SubElement(parent, ns(GENEREF_TAG))
+ set_attrib(gene_elem, "fbc:geneProduct", "G_" + expression.id)
+ else:
+ raise Exception("unsupported operation " + repr(expression))
+
+
+def parse_xml_into_model(xml, number=float):
+ xml_model = xml.find(ns("sbml:model"))
+ if get_attrib(xml_model, "fbc:strict") != "true":
+ warn('loading SBML model without fbc:strict="true"')
+
+ model_id = get_attrib(xml_model, "id")
+ model = Model(model_id)
+
+ model.compartments = {c.get("id"): c.get("name") for c in
+ xml.findall(ns(COMPARTMENT_XPATH))}
+
+ # add metabolites
+ for species in xml_model.findall(ns(SPECIES_XPATH) % 'false'):
+ met = Metabolite(clip(species.get("id"), "M_"))
+ met.name = species.get("name")
+ met.compartment = species.get("compartment")
+ met.charge = get_attrib(species, "fbc:charge", int)
+ met.formula = get_attrib(species, "fbc:chemicalFormula")
+ model.add_metabolites([met])
+ # Detect boundary metabolites - In case they have been mistakenly
+ # added. They should not actually appear in a model
+ boundary_metabolites = {clip(i.get("id"), "M_")
+ for i in xml_model.findall(ns(SPECIES_XPATH)
+ % 'true')}
+
+ # add genes
+ for sbml_gene in xml_model.findall(ns(GENES_XPATH)):
+ gene_id = get_attrib(sbml_gene, "fbc:id").replace(SBML_DOT, ".")
+ gene = Gene(clip(gene_id, "G_"))
+ gene.name = get_attrib(sbml_gene, "fbc:label")
+ model.genes.append(gene)
+
+ or_tag = ns(OR_TAG)
+ and_tag = ns(AND_TAG)
+ generef_tag = ns(GENEREF_TAG)
+
+ def process_gpr(sub_xml):
+ """recursively convert gpr xml to a gpr string"""
+ if sub_xml.tag == or_tag:
+ return "( " + ' or '.join(process_gpr(i) for i in sub_xml) + " )"
+ elif sub_xml.tag == and_tag:
+ return "( " + ' and '.join(process_gpr(i) for i in sub_xml) + " )"
+ elif sub_xml.tag == generef_tag:
+ gene_id = get_attrib(sub_xml, "fbc:geneProduct", require=True)
+ return clip(gene_id, "G_")
+ else:
+ raise Exception("unsupported tag " + sub_xml.tag)
+
+ # options for get_attrib for numbers
+ opts = {"type": number, "require": True}
+ # TODO handle infinity
+ bounds = {bound.get("id"): get_attrib(bound, "value", **opts)
+ for bound in xml_model.findall(ns(BOUND_XPATH))}
+ # add reactions
+ reactions = []
+ for sbml_reaction in xml_model.findall(
+ ns("sbml:listOfReactions/sbml:reaction")):
+ reaction = Reaction(clip(sbml_reaction.get("id"), "R_"))
+ reaction.name = sbml_reaction.get("name")
+ lb_id = get_attrib(sbml_reaction, "fbc:lowerFluxBound", require=True)
+ reaction.lower_bound = bounds[lb_id]
+ ub_id = get_attrib(sbml_reaction, "fbc:upperFluxBound", require=True)
+ reaction.upper_bound = bounds[ub_id]
+ reactions.append(reaction)
+
+ stoichiometry = defaultdict(lambda: 0)
+ for species_reference in sbml_reaction.findall(
+ ns("sbml:listOfReactants/sbml:speciesReference")):
+ met_name = clip(species_reference.get("species"), "M_")
+ stoichiometry[met_name] -= \
+ number(species_reference.get("stoichiometry"))
+ for species_reference in sbml_reaction.findall(
+ ns("sbml:listOfProducts/sbml:speciesReference")):
+ met_name = clip(species_reference.get("species"), "M_")
+ stoichiometry[met_name] += \
+ get_attrib(species_reference, "stoichiometry", **opts)
+ # needs to have keys of metabolite objects, not ids
+ object_stoichiometry = {}
+ for met_id in stoichiometry:
+ if met_id in boundary_metabolites:
+ continue
+ try:
+ metabolite = model.metabolites.get_by_id(met_id)
+ except KeyError:
+ warn("ignoring unknown metabolite '%s' in %s" %
+ (met_id, repr(reaction)))
+ continue
+ object_stoichiometry[metabolite] = stoichiometry[met_id]
+ reaction.add_metabolites(object_stoichiometry)
+ # set gene reaction rule
+ gpr_xml = sbml_reaction.find(ns(GPR_TAG))
+ if gpr_xml is not None and len(gpr_xml) != 1:
+ warn("ignoring invalid geneAssocation for " + repr(reaction))
+ gpr_xml = None
+ gpr = process_gpr(gpr_xml[0]) if gpr_xml is not None else ''
+ # remove outside parenthesis, if any
+ if gpr.startswith("(") and gpr.endswith(")"):
+ gpr = gpr[1:-1].strip()
+ gpr = gpr.replace(SBML_DOT, ".")
+ reaction.gene_reaction_rule = gpr
+ model.add_reactions(reactions)
+
+ # objective coefficients are handled after all reactions are added
+ obj_list = xml_model.find(ns("fbc:listOfObjectives"))
+ target_objective = get_attrib(obj_list, "fbc:activeObjective")
+ obj_query = ns(OBJECTIVES_XPATH) % target_objective
+ for sbml_objective in obj_list.findall(obj_query):
+ rxn_id = clip(get_attrib(sbml_objective, "fbc:reaction"), "R_")
+ model.reactions.get_by_id(rxn_id).objective_coefficient = \
+ get_attrib(sbml_objective, "fbc:coefficient", type=number)
+
+ return model
+
+
+def model_to_xml(cobra_model, units=True):
+ xml = Element("sbml", xmlns=namespaces["sbml"], level="3", version="1",
+ sboTerm="SBO:0000624")
+ set_attrib(xml, "fbc:required", "false")
+ xml_model = SubElement(xml, "model")
+ set_attrib(xml_model, "fbc:strict", "true")
+ if cobra_model.id is not None:
+ xml_model.set("id", cobra_model.id)
+
+ # if using units, add in mmol/gdw/hr
+ if units:
+ unit_def = SubElement(
+ SubElement(xml_model, "listOfUnitDefinitions"),
+ "unitDefinition", id="mmol_per_gDW_per_hr")
+ list_of_units = SubElement(unit_def, "listOfUnits")
+ SubElement(list_of_units, "unit", kind="mole", scale="-3",
+ multiplier="1", exponent="1")
+ SubElement(list_of_units, "unit", kind="gram", scale="0",
+ multiplier="1", exponent="-1")
+ SubElement(list_of_units, "unit", kind="second", scale="0",
+ multiplier="3600", exponent="-1")
+
+ # create the element for the flux objective
+ obj_list_tmp = SubElement(xml_model, ns("fbc:listOfObjectives"))
+ set_attrib(obj_list_tmp, "fbc:activeObjective", "obj")
+ obj_list_tmp = SubElement(obj_list_tmp, ns("fbc:objective"))
+ set_attrib(obj_list_tmp, "fbc:id", "obj")
+ set_attrib(obj_list_tmp, "fbc:type", "maximize")
+ flux_objectives_list = SubElement(obj_list_tmp,
+ ns("fbc:listOfFluxObjectives"))
+
+ # create the element for the flux bound parameters
+ parameter_list = SubElement(xml_model, "listOfParameters")
+ param_attr = {"constant": "true"}
+ if units:
+ param_attr["units"] = "mmol_per_gDW_per_hr"
+ # the most common bounds are the minimum, maxmium, and 0
+ min_value = min(cobra_model.reactions.list_attr("lower_bound"))
+ max_value = max(cobra_model.reactions.list_attr("upper_bound"))
+ SubElement(parameter_list, "parameter", value=strnum(min_value),
+ id="cobra_default_lb", sboTerm="SBO:0000626", **param_attr)
+ SubElement(parameter_list, "parameter", value=strnum(max_value),
+ id="cobra_default_ub", sboTerm="SBO:0000626", **param_attr)
+ SubElement(parameter_list, "parameter", value="0",
+ id="cobra_0_bound", sboTerm="SBO:0000626", **param_attr)
+
+ def create_bound(reaction, bound_type):
+ """returns the str id of the appropriate bound for the reaction
+
+ The bound will also be created if necessary"""
+ value = getattr(reaction, bound_type)
+ if value == min_value:
+ return "cobra_default_lb"
+ elif value == 0:
+ return "cobra_0_bound"
+ elif value == max_value:
+ return "cobra_default_ub"
+ else:
+ param_id = "R_" + reaction.id + "_" + bound_type
+ SubElement(parameter_list, "parameter", id=param_id,
+ value=strnum(value), sboTerm="SBO:0000625",
+ **param_attr)
+ return param_id
+
+ # add in compartments
+ compartmenst_list = SubElement(xml_model, "listOfCompartments")
+ compartments = cobra_model.compartments
+ for compartment, name in iteritems(compartments):
+ SubElement(compartmenst_list, "compartment", id=compartment, name=name,
+ constant="true")
+
+ # add in metabolites
+ species_list = SubElement(xml_model, "listOfSpecies")
+ for met in cobra_model.metabolites:
+ species = SubElement(species_list, "species",
+ id="M_" + met.id,
+ compartment=str(met.compartment),
+ # Useless required SBML parameters
+ constant="false",
+ boundaryCondition="false",
+ hasOnlySubstanceUnits="false")
+ set_attrib(species, "name", met.name)
+ set_attrib(species, "fbc:charge", met.charge)
+ set_attrib(species, "fbc:chemicalFormula", met.formula)
+
+ # add in genes
+ if len(cobra_model.genes) > 0:
+ genes_list = SubElement(xml_model, ns(GENELIST_TAG))
+ for gene in cobra_model.genes:
+ gene_id = gene.id.replace(".", SBML_DOT)
+ sbml_gene = SubElement(genes_list, ns(GENE_TAG))
+ set_attrib(sbml_gene, "fbc:id", "G_" + gene_id)
+ name = gene.name
+ if name is None or len(name) == 0:
+ name = gene.id
+ set_attrib(sbml_gene, "fbc:label", gene_id)
+ set_attrib(sbml_gene, "fbc:name", gene.name)
+
+ # add in reactions
+ reactions_list = SubElement(xml_model, "listOfReactions")
+ for reaction in cobra_model.reactions:
+ id = "R_" + reaction.id
+ sbml_reaction = SubElement(
+ reactions_list, "reaction",
+ id=id,
+ # Useless required SBML parameters
+ fast="false",
+ reversible=str(reaction.lower_bound < 0).lower())
+ set_attrib(sbml_reaction, "name", reaction.name)
+ # add in bounds
+ set_attrib(sbml_reaction, "fbc:upperFluxBound",
+ create_bound(reaction, "upper_bound"))
+ set_attrib(sbml_reaction, "fbc:lowerFluxBound",
+ create_bound(reaction, "lower_bound"))
+
+ # objective coefficient
+ if reaction.objective_coefficient != 0:
+ objective = SubElement(flux_objectives_list,
+ ns("fbc:fluxObjective"))
+ set_attrib(objective, "fbc:reaction", id)
+ set_attrib(objective, "fbc:coefficient",
+ strnum(reaction.objective_coefficient))
+
+ # stoichiometry
+ reactants = {}
+ products = {}
+ for metabolite, stoichiomety in iteritems(reaction._metabolites):
+ met_id = "M_" + metabolite.id
+ if stoichiomety > 0:
+ products[met_id] = strnum(stoichiomety)
+ else:
+ reactants[met_id] = strnum(-stoichiomety)
+ if len(reactants) > 0:
+ reactant_list = SubElement(sbml_reaction, "listOfReactants")
+ for met_id, stoichiomety in iteritems(reactants):
+ SubElement(reactant_list, "speciesReference", species=met_id,
+ stoichiometry=stoichiomety, constant="true")
+ if len(products) > 0:
+ product_list = SubElement(sbml_reaction, "listOfProducts")
+ for met_id, stoichiomety in iteritems(products):
+ SubElement(product_list, "speciesReference", species=met_id,
+ stoichiometry=stoichiomety, constant="true")
+
+ # gene reaction rule
+ gpr = reaction.gene_reaction_rule
+ if gpr is not None and len(gpr) > 0:
+ gpr = gpr.replace(".", SBML_DOT)
+ gpr_xml = SubElement(sbml_reaction, ns(GPR_TAG))
+ try:
+ parsed = parse_gpr(gpr)[0]
+ construct_gpr_xml(gpr_xml, parsed.body)
+ except Exception as e:
+ print("failed on '%s' in %s" %
+ (reaction.gene_reaction_rule, repr(reaction)))
+ raise e
+
+ return xml
+
+
+def read_sbml_model(filename, number=float, **kwargs):
+ xmlfile = parse(filename)
+ xml = xmlfile.getroot()
+ if xml.get("level") != "3" or xml.get("version") != "1" or \
+ get_attrib(xml, "fbc:required") is None:
+ if libsbml is None:
+ raise Exception("libSBML required for fbc < 2")
+ return read_sbml2(filename, **kwargs)
+ return parse_xml_into_model(xml, number=number)
+
+
+def write_sbml_model(cobra_model, filename, use_fbc_package=True, **kwargs):
+ if not use_fbc_package:
+ write_sbml2(cobra_model, filename, use_fbc_package=False, **kwargs)
+ return
+ xml = model_to_xml(cobra_model, **kwargs)
+ indent_xml(xml)
+ ElementTree(xml).write(filename, encoding="UTF-8")
+
+
+# inspired by http://effbot.org/zone/element-lib.htm#prettyprint
+def indent_xml(elem, level=0):
+ """indent xml for pretty printing"""
+ i = "\n" + level * " "
+ if len(elem):
+ if not elem.text or not elem.text.strip():
+ elem.text = i + " "
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ for elem in elem:
+ indent_xml(elem, level + 1)
+ if not elem.tail or not elem.tail.strip():
+ elem.tail = i
+ else:
+ if level and (not elem.tail or not elem.tail.strip()):
+ elem.tail = i
diff --git a/cobra/manipulation/__init__.py b/cobra/manipulation/__init__.py
index 188be8a..827c4f1 100644
--- a/cobra/manipulation/__init__.py
+++ b/cobra/manipulation/__init__.py
@@ -1,3 +1,3 @@
-from .delete import delete_model_genes, undelete_model_genes
+from .delete import delete_model_genes, undelete_model_genes, remove_genes
from .modify import initialize_growth_medium, convert_to_irreversible, \
- revert_to_reversible
+ revert_to_reversible, escape_ID
diff --git a/cobra/manipulation/delete.py b/cobra/manipulation/delete.py
index 5635984..b2178c3 100644
--- a/cobra/manipulation/delete.py
+++ b/cobra/manipulation/delete.py
@@ -1,12 +1,11 @@
import re
from copy import deepcopy
from warnings import warn
+from ast import NodeTransformer, And
+from six import iteritems, string_types
-# compile regular expressions now instead of in every function call
-spontaneous_re = re.compile('(^|(?<=( |\()))s0001(?=( |\)|$))')
-and_re = re.compile(r'\band\b')
-or_re = re.compile(r'\bor\b')
+from ..core.Gene import eval_gpr, parse_gpr, ast2str
def prune_unused_metabolites(cobra_model):
@@ -85,25 +84,12 @@ def get_compiled_gene_reaction_rules(cobra_model):
rules.
"""
- rules = {}
- # some gene names can not be put through eval
- bad_genes = {g for g in cobra_model.genes if g.id[0].isdigit() or
- not g.id.isalnum()}
- for reaction in cobra_model.reactions:
- try:
- if len(bad_genes.intersection(reaction.genes)) > 0:
- continue
- rules[reaction.id] = compile(reaction.gene_reaction_rule,
- '<string>', 'eval')
- except SyntaxError:
- # This is necessary because some gene_reaction_rules do not
- # compile.
- None
- return rules
+ return {r: parse_gpr(r.gene_reaction_rule)[0]
+ for r in cobra_model.reactions}
def find_gene_knockout_reactions(cobra_model, gene_list,
- compiled_gene_reaction_rules={}):
+ compiled_gene_reaction_rules=None):
"""identify reactions which will be disabled when the genes are knocked out
cobra_model: :class:`~cobra.core.Model.Model`
@@ -118,43 +104,18 @@ def find_gene_knockout_reactions(cobra_model, gene_list,
dict must exclude any rules which can not be used with eval.
"""
-
potential_reactions = set()
- for x in gene_list:
- potential_reactions.update(x._reaction)
-
- knocked_out_reactions = []
- for the_reaction in potential_reactions:
- # Attempt to use the compiled gene reaction rule if provided
- if the_reaction.id in compiled_gene_reaction_rules:
- gene_state = {i.id: False if i in gene_list else True
- for i in the_reaction._genes}
- result = eval(compiled_gene_reaction_rules[the_reaction.id],
- {}, gene_state)
- if result is False:
- knocked_out_reactions.append(the_reaction)
- continue
- elif result is True:
- continue
-
- # operates on a copy
- gene_reaction_rule = and_re.sub("*", the_reaction.gene_reaction_rule)
- gene_reaction_rule = or_re.sub("+", gene_reaction_rule)
- # To prevent shorter gene names from replacing substrings in
- # longer names, go in order from longest to shortest.
- reaction_genes = sorted(the_reaction._genes, reverse=True,
- key=lambda x: len(x.id))
- # Replace each gene in the gpr string with 1 if it is still
- # active, or 0 if it is being knocked out.
- for gene in reaction_genes:
- if gene in gene_list:
- gene_reaction_rule = gene_reaction_rule.replace(gene.id, '0')
- else:
- gene_reaction_rule = gene_reaction_rule.replace(gene.id, '1')
- gene_reaction_rule = spontaneous_re.sub('1', gene_reaction_rule)
- if not eval(gene_reaction_rule): # evaluates to 0 when gpr is false
- knocked_out_reactions.append(the_reaction)
- return knocked_out_reactions
+ for gene in gene_list:
+ if isinstance(gene, string_types):
+ gene = cobra_model.genes.get_by_id(gene)
+ potential_reactions.update(gene._reaction)
+ gene_set = {str(i) for i in gene_list}
+ if compiled_gene_reaction_rules is None:
+ compiled_gene_reaction_rules = {r: parse_gpr(r.gene_reaction_rule)[0]
+ for r in potential_reactions}
+
+ return [r for r in potential_reactions
+ if not eval_gpr(compiled_gene_reaction_rules[r], gene_set)]
def delete_model_genes(cobra_model, gene_list,
@@ -216,3 +177,54 @@ def delete_model_genes(cobra_model, gene_list,
cobra_model._trimmed_genes = list(set(cobra_model._trimmed_genes +
gene_list))
+
+
+class _GeneRemover(NodeTransformer):
+ def __init__(self, target_genes):
+ NodeTransformer.__init__(self)
+ self.target_genes = {str(i) for i in target_genes}
+
+ def visit_Name(self, node):
+ return None if node.id in self.target_genes else node
+
+ def visit_BoolOp(self, node):
+ original_n = len(node.values)
+ self.generic_visit(node)
+ if len(node.values) == 0:
+ return None
+ # AND with any entities removed
+ if len(node.values) < original_n and isinstance(node.op, And):
+ return None
+ # if one entity in an OR was removed, just that entity passed up
+ if len(node.values) == 1:
+ return node.values[0]
+ return node
+
+
+def remove_genes(cobra_model, gene_list, remove_reactions=True):
+ """remove genes entirely from the model
+
+ This will also simplify all gene_reaction_rules with this
+ gene inactivated."""
+ gene_set = {cobra_model.genes.get_by_id(str(i)) for i in gene_list}
+ gene_id_set = {i.id for i in gene_set}
+ remover = _GeneRemover(gene_id_set)
+ ast_rules = get_compiled_gene_reaction_rules(cobra_model)
+ target_reactions = []
+ for reaction, rule in iteritems(ast_rules):
+ if reaction.gene_reaction_rule is None or \
+ len(reaction.gene_reaction_rule) == 0:
+ continue
+ # reactions to remove
+ if remove_reactions and not eval_gpr(rule, gene_id_set):
+ target_reactions.append(reaction)
+ else:
+ # if the reaction is not removed, remove the gene
+ # from its gpr
+ remover.visit(rule)
+ new_rule = ast2str(rule)
+ if new_rule != reaction.gene_reaction_rule:
+ reaction.gene_reaction_rule = new_rule
+ for gene in gene_set:
+ cobra_model.genes.remove(gene)
+ cobra_model.remove_reactions(target_reactions)
diff --git a/cobra/manipulation/modify.py b/cobra/manipulation/modify.py
index ae977d0..18443ab 100644
--- a/cobra/manipulation/modify.py
+++ b/cobra/manipulation/modify.py
@@ -1,7 +1,54 @@
from copy import deepcopy
from warnings import warn
+from itertools import chain
+from ast import NodeTransformer
+
+from six import iteritems
from .. import Reaction
+from .delete import get_compiled_gene_reaction_rules
+from ..core.Gene import ast2str
+
+_renames = (
+ (".", "_DOT_"),
+ ("(", "_LPAREN_"),
+ (")", "_RPAREN_"),
+ ("-", "__"),
+ ("[", "_LSQBKT"),
+ ("]", "_RSQBKT"),
+ (",", "_COMMA_"),
+ (":", "_COLON_"),
+ (">", "_GT_"),
+ ("<", "_LT"),
+ ("/", "_FLASH"),
+ ("\\", "_BSLASH"),
+ ("+", "_PLUS_"),
+ ("=", "_EQ_"),
+ (" ", "_SPACE_"),
+)
+
+
+class _GeneRenamer(NodeTransformer):
+
+ def visit_Name(self, node):
+ for char, escaped_char in _renames:
+ node.id = node.id.replace(char, escaped_char)
+ return node
+
+
+def escape_ID(cobra_model):
+ """makes all ids SBML compliant"""
+ for x in chain([cobra_model],
+ cobra_model.metabolites,
+ cobra_model.reactions,
+ cobra_model.genes):
+ for char, escaped_char in _renames:
+ x.id = x.id.replace(char, escaped_char)
+ cobra_model.repair()
+ gene_renamer = _GeneRenamer()
+ for rxn, rule in iteritems(get_compiled_gene_reaction_rules(cobra_model)):
+ if rule is not None:
+ rxn._gene_reaction_rule = ast2str(gene_renamer.visit(rule))
def initialize_growth_medium(cobra_model, the_medium='MgM',
diff --git a/cobra/mlab/__init__.py b/cobra/mlab/__init__.py
deleted file mode 100644
index 5741d75..0000000
--- a/cobra/mlab/__init__.py
+++ /dev/null
@@ -1,15 +0,0 @@
-from os import name as __name
-from sys import modules as __modules
-from warnings import warn
-if __name == 'java':
- warn("%s is not yet supported on jython"%__modules[__name__])
-else:
- from mlab import *
-del __name, __modules
-
-__doc__ = """
-Provides python functions which are useful for interacting with MATLAB
-by using the mlabwrap library.
-
-To use MATLAB functions directly, see cobra.matlab
-"""
diff --git a/cobra/mlab/matlab_scripts/cell_to_string.m b/cobra/mlab/matlab_scripts/cell_to_string.m
deleted file mode 100644
index bfcf58f..0000000
--- a/cobra/mlab/matlab_scripts/cell_to_string.m
+++ /dev/null
@@ -1,3 +0,0 @@
-function the_string = cell_to_string( the_cell_array )
- the_string = sprintf( '%s\t', the_cell_array{:} );
-
diff --git a/cobra/mlab/matlab_scripts/create_container.m b/cobra/mlab/matlab_scripts/create_container.m
deleted file mode 100644
index ba9f2e7..0000000
--- a/cobra/mlab/matlab_scripts/create_container.m
+++ /dev/null
@@ -1,2 +0,0 @@
-function the_container = create_container(the_keys, the_values)
- the_container = containers.Map(the_keys, the_values);
diff --git a/cobra/mlab/matlab_scripts/load_mat.m b/cobra/mlab/matlab_scripts/load_mat.m
deleted file mode 100644
index 0d21abb..0000000
--- a/cobra/mlab/matlab_scripts/load_mat.m
+++ /dev/null
@@ -1,3 +0,0 @@
-function loaded_object = load_mat( the_filename )
- loaded_object = load( the_filename);
-
diff --git a/cobra/mlab/matlab_scripts/save_from_python.m b/cobra/mlab/matlab_scripts/save_from_python.m
deleted file mode 100644
index ce47cff..0000000
--- a/cobra/mlab/matlab_scripts/save_from_python.m
+++ /dev/null
@@ -1,3 +0,0 @@
-function [] = save_from_python( the_file, the_model )
- save the_file the_model;
-
diff --git a/cobra/mlab/mlab.py b/cobra/mlab/mlab.py
deleted file mode 100644
index 50705a6..0000000
--- a/cobra/mlab/mlab.py
+++ /dev/null
@@ -1,405 +0,0 @@
-#cobra.mlab.py
-#System modules
-import cPickle, numpy, os, cobra, warnings
-from copy import deepcopy
-from scipy.sparse import dok_matrix
-from .. import Model, Reaction, Metabolite, Formula, ArrayBasedModel
-
-from mlabwrap import mlab as matlab
-
-# give an interface to the mlab system through cobra.matlab
-cobra.matlab = matlab
-matlab.__doc__ = """
-This is an mlabwrap connection to MATLAB which can be used to call
-MATLAB functions. For example, if model is a python model, the following
-can be used to optimize the model in MATLAB:
-> matlab_model = cobra.mlab.cobra_model_object_to_cobra_matlab_struct(model)
-> result = cobra.matlab.optimizeCbModel(matlab_model)
-
-Any MATLAB function can be called this way"""
-
-# add path with module's python scripts to the MATLAB path
-mlab_path = os.path.join(cobra.__path__[0], 'mlab', 'matlab_scripts')
-matlab.addpath(mlab_path)
-
-_possible_cobra_locations = ["~/MATLAB/cobra", "~/cobra",
- "~/Documents/MATLAB/cobra", "~/Documents/opencobra/matlab/cobra"]
-
-def init_matlab_toolbox(matlab_cobra_path=None, discover_functions=True):
- """initialize the matlab cobra toolbox, and load its functions
- into mlab's namespace (very useful for ipython tab completion)
-
- matlab_cobra_path: the path to the directory containing the MATLAB
- cobra installation. Using the default None will attempt to find the
- toolbox in the MATLAB path
-
- discover_functions: Whether mlabwrap should autodiscover all cobra toolbox
- functions in matlab. This is convenient for tab completion, but may take
- some time."""
- # find initCobraToolbox.m
- if matlab_cobra_path is None:
- matlab_cobra_path = os.path.split(
- cobra.matlab.which('initCobraToolbox'))[0]
- if matlab_cobra_path == "":
- for i in _possible_cobra_locations:
- poss_path = os.path.expanduser(i)
- if os.path.isfile(poss_path + "/initCobraToolbox.m"):
- matlab_cobra_path = poss_path
- break
- if not os.path.isfile(os.path.join(matlab_cobra_path,
- "initCobraToolbox.m")):
- print "initCobraToolbox not found in given path"
- return
- # store the current directory so we can return to it
- curdir = os.path.abspath(os.curdir)
- os.chdir(matlab_cobra_path)
- matlab.initCobraToolbox()
- os.chdir(curdir)
- # discover MATLAB functions
- for matlab_func in ["plot", "figure", "hist", "load", "find"]:
- getattr(matlab, matlab_func)
- for filename in os.listdir(mlab_path):
- getattr(matlab, filename.replace(".m", ""))
- if not discover_functions:
- return # done now, do not need to find matlab cobra functions
- with warnings.catch_warnings():
- warnings.simplefilter("ignore")
- walker = os.walk(matlab_cobra_path)
- # skip docs and external
- dirpath, dirnames, filenames = walker.next()
- dirnames.pop(dirnames.index("external"))
- dirnames.pop(dirnames.index("docs"))
- for root, dirs, files in walker:
- for filename in files:
- if filename.endswith(".m"):
- try:
- getattr(matlab, filename.replace(".m", ""))
- except:
- continue
-
-
-#Project defined modules
-def matlab_cell_to_python_list(the_cell):
- try:
- import mlabwrap
- except ImportError:
- print 'Could not import mlabwrap: ' + ImportError + '\n'
- return False
- #the_list = mlabwrap.mlab.cell_to_string(the_cell).rstrip('\t').split('\t')
- #Because the mlabwrap.mlab.cell_to_string function will end with a tab, it must
- #be removed. Use indexing instead of rstrip because rstrip will mess up
- #when the last element in the string is empty.
- the_list = mlabwrap.mlab.cell_to_string(the_cell).split('\t')
- return the_list[:len(the_list) - 1]
-
-def matlab_logical_to_python_logical(the_logical):
- try:
- import mlabwrap
- except ImportError:
- print 'Could not import mlabwrap: ' + ImportError + '\n'
- return False
- if mlabwrap.mlab.double(the_logical)[0][0] == 1:
- return True
- else:
- return False
-
-def python_list_to_matlab_cell(the_list, transpose = False):
- try:
- import mlabwrap
- except ImportError:
- print 'Could not load mlabwrap ' + ImportError + '\n'
- return False
- if hasattr(the_list[0], 'id'):
- the_list = [x.id for x in the_list]
- #Remove the single apostrophes because matlab or mlabwrap has
- #problems with them.
- the_list = [x.replace(r"'",'') for x in the_list]
- the_string = '{' + str(the_list).lstrip('[').rstrip(']') + '}'
- if transpose:
- the_string = the_string.replace(',',';')
- return mlabwrap.mlab.eval(the_string)
-
-def matlab_sparse_to_scipy_sparse(matlab_sparse_matrix):
- try:
- import mlabwrap
- import scipy.sparse
- except ImportError:
- print 'Could not load mlabwrap or scipy ' + ImportError + '\n'
- return False
- [row_indices, column_indices, the_values] = mlabwrap.mlab.find(matlab_sparse_matrix , nout = 3)
- #Change to 0-based indices
- row_indices = row_indices - 1
- column_indices = column_indices - 1
- the_shape = mlabwrap.mlab.size(matlab_sparse_matrix)
- the_shape = tuple(map(int, the_shape[0,]))
- #This could be sped up by using a dok_matrix and zipping the indices and values
- #scipy_sparse_matrix = scipy.sparse_dok.matrix(the_shape)
- #scipy_sparse_matrix.update(zip(zip(row_indices, column_indices), the_values))
- #return scipy_sparse_matrix.tolil()
- scipy_sparse_matrix = scipy.sparse.lil_matrix(the_shape)
- for i in range(len(the_values)):
- scipy_sparse_matrix[int(row_indices[i][0]), int(column_indices[i][0])] = the_values[i][0]
- return scipy_sparse_matrix
-
-def scipy_sparse_to_mlab_sparse(scipy_sparse_matrix):
- """A more efficient method is needed for when the
- matrix is so big that making a dense version
- is a waste of computer effort."""
- try:
- import mlabwrap
- except ImportError:
- print 'Could not load mlabwrap ' + ImportError + '\n'
- return False
- return mlabwrap.mlab.sparse(scipy_sparse_matrix.todense())
-
-def matlab_sparse_to_numpy_array(matlab_sparse_matrix):
- try:
- import mlabwrap
- import numpy
- except ImportError:
- print 'Could not load mlabwrap or numpy ' + ImportError + '\n'
- return False
- [row_indices, column_indices, the_values] = mlabwrap.mlab.find(matlab_sparse_matrix , nout = 3)
- #Change to 0-based indices
- row_indices = row_indices - 1
- column_indices = column_indices - 1
- the_shape = mlabwrap.mlab.size(matlab_sparse_matrix)
- numpy_array = numpy.zeros(the_shape[0,])
- for i in range(len(the_values)):
- numpy_array[int(row_indices[i][0]), int(column_indices[i][0])] = the_values[i][0]
- return numpy_array
-
-def numpy_array_to_mlab_sparse(numpy_array):
- """A more efficient method is needed for when the
- matrix is so big that making a dense version
- is a waste of computer effort."""
- try:
- import mlabwrap
- except ImportError:
- print 'Could not load mlabwrap ' + ImportError + '\n'
- return False
-
- return mlabwrap.mlab.sparse(numpy_array)
-
-def matlab_cobra_struct_to_python_cobra_object(matlab_struct):
- """Converts a COBRA toolbox 2.0 struct into a cobra.Model object using the mlabwrap matlab proxy
-
- """
-
- from cobra import Model
- try:
- from mlabwrap import mlab as matlab
- except:
- raise Exception('mlabwrap and MATLAB are required to use these functions. '+\
- 'They only function on Mac OS X and GNU/Linux')
- from copy import deepcopy
- from numpy import array
- from cobra.mlab import matlab_cell_to_python_list, matlab_sparse_to_scipy_sparse
- struct_fields = matlab_cell_to_python_list(matlab.fields(matlab_struct, nout=1))
- _S_dok = dok_matrix(matlab_sparse_to_scipy_sparse(matlab_struct.S))
- model_id = 'Matlab_Import'
- if 'description' in struct_fields:
- model_id = str(deepcopy(matlab_struct.description))
- the_model = Model(model_id)
- #Metabolite section
- #Deal with lack of compartment support in the COBRA Toolbox
- the_metabolites = matlab_cell_to_python_list(matlab_struct.mets)
- cobra_metabolites = []
- if the_metabolites[0].endswith(']'):
- [cobra_metabolites.append(Metabolite('%s_%s'%(x[:-3], x[-2]),
- compartment=x[-2]))
- for x in the_metabolites]
- elif the_metabolites[0][-2] == '_':
- [cobra_metabolites.append(Metabolite('%s_%s'%(x[:-2],x[-1]),
- compartment=x[-1]))
- for x in the_metabolites]
- else:
- raise Exception("Don't know how to extract compartment from %s"%the_metabolites[0])
- _b = deepcopy(matlab_struct.b).tolist()
- if 'metNames' in struct_fields:
- _metabolite_names = matlab_cell_to_python_list(matlab_struct.metNames)
- else:
- _metabolite_names = ['']*len(cobra_metabolites)
-
- if 'csense' in struct_fields:
- if isinstance(matlab_struct.csense, str):
- the_csense = matlab_struct.csense
- _constraint_sense = [the_csense[i] for i in range(len(the_csense))]
- else:
- _constraint_sense = matlab_cell_to_python_list(matlab_struct.csense)
- else:
- _constraint_sense = ['E']*len(cobra_metabolites)
- if 'metFormulas' in struct_fields:
- _metabolite_formulas = matlab_cell_to_python_list(matlab_struct.metFormulas)
- else:
- _metabolite_formulas = ['']*len(the_model.metabolites)
- if 'metCharge' in struct_fields:
- _metabolite_charges = matlab_struct.metCharge.flatten().tolist()
- else:
- _metabolite_charges = [None]*len(cobra_metabolites)
- if 'metCASID' in struct_fields:
- _metabolite_cas_id = matlab_cell_to_python_list(matlab_struct.metCASID)
- else:
- _metabolite_cas_id = [None]*len(cobra_metabolites)
- if 'metKeggID' in struct_fields:
- _metabolite_kegg_id = matlab_cell_to_python_list(matlab_struct.metKeggID)
- else:
- _metabolite_kegg_id = [None]*len(cobra_metabolites)
- the_compartments = {}
- for the_metabolite, b, n, c, f, ch, cas, kegg in zip(cobra_metabolites,
- _b,
- _metabolite_names,
- _constraint_sense,
- _metabolite_formulas,
- _metabolite_charges,
- _metabolite_cas_id,
- _metabolite_kegg_id):
- the_metabolite._bound = b[0]
- the_metabolite.name = n
- the_metabolite._constraint_sense = c
- the_metabolite.formula = Formula(f)
-
- the_compartments[the_metabolite.compartment] = the_metabolite.compartment
- if ch is not None:
- the_metabolite.charge = the_metabolite.notes['CHARGE'] = int(ch)
- if cas is not None and cas != '':
- the_metabolite.notes['CASID'] = cas
- if kegg is not None and kegg != '':
- the_metabolite.notes['KEGGID'] = kegg
-
- metabolite_dict = dict([(x.id, x)
- for x in cobra_metabolites])
- #Reaction section
- cobra_reactions = map(Reaction, matlab_cell_to_python_list(matlab_struct.rxns))
- _objective_coefficients = deepcopy(matlab_struct.c).tolist()
- _lower_bounds = deepcopy(matlab_struct.lb).tolist()
- _upper_bounds = deepcopy(matlab_struct.ub).tolist()
- _reversibility = deepcopy(matlab_struct.rev).tolist()
- if 'rxnNames' in struct_fields:
- _reaction_names = matlab_cell_to_python_list(matlab_struct.rxnNames)
- else:
- _reaction_names = ['']*len(the_model.reactions)
- if 'grRules' in struct_fields:
- _gene_reaction_rules = matlab_cell_to_python_list(matlab_struct.grRules)
- else:
- _gene_reaction_rules = ['']*len(the_model.reactions)
- if 'subSystems' in struct_fields:
- _subsystems = matlab_cell_to_python_list(matlab_struct.subSystems)
- else:
- _subsystems = ['']*len(the_model.reactions)
- for the_reaction, o, l, u, n, r, s, rev in zip(cobra_reactions,
- _objective_coefficients,
- _lower_bounds,
- _upper_bounds,
- _reaction_names,
- _gene_reaction_rules,
- _subsystems, _reversibility ):
- the_reaction.objective_coefficient = o[0]
- the_reaction.lower_bound = l[0]
- the_reaction.upper_bound = u[0]
- the_reaction.name = n
- the_reaction.gene_reaction_rule = r
- the_reaction.subsystem = s
- the_reaction.reversibility = rev[0]
- the_reaction.parse_gene_association()
- index_to_reaction = dict(zip(range(len(cobra_reactions)),
- cobra_reactions))
- index_to_metabolite = dict(zip(range(len(cobra_metabolites)),
- cobra_metabolites))
- for k, coefficient in _S_dok.items():
- the_reaction = index_to_reaction[k[1]]
- the_metabolite = index_to_metabolite[k[0]]
- the_reaction.add_metabolites({the_metabolite: coefficient})
- #solution needs to be redesigned from a matlab proxy.
- #Now populate all of the reactions
- #NOTE: Having a metabolite referenece here would be a good idea
- compartment_dict = {'e': 'extracellular',
- 'c': 'cytosol',
- 'p': 'periplasm'}
- for the_key in the_compartments:
- if the_key in compartment_dict:
- the_compartments[the_key] = compartment_dict[the_key]
- the_model.add_reactions(cobra_reactions)
- the_model.compartments = the_compartments
- the_model.solution = None
- return the_model
-
-
-def cobra_model_object_to_cobra_matlab_struct(cobra_model):
- """This function converts all of the object values to the
- corresponding model fields to update the mlab model.
-
- """
- try:
- from mlabwrap import mlab as matlab
- except:
- raise Exception('mlabwrap and MATLAB are required to use these functions. '+\
- 'They only function on Mac OS X and GNU/Linux')
- from cobra.mlab import python_list_to_matlab_cell, scipy_sparse_to_mlab_sparse
- if hasattr(cobra_model, 'to_array_based_model'):
- cobra_model = cobra_model.to_array_based_model()
- else:
- cobra_model.update()
- matlab_struct = matlab.struct()
- #Things that need a conversion: S, rxnGeneMat,
- matlab_struct.mets = python_list_to_matlab_cell([x.id for x in cobra_model.metabolites],
- transpose = True)
- matlab_struct.metNames = python_list_to_matlab_cell([x.name for x in cobra_model.metabolites],
- transpose = True)
- matlab_struct.metFormulas = python_list_to_matlab_cell([x.formula
- for x in cobra_model.metabolites],
- transpose = True)
- matlab_struct.genes = python_list_to_matlab_cell(cobra_model.genes, transpose = True)
- matlab_struct.grRules = python_list_to_matlab_cell([x.gene_reaction_rule
- for x in cobra_model.reactions],
- transpose = True)
- matlab_struct.rxns = python_list_to_matlab_cell([x.id for x in cobra_model.reactions],
- transpose = True)
- matlab_struct.rxnNames = python_list_to_matlab_cell([x.name
- for x in cobra_model.reactions],
- transpose = True)
- matlab_struct.subSystems = python_list_to_matlab_cell([x.subsystem
- for x in cobra_model.reactions],
- transpose=True)
-
- if hasattr(cobra_model, 'constraint_sense'):
- matlab_struct.csense = reduce(lambda x,y: x+y, cobra_model.constraint_sense)
- #matlab_struct.csense = python_list_to_matlab_cell(['E']*len(cobra_model.metabolites), transpose = True)
- #TODO: inefficient conversion but who cares? matlab's on its way out
- matlab_struct.S = scipy_sparse_to_mlab_sparse(cobra_model.S)
- #Things that can be directly copied
- matlab_struct.b = cobra_model.b
- matlab_struct.c = cobra_model.objective_coefficients
- matlab_struct.lb = cobra_model.lower_bounds
- matlab_struct.ub = cobra_model.upper_bounds
- matlab_struct.rev = [x.reversibility for x in cobra_model.reactions]
- matlab_struct.description = cobra_model.description
- return(matlab_struct)
-
-
-
-if __name__ == '__main__':
- from cPickle import load
- from time import time
- from numpy import round
- from cobra.manipulation import initialize_growth_medium
- try:
- matlab.changeCobraSolver('glpk','LP')
- except AttributeError:
- raise Exception('Could not run matlab function changeCobraSolver. Is the ' +\
- 'COBRA Toolbox in your MATLAB path?')
- test_directory = '../test/data/'
- with open(test_directory + 'salmonella.pickle') as in_file:
- cobra_model = load(in_file)
- initialize_growth_medium(cobra_model, 'LPM')
- py_cobra_solution = repr(cobra_model.solution.f)
- matlab_struct = cobra_model_object_to_cobra_matlab_struct(cobra_model)
-
- matlab_result = matlab.optimizeCbModel(matlab_struct)
- matlab_solution = repr(float(matlab_result.f))
- if py_cobra_solution[:4] == matlab_solution[:4]:
- print 'SUCCESS: growth rate match between pyCOBRA and COBRA Toolbox: %s ~ %s'%(py_cobra_solution,
- matlab_solution)
- else:
- print 'FAILURE: pyCOBRA and COBRA Toolbox do not match: %s !~ %s'%(py_cobra_solution,
- matlab_solution)
diff --git a/cobra/oven/aliebrahim/gapAnalysis.py b/cobra/oven/aliebrahim/gapAnalysis.py
deleted file mode 100644
index e4c9d17..0000000
--- a/cobra/oven/aliebrahim/gapAnalysis.py
+++ /dev/null
@@ -1,209 +0,0 @@
-import cobra
-from cobra import Model, Reaction, Metabolite
-
-
-class SUXModelMILP(cobra.Model):
- """Model with additional Universal and Exchange reactions.
- Adds corresponding dummy reactions and dummy metabolites for each added
- reaction which are used to impose MILP constraints to minimize the
- total number of added reactions. See the figure for more
- information on the structure of the matrix.
- """
- def __init__(self, model, Universal=None, threshold=0.05,
- penalties={"Universal": 1, "Exchange": 1, "Demand": 1},
- dm_rxns=False, ex_rxns=True):
- cobra.Model.__init__(self, "")
- # store parameters
- self.threshold = threshold
- self.penalties = penalties
- # want to only operate on a copy of Universal so as not to mess up
- # is this necessary?
- if Universal is None:
- Universal = cobra.Model("Universal_Reactions")
- else:
- Universal = Universal.copy()
-
- # SUX += Exchange (when exchange generator has been written)
- # For now, adding exchange reactions to Universal - could add to a new model called exchange and allow their addition or not....
- if ex_rxns:
- ex_reactions = [x for x in model.reactions if x.startswith('EX_')]
- else:
- ex_reactions = []
-
- # ADD ALL EXCHANGE REACTIONS TO UNIVERSAL MODEL
- for r in ex_reactions:
- if r.lower_bound >= 0:
- rxn = r.copy()
- #model.remove_reaction(r)
- rxn.id += "_gapfill"
- rxn.lower_bound = -1000
- Universal.add_reaction(rxn)
-
- if dm_rxns:
- # ADD DEMAND REACTIONS FOR ALL METABOLITES TO UNIVERSAL MODEL
- for m in model.metabolites:
- rxn = Reaction('DM_' + m.id)
- rxn.lower_bound = -1000
- rxn.upper_bound = 1000
- rxn.add_metabolites({m: -1.0})
- Universal.add_reaction(rxn)
-
- cobra.manipulation.modify.convert_to_irreversible(Universal)
-
- for rxn in Universal.reactions:
- if rxn.startswith('EX_'):
- rxn.notes["gapfilling_type"] = "Exchange"
- elif rxn.startswith('DM_'):
- rxn.notes["gapfilling_type"] = "Demand"
- else:
- rxn.notes["gapfilling_type"] = "Universal"
- self += model
- self += Universal
-
- # Add MILP dummy reactions
- v = 1000 # maximum flux in a reaction
- # threshold = 0.05
- dummy_reactions = []
- # all reactions with an index < len(model.reactions) were original
- self.original_reactions = self.reactions[:len(model.reactions)]
- self.added_reactions = self.reactions[len(model.reactions):]
-
- # add in the dummy reactions for each added reaction
- # a dict will map from each added reaction (the key) to
- # the dummy reaction (the value)
- self._dummy_reaction_map = {}
- for reaction in self.added_reactions:
- dummy_metabolite = cobra.Metabolite("dummy_met_" + reaction.id)
- dummy_metabolite._constraint_sense = "L"
- reaction.add_metabolites({dummy_metabolite: 1})
- the_dummy_reaction = cobra.Reaction("dummy_rxn_" + reaction.id)
- the_dummy_reaction.add_metabolites({dummy_metabolite: -1 * v})
- the_dummy_reaction.lower_bound = 0
- the_dummy_reaction.upper_bound = 1
- the_dummy_reaction.variable_kind = "integer"
- dummy_reactions.append(the_dummy_reaction)
- self._dummy_reaction_map[reaction] = the_dummy_reaction
- self.add_reactions(dummy_reactions)
- # add in the dummy metabolite for the actual objective function
- self.objective_metabolite = cobra.Metabolite(
- "dummy_metabolite_objective_function")
- self.objective_metabolite._constraint_sense = "G"
- self.objective_metabolite._bound = self.threshold
- self._update_objectives()
- # make .add_reaction(s) call the ._add_reaction(s) functions
- self.add_reaction = self._add_reaction
- self.add_reactions = self._add_reactions
-
-
- def _update_objectives(self):
- """Update the metabolite which encodes the objective function
- with the objective coefficients for the reaction, and impose
- penalties for added reactions.
- """
- for reaction in self.original_reactions:
- reaction.add_metabolites({self.objective_metabolite: \
- reaction.objective_coefficient})
- reaction.objective_coefficient = 0
- # now make the objective coefficient the penalty
- for reaction in self.added_reactions:
- reaction.objective_coefficient += \
- self.penalties[reaction.notes["gapfilling_type"]]
-
- def _add_reaction(self, reaction):
- cobra.Model.add_reaction(self, reaction)
- self.original_reactions.append(reaction)
- self._update_objectives()
-
- def _add_reactions(self, reactions):
- cobra.Model.add_reactions(self, reactions)
- self.original_reactions.extend(reactions)
- self._update_objectives()
-
- def solve(self, solver="glpk", iterations=1, debug=False, time_limit=100, **solver_parameters):
- """solve the MILP problem"""
- used_reactions = {}
- numeric_error_cutoff = 0.0001
- self._update_objectives()
- for i in range(iterations):
- used_reactions[i] = []
- self.optimize(objective_sense="minimize", solver=solver, **solver_parameters)
- if debug:
- print "Iteration %d: Status is %s" % (i, self.solution.status)
- for reaction in self.added_reactions:
- # The dummy reaction should have a flux of either 0 or 1.
- # If it is 1 (nonzero), then the reaction was used in
- # the solution.
-
- if self.solution.x_dict[self._dummy_reaction_map[
- reaction].id] > numeric_error_cutoff:
- used_reactions[i].append(reaction)
- reaction.objective_coefficient += self.penalties[reaction.notes["gapfilling_type"]]
- if debug:
- print '\t', reaction, reaction.objective_coefficient
-
- return used_reactions
-
-
-def growMatch(model, Universal, iterations=1, debug=False,
- dm_rxns=False, ex_rxns=False, solver="glpk", time_limit=60, **solver_parameters):
- """runs growMatch"""
- model = model.copy()
- SUX = SUXModelMILP(model, Universal, dm_rxns=dm_rxns, ex_rxns=ex_rxns)
- used_reactions = SUX.solve(iterations=iterations, debug=debug,
- solver=solver, time_limit=time_limit, **solver_parameters)
- return used_reactions
-
-
-def SMILEY(model, metabolite_id, Universal, iterations=1, debug=False,
- dm_rxns=False, ex_rxns=False, solver="glpk", time_limit=60, **solver_parameters):
- """
- runs the SMILEY algorithm to determine which gaps should be
- filled in order for the model to create the metabolite with the
- given metabolite_id.
-
- This function is good for running the algorithm once. For more fine-
- grained control, create a SUXModelMILP object, add a demand reaction
- for the given metabolite_id, and call the solve function on the
- SUXModelMILP object.
- """
- model = model.copy()
- SUX = SUXModelMILP(model, Universal, dm_rxns=dm_rxns, ex_rxns=ex_rxns)
- # change the objective to be the metabolite
- for reaction in SUX.original_reactions:
- reaction.objective_coefficient = 0
- demand_reaction = cobra.Reaction("SMILEY_DEMAND_RXN_%s" % metabolite_id)
- demand_reaction.objective_coefficient = 1
- demand_reaction.add_metabolites(
- {SUX.metabolites[SUX.metabolites.index(metabolite_id)]: -1})
- SUX.add_reaction(demand_reaction)
- used_reactions = SUX.solve(iterations=iterations, debug=debug,
- solver=solver, time_limit=time_limit, **solver_parameters)
- return used_reactions
-
-
-if __name__ == "__main__":
- from cobra.test import create_test_model
- import cobra
- from time import time
-
- model = create_test_model()
-
- # create a Universal model containing some removed reactions
- Universal = cobra.Model("Universal_Reactions")
- for i in [i.id for i in model.metabolites.f6p_c.reactions]:
- reaction = model.reactions.get_by_id(i)
- Universal.add_reaction(reaction.copy())
- reaction.remove_from_model(model)
-
- # run growMatch
- print "growMatch"
- tic = time()
- results = growMatch(model, Universal, debug=True)
- toc = time()
- print "%.2f sec for growmatch" % (toc - tic)
- # run SMILEY
- print "SMILEY"
- tic = time()
- SMILEY_results = SMILEY(model, "f6p_c", Universal, debug=True)
- toc = time()
- print "%.2f sec for smiley" % (toc - tic)
diff --git a/cobra/solvers/__init__.py b/cobra/solvers/__init__.py
index 7f2be06..ecdb24a 100644
--- a/cobra/solvers/__init__.py
+++ b/cobra/solvers/__init__.py
@@ -77,8 +77,8 @@ def get_solver_name(mip=False, qp=False):
if len(solver_dict) == 0:
raise SolverNotFound("no solvers installed")
# glpk only does lp, not qp. Gurobi and cplex are better at mip
- mip_order = ["gurobi", "cplex", "cglpk", "glpk"]
- lp_order = ["cglpk", "cplex", "glpk", "gurobi"]
+ mip_order = ["gurobi", "cplex", "coin", "cglpk", "glpk"]
+ lp_order = ["cglpk", "cplex", "glpk", "gurobi", "coin"]
qp_order = ["gurobi", "cplex"]
if mip is False and qp is False:
diff --git a/cobra/solvers/cglpk.pyx b/cobra/solvers/cglpk.pyx
index 7a35ae0..6d81299 100644
--- a/cobra/solvers/cglpk.pyx
+++ b/cobra/solvers/cglpk.pyx
@@ -10,6 +10,13 @@ from tempfile import NamedTemporaryFile as _NamedTemporaryFile # for pickling
from os import unlink as _unlink
from warnings import warn as _warn
+try:
+ from sympy import Basic, Number
+except:
+ class Basic:
+ pass
+ Number = Basic
+
__glpk_version__ = str(glp_version())
_SUPPORTS_MILP = True
solver_name = "cglpk"
@@ -74,6 +81,23 @@ cdef dict METHODS = {
"dual": GLP_DUAL
}
+cdef dict PRICINGS = {
+ "std": GLP_PT_STD,
+ "pse": GLP_PT_PSE
+}
+
+cdef dict RATIOS = {
+ "std": GLP_RT_STD,
+ "har": GLP_RT_HAR
+}
+
+cdef dict SCALINGS = {
+ "auto": GLP_SF_AUTO,
+ "gm": GLP_SF_GM,
+ "eq": GLP_SF_EQ,
+ "2n": GLP_SF_2N,
+ "skip": GLP_SF_SKIP
+}
cdef int downcast_pos_size(Py_ssize_t size):
if size > INT_MAX:
@@ -102,6 +126,12 @@ cdef int hook(void *info, const char *s):
print(s)
return 1
+cdef double _to_double(value):
+ if isinstance(value, Basic) and not isinstance(value, Number):
+ return 0.
+ else:
+ return <double>value
+
cdef class GLP:
cdef glp_prob *glp
@@ -126,6 +156,7 @@ cdef class GLP:
cdef int *c_rows
cdef int *c_cols
cdef double *c_values
+ cdef double b
# initialize parameters
self.parameters.msg_lev = GLP_MSG_OFF
@@ -146,7 +177,7 @@ cdef class GLP:
# set metabolite/consraint bounds
for index, metabolite in enumerate(cobra_model.metabolites, 1):
- b = float(metabolite._bound)
+ b = _to_double(metabolite._bound)
c = metabolite._constraint_sense
if c == 'E':
bound_type = GLP_FX # Set metabolite to steady state levels
@@ -170,13 +201,14 @@ cdef class GLP:
else:
bound_type = GLP_DB
glp_set_col_bnds(glp, index, bound_type,
- float(reaction.lower_bound),
- float(reaction.upper_bound))
- glp_set_obj_coef(glp, index, float(reaction.objective_coefficient))
+ _to_double(reaction.lower_bound),
+ _to_double(reaction.upper_bound))
+ glp_set_obj_coef(glp, index,
+ _to_double(reaction.objective_coefficient))
for metabolite, coefficient in reaction._metabolites.iteritems():
- metabolite_index = metabolite_id_to_index[metabolite.id]
- linear_constraint_rows.append(metabolite_index)
+ linear_constraint_rows.append(
+ metabolite_id_to_index[metabolite.id])
linear_constraint_cols.append(index)
linear_constraint_values.append(coefficient)
@@ -191,7 +223,7 @@ cdef class GLP:
for index in range(n_values):
c_rows[index + 1] = linear_constraint_rows[index]
c_cols[index + 1] = linear_constraint_cols[index]
- c_values[index + 1] = float(linear_constraint_values[index])
+ c_values[index + 1] = _to_double(linear_constraint_values[index])
# actually set the values
glp_load_matrix(glp, n_values, c_rows, c_cols, c_values)
# free the c arrays
@@ -317,16 +349,20 @@ cdef class GLP:
"""set a solver parameter"""
if parameter_name == "objective_sense":
self.set_objective_sense(value)
- elif parameter_name == "time_limit":
+ elif parameter_name in {"time_limit", "tm_lim"}:
self.parameters.tm_lim = int(1000 * value)
elif parameter_name == "tolerance_feasibility":
self.parameters.tol_bnd = float(value)
self.parameters.tol_dj = float(value)
- elif parameter_name == "tolerance_markowitz":
+ elif parameter_name == "tol_bnd":
+ self.parameters.tol_bnd = float(value)
+ elif parameter_name == "tol_dj":
+ self.parameters.tol_dj = float(value)
+ elif parameter_name in {"tolerance_markowitz", "tol_piv"}:
self.parameters.tol_piv = float(value)
- elif parameter_name == "tolerance_integer":
+ elif parameter_name in {"tolerance_integer", "tol_int"}:
self.integer_parameters.tol_int = float(value)
- elif parameter_name == "mip_gap" or parameter_name == "MIP_gap":
+ elif parameter_name in {"mip_gap", "MIP_gap"}:
self.integer_parameters.mip_gap = float(value)
elif parameter_name == "verbose":
if not value: # suppress all output
@@ -350,6 +386,20 @@ cdef class GLP:
_warn("multiple threads not supported")
elif parameter_name == "MIP_gap_abs":
_warn("setting aboslute mip gap not supported")
+ elif parameter_name == "presolve":
+ self.parameters.presolve = GLP_ON if value else GLP_OFF
+ elif parameter_name == "pricing":
+ self.parameters.pricing = PRICINGS[value]
+ elif parameter_name == "r_test":
+ self.parameters.r_test = RATIOS[value]
+ elif parameter_name == "scale":
+ if value:
+ if isinstance(value, int):
+ glp_scale_prob(self.glp, value)
+ else:
+ glp_scale_prob(self.glp, SCALINGS[value])
+ else:
+ glp_unscale_prob(self.glp)
else:
raise ValueError("unknown parameter " + str(parameter_name))
diff --git a/cobra/solvers/coin.py b/cobra/solvers/coin.py
new file mode 100644
index 0000000..feda120
--- /dev/null
+++ b/cobra/solvers/coin.py
@@ -0,0 +1,136 @@
+from cylp.cy import CyClpSimplex
+from cylp.py.modeling.CyLPModel import CyLPArray
+from cylp.cy.CyCoinPackedMatrix import CyCoinPackedMatrix
+
+solver_name = "coin"
+_status_translation = {"primal infeasible": "infeasible",
+ "solution": "optimal"}
+
+_SUPPORTS_MILP = True
+
+
+class Coin(CyClpSimplex):
+ cbc = None
+
+ @property
+ def status_(self):
+ return self.cbc.status if self.cbc else self.getStatusString()
+
+ @property
+ def primalVariableSolution_(self):
+ return self.cbc.primalVariableSolution if self.cbc \
+ else self.primalVariableSolution
+
+ @property
+ def objectiveValue_(self):
+ return self.cbc.objectiveValue if self.cbc else self.objectiveValue
+
+
+def create_problem(cobra_model, objective_sense="maximize", **kwargs):
+ m = cobra_model.to_array_based_model()
+ lp = Coin()
+ v = lp.addVariable("v", len(m.reactions))
+ for i, rxn in enumerate(m.reactions):
+ if rxn.variable_kind == "integer":
+ lp.setInteger(v[i])
+ S = m.S
+ v.lower = CyLPArray(m.lower_bounds)
+ v.upper = CyLPArray(m.upper_bounds)
+ inf = float("inf")
+ cons = zip(m.b, m.constraint_sense)
+ b_l = CyLPArray([-inf if s == "L" else b for b, s in cons])
+ b_u = CyLPArray([inf if s == "G" else b for b, s in cons])
+ lp.addConstraint(b_u >= S * v >= b_l, "b")
+ lp.objectiveCoefficients = CyLPArray(m.objective_coefficients)
+ set_parameter(lp, "objective_sense", objective_sense)
+ set_parameter(lp, "tolerance_feasibility", 1e-9)
+ lp.logLevel = 0
+ for key, value in kwargs.items():
+ set_parameter(lp, key, value)
+ return lp
+
+
+def solve(cobra_model, **kwargs):
+ lp = create_problem(cobra_model)
+ for key, value in kwargs.items():
+ set_parameter(lp, key, value)
+ solve_problem(lp)
+ return format_solution(lp, cobra_model)
+
+
+def set_parameter(lp, parameter_name, value):
+ if parameter_name == "objective_sense":
+ v = str(value).lower()
+ if v == "maximize":
+ lp.optimizationDirection = "max"
+ elif v == "minimize":
+ lp.optimizationDirection = "min"
+ else:
+ raise ValueError("unknown objective sense '%s'" % value)
+ elif parameter_name == "tolerance_feasibility":
+ lp.primalTolerance = value
+ elif parameter_name == "verbose":
+ lp.logLevel = value
+ elif parameter_name == "quadratic_component":
+ set_quadratic_objective(lp, value)
+ else:
+ setattr(lp, parameter_name, value)
+
+
+def solve_problem(lp, **kwargs):
+ for key, value in kwargs.items():
+ set_parameter(lp, key, value)
+ if max(lp.integerInformation):
+ lp.cbc = lp.getCbcModel()
+ lp.cbc.logLevel = lp.logLevel
+ return lp.cbc.branchAndBound()
+ else:
+ lp.cbc = None
+ return lp.primal()
+
+
+def format_solution(lp, cobra_model):
+ Solution = cobra_model.solution.__class__
+ status = get_status(lp)
+ if status != "optimal": # todo handle other possible
+ return Solution(None, status=status)
+ solution = Solution(lp.objectiveValue_, status=status)
+ x = lp.primalVariableSolution_["v"].tolist()
+ solution.x_dict = {r.id: x[i] for i, r in enumerate(cobra_model.reactions)}
+ solution.x = x
+ # TODO handle y
+
+ return solution
+
+
+def get_status(lp):
+ status = lp.status_
+ return _status_translation.get(status, status)
+
+
+def get_objective_value(lp):
+ return lp.objectiveValue_
+
+
+def change_variable_bounds(lp, index, lower_bound, upper_bound):
+ lp.variablesLower[index] = lower_bound
+ lp.variablesUpper[index] = upper_bound
+
+
+def change_coefficient(lp, met_index, rxn_index, value):
+ S = lp.coefMatrix
+ S[met_index, rxn_index] = value
+ lp.coefMatrix = S
+
+
+def change_variable_objective(lp, index, value):
+ lp.setObjectiveCoefficient(index, value)
+
+
+def _set_quadratic_objective(lp, quadratic_objective):
+ """The quadratic routines in CLP do not yet work for GEMs"""
+ if not hasattr(quadratic_objective, "tocoo"):
+ raise Exception('quadratic component must have method tocoo')
+ coo = quadratic_objective.tocoo()
+ matrix = CyCoinPackedMatrix(True, coo.row, coo.col, coo.data)
+ lp.loadQuadraticObjective(matrix)
diff --git a/cobra/solvers/cplex_solver.py b/cobra/solvers/cplex_solver.py
index 42f9480..2e8d4dc 100644
--- a/cobra/solvers/cplex_solver.py
+++ b/cobra/solvers/cplex_solver.py
@@ -8,8 +8,8 @@ from cplex import Cplex, SparsePair
from cplex.exceptions import CplexError
from ..core.Solution import Solution
-from ..external.six.moves import zip
-from ..external.six import string_types
+from six.moves import zip
+from six import string_types, iteritems
solver_name = 'cplex'
_SUPPORTS_MILP = True
@@ -21,7 +21,8 @@ parameter_defaults = {'objective_sense': 'maximize',
'tolerance_integer': 1e-9,
'lp_method': 1,
'tolerance_barrier': 1e-8,
- 'verbose': False}
+ 'verbose': False,
+ 'qpmethod': 1}
parameter_mappings = {'lp_method': 'lpmethod',
'lp_parallel': 'threads',
'threads': 'threads',
@@ -52,7 +53,7 @@ status_dict = {'MIP_infeasible': 'infeasible',
def get_status(lp):
status = lp.solution.get_status_string().lower()
- return status_dict[status] if status in status_dict else 'failed'
+ return status_dict.get(status, status)
def get_objective_value(lp):
@@ -61,7 +62,7 @@ def get_objective_value(lp):
def format_solution(lp, cobra_model, **kwargs):
status = get_status(lp)
- if status in ('optimal', 'time_limit'):
+ if status in ('optimal', 'time_limit', 'non-optimal'):
objective_value = lp.solution.get_objective_value()
x_dict = dict(zip(lp.variables.get_names(),
lp.solution.get_values()))
@@ -150,7 +151,7 @@ def create_problem(cobra_model, quadratic_component=None, **kwargs):
# Begin problem creation
lp = Cplex()
- for k, v in the_parameters.iteritems():
+ for k, v in iteritems(the_parameters):
set_parameter(lp, k, v)
objective_coefficients = [float(x.objective_coefficient)
for x in cobra_model.reactions]
@@ -230,7 +231,10 @@ def create_problem(cobra_model, quadratic_component=None, **kwargs):
def set_quadratic_objective(lp, quadratic_objective):
if not hasattr(quadratic_objective, 'todok'):
raise Exception('quadratic component must have method todok')
-
+ # ensure the matrix is properly read in
+ nnz = quadratic_objective.nnz
+ if lp.parameters.read.qpnonzeros < nnz:
+ lp.parameters.read.qpnonzeros.set(nnz + 1)
# Reset the quadratic coefficient if it exists
if lp.objective.get_num_quadratic_nonzeros() > 0:
lp.objective.set_quadratic((0.,) * lp.variables.get_num())
@@ -286,7 +290,7 @@ def update_problem(lp, cobra_model, new_objective=None, **kwargs):
def solve_problem(lp, **kwargs):
# Update parameter settings if provided
- for k, v in kwargs.iteritems():
+ for k, v in iteritems(kwargs):
set_parameter(lp, k, v)
lp.solve()
# If the solver takes more than 0.1 s with a hot start it is likely stuck
diff --git a/cobra/solvers/esolver.py b/cobra/solvers/esolver.py
index 3ed4232..4a46308 100644
--- a/cobra/solvers/esolver.py
+++ b/cobra/solvers/esolver.py
@@ -3,7 +3,7 @@ from os import unlink, devnull
from os.path import isfile
from tempfile import NamedTemporaryFile
from fractions import Fraction
-from ..external.six.moves import zip
+from six.moves import zip
from . import cglpk
from .wrappers import *
diff --git a/cobra/solvers/glpk.pxd b/cobra/solvers/glpk.pxd
index e721117..91993b2 100644
--- a/cobra/solvers/glpk.pxd
+++ b/cobra/solvers/glpk.pxd
@@ -94,6 +94,9 @@ cdef extern from "glpk.h":
double glp_get_col_lb(glp_prob *lp, int i)
double glp_get_col_ub(glp_prob *lp, int i)
+ void glp_scale_prob(glp_prob *lp, int flags)
+ void glp_unscale_prob(glp_prob *lp)
+
int glp_get_prim_stat(glp_prob *lp)
int glp_get_status(glp_prob *lp)
int glp_mip_status(glp_prob *lp)
@@ -108,6 +111,7 @@ cdef extern from "glpk.h":
double glp_get_obj_coef(glp_prob *lp, int)
int glp_get_obj_dir(glp_prob *lp)
void glp_copy_prob(glp_prob *dst, glp_prob *src, int names)
+
const char *glp_version()
# output redirection
@@ -143,6 +147,13 @@ cdef extern from "glpk.h":
int GLP_ON
int GLP_OFF
+ # constants for scaling the problem
+ int GLP_SF_AUTO
+ int GLP_SF_GM
+ int GLP_SF_EQ
+ int GLP_SF_2N
+ int GLP_SF_SKIP
+
# constants for iocp control, not already in simplex
int GLP_BR_FFV
diff --git a/cobra/solvers/gurobi_solver.py b/cobra/solvers/gurobi_solver.py
index ec7a7dd..d69308e 100644
--- a/cobra/solvers/gurobi_solver.py
+++ b/cobra/solvers/gurobi_solver.py
@@ -7,7 +7,7 @@ from gurobipy import Model, LinExpr, GRB, QuadExpr
from ..core.Solution import Solution
-from ..external.six import string_types
+from six import string_types
solver_name = 'gurobi'
_SUPPORTS_MILP = True
diff --git a/cobra/solvers/mosek.py b/cobra/solvers/mosek.py
index d37892f..077ab93 100644
--- a/cobra/solvers/mosek.py
+++ b/cobra/solvers/mosek.py
@@ -2,8 +2,8 @@ from __future__ import absolute_import, print_function
import mosek
-from ..external.six.moves import zip
-from ..external.six import iteritems, string_types
+from six.moves import zip
+from six import iteritems, string_types
env = mosek.Env()
diff --git a/cobra/test/__init__.py b/cobra/test/__init__.py
index e11c334..87bca3c 100644
--- a/cobra/test/__init__.py
+++ b/cobra/test/__init__.py
@@ -1,62 +1,58 @@
-from __future__ import with_statement, absolute_import
-import sys
+from __future__ import absolute_import
+from os.path import join, abspath, dirname
+import unittest as _unittest
+
+try:
+ from cPickle import load as _load
+except:
+ from pickle import load as _load
+
+from ..io import read_sbml_model
+
+
available_tests = ['unit_tests', 'solvers', 'flux_analysis', 'io_tests']
-from os.path import abspath, join, split, sep
-cobra_directory = abspath(join(split(abspath(__file__))[0], ".."))
+cobra_directory = abspath(join(dirname(abspath(__file__)), ".."))
cobra_location = abspath(join(cobra_directory, ".."))
-data_directory = join(split(abspath(__file__))[0], "data")
-if not data_directory.endswith(sep):
- data_directory += sep
+data_directory = join(cobra_directory, "test", "data", "")
salmonella_sbml = join(data_directory, "salmonella.xml")
-salmonella_fbc_sbml = join(data_directory, "salmonella_fbc.xml")
salmonella_pickle = join(data_directory, "salmonella.pickle")
+
ecoli_sbml = join(data_directory, "iJO1366.xml")
-ecoli_pickle = join(data_directory, "iJO1366.pickle")
-ecoli_mat = join(data_directory, "iJO1366.mat")
-ecoli_json = join(data_directory, "iJO1366.json")
-
-__test_pickles = {'Salmonella_enterica': salmonella_pickle,
- 'Escherichia_coli': ecoli_pickle,
- }
-__test_xml = {'Salmonella_enterica': salmonella_sbml,
- 'Escherichia_coli': ecoli_sbml,
- }
-del abspath, join, split, sep
-
-
-def create_test_model(test_pickle=salmonella_pickle):
- """Returns a cobra model for testing. The default model is the up to date
- version of the Salmonella enterica Typhimurium LT2 model published in
- Thiele et al. 2011 BMC Sys Bio 5:8
-
- test_pickle: The filename of a pickled cobra.Model
- We currently provide Salmonella enterica Typhimurium and Escherichia coli
- models whose paths are stored in cobra.test.salmonella_pickle and
- cobra.test.ecoli_pickle, respectively. The ecoli model is a variant of the
- model published in Orth et al. 2011 Mol Syst Biol 7:535
+textbook_sbml = join(data_directory, "textbook.xml")
+mini_sbml = join(data_directory, "mini_fbc2.xml")
+
+del abspath, join, dirname
+
+
+def create_test_model(model_name="salmonella"):
+ """Returns a cobra model for testing
+
+ model_name: str
+ One of 'ecoli', 'textbook', or 'salmonella', or the
+ path to a pickled cobra.Model
"""
- try:
- from cPickle import load
- except:
- from pickle import load
- if test_pickle == "salmonella":
- test_pickle = salmonella_pickle
- elif test_pickle == "ecoli":
- test_pickle = ecoli_pickle
- with open(test_pickle, "rb") as infile:
- return load(infile)
+ if model_name == "ecoli":
+ return read_sbml_model(ecoli_sbml)
+ elif model_name == "textbook":
+ return read_sbml_model(textbook_sbml)
+ elif model_name == "mini":
+ return read_sbml_model(mini_sbml)
+
+ if model_name == "salmonella":
+ model_name = salmonella_pickle
+ with open(model_name, "rb") as infile:
+ return _load(infile)
def create_test_suite():
"""create a unittest.TestSuite with available tests"""
- from unittest import TestLoader, TestSuite
- loader = TestLoader()
- suite = TestSuite()
+ loader = _unittest.TestLoader()
+ suite = _unittest.TestSuite()
for test_name in available_tests:
exec("from . import " + test_name)
suite.addTests(loader.loadTestsFromModule(eval(test_name)))
@@ -67,5 +63,4 @@ suite = create_test_suite()
def test_all():
"""###running unit tests on cobra py###"""
- from unittest import TextTestRunner
- TextTestRunner(verbosity=2).run(create_test_suite())
+ _unittest.TextTestRunner(verbosity=2).run(create_test_suite())
diff --git a/cobra/test/data/iJO1366.json b/cobra/test/data/iJO1366.json
deleted file mode 100644
index 7c21d8a..0000000
--- a/cobra/test/data/iJO1366.json
+++ /dev/null
@@ -1 +0,0 @@
-{"reactions": [{"subsystem": "", "name": "Sink needed to allow p-Cresol to leave system", "upper_bound": 1000.0, "lower_bound": 0.0, "notes": {}, "metabolites": {"4crsol_c": -1.0}, "objective_coefficient": 0.0, "variable_kind": "continuous", "id": "DM_4CRSOL", "gene_reaction_rule": ""}, {"subsystem": "", "name": "Sink needed to allow 5'-deoxyribose to leave system", "upper_bound": 1000.0, "lower_bound": 0.0, "notes": {}, "metabolites": {"5drib_c": -1.0}, "objective_coefficient": 0.0, "va [...]
\ No newline at end of file
diff --git a/cobra/test/data/iJO1366.mat b/cobra/test/data/iJO1366.mat
deleted file mode 100644
index aa88bf4..0000000
Binary files a/cobra/test/data/iJO1366.mat and /dev/null differ
diff --git a/cobra/test/data/iJO1366.xml b/cobra/test/data/iJO1366.xml
index 066eb10..1cf5ef0 100644
--- a/cobra/test/data/iJO1366.xml
+++ b/cobra/test/data/iJO1366.xml
@@ -1,85978 +1,39002 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
- <model id="iJO1366">
- <listOfUnitDefinitions>
- <unitDefinition id="mmol_per_gDW_per_hr">
- <listOfUnits>
- <unit kind="mole" scale="-3"/>
- <unit kind="gram" exponent="-1"/>
- <unit kind="second" exponent="-1" multiplier="0.000277777777777778"/>
- </listOfUnits>
- </unitDefinition>
- </listOfUnitDefinitions>
- <listOfCompartments>
- <compartment id="c" name="Cytoplasm"/>
- <compartment id="e" name="Extracellular"/>
- <compartment id="p" name="Periplasm"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="M_10fthf_c" name="10-Formyltetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H21N7O7</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr120_c" name="1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H52O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr140_c" name="1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H60O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr141_c" name="1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H56O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr160_c" name="1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H68O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr161_c" name="1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H64O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr180_c" name="1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H76O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr181_c" name="1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H72O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_R_c" name="(R)-Propane-1,2-diol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_S_c" name="(S)-Propane-1,2-diol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H4O10P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_14dhncoa_c" name="1,4-dihydroxy-2-napthoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C32H38N7O19P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_14glucan_c" name="1,4-alpha-D-glucan" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_15dap_c" name="1,5-Diaminopentane" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_1ddecg3p_c" name="1-dodecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H29O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1hdec9eg3p_c" name="1-hexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H35O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1hdecg3p_c" name="1-hexadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H37O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1odec11eg3p_c" name="1-octadec-11-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H39O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1odecg3p_c" name="1-octadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H41O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1pyr5c_c" name="1-Pyrroline-5-carboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H6NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1tdec7eg3p_c" name="1-tetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H31O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1tdecg3p_c" name="1-tetradecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H33O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_23dappa_c" name="2,3-diaminopropionate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_23ddhb_c" name="2,3-Dihydro-2,3-dihydroxybenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhacoa_c" name="2,3-dehydroadipyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H37N7O19P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhb_c" name="2,3-Dihydroxybenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhba_c" name="(2,3-Dihydroxybenzoyl)adenylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H17N5O10P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhbzs_c" name="2,3-dihydroxybenzoylserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10NO6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhdp_c" name="2,3-Dihydrodipicolinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5NO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhmb_c" name="(R)-2,3-Dihydroxy-3-methylbutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dhmp_c" name="(R)-2,3-Dihydroxy-3-methylpentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23doguln_c" name="2,3-Dioxo-L-gulonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H7O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_25aics_c" name="(S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C13H15N4O12P</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_25dkglcn_c" name="2,5-diketo-D-gluconate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H7O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_25drapp_c" name="2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H14N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_26dap_DASH_LL_c" name="LL-2,6-Diaminoheptanedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_26dap_DASH_M_c" name="meso-2,6-Diaminoheptanedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe120_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H36NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe140_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H40NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe141_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H38NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe160_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H44NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe161_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H42NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe180_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H48NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe181_c" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H46NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg120_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H36O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg140_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H40O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg141_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H38O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg160_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H44O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg161_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H42O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg180_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H48O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg181_c" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H46O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ahbut_c" name="(S)-2-Aceto-2-hydroxybutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2amsa_c" name="2-Aminomalonate semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2aobut_c" name="L-2-Amino-3-oxobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2cpr5p_c" name="1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H13NO9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2dda7p_c" name="2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H10O10P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddecg3p_c" name="2-dodecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H30O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddg6p_c" name="2-Dehydro-3-deoxy-D-gluconate 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddglcn_c" name="2-Dehydro-3-deoxy-D-gluconate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2dh3dgal_c" name="2-Dehydro-3-deoxy-D-galactonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2dh3dgal6p_c" name="2-Dehydro-3-deoxy-D-galactonate 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2dhguln_c" name="2-Dehydro-L-gulonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2dhp_c" name="2-Dehydropantoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2dmmq8_c" name="2-Demethylmenaquinone 8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C50H70O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2dmmql8_c" name="2-Demethylmenaquinol 8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C50H72O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2dr1p_c" name="2-Deoxy-D-ribose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2dr5p_c" name="2-Deoxy-D-ribose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2fe1s_c" name="[2Fe-1S] desulfurated iron-sulfur cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: SFe2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_2fe2s_c" name="[2Fe-2S] iron-sulfur cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: S2Fe2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_2h3oppan_c" name="2-Hydroxy-3-oxopropanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2hdec9eg3p_c" name="2-hexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H36O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2hdecg3p_c" name="2-hexadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H38O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ippm_c" name="2-Isopropylmaleate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2mahmp_c" name="2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8N3O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2mcacn_c" name="cis-2-Methylaconitate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5O6</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2mcit_c" name="2-Methylcitrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H7O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2me4p_c" name="2-C-methyl-D-erythritol 4-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2mecdp_c" name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O9P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2obut_c" name="2-Oxobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2odec11eg3p_c" name="2-octadec-11-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H40O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2odecg3p_c" name="2-octadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H42O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ohph_c" name="2-Octaprenyl-6-hydroxyphenol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C46H70O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2ombzl_c" name="2-Octaprenyl-6-methoxy-1,4-benzoquinol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C47H72O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2omhmbl_c" name="2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H74O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2ommbl_c" name="2-Octaprenyl-3-methyl-6-methoxy- 1,4-benzoquinol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H74O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2omph_c" name="2-Octaprenyl-6-methoxyphenol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C47H72O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2oph_c" name="2-Octaprenylphenol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C46H70O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2oxpaccoa_c" name="2-oxepin-2(3H)-ylideneacetyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H38N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_2p4c2me_c" name="2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H22N3O17P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_2pg_c" name="D-Glycerate 2-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H4O7P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2pglyc_c" name="2-Phosphoglycolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2O6P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2sephchc_c" name="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H13O9</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_2shchc_c" name="2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H10O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_2tdec7eg3p_c" name="2-tetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H32O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2tdecg3p_c" name="2-tetradecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H34O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2tpr3dpcoa_c" name="2'-(5''-triphosphoribosyl)-3'-dephospho-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C26H40N7O26P5S</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_34hpp_c" name="3-(4-Hydroxyphenyl)pyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_35cgmp_c" name="3',5'-Cyclic GMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3amac_c" name="3-Aminoacrylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H4NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3c2hmp_c" name="3-Carboxy-2-hydroxy-4-methylpentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H10O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3c3hmp_c" name="3-Carboxy-3-hydroxy-4-methylpentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H10O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3c4mop_c" name="3-Carboxy-4-methyl-2-oxopentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3dhguln_c" name="3-Dehydro-L-gulonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3dhgulnp_c" name="3-keto-L-gulonate-6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O10P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_3dhq_c" name="3-Dehydroquinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3dhsk_c" name="3-Dehydroshikimate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H7O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3fe4s_c" name="[3Fe-4S] damaged iron-sulfur cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: S4Fe3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_3haACP_c" name="(3R)-3-Hydroxyacyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H27N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hadpcoa_c" name="(3S)-3-Hydroxyadipyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H39N7O20P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_3hbcoa_c" name="(S)-3-Hydroxybutanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H38N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcddec5eACP_c" name="(R)-3-hydroxy-cis-dodec-5-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H41N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcinnm_c" name="3-hydroxycinnamic acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcmrs7eACP_c" name="(R)-3-hydroxy-cis-myristol-7-eoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H45N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcpalm9eACP_c" name="(R)-3-hydroxy-cis-palm-9-eoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H49N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcvac11eACP_c" name="(R)-3-hydroxy-cis-vacc-11-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H53N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hdcoa_c" name="(S)-3-Hydroxydecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H50N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hddcoa_c" name="(S)-3-Hydroxydodecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H54N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hddecACP_c" name="(R)-3-Hydroxydodecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H43N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hdecACP_c" name="(R)-3-Hydroxydecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H39N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hhcoa_c" name="(S)-3-Hydroxyhexanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hhdcoa_c" name="(S)-3-Hydroxyhexadecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H62N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hhexACP_c" name="(R)-3-Hydroxyhexanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H31N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hmrsACP_c" name="(R)-3-Hydroxytetradecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H47N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hocoa_c" name="(S)-3-Hydroxyoctanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H46N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hoctACP_c" name="(R)-3-Hydroxyoctanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H35N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hoctaACP_c" name="(R)-3-Hydroxyoctadecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H55N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hodcoa_c" name="(S)-3-Hydroxyoctadecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H66N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpalmACP_c" name="R-3-hydroxypalmitoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H51N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpp_c" name="3-Hydroxypropanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpppn_c" name="3-(3-hydroxy-phenyl)propionate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3htdcoa_c" name="(S)-3-Hydroxytetradecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H58N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3ig3p_c" name="C'-(3-Indolyl)-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3mob_c" name="3-Methyl-2-oxobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3mop_c" name="(S)-3-Methyl-2-oxopentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ocddec5eACP_c" name="3-oxo-cis-dodec-5-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H39N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ocmrs7eACP_c" name="3-oxo-cis-myristol-7-eoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H43N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ocpalm9eACP_c" name="3-oxo-cis-palm-9-eoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H47N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ocvac11eACP_c" name="3-oxo-cis-vacc-11-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H51N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3odcoa_c" name="3-Oxodecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H48N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3oddcoa_c" name="3-Oxododecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H52N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3oddecACP_c" name="3-Oxododecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H41N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3odecACP_c" name="3-Oxodecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H37N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ohcoa_c" name="3-Oxohexanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H40N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3ohdcoa_c" name="3-Oxohexadecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H60N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3ohexACP_c" name="3-Oxohexanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H29N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3omrsACP_c" name="3-Oxotetradecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H45N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3oocoa_c" name="3-Oxooctanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H44N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3ooctACP_c" name="3-Oxooctanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H33N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ooctdACP_c" name="3-Oxooctadecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H53N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3oodcoa_c" name="3-Oxooctadecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H64N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3opalmACP_c" name="3-Oxohexadecanoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H49N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ophb_c" name="3-Octaprenyl-4-hydroxybenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C47H69O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3otdcoa_c" name="3-Oxotetradecanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H56N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3oxdhscoa_c" name="3-oxo-5,6-dehydrosuberyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H39N7O20P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_3pg_c" name="3-Phospho-D-glycerate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H4O7P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_3php_c" name="3-Phosphohydroxypyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H2O7P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_3psme_c" name="5-O-(1-Carboxyvinyl)-3-phosphoshikimate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H9O10P</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_3sala_c" name="3-Sulfino-L-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5NO4S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4abut_c" name="4-Aminobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4abutn_c" name="4-Aminobutanal" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H10NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_4abz_c" name="4-Aminobenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H6NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_4adcho_c" name="4-amino-4-deoxychorismate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10NO5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_4ahmmp_c" name="4-Amino-5-hydroxymethyl-2-methylpyrimidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9N3O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4ampm_c" name="4-Amino-2-methyl-5-phosphomethylpyrimidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8N3O4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4c2me_c" name="4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H23N3O14P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4crsol_c" name="p-Cresol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4fe4s_c" name="[4Fe-4S] iron-sulfur cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: S4Fe4</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_4h2opntn_c" name="4-Hydroxy-2-oxopentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_4hbz_c" name="4-Hydroxybenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_4hthr_c" name="4-Hydroxy-L-threonine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4mhetz_c" name="4-Methyl-5-(2-hydroxyethyl)-thiazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9NOS</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4mop_c" name="4-Methyl-2-oxopentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_4mpetz_c" name="4-Methyl-5-(2-phosphoethyl)-thiazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8NO4PS</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4pasp_c" name="4-Phospho-L-aspartate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6NO7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4per_c" name="4-Phospho-D-erythronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6O8P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_4ppan_c" name="D-4'-Phosphopantothenate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15NO8P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_4ppcys_c" name="N-((R)-4-Phosphopantothenoyl)-L-cysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H20N2O9PS</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_4r5au_c" name="4-(1-D-Ribitylamino)-5-aminouracil" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H16N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_56dura_c" name="5,6-dihydrouracil" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5aizc_c" name="5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N3O9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_5aop_c" name="5-Amino-4-oxopentanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5aprbu_c" name="5-Amino-6-(5'-phosphoribitylamino)uracil" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_5apru_c" name="5-Amino-6-(5'-phosphoribosylamino)uracil" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_5caiz_c" name="5-phosphoribosyl-5-carboxyaminoimidazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N3O9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_5dglcn_c" name="5-Dehydro-D-gluconate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_5dh4dglc_c" name="5-Dehydro-4-deoxy-D-glucarate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6O7</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_5drib_c" name="5'-deoxyribose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5fthf_c" name="5-Formyltetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H21N7O7</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_5mta_c" name="5-Methylthioadenosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H15N5O3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5mthf_c" name="5-Methyltetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H24N7O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_5mtr_c" name="5-Methylthio-D-ribose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O4S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5prdmbz_c" name="N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H17N2O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_6hmhpt_c" name="6-hydroxymethyl dihydropterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9N5O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_6hmhptpp_c" name="6-hydroxymethyl-dihydropterin pyrophosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8N5O8P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_6pgc_c" name="6-Phospho-D-gluconate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10O10P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_6pgl_c" name="6-phospho-D-glucono-1,5-lactone" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_8aonn_c" name="8-Amino-7-oxononanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H17NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ACP_c" name="acyl carrier protein" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H21N2O7PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDglu_c" name="L-alanine-D-glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdap_c" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25N4O8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdapDala_c" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H30N5O9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaLglu_c" name="L-alanine-L-glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_N1aspmd_c" name="N1-Acetylspermidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H23N3O</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_Nmtrp_c" name="N-Methyltryptophan" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H14N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_Sfglutth_c" name="S-Formylglutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H16N3O7S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_aacald_c" name="Aminoacetaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_aacoa_c" name="Acetoacetyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H36N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_aact_c" name="Aminoacetone" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ac_c" name="Acetate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acACP_c" name="Acetyl-ACP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C13H23N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acac_c" name="Acetoacetate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acald_c" name="Acetaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acanth_c" name="N-Acetylanthranilate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H8NO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_accoa_c" name="Acetyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H34N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_acetol_c" name="Acetol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acg5p_c" name="N-Acetyl-L-glutamyl 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9NO8P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_acg5sa_c" name="N-Acetyl-L-glutamate 5-semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H10NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam_c" name="N-Acetyl-D-glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam1p_c" name="N-Acetyl-D-glucosamine 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam6p_c" name="N-Acetyl-D-glucosamine 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acglc_DASH_D_c" name="6-Acetyl-D-glucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14O7</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acglu_c" name="N-Acetyl-L-glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9NO5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acmalt_c" name="Acetyl-maltose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H24O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acmana_c" name="N-Acetyl-D-mannosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acmanap_c" name="N-Acetyl-D-mannosamine 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acmum6p_c" name="N-acetylmuramate 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H17NO11P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_acnam_c" name="N-Acetylneuraminate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18NO9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acon_DASH_C_c" name="cis-Aconitate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H3O6</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_acon_DASH_T_c" name="trans-Aconitate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H3O6</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_aconm_c" name="E-3-carboxy-2-pentenedioate 6-methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H6O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acorn_c" name="N2-Acetyl-L-ornithine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acser_c" name="O-Acetyl-L-serine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_actACP_c" name="Acetoacetyl-ACP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25N2O9PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_actp_c" name="Acetyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O5P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ade_c" name="Adenine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adn_c" name="Adenosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adocbi_c" name="Adenosyl cobinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C58H84CoN16O11</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_adocbip_c" name="Adenosyl cobinamide phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C58H83CoN16O14P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_adocbl_c" name="Adenosylcobalamin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C72H100CoN18O17P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adp_c" name="ADP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O10P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_adpglc_c" name="ADPglucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H23N5O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_adphep_DASH_DD_c" name="ADP-D-glycero-D-manno-heptose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N5O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_adphep_DASH_LD_c" name="ADP-L-glycero-D-manno-heptose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N5O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_adprib_c" name="ADPribose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H21N5O14P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ag_c" name="silver" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ag</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_agdpcbi_c" name="Adenosine-GDP-cobinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C68H95CoN21O21P2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_agm_c" name="Agmatine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N4</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_ahcys_c" name="S-Adenosyl-L-homocysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H20N6O5S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ahdt_c" name="2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N5O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_aicar_c" name="5-Amino-1-(5-Phospho-D-ribosyl)imidazole-4-carboxamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N4O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_air_c" name="5-amino-1-(5-phospho-D-ribosyl)imidazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12N3O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_akg_c" name="2-Oxoglutarate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_B_c" name="beta-Alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_D_c" name="D-Alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_L_c" name="L-Alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alaala_c" name="D-Alanyl-D-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alac_DASH_S_c" name="(S)-2-Acetolactate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_alatrna_c" name="L-Alanyl-tRNA(Ala)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_all_DASH_D_c" name="D-Allose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_all6p_c" name="D-Allose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_alltn_c" name="Allantoin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6N4O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alltt_c" name="Allantoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7N4O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_allul6p_c" name="Allulose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_altrn_c" name="D-Altronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_amet_c" name="S-Adenosyl-L-methionine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H23N6O5S</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ametam_c" name="S-Adenosylmethioninamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H24N6O3S</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_amob_c" name="S-Adenosyl-4-methylthio-2-oxobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N5O6S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_amp_c" name="AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm_c" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H29N2O12</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm3p_c" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H52N6O19</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm4p_c" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H57N7O20</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhm_c" name="1,6-anhydrous-N-Acetylmuramate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H16NO7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_anhm3p_c" name="1,6-anhydrous-N-Acetylmuramyl-tripeptide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C26H39N5O14</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhm4p_c" name="1,6-anhydrous-N-Acetylmuramyl-tetrapeptide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H44N6O15</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anth_c" name="Anthranilate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H6NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ap4a_c" name="P1,P4-Bis(5'-adenosyl) tetraphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H24N10O19P4</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ap5a_c" name="P1,P5-Bis(5'-adenosyl) pentaphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H24N10O22P5</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_apg120_c" name="acyl phosphatidylglycerol (n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H80O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg140_c" name="acyl phosphatidylglycerol (n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H92O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg141_c" name="acyl phosphatidylglycerol (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H86O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg160_c" name="acyl phosphatidylglycerol (n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C54H104O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg161_c" name="acyl phosphatidylglycerol (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C54H98O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg180_c" name="acyl phosphatidylglycerol (n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C60H116O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apg181_c" name="acyl phosphatidylglycerol (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C60H110O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_apoACP_c" name="apoprotein [acyl carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: RHO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_appl_c" name="1-Aminopropan-2-ol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H10NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_aps_c" name="Adenosine 5'-phosphosulfate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O10PS</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ara5p_c" name="D-Arabinose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_arab_DASH_L_c" name="L-Arabinose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_aragund_c" name="O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C71H115N1O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_arbt6p_c" name="Arbutin 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H15O10P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_c" name="aerobactin minus Fe3" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33N4O13</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_DASH_fe3_c" name="Aerobactin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33FeN4O13</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arg_DASH_L_c" name="L-Arginine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N4O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_argsuc_c" name="N(omega)-(L-Arginino)succinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H17N4O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_argtrna_c" name="L-Arginyl-tRNA(Arg)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14N4OR</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_ascb6p_c" name="L-ascorbate-6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H7O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_asn_DASH_L_c" name="L-Asparagine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_asntrna_c" name="L-Asparaginyl-tRNA(Asn)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H24N2O12PR2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_aso3_c" name="arsenite" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: AsO3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_aso4_c" name="arsenate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: AsO4</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_asp_DASH_L_c" name="L-Aspartate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_aspsa_c" name="L-Aspartate 4-semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_asptrna_c" name="L-Aspartyl-tRNA(Asp)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5NO3R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_athr_DASH_L_c" name="L-Allo-threonine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_athtp_c" name="adenosine thiamine triphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H28N9O13P3S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_atp_c" name="ATP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_b2coa_c" name="Crotonoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H36N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_bbtcoa_c" name="gamma-butyrobetainyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C28H46N8O17P3S</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_betald_c" name="Betaine aldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H12NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_bglycogen_c" name="branching glycogen" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_bmoco_c" name="bis-molybdenum cofactor" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H20N10O13P2S4Mo</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_bmoco1gdp_c" name="bis-molybdopterin mono-guanine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H32N15O20P3S4Mo</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_bmocogdp_c" name="bis-molybdopterin guanine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H44N20O27P4S4Mo</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_btal_c" name="Butanal" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_btcoa_c" name="Butanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H38N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_btn_c" name="Biotin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H15N2O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_btnso_c" name="d-biotin d-sulfoxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H15N2O4S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_but_c" name="Butyrate (n-C4:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_but2eACP_c" name="But-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_butACP_c" name="Butyryl-ACP (n-C4:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H27N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_butso3_c" name="butanesulfonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_bwco_c" name="tungsten bispterin cofactor" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H20N10O13P2S4W</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_bwco1gdp_c" name="tungsten bispterin cofactor mono-guanine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H32N15O20P3S4W</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_bwcogdp_c" name="tungsten bispterin cofactor guanine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H44N20O27P4S4W</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ca2_c" name="Calcium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ca</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_camp_c" name="cAMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O6P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cbasp_c" name="N-Carbamoyl-L-aspartate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H6N2O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cbi_c" name="Cobinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H72CoN11O8</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cbl1_c" name="Cob(I)alamin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C62H88CoN13O14P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cbm_c" name="Carbamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH2NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cbp_c" name="Carbamoyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH2NO5P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cd2_c" name="Cadmium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cd</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cddec5eACP_c" name="cis-dodec-5-enoyl-[acyl-carrier protein] (n-C12:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H41N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cdec3eACP_c" name="cis-dec-3-enoyl-[acyl-carrier protein] (n-C10:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H37N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cdg_c" name="7-deaza-7-carboxyguanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5N4O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cdp_c" name="CDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdddecg_c" name="CDP-1,2-didodecanoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H63N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdhdec9eg_c" name="CDP-1,2-dihexadec-9-enoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C44H75N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdhdecg_c" name="CDP-1,2-dihexadecanoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C44H79N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdodec11eg_c" name="CDP-1,2-dioctadec-11-enoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H83N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdodecg_c" name="CDP-1,2-dioctadecanoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H87N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdtdec7eg_c" name="CDP-1,2-ditetradec-7-enoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H67N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cdpdtdecg_c" name="CDP-1,2-ditetradecanoylglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H71N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cechddd_c" name="cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cenchddd_c" name="cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cgly_c" name="Cys-Gly" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_chol_c" name="Choline" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_chor_c" name="chorismate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H8O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_chtbs6p_c" name="diacetylchitobiose-6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H27N2O14P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cinnm_c" name="trans-Cinnamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cit_c" name="Citrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H5O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_citr_DASH_L_c" name="L-Citrulline" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13N3O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ckdo_c" name="CMP-3-deoxy-D-manno-octulosonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H24N3O15P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cl_c" name="Chloride" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cl</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cmp_c" name="CMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_co2_c" name="CO2" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_coa_c" name="Coenzyme A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H32N7O16P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_cobalt2_c" name="Co2+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Co</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_colipa_c" name="core oligosaccharide lipid A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C176H303N2O100P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_cpe160_c" name="cyclopropane phosphatidylethanolamine (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H74N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cpe180_c" name="cyclopropane phosphatidylethanolamine (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C43H82N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cpg160_c" name="cyclopropane phosphatidylglycerol (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H74O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpg180_c" name="cyclopropane phosphatidylglycerol (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C44H82O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_c" name="coprogen" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13Fe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_DASH_un_c" name="coprogen unloaded (no Fe(III))" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_cph4_c" name="6-carboxy-5,6,7,8-tetrahydropterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8N5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpmp_c" name="cyclic pyranopterin monophosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpppg3_c" name="Coproporphyrinogen III" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H40N4O8</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_c" name="L-Carnitine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_DASH_D_c" name="D-Carnitine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_crnDcoa_c" name="D-carnitinyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C28H46N8O18P3S</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_crncoa_c" name="L-Carnitinyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C28H46N8O18P3S</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_csn_c" name="Cytosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5N3O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ctbt_c" name="crotonobetaine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ctbtcoa_c" name="crotonobetainyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C28H44N8O17P3S</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ctp_c" name="CTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_cu_c" name="Cu+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_cu2_c" name="Cu2+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cyan_c" name="Hydrogen cyanide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CHN</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cynt_c" name="Cyanate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNO</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_D_c" name="D-Cysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_L_c" name="L-Cysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cyst_DASH_L_c" name="L-Cystathionine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O4S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cystrna_c" name="L-Cysteinyl-tRNA(Cys)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NOSR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_cytd_c" name="Cytidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dad_DASH_2_c" name="Deoxyadenosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dad_DASH_5_c" name="5'-Deoxyadenosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dadp_c" name="dADP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O9P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_damp_c" name="dAMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dann_c" name="7,8-Diaminononanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H21N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_datp_c" name="dATP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O12P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_db4p_c" name="3,4-dihydroxy-2-butanone 4-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dc2coa_c" name="trans-Dec-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H48N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dca_c" name="Decanoate (n-C10:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H19O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dcaACP_c" name="Decanoyl-ACP (n-C10:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H39N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dcacoa_c" name="Decanoyl-CoA (n-C10:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H50N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dcamp_c" name="N6-(1,2-Dicarboxyethyl)-AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H14N5O11P</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dcdp_c" name="dCDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O10P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dcmp_c" name="dCMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dctp_c" name="dCTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dcyt_c" name="Deoxycytidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dd2coa_c" name="trans-Dodec-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H52N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ddca_c" name="Dodecanoate (n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H23O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ddcaACP_c" name="Dodecanoyl-ACP (n-C12:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H43N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ddcacoa_c" name="Dodecanoyl-CoA (n-C12:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H54N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ddcap_c" name="Dodecanoly-phosphate (n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H24O5P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dgdp_c" name="dGDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O10P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dgmp_c" name="dGMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dgslnt_c" name="Selenodiglutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H30N6O12S2Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dgsn_c" name="Deoxyguanosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dgtp_c" name="dGTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dha_c" name="Dihydroxyacetone" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dhap_c" name="Dihydroxyacetone phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dhcinnm_c" name="2,3-dihydroxicinnamic acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhf_c" name="7,8-Dihydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H19N7O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dhgly_c" name="dehydroglycine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhmpt_c" name="Dihydromonapterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dhmptp_c" name="dihydromonapterin-triphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N5O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dhna_c" name="1,4-Dihydroxy-2-naphthoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H7O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhnpt_c" name="Dihydroneopterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dhor_DASH_S_c" name="(S)-Dihydroorotate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhpmp_c" name="Dihydroneopterin monophosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dhpppn_c" name="3-(2,3-Dihydroxyphenyl)propanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhpt_c" name="Dihydropteroate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H13N6O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dhptd_c" name="4,5-dihydroxy-2,3-pentanedione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dhptdn_c" name="6,7-Dihydropteridine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6N4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_didp_c" name="dIDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O10P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dimp_c" name="dIMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_din_c" name="Deoxyinosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ditp_c" name="dITP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O13P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dmbzid_c" name="5,6-Dimethylbenzimidazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10N2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dmlz_c" name="6,7-Dimethyl-8-(1-D-ribityl)lumazine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C13H18N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dmpp_c" name="Dimethylallyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dms_c" name="Dimethyl sulfide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dmso_c" name="Dimethyl sulfoxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6OS</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dnad_c" name="Deamino-NAD+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H24N6O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dpcoa_c" name="Dephospho-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H33N7O13P2S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbdox_c" name="fused thiol:disulfide interchange protein (oxidized)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbdrd_c" name="fused thiol:disulfide interchange protein (reduced)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dscl_c" name="dihydrosirohydrochlorin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H41N4O16</p>
- <p>CHARGE: -7</p>
- </body>
- </notes>
- </species>
- <species id="M_dtbt_c" name="Dethiobiotin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H17N2O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdp_c" name="dTDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdp4aaddg_c" name="dTDP-4-acetamido-4,6-dideoxy-D-galactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H27N3O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdp4addg_c" name="dTDP-4-amino-4,6-dideoxy-D-galactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H26N3O14P2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdp4d6dg_c" name="dTDP-4-dehydro-6-deoxy-D-glucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H22N2O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdp4d6dm_c" name="dTDP-4-dehydro-6-deoxy-L-mannose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H22N2O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdpglu_c" name="dTDPglucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H24N2O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dtdprmn_c" name="dTDP-L-rhamnose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H24N2O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dtmp_c" name="dTMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dttp_c" name="dTTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dudp_c" name="dUDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_dump_c" name="dUMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_duri_c" name="Deoxyuridine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dutp_c" name="dUTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_dxyl_c" name="1-deoxy-D-xylulose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dxyl5p_c" name="1-deoxy-D-xylulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_e4p_c" name="D-Erythrose 4-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_egmeACP_c" name="Enoylglutaryl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H27N2O10PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_eig3p_c" name="D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9N2O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_enter_c" name="Enterochelin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27N3O15</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_epmeACP_c" name="Enoylpimeloyl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H31N2O10PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_etha_c" name="Ethanolamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H8NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ethso3_c" name="ethanesulfonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_etoh_c" name="Ethanol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_f1p_c" name="D-Fructose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_f6p_c" name="D-Fructose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fad_c" name="Flavin adenine dinucleotide oxidized" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H31N9O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fadh2_c" name="Flavin adenine dinucleotide reduced" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H33N9O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fald_c" name="Formaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fc1p_c" name="L-Fuculose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fcl_DASH_L_c" name="L-fuculose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fdp_c" name="D-Fructose 1,6-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10O12P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_fe2_c" name="Fe2+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3_c" name="Fe3+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3dhbzs_c" name="ferric 2,3-dihydroxybenzoylserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10NO6Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_c" name="Fe(III)hydroxamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3Fe</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_DASH_un_c" name="Fe(III)hydoxamate, unloaded" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_c" name="Ferrichrome" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42FeN9O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_DASH_un_c" name="Ferrichrome minus Fe(III)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42N9O12</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_feenter_c" name="Fe-enterobactin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27FeN3O15</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_c" name="ferroxamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46FeN6O8</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_DASH_un_c" name="ferroxamine minus Fe(3)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46N6O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fgam_c" name="N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_flxr_c" name="Flavodoxin reduced" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_flxso_c" name="flavodoxin semi oxidized" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fmettrna_c" name="N-Formylmethionyl-tRNA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9NO2SR</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fmn_c" name="FMN" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H19N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fmnh2_c" name="Reduced FMN" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H21N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_for_c" name="Formate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH1O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_forcoa_c" name="Formyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H32N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_fpram_c" name="2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15N3O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fprica_c" name="5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_frdp_c" name="Farnesyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fru_c" name="D-Fructose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_frulys_c" name="fructoselysine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_frulysp_c" name="fructoselysine Phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H24N2O10P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fruur_c" name="D-Fructuronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fuc_DASH_L_c" name="L-Fucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fum_c" name="Fumarate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H2O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_g1p_c" name="D-Glucose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_g3p_c" name="Glyceraldehyde 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pc_c" name="sn-Glycero-3-phosphocholine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H20NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pe_c" name="sn-Glycero-3-phosphoethanolamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pg_c" name="Glycerophosphoglycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pi_c" name="sn-Glycero-3-phospho-1-inositol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3ps_c" name="Glycerophosphoserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g6p_c" name="D-Glucose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gagicolipa_c" name="galactosyl-glucosyl-inner core oligosaccharide lipid A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C157H271N2O84P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_gal_c" name="D-Galactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gal1p_c" name="alpha-D-Galactose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galct_DASH_D_c" name="D-Galactarate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_D_c" name="D-Galactonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_L_c" name="L-Galactonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galt1p_c" name="Galactitol 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galur_c" name="D-Galacturonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam1p_c" name="D-Glucosamine 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam6p_c" name="D-Glucosamine 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gar_c" name="N1-(5-Phospho-D-ribosyl)glycinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_garagund_c" name="glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C77H125N1O22P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gbbtn_c" name="gamma-butyrobetaine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gcald_c" name="Glycolaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H4O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gdp_c" name="GDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_gdpddman_c" name="GDP-4-dehydro-6-deoxy-D-mannose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H21N5O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gdpfuc_c" name="GDP-L-fucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H23N5O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gdpmann_c" name="GDP-D-mannose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H23N5O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gdpofuc_c" name="GDP-4-oxo-L-fucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H21N5O15P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gdptp_c" name="Guanosine 3'-diphosphate 5'-triphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O20P5</p>
- <p>CHARGE: -7</p>
- </body>
- </notes>
- </species>
- <species id="M_gfgaragund_c" name="galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C83H135N1O27P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gg4abut_c" name="gamma-glutamyl-gamma aminobutyric acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15O5N2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ggagicolipa_c" name="glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C163H281N2O89P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_ggbutal_c" name="gamma-glutamyl-gamma-butyraldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H16O4N2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gggagicolipa_c" name="glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C169H291N2O94P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_ggptrc_c" name="gamma-glutamyl-putrescine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H20O3N3</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ghb_c" name="gamma-hydroxybutyrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gicolipa_c" name="glucosyl-inner core oligosaccharide lipid A" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C151H261N2O79P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_glc_DASH_D_c" name="D-Glucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glcn_c" name="D-Gluconate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glcr_c" name="D-Glucarate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glcur_c" name="D-Glucuronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gln_DASH_L_c" name="L-Glutamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glntrna_c" name="L-Glutaminyl-tRNA(Gln)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9N2O2R</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_glu_DASH_D_c" name="D-Glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glu_DASH_L_c" name="L-Glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glu1sa_c" name="L-Glutamate 1-semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glu5p_c" name="L-Glutamate 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NO7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glu5sa_c" name="L-Glutamate 5-semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glucys_c" name="gamma-L-Glutamyl-L-cysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glutrna_c" name="L-Glutamyl-tRNA(Glu)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H7NO3R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glx_c" name="Glyoxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H1O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gly_c" name="Glycine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyald_c" name="D-Glyceraldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyb_c" name="Glycine betaine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_c" name="Glycerol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_DASH_R_c" name="(R)-Glycerate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc2p_c" name="Glycerol 2-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc3p_c" name="Glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyclt_c" name="Glycolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glycogen_c" name="glycogen" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glytrna_c" name="Glycyl-tRNA(Gly)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H4NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_gmeACP_c" name="Glutaryl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H29N2O10PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gmhep17bp_c" name="D-Glycero-D-manno-heptose 1,7-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12O13P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_gmhep1p_c" name="D-Glycero-D-manno-heptose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H13O10P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gmhep7p_c" name="D-Glycero-D-manno-heptose 7-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H13O10P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gmp_c" name="GMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gp4g_c" name="P1,P4-Bis(5'-guanosyl) tetraphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H24N10O21P4</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_grdp_c" name="Geranyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H17O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_grxox_c" name="glutaredoxin (oxidized)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_grxrd_c" name="glutaredoxin (reduced)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gslnt_c" name="Glutathiolselenolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H16N3O6SSe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gsn_c" name="Guanosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gthox_c" name="Oxidized glutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H30N6O12S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gthrd_c" name="Reduced glutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H16N3O6S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gtp_c" name="GTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_gtspmd_c" name="Glutathionylspermidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H36N6O5S</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_gua_c" name="Guanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h_c" name="H+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_h2_c" name="H2" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2mb4p_c" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o_c" name="H2O" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o2_c" name="Hydrogen peroxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2s_c" name="Hydrogen sulfide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hco3_c" name="Bicarbonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CHO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hcys_DASH_L_c" name="L-Homocysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hdca_c" name="Hexadecanoate (n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H31O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdcap_c" name="Hexadecanoyl-phosphate (n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H32O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdcea_c" name="Hexadecenoate (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H29O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdceap_c" name="Hexadecanoyl-phosphate (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H30O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdcoa_c" name="Hexadecenoyl-CoA (n-C16:1CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H60N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_hdd2coa_c" name="trans-Hexadec-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H60N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_hdeACP_c" name="cis-hexadec-9-enoyl-[acyl-carrier protein] (n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H49N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hemeO_c" name="Heme O" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C49H56FeN4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_hexACP_c" name="Hexanoyl-ACP (n-C6:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H31N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hg2_c" name="Hg2+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Hg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_hgmeACP_c" name="3-Hydroxyglutaryl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H29N2O11PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hhlipa_c" name="heptosyl-heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C124H220N2O51P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_his_DASH_L_c" name="L-Histidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9N3O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hisp_c" name="L-Histidinol phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11N3O4P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_histd_c" name="L-Histidinol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12N3O</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_histrna_c" name="L-Histidyl-tRNA(His)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8N3OR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_hkndd_c" name="2-Hydroxy-6-oxonona-2,4-diene-1,9-dioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H8O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_hkntd_c" name="2-hydroxy-6-ketononatrienedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H6O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_hlipa_c" name="heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C117H208N2O45P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_hmbil_c" name="Hydroxymethylbilane" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H38N4O17</p>
- <p>CHARGE: -8</p>
- </body>
- </notes>
- </species>
- <species id="M_hmgth_c" name="hydroxymethylglutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18N3O7S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hom_DASH_L_c" name="L-Homoserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hphhlipa_c" name="heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C131H231N2O60P3</p>
- <p>CHARGE: -8</p>
- </body>
- </notes>
- </species>
- <species id="M_hpmeACP_c" name="3-Hydroxypimeloyl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H33N2O11PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hpyr_c" name="Hydroxypyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hqn_c" name="Hydroquinone" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hx2coa_c" name="trans-Hex-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H40N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_hxa_c" name="Hexanoate (n-C6:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hxan_c" name="Hypoxanthine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hxcoa_c" name="Hexanoyl-CoA (n-C6:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_iasp_c" name="Iminoaspartate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H3NO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ichor_c" name="Isochorismate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H8O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_icit_c" name="Isocitrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H5O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_icolipa_c" name="inner core oligosaccharide lipid A (E coli)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C145H251N2O74P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_idon_DASH_L_c" name="L-Idonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_idp_c" name="IDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ile_DASH_L_c" name="L-Isoleucine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_iletrna_c" name="L-Isoleucyl-tRNA(Ile)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_imacp_c" name="3-(Imidazol-4-yl)-2-oxopropyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H7N2O5P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_imp_c" name="IMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_indole_c" name="Indole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H7N</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_inost_c" name="myo-Inositol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ins_c" name="Inosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ipdp_c" name="Isopentenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_iscs_c" name="IscS sulfur acceptor protein" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HSR</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_iscssh_c" name="IscS with bound sulfur" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HS2R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_iscu_c" name="IscU scaffold protein" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H8O2S6R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_iscu_DASH_2fe2s_c" name="IscU with bound [2Fe-2S] cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4O2S8Fe2R</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_iscu_DASH_2fe2s2_c" name="IscU with two bound [2Fe-2S] clusters" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2S10Fe4R</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_iscu_DASH_4fe4s_c" name="IscU with bound [4Fe-4S] cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4O2S10Fe4R</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_isetac_c" name="Isethionic acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O4S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_itp_c" name="ITP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_k_c" name="potassium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: K</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo_c" name="3-Deoxy-D-manno-2-octulosonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13O8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo2lipid4_c" name="KDO(2)-lipid IV(A)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C84H148N2O37P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo2lipid4L_c" name="KDO(2)-lipid IV(A) with laurate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C96H170N2O38P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo2lipid4p_c" name="KDO(2)-lipid IV(A) with palmitoleoyl" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C100H176N2O38P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo8p_c" name="3-Deoxy-D-manno-octulosonate 8-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12O11P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_kdolipid4_c" name="KDO-lipid IV(A)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C76H137N2O30P2</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_kphphhlipa_c" name="kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C139H241N2O70P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_D_c" name="D-Lactate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_L_c" name="L-Lactate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lald_DASH_D_c" name="D-Lactaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lald_DASH_L_c" name="L-Lactaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lcts_c" name="Lactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_leu_DASH_L_c" name="L-Leucine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_leutrna_c" name="L-Leucyl-tRNA(Leu)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_lgt_DASH_S_c" name="(R)-S-Lactoylglutathione" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C13H20N3O8S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_c" name="KDO(2)-lipid (A)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C110H196N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_cold_c" name="cold adapted KDO(2)-lipid (A)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C114H202N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipidA_c" name="2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C68H126N2O23P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_lipidAds_c" name="Lipid A Disaccharide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C68H127N2O20P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_lipidX_c" name="2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H64NO12P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_lipoamp_c" name="lipoyl-AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H25N5O8PS2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lipoate_c" name="Lipoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14O2S2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lipopb_c" name="lipoate (protein bound)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13OS2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_lys_DASH_L_c" name="L-Lysine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_lystrna_c" name="L-Lysine-tRNA (Lys)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14N2OR</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_lyx_DASH_L_c" name="L-Lyxose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_D_c" name="D-Malate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_L_c" name="L-Malate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_malACP_c" name="Malonyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H22N2O10PRS</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_malcoa_c" name="Malonyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H33N7O19P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_malcoame_c" name="malonyl-CoA methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H36N7O19P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_malt_c" name="Maltose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malt6p_c" name="Maltose 6'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H21O14P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_malthp_c" name="Maltoheptaose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H72O36</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malthx_c" name="Maltohexaose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltpt_c" name="Maltopentaose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H52O26</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malttr_c" name="Maltotriose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H32O16</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltttr_c" name="Maltotetraose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H42O21</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man_c" name="D-Mannose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man1p_c" name="D-Mannose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_man6p_c" name="D-Mannose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_man6pglyc_c" name="2(alpha-D-Mannosyl-6-phosphate)-D-glycerate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H14O12P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_mana_c" name="D-Mannonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_mdhdhf_c" name="(2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-3-one" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_melib_c" name="Melibiose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_meoh_c" name="Methanol" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4O1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mercppyr_c" name="Mercaptopyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_D_c" name="D-Methionine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_L_c" name="L-Methionine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_methf_c" name="5,10-Methenyltetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H20N7O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_R_DASH_L_c" name="L-methionine-R-sulfoxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_S_DASH_L_c" name="L-Methionine Sulfoxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mettrna_c" name="L-Methionyl-tRNA (Met)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10NOSR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_mg2_c" name="magnesium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mi1p_DASH_D_c" name="1D-myo-Inositol 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_micit_c" name="methylisocitrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H7O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_mlthf_c" name="5,10-Methylenetetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H21N7O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mmcoa_DASH_S_c" name="(S)-Methylmalonyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H35N7O19P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_mmet_c" name="S-Methyl-L-methionine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14NO2S</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_mn2_c" name="Mn2+" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mnl1p_c" name="D-Mannitol 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_moadamp_c" name="MoaD Protein with bound AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12N5O8P1X</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_moadcoo_c" name="MoaD Protein with carboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C1O2X</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_moadcosh_c" name="MoaD Protein with thiocarboxylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C1H1O1S1X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mobd_c" name="Molybdate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: MoO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_moco_c" name="molybdenum cofactor" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10N5O8PS2Mo</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mococdp_c" name="molybdopterin cytosine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H22N8O15P2S2Mo</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mocogdp_c" name="molybdopterin guanine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H22N10O15P2S2Mo</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mpt_c" name="molybdopterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10N5O6PS2Cu</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mptamp_c" name="adenylated molybdopterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H22N10O12P2S2Cu</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mql8_c" name="Menaquinol 8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C51H74O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mqn8_c" name="Menaquinone 8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C51H72O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_msa_c" name="Malonate semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_mso3_c" name="methanesulfonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH3O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_mthgxl_c" name="Methylglyoxal" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H4O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mththf_c" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_myrsACP_c" name="Myristoyl-ACP (n-C14:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H47N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_n2o_c" name="Nitrous oxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_n8aspmd_c" name="N8-Acetylspermidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H23N3O</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_na1_c" name="Sodium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Na</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_na15dap_c" name="N-3-aminopropyl-1,5-diaminopentane" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H24N3</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_nac_c" name="Nicotinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H4NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_nad_c" name="Nicotinamide adenine dinucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H26N7O14P2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H27N7O14P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_nadp_c" name="Nicotinamide adenine dinucleotide phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H25N7O17P3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_nadph_c" name="Nicotinamide adenine dinucleotide phosphate - reduced" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H26N7O17P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ncam_c" name="Nicotinamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_nh4_c" name="Ammonium" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ni2_c" name="nickel" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ni</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_nicrnt_c" name="Nicotinate D-ribonucleotide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_nmn_c" name="NMN" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H14N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no_c" name="Nitric oxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_no2_c" name="Nitrite" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no3_c" name="Nitrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_o16aund_c" name="O16 antigen undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C89H145N1O32P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_o2_c" name="O2" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_o2s_c" name="Superoxide anion" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_oaa_c" name="Oxaloacetate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H2O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_oc2coa_c" name="trans-Oct-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H44N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ocACP_c" name="Octanoyl-ACP (n-C8:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H35N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_occoa_c" name="Octanoyl-CoA (n-C8:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H46N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdca_c" name="octadecanoate (n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H35O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdcaACP_c" name="Octadecanoyl-ACP (n-C18:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H55N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdcap_c" name="Octadecanoyl-phosphate (n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H36O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdcea_c" name="octadecenoate (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H33O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdceap_c" name="Octadecanoyl-phosphate (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H34O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_octa_c" name="octanoate (n-C8:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_octapb_c" name="octanoate (protein bound)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15O</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_octdp_c" name="all-trans-Octaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H65O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_octeACP_c" name="cis-octadec-11-enoyl-[acyl-carrier protein] (n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H53N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_od2coa_c" name="trans-Octadec-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H64N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_odecoa_c" name="Octadecenoyl-CoA (n-C18:1CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H64N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ogmeACP_c" name="3-Oxo-glutaryl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H27N2O11PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ohpb_c" name="2-Oxo-3-hydroxy-4-phosphobutanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O8P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_op4en_c" name="2-Oxopent-4-enoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_opmeACP_c" name="3-Oxo-pimeloyl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H31N2O11PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_orn_c" name="Ornithine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_orot_c" name="Orotate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H3N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_orot5p_c" name="Orotidine 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10N2O11P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_oxa_c" name="Oxalate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_oxadpcoa_c" name="3-Oxoadipyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H37N7O20P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_oxalcoa_c" name="Oxalyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H31N7O19P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_oxam_c" name="Oxamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2NO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_oxur_c" name="Oxalureate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pa120_c" name="1,2-didodecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H51O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa140_c" name="1,2-ditetradecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H59O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa141_c" name="1,2-ditetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H55O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa160_c" name="1,2-dihexadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H67O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa161_c" name="1,2-dihexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H63O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa180_c" name="1,2-dioctadecanoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H75O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa181_c" name="1,2-dioctadec-11-enoyl-sn-glycerol 3-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H71O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pac_c" name="Phenylacetic acid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H7O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pacald_c" name="Phenylacetaldehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_palmACP_c" name="Palmitoyl-ACP (n-C16:0ACP)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H51N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pan4p_c" name="Pantetheine 4'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H21N2O7PS</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pant_DASH_R_c" name="(R)-Pantoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pap_c" name="Adenosine 3',5'-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O10P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_paps_c" name="3'-Phosphoadenylyl sulfate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O13P2S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_pdx5p_c" name="Pyridoxine 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H10NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pe120_c" name="phosphatidylethanolamine (didodecanoyl, n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H58N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe140_c" name="phosphatidylethanolamine (ditetradecanoyl, n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H66N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe141_c" name="phosphatidylethanolamine (ditetradec-7-enoyl, n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H62N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe160_c" name="phosphatidylethanolamine (dihexadecanoyl, n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H74N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe161_c" name="phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H70N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe180_c" name="phosphatidylethanolamine (dioctadecanoyl, n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C41H82N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe181_c" name="phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C41H78N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pep_c" name="Phosphoenolpyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H2O6P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pg120_c" name="Phosphatidylglycerol (didodecanoyl, n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H58O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg140_c" name="Phosphatidylglycerol (ditetradecanoyl, n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H66O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg141_c" name="Phosphatidylglycerol (ditetradec-7-enoyl, n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H62O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg160_c" name="Phosphatidylglycerol (dihexadecanoyl, n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H74O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg161_c" name="Phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H70O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg180_c" name="Phosphatidylglycerol (dioctadecanoyl, n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H82O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg181_c" name="Phosphatidylglycerol (dioctadec-11-enoyl, n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H78O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp120_c" name="Phosphatidylglycerophosphate (didodecanoyl, n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H57O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp140_c" name="Phosphatidylglycerophosphate (ditetradecanoyl, n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H65O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp141_c" name="Phosphatidylglycerophosphate (ditetradec-7-enoyl, n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H61O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp160_c" name="Phosphatidylglycerophosphate (dihexadecanoyl, n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H73O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp161_c" name="Phosphatidylglycerophosphate (dihexadec-9-enoyl, n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H69O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp180_c" name="Phosphatidylglycerophosphate (dioctadecanoyl, n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H81O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp181_c" name="Phosphatidylglycerophosphate (dioctadec-11-enoyl, n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H77O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_phaccoa_c" name="Phenylacetyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H38N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_phe_DASH_L_c" name="L-Phenylalanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pheme_c" name="Protoheme" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H30FeN4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_phetrna_c" name="L-Phenylalanyl-tRNA(Phe)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_phhlipa_c" name="phospho-heptosyl-heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C124H219N2O54P3</p>
- <p>CHARGE: -8</p>
- </body>
- </notes>
- </species>
- <species id="M_phom_c" name="O-Phospho-L-homoserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_phphhlipa_c" name="phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C131H230N2O63P4</p>
- <p>CHARGE: -10</p>
- </body>
- </notes>
- </species>
- <species id="M_phpyr_c" name="Phenylpyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_phthr_c" name="O-Phospho-4-hydroxy-L-threonine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8NO7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pi_c" name="Phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pimACP_c" name="Pimeloyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H31N2O10PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pmeACP_c" name="Pimeloyl-[acyl-carrier protein] methyl ester" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H33N2O10PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pmtcoa_c" name="Palmitoyl-CoA (n-C16:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H62N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_pnto_DASH_R_c" name="(R)-Pantothenate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H16NO5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_poaac_c" name="Peroxyaminoacrylate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ppa_c" name="Propionate (n-C3:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppal_c" name="Propanal" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ppap_c" name="Propanoyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O5P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ppbng_c" name="Porphobilinogen" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppcoa_c" name="Propanoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H36N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ppgpp_c" name="Guanosine 3',5'-bis(diphosphate)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O17P4</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_pphn_c" name="Prephenate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H8O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ppi_c" name="Diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ppp9_c" name="Protoporphyrin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H32N4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pppg9_c" name="Protoporphyrinogen IX" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H38N4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pppi_c" name="Inorganic triphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO10P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_pppn_c" name="Phenylpropanoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pram_c" name="5-Phospho-beta-D-ribosylamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pran_c" name="N-(5-Phospho-D-ribosyl)anthranilate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H13NO9P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_prbamp_c" name="1-(5-Phosphoribosyl)-AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N5O14P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_prbatp_c" name="1-(5-Phosphoribosyl)-ATP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N5O20P4</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_preq0_c" name="7-cyano-7-carbaguanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H5N5O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_preq1_c" name="7-aminomethyl-7-deazaguanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H10N5O</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_prfp_c" name="1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H21N5O15P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_prlp_c" name="5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H21N5O15P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_pro_DASH_L_c" name="L-Proline" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_progly_c" name="L-Prolinylglycine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_protrna_c" name="L-Prolyl-tRNA(Pro)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_prpp_c" name="5-Phospho-alpha-D-ribose 1-diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8O14P3</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_ps120_c" name="phosphatidylserine (didodecanoyl, n-C12:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H57N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps140_c" name="phosphatidylserine (ditetradecanoyl, n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H65N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps141_c" name="phosphatidylserine (ditetradec-7-enoyl, n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H61N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps160_c" name="phosphatidylserine (dihexadecanoyl, n-C16:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H73N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps161_c" name="phosphatidylserine (dihexadec-9-enoyl, n-C16:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H69N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps180_c" name="phosphatidylserine (dioctadecanoyl, n-C18:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H81N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ps181_c" name="phosphatidylserine (dioctadec-11-enoyl, n-C18:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H77N1O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_psclys_c" name="psicoselysine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pser_DASH_L_c" name="O-Phospho-L-serine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ptrc_c" name="Putrescine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H14N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_pyam5p_c" name="Pyridoxamine 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12N2O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pydam_c" name="Pyridoxamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pydx_c" name="Pyridoxal" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pydx5p_c" name="Pyridoxal 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pydxn_c" name="Pyridoxine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pyr_c" name="Pyruvate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_q8_c" name="Ubiquinone-8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C49H74O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_q8h2_c" name="Ubiquinol-8" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C49H76O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_quin_c" name="Quinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_quln_c" name="Quinolinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H3NO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_r15bp_c" name="D-Ribose 1,5-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8O11P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_r1p_c" name="alpha-D-Ribose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_r5p_c" name="alpha-D-Ribose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ragund_c" name="rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C69H113N1O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_rbflvrd_c" name="Reduced riboflavin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H22N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rbl_DASH_L_c" name="L-Ribulose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rdmbzi_c" name="N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H18N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rephaccoa_c" name="Ring 1,2-epoxyphenylacetyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H38N7O18P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_rhcys_c" name="S-Ribosyl-L-homocysteine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H17NO6S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rib_DASH_D_c" name="D-Ribose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ribflv_c" name="Riboflavin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H20N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rml_c" name="L-Rhamnulose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rml1p_c" name="L-Rhamnulose 1-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_rmn_c" name="L-Rhamnose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ru5p_DASH_D_c" name="D-Ribulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ru5p_DASH_L_c" name="L-Ribulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_s17bp_c" name="Sedoheptulose 1,7-bisphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12O13P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_s7p_c" name="Sedoheptulose 7-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H13O10P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sarcs_c" name="Sarcosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sbt6p_c" name="D-Sorbitol 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sbzcoa_c" name="O-Succinylbenzoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C32H39N7O20P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_scl_c" name="sirohydrochlorin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H39N4O16</p>
- <p>CHARGE: -7</p>
- </body>
- </notes>
- </species>
- <species id="M_sectrna_c" name="L-Selenocysteinyl-tRNA(Sec)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NOSeR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_sel_c" name="Selenate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_seln_c" name="Selenide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HSe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_selnp_c" name="Selenophosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O3PSe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_D_c" name="D-Serine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_L_c" name="L-Serine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_seramp_c" name="L-seryl-AMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C13H19N6O9P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sertrna_c" name="L-Seryl-tRNA(Ser)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NO2R</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_sertrna_LSQBKT_sec_RSQBKT__c" name="L-Seryl-tRNA(Sec)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NO2R</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_sheme_c" name="Siroheme" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H36FeN4O16</p>
- <p>CHARGE: -8</p>
- </body>
- </notes>
- </species>
- <species id="M_skm_c" name="Shikimate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_skm5p_c" name="Shikimate 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H8O8P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_sl26da_c" name="N-Succinyl-LL-2,6-diaminoheptanedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H16N2O7</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sl2a6o_c" name="N-Succinyl-2-L-amino-6-oxoheptanedioate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12NO8</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_slnt_c" name="selenite" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so2_c" name="sulfur dioxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_so3_c" name="Sulfite" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so4_c" name="Sulfate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_spmd_c" name="Spermidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H22N3</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_stcoa_c" name="Stearoyl-CoA (n-C18:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H66N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_suc6p_c" name="Sucrose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H21O14P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sucarg_c" name="N2-Succinyl-L-arginine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H17N4O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_sucbz_c" name="o-Succinylbenzoate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H8O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_succ_c" name="Succinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_succoa_c" name="Succinyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H35N7O19P3S</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_sucglu_c" name="N2-Succinyl-L-glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10NO7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_sucgsa_c" name="N2-Succinyl-L-glutamate 5-semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_suchms_c" name="O-Succinyl-L-homoserine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12NO6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_sucorn_c" name="N2-Succinyl-L-ornithine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_sucsal_c" name="Succinic semialdehyde" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_sufbcd_c" name="SufBCD scaffold complex" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H8O2S6R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sufbcd_DASH_2fe2s_c" name="SufBCD with bound [2Fe-2S] cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4O2S8Fe2R</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sufbcd_DASH_2fe2s2_c" name="SufBCD with two bound [2Fe-2S] clusters" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2S10Fe4R</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_sufbcd_DASH_4fe4s_c" name="SufBCD with bound [4Fe-4S] cluster" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4O2S10Fe4R</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sufse_c" name="SufSE sulfur acceptor complex" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HSR</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sufsesh_c" name="SufSE with bound sulfur" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HS2R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sulfac_c" name="sulfoacetate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2O5S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_t3c11vaceACP_c" name="trans-3-cis-11-vacceoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H51N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_t3c5ddeceACP_c" name="trans-3-cis-5-dodecenoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H39N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_t3c7mrseACP_c" name="trans-3-cis-7-myristoleoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H43N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_t3c9palmeACP_c" name="trans-3-cis-9-palmitoleoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H47N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tag6p_DASH_D_c" name="D-Tagatose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tagdp_DASH_D_c" name="D-Tagatose 1,6-biphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10O12P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_tagur_c" name="D-Tagaturonate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_D_c" name="D-tartrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_L_c" name="L-tartrate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_taur_c" name="Taurine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H7NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tcynt_c" name="Thiocyanate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_td2coa_c" name="trans-Tetradec-2-enoyl-CoA" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H56N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_tdcoa_c" name="Tetradecanoyl-CoA (n-C14:0CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H58N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_tddec2eACP_c" name="trans-Dodec-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H41N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tdeACP_c" name="cis-tetradec-7-enoyl-[acyl-carrier protein] (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H45N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tdec2eACP_c" name="trans-Dec-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H37N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tdecoa_c" name="Tetradecenoyl-CoA (n-C14:1CoA)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H56N7O17P3S</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_thdp_c" name="2,3,4,5-Tetrahydrodipicolinate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H7NO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_thex2eACP_c" name="trans-Hex-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H29N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_thf_c" name="5,6,7,8-Tetrahydrofolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H21N7O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_thm_c" name="Thiamin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H17N4OS</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_thmmp_c" name="Thiamin monophosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H16N4O4PS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_thmnp_c" name="Tetrahydromonapterin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thmpp_c" name="Thiamine diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H16N4O7P2S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_thptdn_c" name="5,6,7,8-tetrahydropteridine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H10N4</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_thr_DASH_L_c" name="L-Threonine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thrtrna_c" name="L-Threonyl-tRNA(Thr)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8NO2R</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_thym_c" name="Thymine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H6N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thymd_c" name="Thymidine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H14N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tma_c" name="trimethylamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H10N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tmao_c" name="Trimethylamine N-oxide" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tmrs2eACP_c" name="trans-Tetradec-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H45N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_toct2eACP_c" name="trans-Oct-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H33N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_toctd2eACP_c" name="trans-octadec-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H53N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tpalm2eACP_c" name="trans-Hexadec-2-enoyl-[acyl-carrier protein]" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H49N2O8PRS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_trdox_c" name="Oxidized thioredoxin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trdrd_c" name="Reduced thioredoxin" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tre_c" name="Trehalose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tre6p_c" name="alpha,alpha'-Trehalose 6-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H21O14P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaala_c" name="tRNA(Ala)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaarg_c" name="tRNA(Arg)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaasn_c" name="tRNA(Asn)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H17O10PR2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaasp_c" name="tRNA(Asp)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnacys_c" name="tRNA(Cys)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnagln_c" name="tRNA(Gln)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaglu_c" name="tRNA (Glu)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnagly_c" name="tRNA(Gly)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnahis_c" name="tRNA(His)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaile_c" name="tRNA(Ile)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaleu_c" name="tRNA(Leu)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnalys_c" name="tRNA(Lys)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnamet_c" name="tRNA(Met)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaphe_c" name="tRNA(Phe)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnapro_c" name="tRNA(Pro)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnasecys_c" name="tRNA(SeCys)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaser_c" name="tRNA(Ser)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnathr_c" name="tRNA(Thr)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnatrp_c" name="tRNA(Trp)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnatyr_c" name="tRNA(Tyr)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trnaval_c" name="tRNA(Val)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: R</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trp_DASH_L_c" name="L-Tryptophan" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trptrna_c" name="L-Tryptophanyl-tRNA(Trp)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H11N2OR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tsul_c" name="Thiosulfate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdca_c" name="tetradecanoate (n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H27O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdcap_c" name="Tetradecanoyl-phosphate (n-C14:0)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H28O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdcea_c" name="tetradecenoate (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H25O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdceap_c" name="Tetradecanoyl-phosphate (n-C14:1)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H26O5P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_tungs_c" name="tungstate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4W1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tyr_DASH_L_c" name="L-Tyrosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tyrtrna_c" name="L-Tyrosyl-tRNA(Tyr)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10NO2R</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_u23ga_c" name="UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C43H75N3O20P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_u3aga_c" name="UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H51N3O19P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_u3hga_c" name="UDP-3-O-(3-hydroxytetradecanoyl)-D-glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H50N3O18P2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_uLa4fn_c" name="undecaprenyl phosphate-4-amino-4-formyl-L-arabinose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C61H99N1O8P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_uLa4n_c" name="undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C60H100N1O7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uaagmda_c" name="Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C95H152N8O28P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_uaccg_c" name="UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H26N3O19P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_uacgam_c" name="UDP-N-acetyl-D-glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_uacmam_c" name="UDP-N-acetyl-D-mannosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_uacmamu_c" name="UDP-N-acetyl-D-mannosaminouronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H22N3O18P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_uagmda_c" name="Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C87H139N7O23P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_uama_c" name="UDP-N-acetylmuramoyl-L-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H33N4O20P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_uamag_c" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C28H39N5O23P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_uamr_c" name="UDP-N-acetylmuramate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H28N3O19P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_udcpdp_c" name="Undecaprenyl diphosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C55H89O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_udcpp_c" name="Undecaprenyl phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C55H89O4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udp_c" name="UDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O12P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_udpLa4fn_c" name="uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H21N3O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpLa4n_c" name="uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H22N3O15P2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_udpLa4o_c" name="UDP-4-keto-pyranose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H18N2O16P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpg_c" name="UDPglucose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpgal_c" name="UDPgalactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpgalfur_c" name="UDP-D-galacto-1,4-furanose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpglcur_c" name="UDP-D-glucuronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N2O18P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ugmd_c" name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H51N7O26P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ugmda_c" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C41H61N9O28P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_um4p_c" name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H56N8O27P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_ump_c" name="UMP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_unaga_c" name="Undecaprenyl diphospho N-acetyl-glucosamine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C63H103NO12P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_unagamu_c" name="Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C71H113N2O18P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_unagamuf_c" name="Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C79H126N3O22P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_uppg3_c" name="Uroporphyrinogen III" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C40H36N4O16</p>
- <p>CHARGE: -8</p>
- </body>
- </notes>
- </species>
- <species id="M_ura_c" name="Uracil" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uracp_c" name="Ureidoacrylate peracid" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_urate_c" name="Urate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_urdglyc_c" name="(-)-Ureidoglycolate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_urea_c" name="Urea" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uri_c" name="Uridine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_utp_c" name="UTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O15P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_val_DASH_L_c" name="L-Valine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_valtrna_c" name="L-Valyl-tRNA(Val)" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10NOR</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_wco_c" name="tungsten binding cofactor" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10N5O8PS2W</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xan_c" name="Xanthine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xdp_c" name="XDP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O12P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_xmp_c" name="Xanthosine 5'-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xtp_c" name="XTP" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O15P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_xtsn_c" name="Xanthosine" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xu5p_DASH_D_c" name="D-Xylulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xu5p_DASH_L_c" name="L-Xylulose 5-phosphate" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xyl_DASH_D_c" name="D-Xylose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xylu_DASH_D_c" name="D-Xylulose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xylu_DASH_L_c" name="L-Xylulose" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_zn2_c" name="Zinc" compartment="c">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Zn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_R_e" name="(R)-Propane-1,2-diol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_S_e" name="(S)-Propane-1,2-diol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_14glucan_e" name="1,4-alpha-D-glucan" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_15dap_e" name="1,5-Diaminopentane" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_23camp_e" name="2',3'-Cyclic AMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O6P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23ccmp_e" name="2',3'-Cyclic CMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N3O7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23cgmp_e" name="2',3'-Cyclic GMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23cump_e" name="2',3'-Cyclic UMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dappa_e" name="2,3-diaminopropionate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_26dap_DASH_M_e" name="meso-2,6-Diaminoheptanedioate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddglcn_e" name="2-Dehydro-3-deoxy-D-gluconate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_34dhpac_e" name="3,4-Dihydroxyphenylacetaldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_3amp_e" name="3'-AMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3cmp_e" name="3'-cmp" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3gmp_e" name="3'-GMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcinnm_e" name="3-hydroxycinnamic acid" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpp_e" name="3-Hydroxypropanoate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpppn_e" name="3-(3-hydroxy-phenyl)propionate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ump_e" name="3'-UMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4abut_e" name="4-Aminobutanoate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4hoxpacd_e" name="4-Hydroxyphenylacetaldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5dglcn_e" name="5-Dehydro-D-gluconate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_5mtr_e" name="5-Methylthio-D-ribose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O4S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDglu_e" name="L-alanine-D-glutamate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdap_e" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25N4O8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdapDala_e" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H30N5O9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaLglu_e" name="L-alanine-L-glutamate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ac_e" name="Acetate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acac_e" name="Acetoacetate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acald_e" name="Acetaldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgal_e" name="N-Acetyl-D-galactosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgal1p_e" name="N-Acetyl-D-galactosamine 1-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam_e" name="N-Acetyl-D-glucosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam1p_e" name="N-Acetyl-D-glucosamine 1-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acmana_e" name="N-Acetyl-D-mannosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acmum_e" name="N-Acetylmuramate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18NO8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acnam_e" name="N-Acetylneuraminate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18NO9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acolipa_e" name="4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C181H314N3O103P4</p>
- <p>CHARGE: -9</p>
- </body>
- </notes>
- </species>
- <species id="M_acser_e" name="O-Acetyl-L-serine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ade_e" name="Adenine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adn_e" name="Adenosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adocbl_e" name="Adenosylcobalamin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C72H100CoN18O17P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ag_e" name="silver" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ag</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_agm_e" name="Agmatine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N4</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_akg_e" name="2-Oxoglutarate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_B_e" name="beta-Alanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_D_e" name="D-Alanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_L_e" name="L-Alanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alaala_e" name="D-Alanyl-D-alanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_all_DASH_D_e" name="D-Allose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alltn_e" name="Allantoin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6N4O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_amp_e" name="AMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm_e" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H29N2O12</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_arab_DASH_L_e" name="L-Arabinose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arbt_e" name="Arbutin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H16O7</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_e" name="aerobactin minus Fe3" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33N4O13</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_DASH_fe3_e" name="Aerobactin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33FeN4O13</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arg_DASH_L_e" name="L-Arginine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N4O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ascb_DASH_L_e" name="L-Ascorbate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_asn_DASH_L_e" name="L-Asparagine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_aso3_e" name="arsenite" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: AsO3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_asp_DASH_L_e" name="L-Aspartate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_btn_e" name="Biotin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H15N2O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_but_e" name="Butyrate (n-C4:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_butso3_e" name="butanesulfonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ca2_e" name="Calcium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ca</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cbi_e" name="Cobinamide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H72CoN11O8</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cbl1_e" name="Cob(I)alamin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C62H88CoN13O14P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cd2_e" name="Cadmium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cd</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cgly_e" name="Cys-Gly" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_chol_e" name="Choline" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_chtbs_e" name="N,N'-diacetylchitobiose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H28N2O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cit_e" name="Citrate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H5O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_cl_e" name="Chloride" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cl</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cm_e" name="Chloramphenicol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12Cl2N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cmp_e" name="CMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_co2_e" name="CO2" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cobalt2_e" name="Co2+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Co</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_colipa_e" name="core oligosaccharide lipid A" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C176H303N2O100P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_colipap_e" name="core oligosaccharide lipid A diphosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C176H303N2O103P5</p>
- <p>CHARGE: -12</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_e" name="coprogen" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13Fe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_DASH_un_e" name="coprogen unloaded (no Fe(III))" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_e" name="L-Carnitine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_DASH_D_e" name="D-Carnitine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_csn_e" name="Cytosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5N3O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cu_e" name="Cu+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_cu2_e" name="Cu2+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cyan_e" name="Hydrogen cyanide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CHN</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cynt_e" name="Cyanate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNO</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_D_e" name="D-Cysteine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_L_e" name="L-Cysteine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cytd_e" name="Cytidine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dad_DASH_2_e" name="Deoxyadenosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_damp_e" name="dAMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dca_e" name="Decanoate (n-C10:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H19O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dcmp_e" name="dCMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dcyt_e" name="Deoxycytidine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ddca_e" name="Dodecanoate (n-C12:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H23O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dgmp_e" name="dGMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dgsn_e" name="Deoxyguanosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dha_e" name="Dihydroxyacetone" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dimp_e" name="dIMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_din_e" name="Deoxyinosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dms_e" name="Dimethyl sulfide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dmso_e" name="Dimethyl sulfoxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6OS</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dopa_e" name="Dopamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12NO2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_doxrbcn_e" name="doxorubicin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H29NO11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dtmp_e" name="dTMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dump_e" name="dUMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_duri_e" name="Deoxyuridine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_eca4colipa_e" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C272H447N14O160P4</p>
- <p>CHARGE: -15</p>
- </body>
- </notes>
- </species>
- <species id="M_enlipa_e" name="phosphoethanolamine KDO(2)-lipid (A)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C112H202N3O42P3</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_enter_e" name="Enterochelin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27N3O15</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_etha_e" name="Ethanolamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H8NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ethso3_e" name="ethanesulfonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_etoh_e" name="Ethanol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_f6p_e" name="D-Fructose 6-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fald_e" name="Formaldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fe2_e" name="Fe2+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3_e" name="Fe3+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3dcit_e" name="Fe(III)dicitrate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H10FeO14</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3dhbzs_e" name="ferric 2,3-dihydroxybenzoylserine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10NO6Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_e" name="Fe(III)hydroxamate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3Fe</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_DASH_un_e" name="Fe(III)hydoxamate, unloaded" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_e" name="Ferrichrome" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42FeN9O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_DASH_un_e" name="Ferrichrome minus Fe(III)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42N9O12</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_feenter_e" name="Fe-enterobactin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27FeN3O15</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_e" name="ferroxamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46FeN6O8</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_DASH_un_e" name="ferroxamine minus Fe(3)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46N6O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_for_e" name="Formate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH1O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fru_e" name="D-Fructose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_frulys_e" name="fructoselysine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_fruur_e" name="D-Fructuronate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fuc_DASH_L_e" name="L-Fucose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fum_e" name="Fumarate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H2O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fusa_e" name="fusidic acid" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H48O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g1p_e" name="D-Glucose 1-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pc_e" name="sn-Glycero-3-phosphocholine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H20NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pe_e" name="sn-Glycero-3-phosphoethanolamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pg_e" name="Glycerophosphoglycerol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pi_e" name="sn-Glycero-3-phospho-1-inositol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3ps_e" name="Glycerophosphoserine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g6p_e" name="D-Glucose 6-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gal_e" name="D-Galactose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gal_DASH_bD_e" name="beta D-Galactose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gal1p_e" name="alpha-D-Galactose 1-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galct_DASH_D_e" name="D-Galactarate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_D_e" name="D-Galactonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_L_e" name="L-Galactonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galt_e" name="Galactitol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_galur_e" name="D-Galacturonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam_e" name="D-Glucosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14NO5</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam6p_e" name="D-Glucosamine 6-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gbbtn_e" name="gamma-butyrobetaine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gdp_e" name="GDP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_glc_DASH_D_e" name="D-Glucose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glcn_e" name="D-Gluconate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glcr_e" name="D-Glucarate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glcur_e" name="D-Glucuronate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glcur1p_e" name="D-Glucuronate 1-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O10P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_gln_DASH_L_e" name="L-Glutamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glu_DASH_L_e" name="L-Glutamate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gly_e" name="Glycine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyald_e" name="D-Glyceraldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyb_e" name="Glycine betaine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_e" name="Glycerol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_DASH_R_e" name="(R)-Glycerate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc2p_e" name="Glycerol 2-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc3p_e" name="Glycerol 3-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyclt_e" name="Glycolate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gmp_e" name="GMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gsn_e" name="Guanosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gthox_e" name="Oxidized glutathione" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H30N6O12S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gthrd_e" name="Reduced glutathione" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H16N3O6S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gtp_e" name="GTP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_gua_e" name="Guanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h_e" name="H+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_h2_e" name="H2" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o_e" name="H2O" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o2_e" name="Hydrogen peroxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2s_e" name="Hydrogen sulfide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hacolipa_e" name="hepta-acylated core oligosaccharide lipid A (E. coli)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C192H333N2O101P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_halipa_e" name="hepta-acylated KDO(2)-lipid (A)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C126H226N2O40P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_hdca_e" name="Hexadecanoate (n-C16:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H31O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdcea_e" name="Hexadecenoate (n-C16:1)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H29O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hg2_e" name="Hg2+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Hg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_his_DASH_L_e" name="L-Histidine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9N3O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hom_DASH_L_e" name="L-Homoserine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hxa_e" name="Hexanoate (n-C6:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hxan_e" name="Hypoxanthine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_idon_DASH_L_e" name="L-Idonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ile_DASH_L_e" name="L-Isoleucine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_imp_e" name="IMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_indole_e" name="Indole" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H7N</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_inost_e" name="myo-Inositol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ins_e" name="Inosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_isetac_e" name="Isethionic acid" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O4S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_k_e" name="potassium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: K</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo2lipid4_e" name="KDO(2)-lipid IV(A)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C84H148N2O37P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_D_e" name="D-Lactate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_L_e" name="L-Lactate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lcts_e" name="Lactose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_leu_DASH_L_e" name="L-Leucine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_e" name="KDO(2)-lipid (A)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C110H196N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_cold_e" name="cold adapted KDO(2)-lipid (A)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C114H202N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipoate_e" name="Lipoate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14O2S2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lys_DASH_L_e" name="L-Lysine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_lyx_DASH_L_e" name="L-Lyxose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_D_e" name="D-Malate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_L_e" name="L-Malate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_malt_e" name="Maltose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malthx_e" name="Maltohexaose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltpt_e" name="Maltopentaose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H52O26</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malttr_e" name="Maltotriose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H32O16</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltttr_e" name="Maltotetraose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H42O21</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man_e" name="D-Mannose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man6p_e" name="D-Mannose 6-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_manglyc_e" name="2(alpha-D-Mannosyl)-D-glycerate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15O9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_melib_e" name="Melibiose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_meoh_e" name="Methanol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4O1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_D_e" name="D-Methionine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_L_e" name="L-Methionine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_R_DASH_L_e" name="L-methionine-R-sulfoxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_S_DASH_L_e" name="L-Methionine Sulfoxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mg2_e" name="magnesium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mincyc_e" name="minocycline" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H27N3O7</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_minohp_e" name="myo-Inositol hexakisphosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6O24P6</p>
- <p>CHARGE: -12</p>
- </body>
- </notes>
- </species>
- <species id="M_mmet_e" name="S-Methyl-L-methionine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14NO2S</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_mn2_e" name="Mn2+" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mnl_e" name="D-Mannitol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mobd_e" name="Molybdate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: MoO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mso3_e" name="methanesulfonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH3O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_n2o_e" name="Nitrous oxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_na1_e" name="Sodium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Na</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_nac_e" name="Nicotinate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H4NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_nh4_e" name="Ammonium" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ni2_e" name="nickel" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ni</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_nmn_e" name="NMN" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H14N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no_e" name="Nitric oxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_no2_e" name="Nitrite" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no3_e" name="Nitrate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_novbcn_e" name="novobiocin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H36N2O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_o16a4colipa_e" name="(O16 antigen)x4 core oligosaccharide lipid A" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C312H523N6O200P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_o2_e" name="O2" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_o2s_e" name="Superoxide anion" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdca_e" name="octadecanoate (n-C18:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H35O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdcea_e" name="octadecenoate (n-C18:1)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H33O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_octa_e" name="octanoate (n-C8:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_orn_e" name="Ornithine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_orot_e" name="Orotate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H3N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pacald_e" name="Phenylacetaldehyde" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_peamn_e" name="Phenethylamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_phe_DASH_L_e" name="L-Phenylalanine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pheme_e" name="Protoheme" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H30FeN4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pi_e" name="Phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pnto_DASH_R_e" name="(R)-Pantothenate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H16NO5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppa_e" name="Propionate (n-C3:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppal_e" name="Propanal" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pppn_e" name="Phenylpropanoate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppt_e" name="Phosphonate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO3P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pro_DASH_L_e" name="L-Proline" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_progly_e" name="L-Prolinylglycine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_psclys_e" name="psicoselysine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pser_DASH_L_e" name="O-Phospho-L-serine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ptrc_e" name="Putrescine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H14N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_pydam_e" name="Pyridoxamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pydx_e" name="Pyridoxal" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pydxn_e" name="Pyridoxine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pyr_e" name="Pyruvate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_quin_e" name="Quinate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_r5p_e" name="alpha-D-Ribose 5-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_rfamp_e" name="rifampin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C43H58N4O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rib_DASH_D_e" name="D-Ribose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rmn_e" name="L-Rhamnose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sbt_DASH_D_e" name="D-Sorbitol" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sel_e" name="Selenate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_D_e" name="D-Serine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_L_e" name="L-Serine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_skm_e" name="Shikimate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_slnt_e" name="selenite" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so2_e" name="sulfur dioxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_so3_e" name="Sulfite" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so4_e" name="Sulfate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_spmd_e" name="Spermidine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H22N3</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_succ_e" name="Succinate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sucr_e" name="Sucrose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sulfac_e" name="sulfoacetate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2O5S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_D_e" name="D-tartrate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_L_e" name="L-tartrate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_taur_e" name="Taurine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H7NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tcynt_e" name="Thiocyanate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_thm_e" name="Thiamin" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H17N4OS</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_thr_DASH_L_e" name="L-Threonine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thrp_e" name="L-Threonine O-3-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_thym_e" name="Thymine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H6N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thymd_e" name="Thymidine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H14N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tma_e" name="trimethylamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H10N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tmao_e" name="Trimethylamine N-oxide" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tre_e" name="Trehalose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trp_DASH_L_e" name="L-Tryptophan" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tsul_e" name="Thiosulfate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdca_e" name="tetradecanoate (n-C14:0)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H27O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdcea_e" name="tetradecenoate (n-C14:1)" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H25O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttrcyc_e" name="tetracycline" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H24N2O8</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tungs_e" name="tungstate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4W1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tym_e" name="Tyramine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tyr_DASH_L_e" name="L-Tyrosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tyrp_e" name="Phosphotyrosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_uacgam_e" name="UDP-N-acetyl-D-glucosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpacgal_e" name="UDP-N-acetyl-D-galactosamine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpg_e" name="UDPglucose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpgal_e" name="UDPgalactose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpglcur_e" name="UDP-D-glucuronate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N2O18P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ump_e" name="UMP" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ura_e" name="Uracil" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_urea_e" name="Urea" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uri_e" name="Uridine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_val_DASH_L_e" name="L-Valine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xan_e" name="Xanthine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xmp_e" name="Xanthosine 5'-phosphate" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xtsn_e" name="Xanthosine" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xyl_DASH_D_e" name="D-Xylose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xylu_DASH_L_e" name="L-Xylulose" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_zn2_e" name="Zinc" compartment="e">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Zn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr120_p" name="1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H52O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr140_p" name="1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H60O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr141_p" name="1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H56O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr160_p" name="1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H68O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr161_p" name="1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H64O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr180_p" name="1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H76O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12dgr181_p" name="1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H72O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_R_p" name="(R)-Propane-1,2-diol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_12ppd_DASH_S_p" name="(S)-Propane-1,2-diol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_14glucan_p" name="1,4-alpha-D-glucan" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_15dap_p" name="1,5-Diaminopentane" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe120_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H36NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe140_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H40NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe141_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H38NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe160_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H44NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe161_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H42NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe180_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H48NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpe181_p" name="1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H46NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg120_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H36O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg140_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H40O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg141_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H38O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg160_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H44O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg161_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H42O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg180_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H48O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1agpg181_p" name="1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H46O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_1ddecg3p_p" name="1-dodecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H29O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1hdec9eg3p_p" name="1-hexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H35O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1hdecg3p_p" name="1-hexadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H37O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1odec11eg3p_p" name="1-octadec-11-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H39O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1odecg3p_p" name="1-octadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H41O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1tdec7eg3p_p" name="1-tetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H31O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_1tdecg3p_p" name="1-tetradecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H33O7P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_23camp_p" name="2',3'-Cyclic AMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O6P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23ccmp_p" name="2',3'-Cyclic CMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N3O7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23cgmp_p" name="2',3'-Cyclic GMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N5O7P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23cump_p" name="2',3'-Cyclic UMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_23dappa_p" name="2,3-diaminopropionate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_26dap_DASH_M_p" name="meso-2,6-Diaminoheptanedioate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H14N2O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe120_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H36NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe140_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H40NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe141_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H38NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe160_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H44NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe161_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H42NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe180_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H48NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpe181_p" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H46NO7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg120_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H36O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg140_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H40O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg141_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H38O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg160_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H44O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg161_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H42O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg180_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H48O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2agpg181_p" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H46O9P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddecg3p_p" name="2-dodecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H30O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2ddglcn_p" name="2-Dehydro-3-deoxy-D-gluconate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O6</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2hdec9eg3p_p" name="2-hexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H36O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2hdecg3p_p" name="2-hexadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H38O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2odec11eg3p_p" name="2-octadec-11-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H40O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2odecg3p_p" name="2-octadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C21H42O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2tdec7eg3p_p" name="2-tetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H32O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_2tdecg3p_p" name="2-tetradecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H34O7P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_34dhpac_p" name="3,4-Dihydroxyphenylacetaldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_3amp_p" name="3'-AMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3cmp_p" name="3'-cmp" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3gmp_p" name="3'-GMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_3hcinnm_p" name="3-hydroxycinnamic acid" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H7O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpp_p" name="3-Hydroxypropanoate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3hpppn_p" name="3-(3-hydroxy-phenyl)propionate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_3ump_p" name="3'-UMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_4abut_p" name="4-Aminobutanoate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_4hoxpacd_p" name="4-Hydroxyphenylacetaldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_5dglcn_p" name="5-Dehydro-D-gluconate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_5mtr_p" name="5-Methylthio-D-ribose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O4S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDglu_p" name="L-alanine-D-glutamate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdap_p" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H25N4O8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaDgluMdapDala_p" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H30N5O9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_LalaLglu_p" name="L-alanine-L-glutamate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ac_p" name="Acetate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acac_p" name="Acetoacetate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acald_p" name="Acetaldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgal_p" name="N-Acetyl-D-galactosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgal1p_p" name="N-Acetyl-D-galactosamine 1-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam_p" name="N-Acetyl-D-glucosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acgam1p_p" name="N-Acetyl-D-glucosamine 1-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14NO9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_acmana_p" name="N-Acetyl-D-mannosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15NO6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_acmum_p" name="N-Acetylmuramate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18NO8</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acnam_p" name="N-Acetylneuraminate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H18NO9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_acolipa_p" name="4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C181H314N3O103P4</p>
- <p>CHARGE: -9</p>
- </body>
- </notes>
- </species>
- <species id="M_acser_p" name="O-Acetyl-L-serine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ade_p" name="Adenine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adn_p" name="Adenosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_adocbl_p" name="Adenosylcobalamin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C72H100CoN18O17P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_agm_p" name="Agmatine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H16N4</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_akg_p" name="2-Oxoglutarate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_B_p" name="beta-Alanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_D_p" name="D-Alanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ala_DASH_L_p" name="L-Alanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alaala_p" name="D-Alanyl-D-alanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_all_DASH_D_p" name="D-Allose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alltn_p" name="Allantoin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6N4O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_alpp_p" name="applipoprotein" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_amp_p" name="AMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm_p" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C19H29N2O12</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm3p_p" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H52N6O19</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_anhgm4p_p" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H57N7O20</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_arab_DASH_L_p" name="L-Arabinose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arbt_p" name="Arbutin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H16O7</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_p" name="aerobactin minus Fe3" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33N4O13</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_arbtn_DASH_fe3_p" name="Aerobactin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H33FeN4O13</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_arg_DASH_L_p" name="L-Arginine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N4O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ascb_DASH_L_p" name="L-Ascorbate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_asn_DASH_L_p" name="L-Asparagine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_aso3_p" name="arsenite" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: AsO3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_asp_DASH_L_p" name="L-Aspartate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H6NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_btn_p" name="Biotin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H15N2O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_but_p" name="Butyrate (n-C4:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H7O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_butso3_p" name="butanesulfonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ca2_p" name="Calcium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ca</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cbi_p" name="Cobinamide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C48H72CoN11O8</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cbl1_p" name="Cob(I)alamin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C62H88CoN13O14P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cd2_p" name="Cadmium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cd</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cgly_p" name="Cys-Gly" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_chol_p" name="Choline" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_chtbs_p" name="N,N'-diacetylchitobiose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H28N2O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cit_p" name="Citrate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H5O7</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_cl_p" name="Chloride" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cl</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn120_p" name="cardiolipin (tetradodecanoyl, n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C57H108O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn140_p" name="cardiolipin (tetratetradecanoyl, n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C65H124O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn141_p" name="cardiolipin (tetratetradec-7-enoyl, n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C65H116O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn160_p" name="cardiolipin (tetrahexadecanoyl, n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C73H140O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn161_p" name="cardiolipin (tetrahexadec-9-enoyl, n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C73H132O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn180_p" name="cardiolipin (tetraoctadecanoyl, n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C81H156O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_clpn181_p" name="cardiolipin (tetraoctadec-11-enoyl, n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C81H148O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_cm_p" name="Chloramphenicol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12Cl2N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cmp_p" name="CMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_co2_p" name="CO2" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cobalt2_p" name="Co2+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Co</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_colipa_p" name="core oligosaccharide lipid A" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C176H303N2O100P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_colipap_p" name="core oligosaccharide lipid A diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C176H303N2O103P5</p>
- <p>CHARGE: -12</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_p" name="coprogen" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13Fe</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cpgn_DASH_un_p" name="coprogen unloaded (no Fe(III))" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H52N6O13</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_p" name="L-Carnitine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_crn_DASH_D_p" name="D-Carnitine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_csn_p" name="Cytosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H5N3O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ctbt_p" name="crotonobetaine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cu_p" name="Cu+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_cu2_p" name="Cu2+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Cu</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_cyan_p" name="Hydrogen cyanide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CHN</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cynt_p" name="Cyanate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNO</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_D_p" name="D-Cysteine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cys_DASH_L_p" name="L-Cysteine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_cytd_p" name="Cytidine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dad_DASH_2_p" name="Deoxyadenosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_damp_p" name="dAMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dca_p" name="Decanoate (n-C10:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H19O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dcmp_p" name="dCMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N3O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dcyt_p" name="Deoxycytidine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H13N3O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ddca_p" name="Dodecanoate (n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H23O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_dgmp_p" name="dGMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dgsn_p" name="Deoxyguanosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dha_p" name="Dihydroxyacetone" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dimp_p" name="dIMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O7P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_din_p" name="Deoxyinosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O4</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dms_p" name="Dimethyl sulfide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dmso_p" name="Dimethyl sulfoxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6OS</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dopa_p" name="Dopamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12NO2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_doxrbcn_p" name="doxorubicin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H29NO11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbaox_p" name="periplasmic protein disulfide isomerase I (oxidized)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbard_p" name="periplasmic protein disulfide isomerase I (reduced)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbcox_p" name="protein disulfide isomerase II (oxidized)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbcrd_p" name="protein disulfide isomerase II (reduced)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbgox_p" name="periplasmic disulfide isomerase/thiol-disulphide oxidase (oxidized)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: X</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dsbgrd_p" name="periplasmic disulfide isomerase/thiol-disulphide oxidase (reduced)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XH2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_dtmp_p" name="dTMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_dump_p" name="dUMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_duri_p" name="Deoxyuridine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_eca2und_p" name="(enterobacterial common antigen)x2 undecaprenyl-diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C103H162N6O37P2</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_eca3und_p" name="(enterobacterial common antigen)x3 undecaprenyl-diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C127H198N9O52P2</p>
- <p>CHARGE: -5</p>
- </body>
- </notes>
- </species>
- <species id="M_eca4colipa_p" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C272H447N14O160P4</p>
- <p>CHARGE: -15</p>
- </body>
- </notes>
- </species>
- <species id="M_eca4und_p" name="(enterobacterial common antigen)x4 undecaprenyl-diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C151H234N12O67P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_enlipa_p" name="phosphoethanolamine KDO(2)-lipid (A)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C112H202N3O42P3</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_enter_p" name="Enterochelin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27N3O15</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_etha_p" name="Ethanolamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H8NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ethso3_p" name="ethanesulfonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_etoh_p" name="Ethanol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_f6p_p" name="D-Fructose 6-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fald_p" name="Formaldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fe2_p" name="Fe2+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3_p" name="Fe3+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Fe</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3dcit_p" name="Fe(III)dicitrate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H10FeO14</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3dhbzs_p" name="ferric 2,3-dihydroxybenzoylserine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H10NO6Fe</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_p" name="Fe(III)hydroxamate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3Fe</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fe3hox_DASH_un_p" name="Fe(III)hydoxamate, unloaded" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O6N3</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_p" name="Ferrichrome" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42FeN9O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fecrm_DASH_un_p" name="Ferrichrome minus Fe(III)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H42N9O12</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_feenter_p" name="Fe-enterobactin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H27FeN3O15</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_p" name="ferroxamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46FeN6O8</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_feoxam_DASH_un_p" name="ferroxamine minus Fe(3)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C25H46N6O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_for_p" name="Formate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH1O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fru_p" name="D-Fructose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_frulys_p" name="fructoselysine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_fruur_p" name="D-Fructuronate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_fuc_DASH_L_p" name="L-Fucose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_fum_p" name="Fumarate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H2O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_fusa_p" name="fusidic acid" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H48O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g1p_p" name="D-Glucose 1-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pc_p" name="sn-Glycero-3-phosphocholine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H20NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pe_p" name="sn-Glycero-3-phosphoethanolamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H14NO6P</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pg_p" name="Glycerophosphoglycerol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3pi_p" name="sn-Glycero-3-phospho-1-inositol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H18O11P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g3ps_p" name="Glycerophosphoserine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_g6p_p" name="D-Glucose 6-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gal_p" name="D-Galactose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gal_DASH_bD_p" name="beta D-Galactose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gal1p_p" name="alpha-D-Galactose 1-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galct_DASH_D_p" name="D-Galactarate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_D_p" name="D-Galactonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galctn_DASH_L_p" name="L-Galactonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_galt_p" name="Galactitol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_galur_p" name="D-Galacturonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam_p" name="D-Glucosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14NO5</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_gam6p_p" name="D-Glucosamine 6-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gbbtn_p" name="gamma-butyrobetaine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H15NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gdp_p" name="GDP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O11P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_glc_DASH_D_p" name="D-Glucose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glcn_p" name="D-Gluconate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glcr_p" name="D-Glucarate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O8</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glcur_p" name="D-Glucuronate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glcur1p_p" name="D-Glucuronate 1-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H8O10P</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_gln_DASH_L_p" name="L-Glutamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glu_DASH_L_p" name="L-Glutamate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H8NO4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gly_p" name="Glycine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyald_p" name="D-Glyceraldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyb_p" name="Glycine betaine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_p" name="Glycerol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H8O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc_DASH_R_p" name="(R)-Glycerate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc2p_p" name="Glycerol 2-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyc3p_p" name="Glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7O6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_glyclt_p" name="Glycolate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gmp_p" name="GMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gsn_p" name="Guanosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H13N5O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_gthox_p" name="Oxidized glutathione" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C20H30N6O12S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_gthrd_p" name="Reduced glutathione" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H16N3O6S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_gtp_p" name="GTP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N5O14P3</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_gua_p" name="Guanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H5N5O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h_p" name="H+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_h2_p" name="H2" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o_p" name="H2O" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2o2_p" name="Hydrogen peroxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_h2s_p" name="Hydrogen sulfide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hdca_p" name="Hexadecanoate (n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H31O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hdcea_p" name="Hexadecenoate (n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C16H29O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hg2_p" name="Hg2+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Hg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_his_DASH_L_p" name="L-Histidine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H9N3O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hom_DASH_L_p" name="L-Homoserine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_hxa_p" name="Hexanoate (n-C6:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_hxan_p" name="Hypoxanthine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_idon_DASH_L_p" name="L-Idonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O7</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ile_DASH_L_p" name="L-Isoleucine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_imp_p" name="IMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_indole_p" name="Indole" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H7N</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_inost_p" name="myo-Inositol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ins_p" name="Inosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_isetac_p" name="Isethionic acid" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H5O4S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_k_p" name="potassium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: K</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_kdo2lipid4_p" name="KDO(2)-lipid IV(A)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C84H148N2O37P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_D_p" name="D-Lactate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lac_DASH_L_p" name="L-Lactate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_lcts_p" name="Lactose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_leu_DASH_L_p" name="L-Leucine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H13NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_p" name="KDO(2)-lipid (A)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C110H196N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipa_cold_p" name="cold adapted KDO(2)-lipid (A)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C114H202N2O39P2</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_lipoate_p" name="Lipoate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H14O2S2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lpp_p" name="lipoprotein" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: XC16H30O1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_lys_DASH_L_p" name="L-Lysine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H15N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_lyx_DASH_L_p" name="L-Lyxose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_D_p" name="D-Malate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mal_DASH_L_p" name="L-Malate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O5</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_malt_p" name="Maltose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malthx_p" name="Maltohexaose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C36H62O31</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltpt_p" name="Maltopentaose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H52O26</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_malttr_p" name="Maltotriose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H32O16</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_maltttr_p" name="Maltotetraose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C24H42O21</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man_p" name="D-Mannose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_man6p_p" name="D-Mannose 6-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H11O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_manglyc_p" name="2(alpha-D-Mannosyl)-D-glycerate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H15O9</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_melib_p" name="Melibiose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_meoh_p" name="Methanol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4O1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_D_p" name="D-Methionine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_met_DASH_L_p" name="L-Methionine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_R_DASH_L_p" name="L-methionine-R-sulfoxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_metsox_DASH_S_DASH_L_p" name="L-Methionine Sulfoxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mg2_p" name="magnesium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mg</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mincyc_p" name="minocycline" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C23H27N3O7</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_minohp_p" name="myo-Inositol hexakisphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H6O24P6</p>
- <p>CHARGE: -12</p>
- </body>
- </notes>
- </species>
- <species id="M_mmet_p" name="S-Methyl-L-methionine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14NO2S</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_mn2_p" name="Mn2+" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Mn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_mnl_p" name="D-Mannitol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_mobd_p" name="Molybdate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: MoO4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_mso3_p" name="methanesulfonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH3O3S</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_murein3p3p_p" name="two linked disacharide tripeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C68H104N12O38</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein3px3p_p" name="two disacharide linked murein units, tripeptide crosslinked tripeptide (A2pm->A2pm) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C68H102N12O37</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein3px4p_p" name="two disacharide linked murein units, tripeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C71H107N13O38</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein4p3p_p" name="two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C71H109N13O39</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein4p4p_p" name="two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C74H114N14O40</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein4px4p_p" name="two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C74H112N14O39</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein4px4p4p_p" name="three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala), one uncrosslinked tetrapaptide) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C111H169N21O59</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_murein4px4px4p_p" name="three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C111H167N21O58</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5p3p_p" name="two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C74H114N14O40</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5p4p_p" name="two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C77H119N15O41</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5p5p_p" name="two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C80H124N16O42</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5p5p5p_p" name="three linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C120H186N24O63</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5px3p_p" name="two disacharide linked murein units, pentapeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C74H112N14O39</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5px4p_p" name="two disacharide linked murein units, pentapeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C77H117N15O40</p>
- <p>CHARGE: -4</p>
- </body>
- </notes>
- </species>
- <species id="M_murein5px4px4p_p" name="three disacharide linked murein units (pentapeptide crosslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C114H172N22O59</p>
- <p>CHARGE: -6</p>
- </body>
- </notes>
- </species>
- <species id="M_n2o_p" name="Nitrous oxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_na1_p" name="Sodium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Na</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_nac_p" name="Nicotinate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H4NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_nh4_p" name="Ammonium" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: H4N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_ni2_p" name="nickel" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Ni</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_nmn_p" name="NMN" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H14N2O8P</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no_p" name="Nitric oxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_no2_p" name="Nitrite" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_no3_p" name="Nitrate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: NO3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_novbcn_p" name="novobiocin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H36N2O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_o16a2und_p" name="(O16 antigen)x2 undecaprenyl diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C123H200N2O57P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_o16a3und_p" name="(O16 antigen)x3 undecaprenyl diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C157H255N3O82P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_o16a4colipa_p" name="(O16 antigen)x4 core oligosaccharide lipid A" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C312H523N6O200P4</p>
- <p>CHARGE: -11</p>
- </body>
- </notes>
- </species>
- <species id="M_o16a4und_p" name="(O16 antigen)x4 undecaprenyl diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C191H310N4O107P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_o16aund_p" name="O16 antigen undecaprenyl diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C89H145N1O32P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_o2_p" name="O2" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_o2s_p" name="Superoxide anion" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdca_p" name="octadecanoate (n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H35O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ocdcea_p" name="octadecenoate (n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C18H33O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_octa_p" name="octanoate (n-C8:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H15O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_orn_p" name="Ornithine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_orot_p" name="Orotate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H3N2O4</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pa120_p" name="1,2-didodecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C27H51O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa140_p" name="1,2-ditetradecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H59O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa141_p" name="1,2-ditetradec-7-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C31H55O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa160_p" name="1,2-dihexadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H67O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa161_p" name="1,2-dihexadec-9-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C35H63O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa180_p" name="1,2-dioctadecanoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H75O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pa181_p" name="1,2-dioctadec-11-enoyl-sn-glycerol 3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C39H71O8P1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pacald_p" name="Phenylacetaldehyde" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H8O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe120_p" name="phosphatidylethanolamine (didodecanoyl, n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C29H58N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe140_p" name="phosphatidylethanolamine (ditetradecanoyl, n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H66N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe141_p" name="phosphatidylethanolamine (ditetradec-7-enoyl, n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C33H62N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe160_p" name="phosphatidylethanolamine (dihexadecanoyl, n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H74N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe161_p" name="phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C37H70N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe180_p" name="phosphatidylethanolamine (dioctadecanoyl, n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C41H82N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pe181_p" name="phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C41H78N1O8P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_peamn_p" name="Phenethylamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg120_p" name="Phosphatidylglycerol (didodecanoyl, n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H58O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg140_p" name="Phosphatidylglycerol (ditetradecanoyl, n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H66O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg141_p" name="Phosphatidylglycerol (ditetradec-7-enoyl, n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H62O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg160_p" name="Phosphatidylglycerol (dihexadecanoyl, n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H74O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg161_p" name="Phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H70O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg180_p" name="Phosphatidylglycerol (dioctadecanoyl, n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H82O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pg181_p" name="Phosphatidylglycerol (dioctadec-11-enoyl, n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H78O10P1</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp120_p" name="Phosphatidylglycerophosphate (didodecanoyl, n-C12:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C30H57O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp140_p" name="Phosphatidylglycerophosphate (ditetradecanoyl, n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H65O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp141_p" name="Phosphatidylglycerophosphate (ditetradec-7-enoyl, n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H61O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp160_p" name="Phosphatidylglycerophosphate (dihexadecanoyl, n-C16:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H73O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp161_p" name="Phosphatidylglycerophosphate (dihexadec-9-enoyl, n-C16:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C38H69O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp180_p" name="Phosphatidylglycerophosphate (dioctadecanoyl, n-C18:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H81O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_pgp181_p" name="Phosphatidylglycerophosphate (dioctadec-11-enoyl, n-C18:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C42H77O13P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_phe_DASH_L_p" name="L-Phenylalanine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pheme_p" name="Protoheme" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C34H30FeN4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pi_p" name="Phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pnto_DASH_R_p" name="(R)-Pantothenate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H16NO5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppa_p" name="Propionate (n-C3:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H5O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppal_p" name="Propanal" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pppn_p" name="Phenylpropanoate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H9O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ppt_p" name="Phosphonate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: HO3P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_pro_DASH_L_p" name="L-Proline" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_progly_p" name="L-Prolinylglycine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12N2O3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_psclys_p" name="psicoselysine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H25N2O7</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pser_DASH_L_p" name="O-Phospho-L-serine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H6NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ptrc_p" name="Putrescine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H14N2</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- <species id="M_pydam_p" name="Pyridoxamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H13N2O2</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_pydx_p" name="Pyridoxal" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pydxn_p" name="Pyridoxine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_pyr_p" name="Pyruvate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H3O3</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_quin_p" name="Quinate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H12O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_r5p_p" name="alpha-D-Ribose 5-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H9O8P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_rfamp_p" name="rifampin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C43H58N4O12</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rib_DASH_D_p" name="D-Ribose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_rmn_p" name="L-Rhamnose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H12O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sbt_DASH_D_p" name="D-Sorbitol" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C6H14O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sel_p" name="Selenate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_D_p" name="D-Serine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_ser_DASH_L_p" name="L-Serine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H7NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_skm_p" name="Shikimate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H9O5</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_slnt_p" name="selenite" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3Se</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so2_p" name="sulfur dioxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O2S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_so3_p" name="Sulfite" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_so4_p" name="Sulfate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_spmd_p" name="Spermidine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C7H22N3</p>
- <p>CHARGE: 3</p>
- </body>
- </notes>
- </species>
- <species id="M_succ_p" name="Succinate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O4</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_sucr_p" name="Sucrose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_sulfac_p" name="sulfoacetate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H2O5S</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_D_p" name="D-tartrate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tartr_DASH_L_p" name="L-tartrate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4O6</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_taur_p" name="Taurine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C2H7NO3S</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tcynt_p" name="Thiocyanate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CNS</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_thm_p" name="Thiamin" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H17N4OS</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_thr_DASH_L_p" name="L-Threonine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H9NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thrp_p" name="L-Threonine O-3-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H8NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_thym_p" name="Thymine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H6N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_thymd_p" name="Thymidine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H14N2O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tma_p" name="trimethylamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H10N</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tmao_p" name="Trimethylamine N-oxide" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C3H9NO</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tre_p" name="Trehalose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C12H22O11</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_trp_DASH_L_p" name="L-Tryptophan" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C11H12N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tsul_p" name="Thiosulfate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O3S2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdca_p" name="tetradecanoate (n-C14:0)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H27O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttdcea_p" name="tetradecenoate (n-C14:1)" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C14H25O2</p>
- <p>CHARGE: -1</p>
- </body>
- </notes>
- </species>
- <species id="M_ttrcyc_p" name="tetracycline" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C22H24N2O8</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tungs_p" name="tungstate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: O4W1</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_tym_p" name="Tyramine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C8H12NO</p>
- <p>CHARGE: 1</p>
- </body>
- </notes>
- </species>
- <species id="M_tyr_DASH_L_p" name="L-Tyrosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11NO3</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_tyrp_p" name="Phosphotyrosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H10NO6P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_uLa4n_p" name="undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C60H100N1O7P1</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uacgam_p" name="UDP-N-acetyl-D-glucosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udcpdp_p" name="Undecaprenyl diphosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C55H89O7P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_udcpp_p" name="Undecaprenyl phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C55H89O4P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpacgal_p" name="UDP-N-acetyl-D-galactosamine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C17H25N3O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpg_p" name="UDPglucose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpgal_p" name="UDPgalactose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H22N2O17P2</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_udpglcur_p" name="UDP-D-glucuronate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C15H19N2O18P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ump_p" name="UMP" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H11N2O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_unagamuf_p" name="Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C79H126N3O22P2</p>
- <p>CHARGE: -3</p>
- </body>
- </notes>
- </species>
- <species id="M_ura_p" name="Uracil" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C4H4N2O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_urea_p" name="Urea" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: CH4N2O</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_uri_p" name="Uridine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C9H12N2O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_val_DASH_L_p" name="L-Valine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H11NO2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xan_p" name="Xanthine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H4N4O2</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xmp_p" name="Xanthosine 5'-phosphate" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H11N4O9P</p>
- <p>CHARGE: -2</p>
- </body>
- </notes>
- </species>
- <species id="M_xtsn_p" name="Xanthosine" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C10H12N4O6</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xyl_DASH_D_p" name="D-Xylose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_xylu_DASH_L_p" name="L-Xylulose" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: C5H10O5</p>
- <p>CHARGE: 0</p>
- </body>
- </notes>
- </species>
- <species id="M_zn2_p" name="Zinc" compartment="p">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>FORMULA: Zn</p>
- <p>CHARGE: 2</p>
- </body>
- </notes>
- </species>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="R_DM_4CRSOL" name="Sink needed to allow p-Cresol to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_4crsol_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DM_5DRIB" name="Sink needed to allow 5'-deoxyribose to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5drib_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DM_AACALD" name="Sink needed to allow aminoacetaldehyde to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_aacald_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DM_AMOB" name="Sink needed to allow S-Adenosyl-4-methylthio-2-oxobutanoate to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_amob_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DM_MTHTHF" name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mththf_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DM_OXAM" name="Sink needed to allow oxamate to leave system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_oxam_c"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_Ec_biomass_iJO1366_WT_53p95M" name="E. coli biomass objective function (iJO1366) - WT - with 53.95 GAM estimate" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_10fthf_c" stoichiometry="0.000223"/>
- <speciesReference species="M_2dmmql8_c" stoichiometry="0.000223"/>
- <speciesReference species="M_2fe2s_c" stoichiometry="2.5e-005"/>
- <speciesReference species="M_4fe4s_c" stoichiometry="0.000248"/>
- <speciesReference species="M_5mthf_c" stoichiometry="0.000223"/>
- <speciesReference species="M_accoa_c" stoichiometry="0.000279"/>
- <speciesReference species="M_adocbl_c" stoichiometry="0.000223"/>
- <speciesReference species="M_ala_DASH_L_c" stoichiometry="0.499149"/>
- <speciesReference species="M_amet_c" stoichiometry="0.000223"/>
- <speciesReference species="M_arg_DASH_L_c" stoichiometry="0.28742"/>
- <speciesReference species="M_asn_DASH_L_c" stoichiometry="0.234232"/>
- <speciesReference species="M_asp_DASH_L_c" stoichiometry="0.234232"/>
- <speciesReference species="M_atp_c" stoichiometry="54.119975"/>
- <speciesReference species="M_bmocogdp_c" stoichiometry="0.000116"/>
- <speciesReference species="M_btn_c" stoichiometry="2e-006"/>
- <speciesReference species="M_ca2_c" stoichiometry="0.004952"/>
- <speciesReference species="M_chor_c" stoichiometry="0.000223"/>
- <speciesReference species="M_cl_c" stoichiometry="0.004952"/>
- <speciesReference species="M_coa_c" stoichiometry="0.000168"/>
- <speciesReference species="M_cobalt2_c" stoichiometry="2.4e-005"/>
- <speciesReference species="M_ctp_c" stoichiometry="0.129799"/>
- <speciesReference species="M_cu2_c" stoichiometry="0.000674"/>
- <speciesReference species="M_cys_DASH_L_c" stoichiometry="0.088988"/>
- <speciesReference species="M_datp_c" stoichiometry="0.024805"/>
- <speciesReference species="M_dctp_c" stoichiometry="0.025612"/>
- <speciesReference species="M_dgtp_c" stoichiometry="0.025612"/>
- <speciesReference species="M_dttp_c" stoichiometry="0.024805"/>
- <speciesReference species="M_enter_c" stoichiometry="0.000223"/>
- <speciesReference species="M_fad_c" stoichiometry="0.000223"/>
- <speciesReference species="M_fe2_c" stoichiometry="0.006388"/>
- <speciesReference species="M_fe3_c" stoichiometry="0.007428"/>
- <speciesReference species="M_gln_DASH_L_c" stoichiometry="0.255712"/>
- <speciesReference species="M_glu_DASH_L_c" stoichiometry="0.255712"/>
- <speciesReference species="M_gly_c" stoichiometry="0.595297"/>
- <speciesReference species="M_glycogen_c" stoichiometry="0.154187"/>
- <speciesReference species="M_gthrd_c" stoichiometry="0.000223"/>
- <speciesReference species="M_gtp_c" stoichiometry="0.209121"/>
- <speciesReference species="M_h2o_c" stoichiometry="48.752916"/>
- <speciesReference species="M_hemeO_c" stoichiometry="0.000223"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_2fe2s_c" stoichiometry="2.6e-005"/>
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- <listOfProducts>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="1" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_12ppd_DASH_R_LPAREN_e_RPAREN_" name="(R)-Propane-1,2-diol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12ppd_DASH_R_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_12ppd_DASH_S_LPAREN_e_RPAREN_" name="(S)-Propane-1,2-diol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12ppd_DASH_S_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_14glucan_LPAREN_e_RPAREN_" name="1,4-alpha-D-glucan exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_14glucan_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_15dap_LPAREN_e_RPAREN_" name="1,5-Diaminopentane exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_15dap_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_23camp_LPAREN_e_RPAREN_" name="2',3'-Cyclic AMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23camp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_23ccmp_LPAREN_e_RPAREN_" name="2',3'-Cyclic CMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23ccmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_23cgmp_LPAREN_e_RPAREN_" name="2',3'-Cyclic GMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23cgmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_23cump_LPAREN_e_RPAREN_" name="2',3'-Cyclic UMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23cump_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_23dappa_LPAREN_e_RPAREN_" name="2,3-diaminopropionate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23dappa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_26dap_DASH_M_LPAREN_e_RPAREN_" name="meso-2,6-Diaminoheptanedioate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_26dap_DASH_M_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_2ddglcn_LPAREN_e_RPAREN_" name="2-Dehydro-3-deoxy-D-gluconate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2ddglcn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_34dhpac_LPAREN_e_RPAREN_" name="3,4-Dihydroxyphenylacetaldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_34dhpac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3amp_LPAREN_e_RPAREN_" name="3'-AMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3amp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3cmp_LPAREN_e_RPAREN_" name="3'-cmp exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3cmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3gmp_LPAREN_e_RPAREN_" name="3'-GMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3gmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3hcinnm_LPAREN_e_RPAREN_" name="3-hydroxycinnamic acid exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hcinnm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3hpp_LPAREN_e_RPAREN_" name="3-Hydroxypropanoate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hpp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3hpppn_LPAREN_e_RPAREN_" name="3-(3-hydroxy-phenyl)propionate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hpppn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_3ump_LPAREN_e_RPAREN_" name="3'-UMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ump_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_4abut_LPAREN_e_RPAREN_" name="4-Aminobutanoate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_4abut_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_4hoxpacd_LPAREN_e_RPAREN_" name="4-Hydroxyphenylacetaldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_4hoxpacd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_5dglcn_LPAREN_e_RPAREN_" name="5-Dehydro-D-gluconate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5dglcn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_5mtr_LPAREN_e_RPAREN_" name="5-Methylthio-D-ribose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5mtr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_LalaDglu_LPAREN_e_RPAREN_" name="L-alanine-D-glutamate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDglu_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_LalaDgluMdap_LPAREN_e_RPAREN_" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDgluMdap_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_LalaDgluMdapDala_LPAREN_e_RPAREN_" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDgluMdapDala_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_LalaLglu_LPAREN_e_RPAREN_" name="L-alanine-L-glutamate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaLglu_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ac_LPAREN_e_RPAREN_" name="Acetate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acac_LPAREN_e_RPAREN_" name="Acetoacetate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acald_LPAREN_e_RPAREN_" name="Acetaldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acald_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acgal_LPAREN_e_RPAREN_" name="N-Acetyl-D-galactosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acgal_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acgal1p_LPAREN_e_RPAREN_" name="N-Acetyl-D-galactosamine 1-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acgal1p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acgam_LPAREN_e_RPAREN_" name="N-Acetyl-D-glucosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acgam_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acgam1p_LPAREN_e_RPAREN_" name="N-Acetyl-D-glucosamine 1-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acgam1p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acmana_LPAREN_e_RPAREN_" name="N-Acetyl-D-mannosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acmana_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acmum_LPAREN_e_RPAREN_" name="N-Acetylmuramate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acmum_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acnam_LPAREN_e_RPAREN_" name="N-Acetylneuraminate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acnam_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acolipa_LPAREN_e_RPAREN_" name="4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acolipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_acser_LPAREN_e_RPAREN_" name="O-Acetyl-L-serine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acser_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ade_LPAREN_e_RPAREN_" name="Adenine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ade_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_adn_LPAREN_e_RPAREN_" name="Adenosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_adocbl_LPAREN_e_RPAREN_" name="Adenosylcobalamin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adocbl_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ag_LPAREN_e_RPAREN_" name="silver exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ag_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_agm_LPAREN_e_RPAREN_" name="Agmatine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_agm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_akg_LPAREN_e_RPAREN_" name="2-Oxoglutarate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_akg_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ala_DASH_B_LPAREN_e_RPAREN_" name="beta-Alanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_B_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ala_DASH_D_LPAREN_e_RPAREN_" name="D-Alanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ala_DASH_L_LPAREN_e_RPAREN_" name="L-Alanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_alaala_LPAREN_e_RPAREN_" name="D-Alanyl-D-alanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alaala_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_all_DASH_D_LPAREN_e_RPAREN_" name="D-Allose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_all_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_alltn_LPAREN_e_RPAREN_" name="Allantoin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alltn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_amp_LPAREN_e_RPAREN_" name="AMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_amp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_anhgm_LPAREN_e_RPAREN_" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_arab_DASH_L_LPAREN_e_RPAREN_" name="L-Arabinose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_arab_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_arbt_LPAREN_e_RPAREN_" name="Arbutin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_arbt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_arbtn_LPAREN_e_RPAREN_" name="aerobactin minus Fe3 exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_arbtn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_arbtn_DASH_fe3_LPAREN_e_RPAREN_" name="Aerobactin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_arbtn_DASH_fe3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_arg_DASH_L_LPAREN_e_RPAREN_" name="L-Arginine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_arg_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ascb_DASH_L_LPAREN_e_RPAREN_" name="L-Ascorbate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ascb_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_asn_DASH_L_LPAREN_e_RPAREN_" name="L-Asparagine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_asn_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_aso3_LPAREN_e_RPAREN_" name="arsenite exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_aso3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_asp_DASH_L_LPAREN_e_RPAREN_" name="L-Aspartate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_asp_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_btn_LPAREN_e_RPAREN_" name="Biotin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_btn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_but_LPAREN_e_RPAREN_" name="Butyrate (n-C4:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_but_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_butso3_LPAREN_e_RPAREN_" name="butanesulfonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_butso3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ca2_LPAREN_e_RPAREN_" name="Calcium exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ca2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cbi_LPAREN_e_RPAREN_" name="Cobinamide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cbi_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cbl1_LPAREN_e_RPAREN_" name="Cob(I)alamin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cbl1_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-0.01" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cd2_LPAREN_e_RPAREN_" name="Cadmium exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cd2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cgly_LPAREN_e_RPAREN_" name="Cys-Gly exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cgly_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_chol_LPAREN_e_RPAREN_" name="Choline exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_chol_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_chtbs_LPAREN_e_RPAREN_" name="chitobiose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_chtbs_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cit_LPAREN_e_RPAREN_" name="Citrate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cit_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cl_LPAREN_e_RPAREN_" name="Chloride exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cl_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cm_LPAREN_e_RPAREN_" name="Chloramphenicol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cmp_LPAREN_e_RPAREN_" name="CMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_co2_LPAREN_e_RPAREN_" name="CO2 exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_co2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cobalt2_LPAREN_e_RPAREN_" name="Co2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cobalt2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_colipa_LPAREN_e_RPAREN_" name="core oligosaccharide lipid A exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_colipap_LPAREN_e_RPAREN_" name="core oligosaccharide lipid A diphosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipap_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cpgn_LPAREN_e_RPAREN_" name="coprogen exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cpgn_DASH_un_LPAREN_e_RPAREN_" name="coprogen unloaded (no Fe(III)) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_DASH_un_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_crn_LPAREN_e_RPAREN_" name="L-Carnitine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_crn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_crn_DASH_D_LPAREN_e_RPAREN_" name="D-carnitine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_crn_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_csn_LPAREN_e_RPAREN_" name="Cytosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_csn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cu_LPAREN_e_RPAREN_" name="Cu+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cu_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cu2_LPAREN_e_RPAREN_" name="Cu2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cu2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cyan_LPAREN_e_RPAREN_" name="Hydrogen cyanide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cyan_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cynt_LPAREN_e_RPAREN_" name="Cyanate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cynt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cys_DASH_D_LPAREN_e_RPAREN_" name="D-Cysteine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cys_DASH_L_LPAREN_e_RPAREN_" name="L-Cysteine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_cytd_LPAREN_e_RPAREN_" name="Cytidine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cytd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dad_DASH_2_LPAREN_e_RPAREN_" name="Deoxyadenosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dad_DASH_2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_damp_LPAREN_e_RPAREN_" name="dAMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_damp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dca_LPAREN_e_RPAREN_" name="Decanoate (n-C10:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dca_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dcmp_LPAREN_e_RPAREN_" name="dCMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dcmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dcyt_LPAREN_e_RPAREN_" name="Deoxycytidine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dcyt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ddca_LPAREN_e_RPAREN_" name="Dodecanoate (n-C12:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ddca_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dgmp_LPAREN_e_RPAREN_" name="dGMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dgmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dgsn_LPAREN_e_RPAREN_" name="Deoxyguanosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dgsn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dha_LPAREN_e_RPAREN_" name="Dihydroxyacetone exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dha_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dimp_LPAREN_e_RPAREN_" name="dIMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dimp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_din_LPAREN_e_RPAREN_" name="Deoxyinosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_din_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dms_LPAREN_e_RPAREN_" name="Dimethyl sulfide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dms_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dmso_LPAREN_e_RPAREN_" name="Dimethyl sulfoxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dmso_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dopa_LPAREN_e_RPAREN_" name="Dopamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dopa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_doxrbcn_LPAREN_e_RPAREN_" name="doxorubicin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_doxrbcn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dtmp_LPAREN_e_RPAREN_" name="dTMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dtmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_dump_LPAREN_e_RPAREN_" name="dUMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dump_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_duri_LPAREN_e_RPAREN_" name="Deoxyuridine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_duri_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_eca4colipa_LPAREN_e_RPAREN_" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_eca4colipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_enlipa_LPAREN_e_RPAREN_" name="phosphoethanolamine KDO(2)-lipid (A) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_enlipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_enter_LPAREN_e_RPAREN_" name="Enterochelin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_enter_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_etha_LPAREN_e_RPAREN_" name="Ethanolamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_etha_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ethso3_LPAREN_e_RPAREN_" name="ethanesulfonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ethso3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_etoh_LPAREN_e_RPAREN_" name="Ethanol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_etoh_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_f6p_LPAREN_e_RPAREN_" name="D-fructose 6-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_f6p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fald_LPAREN_e_RPAREN_" name="Formaldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fald_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe2_LPAREN_e_RPAREN_" name="Fe2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe3_LPAREN_e_RPAREN_" name="Fe3+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe3dcit_LPAREN_e_RPAREN_" name="Fe(III)dicitrate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3dcit_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe3dhbzs_LPAREN_e_RPAREN_" name="ferric 2,3-dihydroxybenzoylserine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3dhbzs_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe3hox_LPAREN_e_RPAREN_" name="Fe(III)hydroxamate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fe3hox_DASH_un_LPAREN_e_RPAREN_" name="Fe(III)hydoxamate, unloaded exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_DASH_un_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fecrm_LPAREN_e_RPAREN_" name="Ferrichrome exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fecrm_DASH_un_LPAREN_e_RPAREN_" name="Ferrichrome minus Fe(III) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_DASH_un_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_feenter_LPAREN_e_RPAREN_" name="Fe-enterobactin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_feenter_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_feoxam_LPAREN_e_RPAREN_" name="ferroxamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_feoxam_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_feoxam_DASH_un_LPAREN_e_RPAREN_" name="ferroxamine minus Fe(3) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_feoxam_DASH_un_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_for_LPAREN_e_RPAREN_" name="Formate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_for_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fru_LPAREN_e_RPAREN_" name="D-Fructose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fru_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_frulys_LPAREN_e_RPAREN_" name="fructoselysine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_frulys_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fruur_LPAREN_e_RPAREN_" name="D-Fructuronate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fruur_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fuc_DASH_L_LPAREN_e_RPAREN_" name="L-Fucose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fuc_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fum_LPAREN_e_RPAREN_" name="Fumarate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fum_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_fusa_LPAREN_e_RPAREN_" name="fusidic acid exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fusa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g1p_LPAREN_e_RPAREN_" name="D-Glucose 1-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g1p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g3pc_LPAREN_e_RPAREN_" name="sn-Glycero-3-phosphocholine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g3pe_LPAREN_e_RPAREN_" name="sn-Glycero-3-phosphoethanolamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pe_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g3pg_LPAREN_e_RPAREN_" name="Glycerophosphoglycerol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pg_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g3pi_LPAREN_e_RPAREN_" name="sn-Glycero-3-phospho-1-inositol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pi_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g3ps_LPAREN_e_RPAREN_" name="Glycerophosphoserine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3ps_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_g6p_LPAREN_e_RPAREN_" name="D-Glucose 6-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g6p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gal_LPAREN_e_RPAREN_" name="D-Galactose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gal_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gal_DASH_bD_LPAREN_e_RPAREN_" name="beta D-Galactose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gal_DASH_bD_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gal1p_LPAREN_e_RPAREN_" name="alpha-D-Galactose 1-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gal1p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_galct_DASH_D_LPAREN_e_RPAREN_" name="D-Galactarate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galct_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_galctn_DASH_D_LPAREN_e_RPAREN_" name="D-Galactonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_galctn_DASH_L_LPAREN_e_RPAREN_" name="L-Galactonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_EX_galt_LPAREN_e_RPAREN_" name="Galactitol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galt_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_galur_LPAREN_e_RPAREN_" name="D-Galacturonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galur_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gam_LPAREN_e_RPAREN_" name="D-Glucosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gam_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gam6p_LPAREN_e_RPAREN_" name="D-Glucosamine 6-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gam6p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gbbtn_LPAREN_e_RPAREN_" name="gamma-butyrobetaine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gbbtn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gdp_LPAREN_e_RPAREN_" name="GDP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gdp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glc_LPAREN_e_RPAREN_" name="D-Glucose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glc_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-10" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glcn_LPAREN_e_RPAREN_" name="D-Gluconate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glcr_LPAREN_e_RPAREN_" name="D-Glucarate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glcur_LPAREN_e_RPAREN_" name="D-Glucuronate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcur_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glcur1p_LPAREN_e_RPAREN_" name="D-Glucuronate 1-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcur1p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gln_DASH_L_LPAREN_e_RPAREN_" name="L-Glutamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gln_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glu_DASH_L_LPAREN_e_RPAREN_" name="L-Glutamate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glu_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gly_LPAREN_e_RPAREN_" name="Glycine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gly_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyald_LPAREN_e_RPAREN_" name="D-Glyceraldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyald_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyb_LPAREN_e_RPAREN_" name="Glycine betaine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyb_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyc_LPAREN_e_RPAREN_" name="Glycerol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyc_DASH_R_LPAREN_e_RPAREN_" name="(R)-Glycerate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc_DASH_R_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyc2p_LPAREN_e_RPAREN_" name="Glycerol 2-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc2p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyc3p_LPAREN_e_RPAREN_" name="Glycerol 3-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc3p_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_EX_glyclt_LPAREN_e_RPAREN_" name="Glycolate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyclt_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gmp_LPAREN_e_RPAREN_" name="GMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gmp_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gsn_LPAREN_e_RPAREN_" name="Guanosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gsn_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gthox_LPAREN_e_RPAREN_" name="Oxidized glutathione exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthox_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gthrd_LPAREN_e_RPAREN_" name="Reduced glutathione exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthrd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gtp_LPAREN_e_RPAREN_" name="GTP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gtp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_gua_LPAREN_e_RPAREN_" name="Guanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gua_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_h_LPAREN_e_RPAREN_" name="H+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_h2_LPAREN_e_RPAREN_" name="H2 exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_h2o_LPAREN_e_RPAREN_" name="H2O exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_h2o2_LPAREN_e_RPAREN_" name="Hydrogen peroxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_h2s_LPAREN_e_RPAREN_" name="Hydrogen sulfide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2s_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hacolipa_LPAREN_e_RPAREN_" name="hepta-acylated core oligosaccharide lipid A (E. coli) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hacolipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_halipa_LPAREN_e_RPAREN_" name="hepta-acylated KDO(2)-lipid (A) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_halipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hdca_LPAREN_e_RPAREN_" name="Hexadecanoate (n-C16:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hdca_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hdcea_LPAREN_e_RPAREN_" name="hexadecenoate (n-C16:1) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hdcea_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hg2_LPAREN_e_RPAREN_" name="Hg2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hg2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_his_DASH_L_LPAREN_e_RPAREN_" name="L-Histidine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_his_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hom_DASH_L_LPAREN_e_RPAREN_" name="L-Homoserine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hom_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hxa_LPAREN_e_RPAREN_" name="Hexanoate (n-C6:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hxa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_hxan_LPAREN_e_RPAREN_" name="Hypoxanthine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hxan_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_idon_DASH_L_LPAREN_e_RPAREN_" name="L-Idonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_idon_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ile_DASH_L_LPAREN_e_RPAREN_" name="L-Isoleucine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ile_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_imp_LPAREN_e_RPAREN_" name="IMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_imp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_indole_LPAREN_e_RPAREN_" name="Indole exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_indole_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_inost_LPAREN_e_RPAREN_" name="myo-Inositol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_inost_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ins_LPAREN_e_RPAREN_" name="Inosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ins_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_isetac_LPAREN_e_RPAREN_" name="Isethionic acid exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_isetac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_k_LPAREN_e_RPAREN_" name="K+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_k_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_kdo2lipid4_LPAREN_e_RPAREN_" name="KDO(2)-lipid IV(A) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_kdo2lipid4_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lac_DASH_D_LPAREN_e_RPAREN_" name="D-lactate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lac_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lac_DASH_L_LPAREN_e_RPAREN_" name="L-Lactate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lac_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lcts_LPAREN_e_RPAREN_" name="Lactose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lcts_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_leu_DASH_L_LPAREN_e_RPAREN_" name="L-Leucine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_leu_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lipa_LPAREN_e_RPAREN_" name="KDO(2)-lipid (A) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lipa_cold_LPAREN_e_RPAREN_" name="cold adapted KDO(2)-lipid (A) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipa_cold_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lipoate_LPAREN_e_RPAREN_" name="Lipoate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipoate_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lys_DASH_L_LPAREN_e_RPAREN_" name="L-Lysine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lys_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_lyx_DASH_L_LPAREN_e_RPAREN_" name="L-Lyxose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lyx_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mal_DASH_D_LPAREN_e_RPAREN_" name="D-Malate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mal_DASH_L_LPAREN_e_RPAREN_" name="L-Malate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_malt_LPAREN_e_RPAREN_" name="Maltose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_malthx_LPAREN_e_RPAREN_" name="Maltohexaose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malthx_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_maltpt_LPAREN_e_RPAREN_" name="Maltopentaose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_maltpt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_malttr_LPAREN_e_RPAREN_" name="Maltotriose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malttr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_maltttr_LPAREN_e_RPAREN_" name="Maltotetraose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_maltttr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_man_LPAREN_e_RPAREN_" name="D-Mannose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_man_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_man6p_LPAREN_e_RPAREN_" name="D-Mannose 6-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_man6p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_manglyc_LPAREN_e_RPAREN_" name="2(alpha-D-Mannosyl)-D-glycerate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_manglyc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_melib_LPAREN_e_RPAREN_" name="Melibiose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_melib_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_meoh_LPAREN_e_RPAREN_" name="methanol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_meoh_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_met_DASH_D_LPAREN_e_RPAREN_" name="D-Methionine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_met_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_met_DASH_L_LPAREN_e_RPAREN_" name="L-Methionine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_met_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_metsox_DASH_R_DASH_L_LPAREN_e_RPAREN_" name="L-methionine-R-sulfoxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_metsox_DASH_R_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_metsox_DASH_S_DASH_L_LPAREN_e_RPAREN_" name="L-Methionine S-oxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_metsox_DASH_S_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mg2_LPAREN_e_RPAREN_" name="Mg exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mg2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mincyc_LPAREN_e_RPAREN_" name="minocycline exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mincyc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_minohp_LPAREN_e_RPAREN_" name="myo-Inositol hexakisphosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_minohp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mmet_LPAREN_e_RPAREN_" name="S-Methyl-L-methionine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mmet_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mn2_LPAREN_e_RPAREN_" name="Mn2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mn2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mnl_LPAREN_e_RPAREN_" name="D-Mannitol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mnl_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mobd_LPAREN_e_RPAREN_" name="Molybdate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mobd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_mso3_LPAREN_e_RPAREN_" name="methanesulfonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mso3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_n2o_LPAREN_e_RPAREN_" name="Nitrous oxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_n2o_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_na1_LPAREN_e_RPAREN_" name="Sodium exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_na1_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_nac_LPAREN_e_RPAREN_" name="Nicotinate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_nh4_LPAREN_e_RPAREN_" name="Ammonia exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nh4_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ni2_LPAREN_e_RPAREN_" name="Ni2+ exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ni2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_nmn_LPAREN_e_RPAREN_" name="NMN exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nmn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_no_LPAREN_e_RPAREN_" name="Nitric oxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_no2_LPAREN_e_RPAREN_" name="Nitrite exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_no3_LPAREN_e_RPAREN_" name="Nitrate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_novbcn_LPAREN_e_RPAREN_" name="novobiocin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_novbcn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_o16a4colipa_LPAREN_e_RPAREN_" name="(O16 antigen)x4 core oligosaccharide lipid A exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_o16a4colipa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_o2_LPAREN_e_RPAREN_" name="O2 exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_o2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_o2s_LPAREN_e_RPAREN_" name="Superoxide anion exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_o2s_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ocdca_LPAREN_e_RPAREN_" name="octadecanoate (n-C18:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ocdca_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ocdcea_LPAREN_e_RPAREN_" name="octadecenoate (n-C18:1) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ocdcea_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_octa_LPAREN_e_RPAREN_" name="octanoate (n-C8:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_octa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_orn_LPAREN_e_RPAREN_" name="Ornithine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_orn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_orot_LPAREN_e_RPAREN_" name="Orotate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_orot_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pacald_LPAREN_e_RPAREN_" name="Phenylacetaldehyde exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pacald_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_peamn_LPAREN_e_RPAREN_" name="Phenethylamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_peamn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_phe_DASH_L_LPAREN_e_RPAREN_" name="L-Phenylalanine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_phe_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pheme_LPAREN_e_RPAREN_" name="Protoheme exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pheme_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pi_LPAREN_e_RPAREN_" name="Phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pi_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pnto_DASH_R_LPAREN_e_RPAREN_" name="(R)-Pantothenate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pnto_DASH_R_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ppa_LPAREN_e_RPAREN_" name="Propionate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ppa_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ppal_LPAREN_e_RPAREN_" name="Propanal exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ppal_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pppn_LPAREN_e_RPAREN_" name="Phenylpropanoate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pppn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ppt_LPAREN_e_RPAREN_" name="Phosphonate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ppt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pro_DASH_L_LPAREN_e_RPAREN_" name="L-Proline exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pro_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_progly_LPAREN_e_RPAREN_" name="L-Prolinylglycine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_progly_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_psclys_LPAREN_e_RPAREN_" name="psicoselysine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_psclys_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pser_DASH_L_LPAREN_e_RPAREN_" name="O-Phospho-L-serine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pser_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ptrc_LPAREN_e_RPAREN_" name="Putrescine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ptrc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pydam_LPAREN_e_RPAREN_" name="Pyridoxamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pydam_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pydx_LPAREN_e_RPAREN_" name="Pyridoxal exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pydx_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pydxn_LPAREN_e_RPAREN_" name="Pyridoxine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pydxn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_pyr_LPAREN_e_RPAREN_" name="Pyruvate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pyr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_quin_LPAREN_e_RPAREN_" name="Quinate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_quin_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_r5p_LPAREN_e_RPAREN_" name="alpha-D-Ribose 5-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_r5p_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_rfamp_LPAREN_e_RPAREN_" name="rifampin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rfamp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_rib_DASH_D_LPAREN_e_RPAREN_" name="D-Ribose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rib_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_rmn_LPAREN_e_RPAREN_" name="L-Rhamnose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rmn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_sbt_DASH_D_LPAREN_e_RPAREN_" name="D-Sorbitol exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_sbt_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_sel_LPAREN_e_RPAREN_" name="Selenate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_sel_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ser_DASH_D_LPAREN_e_RPAREN_" name="D-Serine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ser_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ser_DASH_L_LPAREN_e_RPAREN_" name="L-Serine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ser_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_skm_LPAREN_e_RPAREN_" name="Shikimate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_skm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_slnt_LPAREN_e_RPAREN_" name="selenite exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_slnt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_so2_LPAREN_e_RPAREN_" name="sulfur dioxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_so2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_so3_LPAREN_e_RPAREN_" name="Sulfite exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_so3_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_so4_LPAREN_e_RPAREN_" name="Sulfate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_so4_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_spmd_LPAREN_e_RPAREN_" name="Spermidine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_spmd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_succ_LPAREN_e_RPAREN_" name="Succinate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_succ_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_sucr_LPAREN_e_RPAREN_" name="Sucrose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_sucr_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_sulfac_LPAREN_e_RPAREN_" name="sulfoacetate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_sulfac_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tartr_DASH_D_LPAREN_e_RPAREN_" name="D-tartrate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tartr_DASH_D_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tartr_DASH_L_LPAREN_e_RPAREN_" name="L-tartrate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tartr_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_taur_LPAREN_e_RPAREN_" name="Taurine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_taur_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tcynt_LPAREN_e_RPAREN_" name="Thiocyanate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tcynt_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_thm_LPAREN_e_RPAREN_" name="Thiamin exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_thm_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_thr_DASH_L_LPAREN_e_RPAREN_" name="L-Threonine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_thr_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_thrp_LPAREN_e_RPAREN_" name="L-Threonine O-3-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_thrp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_thym_LPAREN_e_RPAREN_" name="Thymine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_thym_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_thymd_LPAREN_e_RPAREN_" name="Thymidine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_thymd_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tma_LPAREN_e_RPAREN_" name="Trimethylamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tma_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tmao_LPAREN_e_RPAREN_" name="Trimethylamine N-oxide exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tmao_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tre_LPAREN_e_RPAREN_" name="Trehalose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tre_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_trp_DASH_L_LPAREN_e_RPAREN_" name="L-Tryptophan exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_trp_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tsul_LPAREN_e_RPAREN_" name="Thiosulfate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tsul_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ttdca_LPAREN_e_RPAREN_" name="tetradecanoate (n-C14:0) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ttdca_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ttdcea_LPAREN_e_RPAREN_" name="tetradecenoate (n-C14:1) exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ttdcea_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ttrcyc_LPAREN_e_RPAREN_" name="tetracycline exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ttrcyc_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tungs_LPAREN_e_RPAREN_" name="tungstate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tungs_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tym_LPAREN_e_RPAREN_" name="Tyramine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tym_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tyr_DASH_L_LPAREN_e_RPAREN_" name="L-Tyrosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tyr_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_tyrp_LPAREN_e_RPAREN_" name="Phosphotyrosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tyrp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_uacgam_LPAREN_e_RPAREN_" name="UDP-N-acetyl-D-glucosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_uacgam_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_udpacgal_LPAREN_e_RPAREN_" name="UDP-N-acetyl-D-galactosamine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_udpacgal_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_udpg_LPAREN_e_RPAREN_" name="UDPglucose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_udpg_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_udpgal_LPAREN_e_RPAREN_" name="UDPgalactose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_udpgal_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_udpglcur_LPAREN_e_RPAREN_" name="UDP-D-glucuronate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_udpglcur_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ump_LPAREN_e_RPAREN_" name="UMP exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ump_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_ura_LPAREN_e_RPAREN_" name="Uracil exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ura_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_urea_LPAREN_e_RPAREN_" name="Urea exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_urea_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_uri_LPAREN_e_RPAREN_" name="Uridine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_uri_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_val_DASH_L_LPAREN_e_RPAREN_" name="L-Valine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_val_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_xan_LPAREN_e_RPAREN_" name="Xanthine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_xan_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_xmp_LPAREN_e_RPAREN_" name="Xanthosine 5'-phosphate exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_xmp_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_xtsn_LPAREN_e_RPAREN_" name="Xanthosine exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_xtsn_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_xyl_DASH_D_LPAREN_e_RPAREN_" name="D-Xylose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_xyl_DASH_D_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_xylu_DASH_L_LPAREN_e_RPAREN_" name="L-Xylulose exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_xylu_DASH_L_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EX_zn2_LPAREN_e_RPAREN_" name="Zinc exchange">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: </p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_zn2_e"/>
- </listOfReactants>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR120tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr120_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr120_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR140tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr140_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr140_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR141tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr141_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr141_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR160tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr160_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr160_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR161tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr161_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr161_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR180tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr180_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr180_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12DGR181tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12dgr181_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12dgr181_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12PPDRtex" name="(R)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12ppd_DASH_R_e"/>
- </listOfReactants>
- <listOfProducts>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_12PPDStex" name="(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_12ppd_DASH_S_e"/>
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- <listOfProducts>
- <speciesReference species="M_12ppd_DASH_S_p"/>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_12PPDStpp" name="(S)-Propane-1,2-diol facilitated transport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_12ppd_DASH_S_p"/>
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- <listOfProducts>
- <speciesReference species="M_12ppd_DASH_S_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_14GLUCANabcpp" name="1,4-alpha-D-glucan transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_14glucan_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_14glucan_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_14GLUCANtexi" name="1,4-alpha-D-glucan transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_14glucan_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_14glucan_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23CAMPtex" name="23cAMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23camp_e"/>
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- <listOfProducts>
- <speciesReference species="M_23camp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23CCMPtex" name="23cCMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23ccmp_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_23ccmp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23CGMPtex" name="23cGMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
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- <speciesReference species="M_23cgmp_e"/>
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- <listOfProducts>
- <speciesReference species="M_23cgmp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23CUMPtex" name="23cUMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23cump_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_23cump_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23DAPPAt2pp" name="2,3-diaminopropionate transport in via proton symport" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23dappa_p"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_23dappa_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23DAPPAtex" name="2,3-diaminopropionate transport via diffusion">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <listOfProducts>
- <speciesReference species="M_23dappa_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23PDE2pp" name="2',3'-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_23cump_p"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ump_p"/>
- <speciesReference species="M_h_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.4.16</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_23PDE7pp" name="2',3'-cyclic-nucleotide phosphodiesterase (AMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
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- </body>
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- <listOfProducts>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- </body>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
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- <listOfProducts>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
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- <p>EC Number: </p>
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- </reaction>
- <reaction id="R_2AGPA141tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <speciesReference species="M_2tdec7eg3p_p"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg120_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg120_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG140tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg140_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg140_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG141tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg141_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg141_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG160tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg160_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg160_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG161tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg161_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg161_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG180tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg180_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg180_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPG181tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2835</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg181_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg181_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT120" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg120_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ddca_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_pg120_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT140" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg140_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ttdca_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_pg140_c"/>
- <speciesReference species="M_ppi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT141" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg141_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ttdcea_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_pg141_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT160" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg160_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_hdca_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_pg160_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT161" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg161_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_hdcea_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_pg161_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT180" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg180_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ocdca_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_pg180_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2AGPGAT181" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2836</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg181_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ocdcea_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2DGULRGx" name="2-Dehydro-L-gulonate reductase to gluconate (NADH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dhguln_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcn_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2DGULRGy" name="2-Dehydro-L-gulonate reductase to gluconate (NADPH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.215</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dhguln_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcn_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2DGULRx" name="2-dehydro-L-gulonate reductase (NADH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dhguln_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_idon_DASH_L_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2DGULRy" name="2-dehydro-L-gulonate reductase (NADPH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dhguln_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
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- <listOfProducts>
- <speciesReference species="M_idon_DASH_L_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_2MAHMP" name="2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0446 or b1134)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2mahmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_4ampm_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_34dhpac_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_34dhpac_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_3AMACHYD" name="3-aminoacrylate hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1009</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3amac_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_msa_c"/>
- <speciesReference species="M_nh4_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3AMPtex" name="3AMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_3amp_e"/>
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- <speciesReference species="M_3amp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3CMPtex" name="3CMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_3cmp_e"/>
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- <listOfProducts>
- <speciesReference species="M_3cmp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3GMPtex" name="3GMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0929 or b1377 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3gmp_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3gmp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD100" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.60</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hdecACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_tdec2eACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD120" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0180 or b0954)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hddecACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_tddec2eACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD121" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0180 or b0954)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hcddec5eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_t3c5ddeceACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD140" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hmrsACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_tmrs2eACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD141" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hcmrs7eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_t3c7mrseACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD160" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hpalmACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_tpalm2eACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD161" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0180 or b0954)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hcpalm9eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_t3c9palmeACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_3HAD180" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hoctaACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_toctd2eACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_3HAD181" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.61</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HAD40" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.58</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
- <reaction id="R_3HAD60" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.58</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_thex2eACP_c"/>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_3HAD80" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0954 or b0180)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 4.2.1.58</p>
- </body>
- </notes>
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- </listOfReactants>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- <reaction id="R_3HCINNMH" name="3-hydroxycinnamate hydroxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0347</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_o2_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HPPPNH" name="3-(3-hydroxy-phenyl)propionate hydroxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0347</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HPPtex" name="3-hydroxypropionate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b0929 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hpp_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hpp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3HPPtpp" name="3-hydroxypropionate transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3hpp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hpp_p"/>
- <speciesReference species="M_h_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3KGK" name="3-keto-L-gulonate kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3580</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3dhguln_c"/>
- <speciesReference species="M_atp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3dhgulnp_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3NTD2pp" name="3'-nucleotidase (UMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ump_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_p"/>
- <speciesReference species="M_uri_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3NTD4pp" name="3'-nucleotidase (CMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3cmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cytd_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3NTD7pp" name="3'-nucleotidase (AMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3amp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adn_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3NTD9pp" name="3'-nucleotidase (GMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4213</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3gmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gsn_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR100" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3odecACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hdecACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR120" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3oddecACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hddecACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR121" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ocddec5eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hcddec5eACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR140" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3omrsACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hmrsACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR141" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ocmrs7eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hcmrs7eACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR160" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3opalmACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hpalmACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR161" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ocpalm9eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hcpalm9eACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR180" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ooctdACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hoctaACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR181" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ocvac11eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hcvac11eACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR40" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_actACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3haACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR60" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ohexACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3hhexACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAR80" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C8:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ooctACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
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- <listOfProducts>
- <speciesReference species="M_3hoctACP_c"/>
- <speciesReference species="M_nadp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS100" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2323 or b1095)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- <speciesReference species="M_ocACP_c"/>
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- <listOfProducts>
- <speciesReference species="M_3odecACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS120" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1095 or b2323)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dcaACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
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- <listOfProducts>
- <speciesReference species="M_3oddecACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS121" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2323</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cdec3eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
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- <listOfProducts>
- <speciesReference species="M_3ocddec5eACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS140" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2323 or b1095)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ddcaACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
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- <listOfProducts>
- <speciesReference species="M_3omrsACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS141" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2323</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cddec5eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
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- <listOfProducts>
- <speciesReference species="M_3ocmrs7eACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS160" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2323 or b1095)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- <speciesReference species="M_myrsACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3opalmACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS161" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2323</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- <speciesReference species="M_tdeACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ocpalm9eACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS180" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1095 or b2323)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- <speciesReference species="M_palmACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ooctdACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS181" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1095</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_hdeACP_c"/>
- <speciesReference species="M_malACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ocvac11eACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS60" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1095 or b2323)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_butACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ohexACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OAS80" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2323 or b1095)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_hexACP_c"/>
- <speciesReference species="M_malACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ooctACP_c"/>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3OXCOAT" name="3-oxoadipyl-CoA thiolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1397</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_coa_c"/>
- <speciesReference species="M_oxadpcoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_succoa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3PEPTabcpp" name="tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1329 and b1244 and b1245 and b1246 and b1247)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_LalaDgluMdap_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_LalaDgluMdap_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3PEPTtex" name="LalaDgluMdap (tripeptide) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDgluMdap_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_LalaDgluMdap_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_3UMPtex" name="3UMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ump_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3ump_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_42A12BOOXpp" name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1386</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 1.4.3.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dopa_p"/>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_o2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_34dhpac_p"/>
- <speciesReference species="M_h2o2_p"/>
- <speciesReference species="M_nh4_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4HOXPACDtex" name="4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_4hoxpacd_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_4hoxpacd_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
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- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4HTHRS" name="4-Hydroxy-L-threonine synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0004</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
- <speciesReference species="M_4hthr_c"/>
- <speciesReference species="M_pi_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4PCP" name="tetrapeptide L,D-carboxypeptidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1192</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDgluMdapDala_c"/>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
- <speciesReference species="M_LalaDgluMdap_c"/>
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- </math>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4PCPpp" name="tetrapeptide L,D-carboxypeptidase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h2o_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4PEPTabcpp" name="tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1243 and b1244 and b1245 and b1246 and b1247)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_LalaDgluMdapDala_p"/>
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- <listOfProducts>
- <speciesReference species="M_LalaDgluMdapDala_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_4PEPTtex" name="LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_LalaDgluMdapDala_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_LalaDgluMdapDala_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5DGLCNR" name="5-dehydro-D-gluconate reductase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4266</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.69</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5dglcn_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcn_c"/>
- <speciesReference species="M_nadp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5DGLCNt2rpp" name="5-Dehydro-D-gluconate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4265</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5dglcn_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_5dglcn_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5DGLCNtex" name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b2215 or b1377)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_5dglcn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_5dglcn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5DOAN" name="5'-deoxyadenosine nuclosidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0159</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dad_DASH_5_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_5drib_c"/>
- <speciesReference species="M_ade_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5MTRtex" name="5-Methylthio-D-ribose transport via proton diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b0929 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5mtr_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_5mtr_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_5MTRtpp" name="5-Methylthio-D-ribose transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_A5PISO" name="arabinose-5-phosphate isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3197 or b2708)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ru5p_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ara5p_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AACPS1" name="acyl-[acyl-carrier-protein] synthetase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ttdca_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_AACPS2" name="acyl-[acyl-carrier-protein] synthetase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
- </notes>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AACPS3" name="acyl-[acyl-carrier-protein] synthetase (n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
- </notes>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
- <reaction id="R_AACPS4" name="acyl-[acyl-carrier-protein] synthetase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
- </notes>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </reaction>
- <reaction id="R_AACPS5" name="acyl-[acyl-carrier-protein] synthetase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_ocdcea_c"/>
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- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
- <reaction id="R_AACPS6" name="acyl-[acyl-carrier-protein] synthetase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.20</p>
- </body>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <p>GENE_ASSOCIATION: (b2836 and b1094)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Methylglyoxal Metabolism</p>
- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4481</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1927</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3571</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2901</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2662 or b1302)</p>
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- <p>EC Number: 2.6.1.19</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1444</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2663</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2221 and b2222)</p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
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- <p>GENE_ASSOCIATION: b3959</p>
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- <p>EC Number: 2.7.2.8</p>
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- <p>EC Number: 2.3.1.1</p>
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- <notes>
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- <p>EC Number: 2.7.2.1</p>
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- <p>GENE_ASSOCIATION: b2428</p>
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- <notes>
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- <p>GENE_ASSOCIATION: b3794</p>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0221</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 1.3.99.3</p>
- </body>
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- <speciesReference species="M_ddcacoa_c"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOAD6f" name="acyl-CoA dehydrogenase (tetradecanoyl-CoA)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0221</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 1.3.99.3</p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOAD7f" name="acyl-CoA dehydrogenase (hexadecanoyl-CoA)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0221</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 1.3.99.3</p>
- </body>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOAD8f" name="acyl-CoA dehydrogenase (octadecanoyl-CoA)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0221</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 1.3.99.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_stcoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_od2coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOATA" name="Acetyl-CoA ACP transacylase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1091)</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 2.3.1.38</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ACP_c"/>
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- <speciesReference species="M_coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACODA" name="acetylornithine deacetylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3957</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 3.5.1.16</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acorn_c"/>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_orn_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOLIPAabctex" name="arabinose modified core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_acolipa_p"/>
- </listOfReactants>
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- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACONIs" name="aconitate isomerase (spontaneous)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: 5.3.3.7</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acon_DASH_T_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acon_DASH_C_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACONMT" name="Trans-aconitate methyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1519</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_aconm_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACONTa" name="aconitase (half-reaction A, Citrate hydro-lyase)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0118 or b1276)</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 4.2.1.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cit_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACONTb" name="aconitase (half-reaction B, Isocitrate hydro-lyase)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0118 or b1276)</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
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- </body>
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- <ci> FLUX_VALUE </ci>
- </math>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACOTA" name="acetylornithine transaminase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1748 or b3359)</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 2.6.1.11</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acorn_c"/>
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- <listOfProducts>
- <speciesReference species="M_acg5sa_c"/>
- <speciesReference species="M_glu_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACPPAT120" name="acyl-(acyl carrier protein):phosphate acyltransferase (C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACPPAT141" name="acyl-(acyl carrier protein):phosphate acyltransferase (C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_ACPPAT160" name="acyl-(acyl carrier protein):phosphate acyltransferase (C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACPPAT161" name="acyl-(acyl carrier protein):phosphate acyltransferase (C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACPPAT180" name="acyl-(acyl carrier protein):phosphate acyltransferase (C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ACPPAT181" name="acyl-(acyl carrier protein):phosphate acyltransferase (C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1090)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3475 or b2563)</p>
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- <p>EC Number: 2.7.8.7</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4069</p>
- <p>SUBSYSTEM: Pyruvate Metabolism</p>
- <p>EC Number: 6.2.1.1</p>
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- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
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- <p>EC Number: </p>
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- <p>GENE_ASSOCIATION: (b2578 or b1533)</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4067</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1623</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.5.4.4</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1096</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <notes>
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- <p>GENE_ASSOCIATION: (b3360 and b1812)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3665</p>
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- <p>GENE_ASSOCIATION: (b3654 or b3714)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0030</p>
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- <p>EC Number: 3.2.2.8</p>
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- <p>GENE_ASSOCIATION: (b2964 or b2393)</p>
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- <p>GENE_ASSOCIATION: b2406</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0411</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1993</p>
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- <p>GENE_ASSOCIATION: b1992</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1711 and b1709 and b0158)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3966 and (b1252 and b3005 and b3006))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3397 or b3034)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0469</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2750</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1131</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1131</p>
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- <p>GENE_ASSOCIATION: b0677</p>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4PA" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0110</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_c"/>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
- <speciesReference species="M_LalaDgluMdapDala_c"/>
- <speciesReference species="M_anhgm_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4PApp" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2435 or b2817 or b4169)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_p"/>
- <speciesReference species="M_h2o_p"/>
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- <listOfProducts>
- <speciesReference species="M_LalaDgluMdapDala_p"/>
- <speciesReference species="M_anhgm_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4PCP" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1192</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_c"/>
- <speciesReference species="M_anhgm3p_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4PCPpp" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_p"/>
- <speciesReference species="M_anhgm3p_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4PH" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1107</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acgam_c"/>
- <speciesReference species="M_anhm4p_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGM4Pt2pp" name="GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0433</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm4p_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_anhgm4p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGMH" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1107</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acgam_c"/>
- <speciesReference species="M_anhm_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGMHE" name="ADP-D-glycero-D-manno-heptose epimerase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3619</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: 5.1.3.20</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adphep_DASH_DD_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adphep_DASH_LD_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGMT" name="agmatinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2937</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 3.5.3.11</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_agm_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ptrc_c"/>
- <speciesReference species="M_urea_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGMt2pp" name="GlcNAc-anhMurNAc transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0433</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhgm_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_anhgm_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGMtex" name="agmatine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_agm_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_agm_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT120" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.51</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_1ddecg3p_c"/>
- <speciesReference species="M_ddcaACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_pa120_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT140" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.51</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_1tdecg3p_c"/>
- <speciesReference species="M_myrsACP_c"/>
- </listOfReactants>
- <listOfProducts>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT141" name="1-tetradec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
- </notes>
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- <speciesReference species="M_tdeACP_c"/>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT160" name="1-hexadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- <listOfProducts>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT161" name="1-hexadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
- </notes>
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- <speciesReference species="M_1hdec9eg3p_c"/>
- <speciesReference species="M_hdeACP_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT180" name="1-octadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.51</p>
- </body>
- </notes>
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- <speciesReference species="M_ocdcaACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_pa180_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AGPAT181" name="1-octadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3018</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.51</p>
- </body>
- </notes>
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- <speciesReference species="M_octeACP_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3958</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 1.2.1.38</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0572 and b0573 and b0574 and b0575)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0159</p>
- <p>SUBSYSTEM: Methionine Metabolism</p>
- <p>EC Number: 3.2.2.9</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4006</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 2.1.2.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0522</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0523</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0116 and b0726 and b0727)</p>
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- <p>EC Number: </p>
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- <speciesReference species="M_akg_c"/>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2587</p>
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- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1488</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: 3.4.17.14</p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_alaala_c"/>
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- <ci> FLUX_VALUE </ci>
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- <notes>
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- <p>GENE_ASSOCIATION: ((b1487 and b1486 and b1485 and b1484 and b1483) or (b3544 and b3543 and b3542 and b3541 and b3540))</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0381 or b0092)</p>
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- <p>EC Number: 6.3.2.4</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1325</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: 5.1.1.1</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2551 or b0870)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: 2.6.1.2</p>
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- <p>GENE_ASSOCIATION: (b0870 or b2551)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALAabcpp" name="L-alanine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3454 and b3455 and b3457 and b3460 and b3456)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_ala_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_ala_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALAt2pp" name="L-alanine transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4208</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_L_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALAt2rpp" name="L-alanine reversible transport via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_L_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALAt4pp" name="L-alanine transport in via sodium symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0007</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_L_p"/>
- <speciesReference species="M_na1_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_L_c"/>
- <speciesReference species="M_na1_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALAtex" name="L-alanine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ala_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALCD19" name="alcohol dehydrogenase (glycerol)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0356</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyald_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALCD2x" name="alcohol dehydrogenase (ethanol)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1478 or b1241 or b0356)</p>
- <p>SUBSYSTEM: Pyruvate Metabolism</p>
- <p>EC Number: 1.1.1.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_etoh_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acald_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALDD19xr" name="aldehyde dehydrogenase (phenylacetaldehyde, NAD)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1385</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.2.1.39</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_pacald_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_pac_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALDD2x" name="aldehyde dehydrogenase (acetaldehyde, NAD)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1300</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.2.1.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acald_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALDD2y" name="aldehyde dehydrogenase (acetaldehyde, NADP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3588</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.2.1.4</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acald_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_nadph_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALDD3y" name="aldehyde dehydrogenase (propanal, NADP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3588</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_ppal_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_ppa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALDD4" name="aldehyde dehydrogenase (butanal, NAD)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_btal_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_but_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLK" name="Allose kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4084</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_all_DASH_D_c"/>
- <speciesReference species="M_atp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_all6p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLPI" name="Allose 6-phosphate isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4090</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_all6p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_allul6p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLTAMH" name="allantoate amidohydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0516</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.5.3.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alltt_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nh4_c" stoichiometry="2"/>
- <speciesReference species="M_urdglyc_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLTN" name="allantoinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0512</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 3.5.2.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alltn_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alltt_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLTNt2rpp" name="allantoin transport in via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0511</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alltn_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alltn_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLTNtex" name="allantoin transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alltn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alltn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLULPE" name="Allulose 6-phosphate epimerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4085</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_allul6p_c"/>
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- <listOfProducts>
- <speciesReference species="M_f6p_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLabcpp" name="D-allose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4087 and b4088 and b4086)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_all_DASH_D_p"/>
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- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_all_DASH_D_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALLtex" name="Allose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_all_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_all_DASH_D_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALPATE160pp" name="apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0657 and b1677)</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alpp_p"/>
- <speciesReference species="M_pe160_p"/>
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- <listOfProducts>
- <speciesReference species="M_2agpe160_p"/>
- <speciesReference species="M_lpp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALPATG160pp" name="apolipoprotein N-acyltransferase (phosphatidylglycerol, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0657 and b1677)</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_alpp_p"/>
- <speciesReference species="M_pg160_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2agpg160_p"/>
- <speciesReference species="M_lpp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALR2" name="aldose reductase (methylglyoxal)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3012 or b0207 or b1781 or b3001)</p>
- <p>SUBSYSTEM: Methylglyoxal Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mthgxl_c"/>
- <speciesReference species="M_nadph_c"/>
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- <listOfProducts>
- <speciesReference species="M_acetol_c"/>
- <speciesReference species="M_nadp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALR4x" name="aldose reductase (acetol)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3945</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acetol_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_12ppd_DASH_R_c"/>
- <speciesReference species="M_nad_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ALTRH" name="altronate hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3091</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.7</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_altrn_c"/>
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- <listOfProducts>
- <speciesReference species="M_2ddglcn_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AM3PA" name="anhydrous-N-Acetylmuramyl-tripeptide amidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0110</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhm3p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_LalaDgluMdap_c"/>
- <speciesReference species="M_anhm_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AM4PA" name="anhydrous-N-Acetylmuramyl-tetrapeptide amidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0110</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhm4p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_LalaDgluMdapDala_c"/>
- <speciesReference species="M_anhm_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AM4PCP" name="anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1192</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_anhm4p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_c"/>
- <speciesReference species="M_anhm3p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AMALT1" name="Amylomaltase (maltotriose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3416</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.4.1.25</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malt_c"/>
- <speciesReference species="M_malttr_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_maltttr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AMALT2" name="Amylomaltase (maltotetraose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3416</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.4.1.25</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malt_c"/>
- <speciesReference species="M_maltttr_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_maltpt_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
- <reaction id="R_AMALT3" name="Amylomaltase (maltopentaose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3416</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.4.1.25</p>
- </body>
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- <listOfProducts>
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- <speciesReference species="M_malthx_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_AMALT4" name="Amylomaltase (maltohexaose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3416</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.4.1.25</p>
- </body>
- </notes>
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- <speciesReference species="M_malthp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3223</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acmanap_c"/>
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- <listOfProducts>
- <speciesReference species="M_acgam6p_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3222</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.60</p>
- </body>
- </notes>
- <listOfReactants>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0774</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.6.1.62</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_amet_c"/>
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- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3833</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dmmql8_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <reaction id="R_AMPMS2" name="4-amino-2-methyl-5-phosphomethylpyrimidine synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3994</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b0929 or b1377 or b0241)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1640</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1263</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0049</p>
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- <p>GENE_ASSOCIATION: b4129</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: b3059</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3059</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b3722 and b2415 and b2416) or (b2715 and b2415 and b2416))</p>
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- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
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- <reaction id="R_ARBTtex" name="arbutin transport via diffusion (extracellular to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1901 and b1900 and b4460)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ARBt2rpp" name="L-arabinose transport via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2841</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1528</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ARBtex" name="L-arabinose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4115</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfReactants>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ARGDC" name="arginine decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4117</p>
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- </body>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2938</p>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1605</p>
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- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ARGSL" name="argininosuccinate lyase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3960</p>
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- </body>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3172</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2923</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3433</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4192</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2415 and b2416 and b4195 and b4194 and b4193)</p>
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- <p>EC Number: </p>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1767 or b0828)</p>
- <p>SUBSYSTEM: Alanine and Aspartate Metabolism</p>
- <p>EC Number: 3.5.1.1</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2957</p>
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- <p>EC Number: 3.5.1.1</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0674</p>
- <p>SUBSYSTEM: Alanine and Aspartate Metabolism</p>
- <p>EC Number: 6.3.5.4</p>
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- <reaction id="R_ASNS2" name="asparagine synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3744</p>
- <p>SUBSYSTEM: Alanine and Aspartate Metabolism</p>
- <p>EC Number: 6.3.1.1</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0930</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.22</p>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1453</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3502</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: b0928</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1866</p>
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- <p>GENE_ASSOCIATION: (b0655 and b0654 and b0653 and b0652)</p>
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- <p>GENE_ASSOCIATION: b4077</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: b0827</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3857 or (b3857 and b3856))</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3857 or (b3857 and b3856))</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0827</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1216</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CA2tex" name="calcium (Ca+2) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CADVtpp" name="Lysine/Cadaverine antiporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4132</p>
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- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1732 or b3942)</p>
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- <p>EC Number: 1.11.1.6</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3196</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1270</p>
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- <p>EC Number: 2.5.1.17</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3966 and (b1252 and b3005 and b3006))</p>
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- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1711 and b1709 and b0158)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1711 and b1709 and b0158)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3469</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3915 or b0752)</p>
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- <p>EC Number: </p>
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- <notes>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3040</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3918</p>
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- <p>GENE_ASSOCIATION: b3918</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3544 and b3543 and b3542 and b3541 and b3540)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CGLYtex" name="L-Cysteinylglycine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CHLabcpp" name="choline transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2128 and b2129 and b2130 and b2131)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CHLt2pp" name="choline transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0314 or b1801)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CHLtex" name="choline transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CHOLD" name="choline dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0311</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: 1.1.99.1</p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CHORM" name="chorismate mutase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2599 or b2600)</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 5.4.99.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_chor_c"/>
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- <listOfProducts>
- <speciesReference species="M_pphn_c"/>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2329</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 4.2.3.5</p>
- </body>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4039</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfProducts>
- <speciesReference species="M_4hbz_c"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2416</p>
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- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2538 and b2539 and b2540 and b2542)</p>
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- <p>EC Number: </p>
- </body>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0615 and b0616 and b0617) and b0614)</p>
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- <p>EC Number: 4.1.3.6</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNH141pp" name="cardiolipin hydrolase (periplasm, n-C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_clpn141_p"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNH160pp" name="cardiolipin hydrolase (periplasm, n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNH161pp" name="cardiolipin hydrolase (periplasm, n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNH180pp" name="cardiolipin hydrolase (periplasm, n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNH181pp" name="cardiolipin hydrolase (periplasm, n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_clpn181_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_p"/>
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- <speciesReference species="M_pg181_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS120pp" name="cardiolipin synthase (periplasmic, n-C12:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0789 or b1249)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg120_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_clpn120_p"/>
- <speciesReference species="M_glyc_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS140pp" name="cardiolipin synthase (periplasmic, n-C14:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1249 or b0789)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg140_p" stoichiometry="2"/>
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- <listOfProducts>
- <speciesReference species="M_clpn140_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS141pp" name="cardiolipin synthase (periplasmic, n-C14:1)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0789 or b1249)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg141_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_clpn141_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS160pp" name="cardiolipin synthase (periplasmic, n-C16:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0789 or b1249)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg160_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_clpn160_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS161pp" name="cardiolipin synthase (periplasmic, n-C16:1)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1249 or b0789)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg161_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS180pp" name="cardiolipin synthase (periplasmic, n-C18:0)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0789 or b1249)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLPNS181pp" name="cardiolipin synthase (periplasmic, n-C18:1)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0789 or b1249)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pg181_p" stoichiometry="2"/>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLt3_2pp" name="chloride transport out via proton antiport (2:1) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0155 or b1592)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cl_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cl_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CLtex" name="chloride (Cl-1) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_cl_e"/>
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- <listOfProducts>
- <speciesReference species="M_cl_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CMPN" name="CMP nucleosidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.2.2.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cmp_c"/>
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- <listOfProducts>
- <speciesReference species="M_csn_c"/>
- <speciesReference species="M_r5p_c"/>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CMPtex" name="CMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_cmp_e"/>
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- <listOfProducts>
- <speciesReference species="M_cmp_p"/>
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- </reaction>
- <reaction id="R_CMtex" name="Chloramphenicol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_cm_e"/>
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- <listOfProducts>
- <speciesReference species="M_cm_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
- <reaction id="R_CMtpp" name="Chloramphenicol transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cm_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CO2tex" name="CO2 transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_co2_e"/>
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- <listOfProducts>
- <speciesReference species="M_co2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CO2tpp" name="CO2 transporter via diffusion (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_co2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COBALT2abcpp" name="Cobalt (Co+2) ABC transporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3469</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_cobalt2_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_cobalt2_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COBALT2t3pp" name="cobalt (Co+2) transport out via proton antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0752 or b3915)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cobalt2_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cobalt2_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COBALT2tex" name="cobalt (Co+2) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cobalt2_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cobalt2_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COBALT2tpp" name="cobalt transport in via permease (no H+)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3040 or b3816)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cobalt2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cobalt2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COLIPAKpp" name="Lipid A core kinase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2174</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipa_p"/>
- <speciesReference species="M_udcpdp_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_colipap_p"/>
- <speciesReference species="M_udcpp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COLIPAPabctex" name="core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_colipap_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_colipap_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COLIPAabcpp" name="core oligosaccharide lipid A transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_colipa_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_colipa_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_COLIPAabctex" name="core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_colipa_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_colipa_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNR1" name="coprogen(Fe(III)) reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_c" stoichiometry="2"/>
- <speciesReference species="M_fadh2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cpgn_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNR2" name="coprogen(Fe(III)) reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_c" stoichiometry="2"/>
- <speciesReference species="M_fmnh2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cpgn_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNR3" name="coprogen(Fe(III)) reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_c" stoichiometry="2"/>
- <speciesReference species="M_rbflvrd_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cpgn_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_ribflv_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNUtex" name="coprogen unloaded secretion (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_DASH_un_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cpgn_DASH_un_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNUtpp" name="coprogen unloaded secretion" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_DASH_un_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cpgn_DASH_un_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNabcpp" name="coprogen transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0153 and b0151 and b0152)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_cpgn_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_cpgn_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNexs" name="coprogen Fe-loading reaction (spontaneaous)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_DASH_un_e"/>
- <speciesReference species="M_fe3_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cpgn_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPGNtonex" name="Coprogen transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1102 and (b1252 and b3005 and b3006))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cpgn_e"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_cpgn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CPH4S" name="6-carboxy-5,6,7,8-tetrahydropterin synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2765</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ahdt_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acald_c"/>
- <speciesReference species="M_cph4_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0781 and b0783)</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2436</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.3.3.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3867</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0038</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </reaction>
- <reaction id="R_CRNCAL2" name="Carnitine-CoA Ligase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0037</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <reaction id="R_CRNCAR" name="carnitine-CoA racemase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0036</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_crncoa_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CRNCBCT" name="crotonobetainyl-CoA: carnitine CoA transferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0038</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CRNCDH" name="Carnityl-CoA dehydratse">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0036</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0037</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2677 and b2678 and b2679)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_crn_DASH_D_p"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4111</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
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- </listOfParameters>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2677 and b2678 and b2679)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4111</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0040</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0720</p>
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- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0337</p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CSNt2pp" name="cytosine transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0336</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CSNtex" name="cytosine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_csn_e"/>
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- <speciesReference species="M_csn_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CTBTCAL2" name="Crotonobetaine-CoA Ligase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0037</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CTBTabcpp" name="crotonobetaine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2677 and b2678 and b2679)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4111</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ctbt_p"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CTECOAI6" name="3-cis-2-trans-enoyl-CoA isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3846</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 5.3.3.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_tdecoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_td2coa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CTECOAI7" name="3-cis-2-trans-enoyl-CoA isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3846</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 5.3.3.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hdcoa_c"/>
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- <listOfProducts>
- <speciesReference species="M_hdd2coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CTECOAI8" name="3-cis-2-trans-enoyl-CoA isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3846</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 5.3.3.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_odecoa_c"/>
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- <listOfProducts>
- <speciesReference species="M_od2coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CTPS2" name="CTP synthase (glutamine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2780</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.4.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gln_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_CU1Opp" name="Cuprous Oxidase (Cu+1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0123</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cu_p" stoichiometry="4"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cu2_p" stoichiometry="4"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CU1abcpp" name="Copper (Cu +1) ABC transporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0484</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3469</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b0241 or b0929 or b1377)</p>
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- <p>EC Number: </p>
- </body>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3040</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_cu2_p"/>
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- <listOfProducts>
- <speciesReference species="M_cu2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0572 and b0573 and b0574 and b0575)</p>
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- <p>EC Number: </p>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3425</p>
- <p>SUBSYSTEM: Unassigned</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1308</p>
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <listOfProducts>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYNTAH" name="Cyanate aminohydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0340</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cynt_c"/>
- <speciesReference species="M_h_c" stoichiometry="3"/>
- <speciesReference species="M_hco3_c"/>
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- <listOfProducts>
- <speciesReference species="M_co2_c" stoichiometry="2"/>
- <speciesReference species="M_nh4_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYNTt2pp" name="Cyanate transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0341</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cynt_p"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_cynt_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYNTtex" name="Cyanate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cynt_e"/>
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- <listOfProducts>
- <speciesReference species="M_cynt_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSDDS" name="D-cysteine desulfhydrase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1919</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: 4.4.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_D_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2s_c"/>
- <speciesReference species="M_nh4_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSDS" name="Cysteine Desulfhydrase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3708 or b3008)</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: 4.1.99.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2s_c"/>
- <speciesReference species="M_nh4_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSDabcpp" name="D-cysteine uptake via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_cys_DASH_D_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_cys_DASH_D_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSDtex" name="D-cysteine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cys_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSS" name="cysteine synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2414 or b2421)</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acser_c"/>
- <speciesReference species="M_h2s_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_cys_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSSADS" name="L-cysteine sulfinic acid desulfurase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2810</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: 4.1.1.12</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3sala_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_L_c"/>
- <speciesReference species="M_so2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSTL" name="cystathionine b-lyase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1622 or b3008)</p>
- <p>SUBSYSTEM: Methionine Metabolism</p>
- <p>EC Number: 4.4.1.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cyst_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hcys_DASH_L_c"/>
- <speciesReference species="M_nh4_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSTRS" name="Cysteinyl-tRNA synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0526</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.16</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_cys_DASH_L_c"/>
- <speciesReference species="M_trnacys_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_cystrna_c"/>
- <speciesReference species="M_ppi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSabc2pp" name="L-cysteine export via ABC system (cytoplasm to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0886 and b0887)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_cys_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYSabcpp" name="L-cysteine uptake via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_cys_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_cys_DASH_L_c"/>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYStex" name="L-cysteine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_cys_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cys_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_CYStpp" name="L-cysteine export via facilitated transport" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2578 or b1533)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cys_DASH_L_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cys_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0978 and b0979)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_o2_c" stoichiometry="0.5"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_mqn8_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </reaction>
- <reaction id="R_CYTBDpp" name="cytochrome oxidase bd (ubiquinol-8: 2 protons) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0978 and b0979) or (b0733 and b0734))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_o2_c" stoichiometry="0.5"/>
- <speciesReference species="M_q8h2_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0429 and b0430 and b0431 and b0432)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2143</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.5.4.5</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2162 or b0651 or b0030)</p>
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- <p>EC Number: 3.2.2.8</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2066</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2393 or b2964)</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2406</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_CYTDtex" name="cytidine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0910</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.7.4.14</p>
- </body>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0910</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- </body>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3603 or b2975)</p>
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- </body>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_D_DASH_LACtex" name="D-lactate transport via diffusion (extracellular to periplasm)">
- <notes>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1189</p>
- <p>SUBSYSTEM: Alanine and Aspartate Metabolism</p>
- <p>EC Number: 1.4.99.1</p>
- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1623</p>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4042</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1393</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3771</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
- <p>EC Number: 4.2.1.9</p>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3771</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
- <p>EC Number: </p>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1200 and b1199 and b1198 and b2415 and b2416)</p>
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- <p>EC Number: </p>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_dha_e"/>
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- <kineticLaw>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>EC Number: </p>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0596</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.3.1.28</p>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0594</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.7.7.58</p>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- </body>
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- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2541</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0348</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0031</p>
- <p>SUBSYSTEM: Threonine and Lysine Metabolism</p>
- <p>EC Number: 1.3.1.26</p>
- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2478</p>
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- <p>EC Number: 4.2.1.52</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1606 or b0048)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1606</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3930</p>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0207 or b3012)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <reaction id="R_DKGLCNR2x" name="2,5-diketo-D-gluconate reductase (NADH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DKGLCNR2y" name="2,5-diketo-D-gluconate reductase (NADPH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3553</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMATT" name="dimethylallyltranstransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0421</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.5.1.1</p>
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- <listOfReactants>
- <speciesReference species="M_dmpp_c"/>
- <speciesReference species="M_ipdp_c"/>
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- <listOfProducts>
- <speciesReference species="M_grdp_c"/>
- <speciesReference species="M_ppi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMPPS" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0029</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2mb4p_c"/>
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- <listOfProducts>
- <speciesReference species="M_dmpp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
- <reaction id="R_DMQMT" name="3-Dimethylubiquinonol 3-methyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2232</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2omhmbl_c"/>
- <speciesReference species="M_amet_c"/>
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- <listOfProducts>
- <speciesReference species="M_ahcys_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_q8h2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMSOR1" name="Dimethyl sulfoxide reductase (Menaquinol 8)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1587 and b1588 and b1589 and b1590) or (b0894 and b0895 and b0896))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMSOR1pp" name="Dimethyl sulfoxide reductase (Menaquinol 8) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1872 and b1873)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_dmso_p"/>
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- <listOfProducts>
- <speciesReference species="M_mqn8_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMSOR2" name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0894 and b0895 and b0896)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dmmql8_c"/>
- <speciesReference species="M_dmso_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2dmmq8_c"/>
- <speciesReference species="M_dms_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMSOR2pp" name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1872 and b1873)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2dmmql8_c"/>
- <speciesReference species="M_dmso_p"/>
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- <listOfProducts>
- <speciesReference species="M_2dmmq8_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dmso_e"/>
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- <listOfProducts>
- <speciesReference species="M_dmso_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_DMSOtpp" name="Dimethyl sulfoxide transport via diffusion (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <listOfReactants>
- <speciesReference species="M_dmso_p"/>
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- <listOfProducts>
- <speciesReference species="M_dmso_c"/>
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- <kineticLaw>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_dms_e"/>
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- <speciesReference species="M_dms_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dhpmp_c"/>
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- </listOfReactants>
- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
- <reaction id="R_DNTPPA" name="Dihydroneopterin triphosphate pyrophosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0099 or b1865)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <listOfReactants>
- <speciesReference species="M_ahdt_c"/>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3575</p>
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- <p>EC Number: </p>
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- <listOfProducts>
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- </reaction>
- <reaction id="R_DOPAtex" name="dopamine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <speciesReference species="M_dopa_e"/>
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- <speciesReference species="M_dopa_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <reaction id="R_DOXRBCNtex" name="Doxorubicin transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_doxrbcn_e"/>
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- <listOfProducts>
- <speciesReference species="M_doxrbcn_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <reaction id="R_DOXRBCNtpp" name="Doxorubicin transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <reaction id="R_DURItex" name="deoxyuridine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0411</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- </reaction>
- <reaction id="R_DUTPDP" name="dUTP diphosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3640 or b2251)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.23</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0173</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_DXPS" name="1-deoxy-D-xylulose 5-phosphate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0420</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <listOfReactants>
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- <speciesReference species="M_co2_c"/>
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- <listOfParameters>
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- </listOfParameters>
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- <reaction id="R_DXYLK" name="1-Deoxy-D-xylulose kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3564</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfParameters>
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- <reaction id="R_E4PD" name="Erythrose 4-phosphate dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2927 or b1779)</p>
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- <p>EC Number: </p>
- </body>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_EAR100x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
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- </notes>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR100y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_EAR120x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
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- </reaction>
- <reaction id="R_EAR120y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- </body>
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- </reaction>
- <reaction id="R_EAR121x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- </body>
- </notes>
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- <reaction id="R_EAR121y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
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- <notes>
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- <p>GENE_ASSOCIATION: b1288</p>
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- <notes>
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- <speciesReference species="M_palmACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR161x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_t3c9palmeACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hdeACP_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR161y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_t3c9palmeACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hdeACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR180x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_toctd2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_ocdcaACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR180y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_toctd2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_ocdcaACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR181x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_t3c11vaceACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_octeACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR181y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_t3c11vaceACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_octeACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR40x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_but2eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_butACP_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR40y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_but2eACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_butACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR60x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_thex2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hexACP_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR60y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_thex2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hexACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR80x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_toct2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_ocACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_EAR80y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_toct2eACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_ocACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECA4COLIPAabctex" name="enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_eca4colipa_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_eca4colipa_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECA4OALpp" name="enterobacterial common antigen (x4) O-antigen ligase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3622</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipa_p"/>
- <speciesReference species="M_eca4und_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_eca4colipa_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_udcpdp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECAP1pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3793 and b3785)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_unagamuf_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_eca2und_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_udcpdp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECAP2pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3793 and b3785)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_eca2und_p"/>
- <speciesReference species="M_unagamuf_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_eca3und_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_udcpdp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECAP3pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3793 and b3785)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_eca3und_p"/>
- <speciesReference species="M_unagamuf_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_eca4und_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_udcpdp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ECAtpp" name="enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3792</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_unagamuf_c"/>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1850</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1054</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1855</p>
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- <p>GENE_ASSOCIATION: b1855</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
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- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2779</p>
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- <p>GENE_ASSOCIATION: b0583</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0585</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0585</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1288</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.3.1.10</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2440 and b2441)</p>
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- <p>EC Number: 4.3.1.7</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>GENE_ASSOCIATION: (b0936 and b0933 and b0934)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0822</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0404</p>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FA80ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0404</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 3.1.2.14</p>
- </body>
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- <listOfReactants>
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- <listOfProducts>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE100" name="fatty-acid-CoA thioesterase (decanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE120" name="fatty-acid-CoA thioesterase (dodecanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ddcacoa_c"/>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE140" name="fatty-acid-CoA thioesterase (tetradecanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE141" name="fatty-acid-CoA thioesterase (tetradecenoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE160" name="fatty-acid-CoA thioesterase (hexadecanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_pmtcoa_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_hdca_c"/>
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- <kineticLaw>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE161" name="fatty-acid-CoA thioesterase (hexadecenoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE180" name="fatty-acid-CoA thioesterase (octadecanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
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- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_ocdca_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE181" name="fatty-acid-CoA thioesterase (octadecenoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_odecoa_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_ocdcea_c"/>
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- <kineticLaw>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE60" name="fatty-acid-CoA thioesterase (hexanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_hxcoa_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_h_c"/>
- <speciesReference species="M_hxa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAE80" name="fatty-acid-CoA thioesterase (octanoate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0452</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FACOAL100t2pp" name="fatty-acid-CoA ligase (decanoate transport via vectoral Co-A coupling)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1805 or b1701)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_FACOAL120t2pp" name="fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1701 or b1805)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
- </body>
- </notes>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1701 or b1805)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
- </body>
- </notes>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_FACOAL141t2pp" name="fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1701 or b1805)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
- </body>
- </notes>
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- <listOfParameters>
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- </listOfParameters>
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- <reaction id="R_FACOAL160t2pp" name="fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1701 or b1805)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
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- </notes>
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- <kineticLaw>
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- <listOfParameters>
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- <reaction id="R_FACOAL161t2pp" name="fatty-acid-CoA ligase (hexadecenoate transport via vectoral Co-A coupling)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1805 or b1701)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
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- </notes>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1701 or b1805)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1805 or b1701)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.2.1.3</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1805 or b1701)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1805 or b1701)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3844</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2763 and b2764)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0356</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2097 or b1773 or b2925)</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2925</p>
- <p>SUBSYSTEM: Pentose Phosphate Pathway</p>
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: 3.1.3.11</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2802</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_co2_p"/>
- <speciesReference species="M_h_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FDMO" name="FMNH2-dependent monooxygenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0935</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fmnh2_c"/>
- <speciesReference species="M_isetac_c"/>
- <speciesReference species="M_o2_c"/>
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- <listOfProducts>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_gcald_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_so3_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FDMO2" name="FMNH2-dependent monooxygenase (methanesulfonate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0935</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fmnh2_c"/>
- <speciesReference species="M_mso3_c"/>
- <speciesReference species="M_o2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fald_c"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FDMO3" name="FMNH2-dependent monooxygenase (ethanesulfonate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0935</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ethso3_c"/>
- <speciesReference species="M_fmnh2_c"/>
- <speciesReference species="M_o2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acald_c"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_so3_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FDMO4" name="FMNH2-dependent monooxygenase (butanesulfonate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0935</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_butso3_c"/>
- <speciesReference species="M_fmnh2_c"/>
- <speciesReference species="M_o2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_btal_c"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FDMO6" name="FMNH2-dependent monooxygenase (sulfoacetate)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0935</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fmnh2_c"/>
- <speciesReference species="M_o2_c"/>
- <speciesReference species="M_sulfac_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_glx_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_h2o_c"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE2abcpp" name="iron (II) transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3409</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fe2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fe2_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE2t2pp" name="iron (II) transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2392</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE2t3pp" name="iron (Fe+2) transport out via proton antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3915</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe2_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE2tex" name="iron (II) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE2tpp" name="iron (+2) transport in via permease (no H+)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3040</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3DCITabcpp" name="iron transport from ferric-dicitrate via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4290 and b4289 and b4288 and b4287)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fe3dcit_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_cit_c" stoichiometry="2"/>
- <speciesReference species="M_fe3_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3DCITtonex" name="ferric-dicitrate transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4291 and (b1252 and b3005 and b3006))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3dcit_e"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe3dcit_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3DHBZR" name="release of Fe(III) from ferric 2,3-dihydroxybenzoylserine" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3dhbzs_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_23dhbzs_c"/>
- <speciesReference species="M_fe3_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3DHBZSabcpp" name="ferric 2,3-dihydroxybenzoylserine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0592 and b0588 and b0590 and b0589)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fe3dhbzs_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fe3dhbzs_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3DHBZStonex" name="ferric 2,3-dihydroxybenzoylserine transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0805 and (b1252 and b3005 and b3006)) or (b2155 and (b1252 and b3005 and b3006)))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3dhbzs_e"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe3dhbzs_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXR1" name="Fe(III)hydroxamate reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe3hox_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fe3hox_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXR2" name="Fe(III)hydroxamate reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_c" stoichiometry="2"/>
- <speciesReference species="M_fmnh2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fe3hox_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXR3" name="Fe(III)hydroxamate reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_c" stoichiometry="2"/>
- <speciesReference species="M_rbflvrd_c"/>
- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXUtex" name="Fe(III)hydroxamate unloaded secretion" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_DASH_un_c"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe3hox_DASH_un_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXUtpp" name="Fe(III)hydroxamate unloaded secretion (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_DASH_un_p"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe3hox_DASH_un_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXabcpp" name="ferric-dicitrate transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0153 and b0151 and b0152)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fe3hox_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fe3hox_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXexs" name="Fe(III) hydroxamate Fe-loading reaction (spontaneaous)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3_e"/>
- <speciesReference species="M_fe3hox_DASH_un_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe3hox_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3HOXtonex" name="Fe(III)hydroxamine transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0150 and (b1252 and b3005 and b3006))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3hox_e"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fe3hox_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3Ri" name="Fe(III) reduction" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3844</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe3_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3abcpp" name="iron (III) transport via ABC system (periplasm to cytoplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fe3_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fe3_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FE3tex" name="iron (III) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe3_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMR1" name="Ferrichrome reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fecrm_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fecrm_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMR2" name="Ferrichrome reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_c" stoichiometry="2"/>
- <speciesReference species="M_fmnh2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fecrm_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fmn_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMR3" name="Ferrichrome reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_c" stoichiometry="2"/>
- <speciesReference species="M_rbflvrd_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_fecrm_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_ribflv_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMUtex" name="ferrichrome (minus Fe) secretion (to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_DASH_un_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fecrm_DASH_un_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMUtpp" name="ferrichrome (minus Fe) secretion (to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_DASH_un_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fecrm_DASH_un_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMabcpp" name="ferrichrome transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0153 and b0151 and b0152)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_fecrm_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fecrm_c"/>
- <speciesReference species="M_h_c"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMexs" name="ferrichrome Fe(III)-loading reaction (spontaneous)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe3_e"/>
- <speciesReference species="M_fecrm_DASH_un_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fecrm_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FECRMtonex" name="ferrichrome transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0150 and (b1252 and b3005 and b3006))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fecrm_e"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fecrm_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEENTERR1" name="Fe-enterobactin reduction (Fe(III)-unloading)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_feenter_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_enter_c" stoichiometry="2"/>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEENTERR2" name="Fe-enterobactin reduction (Fe(III)-unloading)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0592 and b0588 and b0590 and b0589)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_enter_e"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_feenter_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEENTERtex" name="enterochelin transport (secretion periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3035</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_enter_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_enter_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEENTERtonex" name="Fe-enterobactin transport via ton system (extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0584 and (b1252 and b3005 and b3006))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_feenter_e"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
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- <speciesReference species="M_feenter_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEENTERtpp" name="enterochelin transport (secretion)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0591</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEOXAMR1" name="ferroxamine reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4367</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_feoxam_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_feoxam_DASH_un_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEOXAMR2" name="ferroxamine reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4367</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_feoxam_c" stoichiometry="2"/>
- <speciesReference species="M_fmnh2_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_feoxam_DASH_un_c" stoichiometry="2"/>
- <speciesReference species="M_fmn_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4367</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_feoxam_DASH_un_e"/>
- </listOfProducts>
- <kineticLaw>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEOXAMUtpp" name="ferroxamine (minus Fe3) secretion (to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_feoxam_DASH_un_p"/>
- </listOfProducts>
- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FEOXAMabcpp" name="ferroxamine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0153 and b0151 and b0152)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_feoxam_e"/>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0150 and (b1252 and b3005 and b3006))</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfProducts>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0123</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: 1.16.3.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fe2_p" stoichiometry="4"/>
- <speciesReference species="M_h_p" stoichiometry="4"/>
- <speciesReference species="M_o2_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fe3_p" stoichiometry="4"/>
- <speciesReference species="M_h2o_p" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h2o2_c"/>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <kineticLaw>
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- <listOfParameters>
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- <reaction id="R_FESR" name="iron-sulfur cluster repair" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4474</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </kineticLaw>
- </reaction>
- <reaction id="R_FRULYSK" name="Fructoselysine Kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3374</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_frulys_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRULYSt2pp" name="Fructoselysine transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3370</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRULYStex" name="fructoselysine transporter via diffusion (extracellular)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_frulys_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_frulys_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRUURt2rpp" name="D-fructuronate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4321</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_fruur_p"/>
- <speciesReference species="M_h_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRUURtex" name="D-fructuronate transport via diffusion (extracellular)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_fruur_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fruur_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRUpts2pp" name="Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1817 and b1818 and b1819 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_pep_c"/>
- <speciesReference species="M_fru_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_f6p_c"/>
- <speciesReference species="M_pyr_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRUptspp" name="D-fructose transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2167 and b2169 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_fru_p"/>
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- <listOfProducts>
- <speciesReference species="M_f1p_c"/>
- <speciesReference species="M_pyr_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FRUtex" name="D-fructose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_fru_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fru_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FTHFD" name="formyltetrahydrofolate deformylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1232</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 3.5.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_10fthf_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_for_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FTHFLi" name="formate-tetrahydrofolate ligase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 6.3.4.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_for_c"/>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUCtex" name="L-fucose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fuc_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fuc_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUCtpp" name="L-fucose transport via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2801</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fuc_DASH_L_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fuc_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUM" name="fumarase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1612 or b4122 or b1611)</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 4.2.1.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fum_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mal_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUMt2_2pp" name="Fumarate transport via proton symport (2 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3528</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h_p" stoichiometry="2"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUMt2_3pp" name="Fumarate transport via proton symport (3 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4138 or b4123 or b0621)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h_p" stoichiometry="3"/>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUMtex" name="Fumarate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_fum_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fum_p"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
- <reaction id="R_FUSAtex" name="Fusidic acid transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_fusa_e"/>
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- <listOfProducts>
- <speciesReference species="M_fusa_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_FUSAtpp" name="Fusidic acid transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fusa_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_fusa_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_G1PACT" name="glucosamine-1-phosphate N-acetyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3730</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.3.1.157</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1002</p>
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- <p>EC Number: 3.1.3.10</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2039 or b3789)</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.7.7.24</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <listOfParameters>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0154</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 5.4.3.8</p>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2533</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4055</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- </reaction>
- <reaction id="R_G3PAT120" name="glycerol-3-phosphate acyltransferase (C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.3.1.15</p>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_G3PAT140" name="glycerol-3-phosphate acyltransferase (C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
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- </body>
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- <listOfParameters>
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- <reaction id="R_G3PAT141" name="glycerol-3-phosphate acyltransferase (C14:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
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- </body>
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- <notes>
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- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
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- </body>
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- <notes>
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- <p>GENE_ASSOCIATION: (b1094 and b4041)</p>
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- <notes>
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- </body>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALBDtex" name="beta D-galactose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gal_DASH_bD_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gal_DASH_bD_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTD" name="galactarate dehydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3128</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.42</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galct_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_5dh4dglc_c"/>
- <speciesReference species="M_h2o_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTLO" name="L-galactonate oxidoreductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4358</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_L_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_tagur_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTND" name="galactonate dehydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4478</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2dh3dgal_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTNLt2pp" name="L-galactonate transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4356</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_L_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galctn_DASH_L_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTNLtex" name="L-galactonate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galctn_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTNt2pp" name="D-galactonate transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3691</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_D_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galctn_DASH_D_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTNtex" name="D-galactonate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galctn_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galctn_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTt2rpp" name="D-galactarte transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2789 or b3127)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galct_DASH_D_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galct_DASH_D_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALCTtex" name="D-galactarte transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galct_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galct_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALKr" name="galactokinase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2045 or b0757)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gal_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_gal1p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALM2pp" name="aldose-1-epimerase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0756</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.1.3.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gal_DASH_bD_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gal_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALS3" name="a-galactosidase (melibiose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4119</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.2.1.22</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_melib_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gal_c"/>
- <speciesReference species="M_glc_DASH_D_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALT1" name="galactosyltransferase I (LPS core synthesis)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3628</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gicolipa_c"/>
- <speciesReference species="M_udpg_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gagicolipa_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALTptspp" name="Galactitol transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2094 and b2093 and b2092 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pep_c"/>
- <speciesReference species="M_galt_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galt1p_c"/>
- <speciesReference species="M_pyr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALTtex" name="Galactitol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galt_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galt_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALURt2rpp" name="D-galacturonate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3093</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALURtex" name="D-galacturonate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galur_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_galur_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GALUi" name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1236</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.7.7.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g1p_c"/>
- <speciesReference species="M_h_c"/>
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- <listOfProducts>
- <speciesReference species="M_ppi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2149 and b2150 and b2148) or (b4231 and b4227 and b4485 and b4230))</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2943</p>
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- <p>EC Number: </p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3666</p>
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- <p>EC Number: </p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1817 and b1818 and b1819 and b2415 and b2416)</p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
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- <p>GENE_ASSOCIATION: b1779</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2500</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <ci> FLUX_VALUE </ci>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1300</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_nadp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GGGABAH" name="gamma-glutamyl-gamma-aminobutyric acid hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1298</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h2o_c"/>
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- <speciesReference species="M_glu_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GGPTRCO" name="gamma glutamyl putrescine oxidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1301</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ggptrc_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_o2_c"/>
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- <listOfProducts>
- <speciesReference species="M_ggbutal_c"/>
- <speciesReference species="M_h2o2_c"/>
- <speciesReference species="M_nh4_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GGPTRCS" name="gamma glutamyl putrescine synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1297</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_ptrc_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_ggptrc_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GHBDHx" name="gamma-hydroxybutyrate dehydrogenase (NADH)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3882</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_sucsal_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ghb_c"/>
- <speciesReference species="M_nad_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GHMT2r" name="glycine hydroxymethyltransferase, reversible">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2551</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: 2.1.2.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ser_DASH_L_c"/>
- <speciesReference species="M_thf_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gly_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_mlthf_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GK1" name="guanylate kinase (GMP:ATP)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3648</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.7.4.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gmp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_gdp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLBRAN2" name="1,4-alpha-glucan branching enzyme (glycogen -> bglycogen)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3432</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.4.1.18</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glycogen_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_bglycogen_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCATr" name="D-glucose O-acetyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0459</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.3.1.79</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_glc_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acglc_DASH_D_c"/>
- <speciesReference species="M_coa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCDpp" name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0124 or b0837)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_q8_c"/>
- <speciesReference species="M_glc_DASH_D_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_q8h2_c"/>
- <speciesReference species="M_glcn_p"/>
- <speciesReference species="M_h_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCNt2rpp" name="D-gluconate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4321 or b4476 or b3415 or b4265)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcn_p"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcn_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCNtex" name="D-gluconate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCP" name="glycogen phosphorylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3428 or b3417)</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.4.1.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glycogen_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_g1p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCP2" name="glycogen phosphorylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3417 or b3428)</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.4.1.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_bglycogen_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_g1p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3126</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.2.20</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5dh4dglc_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2h3oppan_c"/>
- <speciesReference species="M_pyr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2788 or b2787)</p>
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- <p>EC Number: 4.2.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3127 or b2789)</p>
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- <p>EC Number: </p>
- </body>
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- <listOfReactants>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcr_e"/>
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- <listOfProducts>
- <speciesReference species="M_glcr_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_GLCS1" name="glycogen synthase (ADPGlc)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3429</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.4.1.21</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adpglc_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCTR1" name="glucosyltransferase I (LPS core synthesis)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3631</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_icolipa_c"/>
- <speciesReference species="M_udpg_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gicolipa_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_udp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCTR2" name="glucosyltransferase II (LPS core synthesis)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3627</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gagicolipa_c"/>
- <speciesReference species="M_udpg_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ggagicolipa_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_udp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCTR3" name="glucosyltransferase III (LPS core synthesis)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3626</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ggagicolipa_c"/>
- <speciesReference species="M_udpg_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gggagicolipa_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_udp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCUR1Ptex" name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcur1p_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcur1p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCURt2rpp" name="D-glucuronate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3909 or b3093)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcur_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcur_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCURtex" name="D-glucuronat transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glcur_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glcur_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCabcpp" name="D-glucose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2149 and b2150 and b2148)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_glc_DASH_D_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCptspp" name="D-glucose transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2417 and b1621 and b2415 and b2416) or (b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416))</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pep_c"/>
- <speciesReference species="M_glc_DASH_D_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_g6p_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCt2pp" name="D-glucose transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2943</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glc_DASH_D_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCtex" name="glucose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glc_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLCtexi" name="D-glucose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glc_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLDBRAN2" name="glycogen debranching enzyme (bglycogen -> glycogen)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3431</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_bglycogen_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glycogen_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLGC" name="glucose-1-phosphate adenylyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3430</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.7.7.27</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_g1p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adpglc_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLNS" name="glutamine synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3870 or b1297)</p>
- <p>SUBSYSTEM: Glutamate Metabolism </p>
- <p>EC Number: 6.3.1.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_nh4_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_gln_DASH_L_c"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLNTRS" name="Glutaminyl-tRNA synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0680</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.18</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gln_DASH_L_c"/>
- <speciesReference species="M_trnagln_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_glntrna_c"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLNabcpp" name="L-glutamine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0811 and b0810 and b0809)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_gln_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_gln_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLNtex" name="L-glutamine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gln_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gln_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLTPD" name="Galactitol-1-phosphate dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2091</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_galt1p_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_tag6p_DASH_D_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLU5K" name="glutamate 5-kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0242</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 2.7.2.11</p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1492</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUCYS" name="gamma-glutamylcysteine synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2688</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 6.3.2.2</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_glu_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3517 or b1493)</p>
- <p>SUBSYSTEM: Glutamate Metabolism</p>
- <p>EC Number: 4.1.1.15</p>
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- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUDy" name="glutamate dehydrogenase (NADP)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1761</p>
- <p>SUBSYSTEM: Glutamate Metabolism</p>
- <p>EC Number: 1.4.1.4</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
- <speciesReference species="M_akg_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUN" name="glutaminase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1812 or b0485 or b1524)</p>
- <p>SUBSYSTEM: Glutamate Metabolism</p>
- <p>EC Number: 3.5.1.2</p>
- </body>
- </notes>
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- <speciesReference species="M_gln_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUNpp" name="glutaminase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2957</p>
- <p>SUBSYSTEM: Glutamate Metabolism</p>
- <p>EC Number: 3.5.1.2</p>
- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUPRT" name="glutamine phosphoribosyldiphosphate amidotransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2312</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 2.4.2.14</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gln_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_prpp_c"/>
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- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_ppi_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUR" name="glutamate racemase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3967</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 5.1.1.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glu_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUSy" name="glutamate synthase (NADPH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3212 and b3213)</p>
- <p>SUBSYSTEM: Glutamate Metabolism </p>
- <p>EC Number: 1.4.1.13</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_c" stoichiometry="2"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUTRR" name="glutamyl-tRNA reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1210</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_glutrna_c"/>
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- <listOfProducts>
- <speciesReference species="M_glu1sa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLUTRS" name="Glutamyl-tRNA synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2400</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 6.1.1.17</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_trnaglu_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0655 and b0654 and b0653 and b0652)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_glu_DASH_L_p"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4077</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3653</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_na1_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_glu_DASH_L_e"/>
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- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0507</p>
- <p>SUBSYSTEM: Glyoxylate Metabolism</p>
- <p>EC Number: 4.1.1.47</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glx_c" stoichiometry="2"/>
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- <listOfProducts>
- <speciesReference species="M_2h3oppan_c"/>
- <speciesReference species="M_co2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
- <reaction id="R_GLYALDtex" name="Glyceraldehyde transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyald_e"/>
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- <listOfProducts>
- <speciesReference species="M_glyald_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYALDtpp" name="Glyceraldehyde facilitated diffusion (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3927</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_glyald_p"/>
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- <listOfProducts>
- <speciesReference species="M_glyald_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYAT" name="glycine C-acetyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3617</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: 2.3.1.29</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_gly_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2aobut_c"/>
- <speciesReference species="M_coa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYBabcpp" name="Glycine betaine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2128 and b2129 and b2130 and b2131)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_glyb_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_glyb_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYBt2pp" name="Glycine betaine transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1801 or b4111)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyb_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyb_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYBtex" name="Glycine betaine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyb_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyb_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYC2Pabcpp" name="sn-Glycerol 2-phosphate transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3452 and b3453 and b3450 and b3451)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_glyc2p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_glyc2p_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYC2Ptex" name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b0241 or b0929 or b1377)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc2p_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc2p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYC3Pabcpp" name="sn-Glycerol 3-phosphate transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3452 and b3453 and b3450 and b3451)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_glyc3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYC3Pt6pp" name="Glycerol-3-phosphate : phosphate antiporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2240</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_glyc3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYC3Ptex" name="Glycerol-3-phosphate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc3p_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCAt2rpp" name="D-glycerate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2789 or b3127)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc_DASH_R_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc_DASH_R_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCAtex" name="D-glycerate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc_DASH_R_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc_DASH_R_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCDx" name="Glycerol dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3945</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyc_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dha_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCK" name="glycerate kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0514</p>
- <p>SUBSYSTEM: Glyoxylate Metabolism</p>
- <p>EC Number: 2.7.1.31</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glyc_DASH_R_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3pg_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCK2" name="glycerate kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3124</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: 2.7.1.31</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glyc_DASH_R_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2pg_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCL" name="Glycine Cleavage System" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2904 and b2903 and b2905 and b0116)</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gly_c"/>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_thf_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_mlthf_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_nh4_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCLTDx" name="Glycolate dehydrogenase (NAD)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3553 or b1033)</p>
- <p>SUBSYSTEM: Glyoxylate Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glx_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyclt_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCLTDy" name="Glycolate dehydrogenase (NADP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1033 or b3553)</p>
- <p>SUBSYSTEM: Glyoxylate Metabolism</p>
- <p>EC Number: 1.1.1.26</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glx_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyclt_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCLTt2rpp" name="glycolate transport via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3603 or b2975)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_glyclt_p"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyclt_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GLYCLTt4pp" name="glycolate transport via sodium symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4067</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2979 and b4467 and b4468)</p>
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- <p>EC Number: </p>
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- <p>GENE_ASSOCIATION: (b2979 and b4467 and b4468)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2979 and b4467 and b4468)</p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3927 or s0001)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3926</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0212</p>
- <p>SUBSYSTEM: Methylglyoxal Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4208 or b1801)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_nh4_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GMPS2" name="GMP synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2507</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.5.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gln_DASH_L_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_xmp_c"/>
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- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_glu_DASH_L_c"/>
- <speciesReference species="M_gmp_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GMPtex" name="GMP transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gmp_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gmp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GND" name="phosphogluconate dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2029</p>
- <p>SUBSYSTEM: Pentose Phosphate Pathway</p>
- <p>EC Number: 1.1.1.44</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_6pgc_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_ru5p_DASH_D_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GNK" name="gluconokinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4268 or b3437)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.12</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_glcn_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_6pgc_c"/>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GOFUCR" name="GDP-4-oxo-L-fucose reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2052</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gdpofuc_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gdpfuc_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GP4GH" name="Gp4G hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0049</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gp4g_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gdp_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA1" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3449</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pc_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_chol_c"/>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA1pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2239</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pc_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_chol_p"/>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA2" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3449</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pe_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_etha_c"/>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA2pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2239</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pe_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_etha_p"/>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA3" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3449</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3ps_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ser_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA3pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2239</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3ps_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_ser_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA4" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3449</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pg_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc_c"/>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA4pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2239</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pg_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc_p"/>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA5" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3449</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pi_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_c"/>
- <speciesReference species="M_h_c"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GPDDA5pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2239</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.4.46</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_g3pi_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_inost_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GRTT" name="geranyltranstransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0421</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.5.1.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_grdp_c"/>
- <speciesReference species="M_ipdp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_frdp_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GRXR" name="glutaredoxin reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1064 or b3610 or b1654 or b0849)</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: 1.8.4.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_grxox_c"/>
- <speciesReference species="M_gthrd_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_grxrd_c"/>
- <speciesReference species="M_gthox_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GSNK" name="guanosine kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0477</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GSNt2pp" name="guanosine transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2964</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GSNtex" name="guanosine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_gsn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gsn_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GSPMDA" name="Glutathionylspermidine amidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2988</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 3.5.1.78</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gtspmd_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gthrd_c"/>
- <speciesReference species="M_spmd_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GSPMDS" name="Glutathionylspermidine synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2988</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 6.3.1.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gthrd_c"/>
- <speciesReference species="M_spmd_c"/>
- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_gtspmd_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHOXtex" name="glutathione (ox) transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthox_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gthox_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHOr" name="glutathione oxidoreductase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3500</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.8.1.7</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthox_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gthrd_c" stoichiometry="2"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHPi" name="glutathione peridoxase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1710</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: 1.11.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthrd_c" stoichiometry="2"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gthox_c"/>
- <speciesReference species="M_h2o_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHRDHpp" name="glutathione hydralase (periplasmic)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3447</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_gthrd_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cgly_p"/>
- <speciesReference species="M_glu_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHRDabc2pp" name="glutathione export via ABC system (cytoplasm to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0886 and b0887)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gthrd_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHRDabcpp" name="Reduced glutathione via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0829 and b0830 and b0831 and b0832)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHRDtex" name="glutathione transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthrd_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gthrd_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_GTHS" name="glutathione synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2947</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 6.3.2.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_glucys_c"/>
- <speciesReference species="M_gly_c"/>
- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2153</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.5.4.16</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_for_c"/>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1277</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h2o_c" stoichiometry="3"/>
- </listOfReactants>
- <listOfProducts>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3779</p>
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- <p>EC Number: 3.6.1.40</p>
- </body>
- </notes>
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- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
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- <reaction id="R_GTPDPK" name="GTP diphosphokinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2784</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.7.6.5</p>
- </body>
- </notes>
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- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 4.6.1.2</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2883</p>
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- <p>EC Number: 3.5.4.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0238 or b0125)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.4.2.8</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3654</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <reaction id="R_GUAtex" name="Guanine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0411</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3092</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.12</p>
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- <speciesReference species="M_fruur_c"/>
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- <reaction id="R_GUI2" name="glucuronate isomerase (D-galacturonate)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3092</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.12</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <speciesReference species="M_h2o2_e"/>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (s0001 or b0957 or b3875 or b2215 or b0241 or b1319 or b1377 or b0929)</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (s0001 or b0875)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3846 or b2341)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0352</p>
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- <p>GENE_ASSOCIATION: b0142</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2221 and b2222)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.8.3.8</p>
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- </notes>
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- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_hxa_c"/>
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- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_hxcoa_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_HXPRT" name="hypoxanthine phosphoribosyltransferase (Hypoxanthine)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0238 or b0125)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.4.2.8</p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_hxan_c"/>
- <speciesReference species="M_prpp_c"/>
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- <listOfProducts>
- <speciesReference species="M_imp_c"/>
- <speciesReference species="M_ppi_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0972 and b0973 and b0974) or (b2994 and b2995 and b2996 and b2997) or (b2719 and b2720 and b2721 and b2722 and b2723 and b2724))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.18.99.1</p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0972 and b0973 and b0974) or (b2994 and b2995 and b2996 and b2997))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.18.99.1</p>
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- <speciesReference species="M_h2_c"/>
- <speciesReference species="M_mqn8_c"/>
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- <listOfProducts>
- <speciesReference species="M_mql8_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_HYD3pp" name="Hydrogenase (Demethylmenaquinone-8: 2 protons) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0972 and b0973 and b0974) or (b2994 and b2995 and b2996 and b2997))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.18.99.1</p>
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- <listOfReactants>
- <speciesReference species="M_2dmmq8_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_h2_c"/>
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- <listOfProducts>
- <speciesReference species="M_2dmmql8_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_HYPOE" name="hypothetical enyme" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_pyam5p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_pydam_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_HYXNtex" name="Hypoxanthine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hxan_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hxan_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_HYXNtpp" name="Hypoxanthine transport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hxan_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hxan_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_Htex" name="proton transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0929 or b1377 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_I2FE2SR" name="ISC [2Fe-2S] regeneration" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2530 and b2529)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2fe1s_c"/>
- <speciesReference species="M_iscssh_c"/>
- <speciesReference species="M_iscu_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="4"/>
- <speciesReference species="M_iscs_c"/>
- <speciesReference species="M_iscu_DASH_2fe2s_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_I2FE2SS" name="ISC [2Fe-2S] Synthesis" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3807 and b2530 and b2529)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_iscssh_c" stoichiometry="2"/>
- <speciesReference species="M_iscu_c"/>
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- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_h_c" stoichiometry="6"/>
- <speciesReference species="M_iscs_c" stoichiometry="2"/>
- <speciesReference species="M_iscu_DASH_2fe2s_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_I2FE2SS2" name="ISC [2Fe-2S] Synthesis II" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3807 and b2530 and b2529)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_iscssh_c" stoichiometry="2"/>
- <speciesReference species="M_iscu_DASH_2fe2s_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_h_c" stoichiometry="6"/>
- <speciesReference species="M_iscs_c" stoichiometry="2"/>
- <speciesReference species="M_iscu_DASH_2fe2s2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_I2FE2ST" name="ISC [2Fe-2S] Transfer" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2528 and b2529)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="4"/>
- <speciesReference species="M_iscu_DASH_2fe2s_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2fe2s_c"/>
- <speciesReference species="M_iscu_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2529</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_iscu_DASH_2fe2s2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2528 and b2529)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="4"/>
- <speciesReference species="M_iscu_DASH_4fe4s_c"/>
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- <listOfProducts>
- <speciesReference species="M_4fe4s_c"/>
- <speciesReference species="M_iscu_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- <reaction id="R_ICDHyr" name="isocitrate dehydrogenase (NADP)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1136</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 1.1.1.42</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_icit_c"/>
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- <listOfProducts>
- <speciesReference species="M_akg_c"/>
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- <speciesReference species="M_nadph_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
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- <reaction id="R_ICHORS" name="isochorismate synthase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2265</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 5.4.99.6</p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_chor_c"/>
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- <listOfProducts>
- <speciesReference species="M_ichor_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
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- <reaction id="R_ICHORSi" name="Isochorismate Synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0593</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_chor_c"/>
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- <listOfProducts>
- <speciesReference species="M_ichor_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ICHORT" name="isochorismatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0595</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.3.2.1</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4015</p>
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- <p>EC Number: 4.1.3.1</p>
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- <p>GENE_ASSOCIATION: b2530</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4267</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4267</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4265</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2023 and b2025)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2022</p>
- <p>SUBSYSTEM: Histidine Metabolism</p>
- <p>EC Number: 4.2.1.19</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1262</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 4.1.1.48</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3770</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3161</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_INDOLEtex" name="Indole transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_indole_e"/>
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- <listOfProducts>
- <speciesReference species="M_indole_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INOSTt4pp" name="Na+/myo-inositol symporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3679</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_na1_p"/>
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- <speciesReference species="M_na1_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INSH" name="Inosine hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0030</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.2.2.8</p>
- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_hxan_c"/>
- <speciesReference species="M_rib_DASH_D_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INSK" name="insosine kinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0477</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.7.1.73</p>
- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INSTtex" name="inositol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_inost_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_inost_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INSt2pp" name="inosine transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2964</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ins_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INSt2rpp" name="inosine transport in via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2406</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_INStex" name="inosine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0411</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_ins_e"/>
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- <listOfProducts>
- <speciesReference species="M_ins_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_IPDDI" name="isopentenyl-diphosphate D-isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2889</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 5.3.3.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ipdp_c"/>
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- <listOfProducts>
- <speciesReference species="M_dmpp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_IPDPS" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0029</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
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- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
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- <ci> FLUX_VALUE </ci>
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- </reaction>
- <reaction id="R_IPMD" name="3-isopropylmalate dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0073</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
- <p>EC Number: 1.1.1.85</p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0071 and b0072)</p>
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- <p>EC Number: 4.2.1.33</p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_IPPMIb" name="2-isopropylmalate hydratase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0071 and b0072)</p>
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- <p>EC Number: 4.2.1.33</p>
- </body>
- </notes>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0074</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
- <p>EC Number: 4.1.3.12</p>
- </body>
- </notes>
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- <speciesReference species="M_3c3hmp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0365 and b0366 and b0367) or (b0936 and b0933 and b0934))</p>
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- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_isetac_e"/>
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- <listOfProducts>
- <speciesReference species="M_isetac_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_kdo2lipid4_c"/>
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- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <reaction id="R_K2L4Aabctex" name="KDO(2)-lipid IV A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_kdo2lipid4_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3774</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
- <p>EC Number: 1.1.1.86</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3774</p>
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- <p>EC Number: 1.1.1.86</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2323 or b1095)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1091</p>
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- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_KDOCT2" name="3-deoxy-manno-octulosonate cytidylyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0918</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: 2.7.7.38</p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_KDOPP" name="3-deoxy-manno-octulosonate-8-phosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3198</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: 3.1.3.45</p>
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- <reaction id="R_KDOPS" name="3-deoxy -D-manno-octulosonic -acid 8-phosphate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1215</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4196 or b3581)</p>
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- </reaction>
- <reaction id="R_Kabcpp" name="Potassium ABC transporter (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0698 and b0697 and b0696) or (b0698 and b0697 and b0696 and b4513))</p>
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- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1291 and b3290 and b3849) or b1250 or (b1291 and b3290 and b1363) or b3747)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1216 or b0842 or b3350 or b0047)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3605 or (b0306 and b0307 and b0308))</p>
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- </notes>
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- <p>GENE_ASSOCIATION: (b3603 or b2975)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2257</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LEUabcpp" name="L-leucine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b3454 and b3455 and b3457 and b3460 and b3456) or (b3454 and b3455 and b3457 and b3458 and b3456))</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_leu_DASH_L_p"/>
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- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LEUt2rpp" name="L-leucine reversible transport via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0401</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_leu_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_leu_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LEUtex" name="L-leucine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_leu_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_leu_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LGTHL" name="lactoylglutathione lyase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1651</p>
- <p>SUBSYSTEM: Methylglyoxal Metabolism</p>
- <p>EC Number: 4.4.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gthrd_c"/>
- <speciesReference species="M_mthgxl_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_lgt_DASH_S_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPACabcpp" name="lipid (cold) A transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_lipa_cold_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_lipa_cold_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPAHT2ex" name="core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0622</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipa_e"/>
- <speciesReference species="M_h_e"/>
- <speciesReference species="M_hdca_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_e"/>
- <speciesReference species="M_hacolipa_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPAHTex" name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0622</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_e"/>
- <speciesReference species="M_hdca_e"/>
- <speciesReference species="M_lipa_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_e"/>
- <speciesReference species="M_halipa_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPAMPL" name="Lipoyl-adenylate protein ligase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4386</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipoamp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_lipopb_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPATPT" name="Lipoate-ATP adenylate transferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4386</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_lipoate_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_lipoamp_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPAabcpp" name="lipid A transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_lipa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_lipa_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPAabctex" name="lipid A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_lipa_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
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- <speciesReference species="M_lipa_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPOCT" name="Lipoyl(octanoyl) transferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0630</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ocACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_octapb_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPOS" name="Lipoate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0628</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_4fe4s_c"/>
- <speciesReference species="M_amet_c" stoichiometry="2"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nad_c"/>
- <speciesReference species="M_octapb_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2fe2s_c"/>
- <speciesReference species="M_dad_DASH_5_c" stoichiometry="2"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
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- <speciesReference species="M_met_DASH_L_c" stoichiometry="2"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPOt2pp" name="Lipoate transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lipoate_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LIPOtex" name="lipoate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipoate_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_lipoate_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LPADSS" name="Lipid A disaccaride synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0182</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: 2.4.1.182</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lipidX_c"/>
- <speciesReference species="M_u23ga_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lipidAds_c"/>
- <speciesReference species="M_udp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LPLIPAL1A120pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C12:0) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0494</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_1ddecg3p_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ddca_p"/>
- <speciesReference species="M_glyc3p_p"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LPLIPAL1A140pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:0) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0494</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_1tdecg3p_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glyc3p_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_ttdca_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <p>EC Number: 3.1.1.5</p>
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- <p>EC Number: 3.1.1.5</p>
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- <p>GENE_ASSOCIATION: b3825</p>
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- <p>GENE_ASSOCIATION: b3825</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: </p>
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- <p>EC Number: </p>
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- <notes>
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- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- <notes>
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- </body>
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- <notes>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LPLIPAL2G181" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3825</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2agpg181_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_g3pg_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ocdcea_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LSERDHr" name="L-serine dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1539</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nadp_c"/>
- <speciesReference species="M_ser_DASH_L_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2amsa_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYSDC" name="lysine decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0186 or b4131)</p>
- <p>SUBSYSTEM: Threonine and Lysine Metabolism</p>
- <p>EC Number: 4.1.1.18</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lys_DASH_L_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_15dap_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYSTRS" name="Lysyl-tRNA synthetase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4129 or b2890)</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_lys_DASH_L_c"/>
- <speciesReference species="M_trnalys_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_lystrna_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYSabcpp" name="L-lysine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2310 and b2307 and b2306 and b2308)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_lys_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lys_DASH_L_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYSt2pp" name="L-lysine transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2156</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_lys_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lys_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYSt3pp" name="L-lysine transport out via proton antiport (cytoplasm to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2923</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lys_DASH_L_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lys_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYStex" name="L-lysine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lys_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_lys_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYXI" name="Lyxose isomerase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3903</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lyx_DASH_L_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_xylu_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYXt2pp" name="L-Lyxose transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3907</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_lyx_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_lyx_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_LYXtex" name="L-Lyxose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_lyx_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_lyx_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_M1PD" name="mannitol-1-phosphate 5-dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3600</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.17</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mnl1p_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_f6p_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MACPD" name="Malonyl-ACP decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2323</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acACP_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALCOAMT" name="Malonyl-CoA methyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0777</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_amet_c"/>
- <speciesReference species="M_malcoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ahcys_c"/>
- <speciesReference species="M_malcoame_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALDDH" name="malate decarboxylating oxidoreductase (decarboxylating)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1800</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.83</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_D_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
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- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALDt2_2pp" name="D-Malate transport via proton symport (2 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3528</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p" stoichiometry="2"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_mal_DASH_D_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALDtex" name="D-Malate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mal_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALS" name="malate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4014 or b2976)</p>
- <p>SUBSYSTEM: Anaplerotic Reactions</p>
- <p>EC Number: 4.1.3.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_glx_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTATr" name="maltose O-acetyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0459</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.3.1.79</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_accoa_c"/>
- <speciesReference species="M_malt_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_acmalt_c"/>
- <speciesReference species="M_coa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTHXabcpp" name="maltohexaose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malthx_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malthx_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTHXtexi" name="maltohexaose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malthx_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_malthx_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTPTabcpp" name="maltopentaose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_maltpt_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_maltpt_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTPTtexi" name="maltopentaoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_maltpt_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_maltpt_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTTRabcpp" name="Maltotriose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malttr_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malttr_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTTRtexi" name="Maltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malttr_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_malttr_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTTTRabcpp" name="maltotetraose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_maltttr_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_maltttr_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTTTRtexi" name="maltotetraoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_maltttr_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_maltttr_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTabcpp" name="maltose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4034 and b4033 and b4032 and b4035)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malt_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malt_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTptspp" name="maltose transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2417 and b1621 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pep_c"/>
- <speciesReference species="M_malt_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_malt6p_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALTtexi" name="maltoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4036</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malt_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_malt_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALt2_2pp" name="Malate transport via proton symport (2 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3528</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p" stoichiometry="2"/>
- <speciesReference species="M_mal_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_mal_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALt2_3pp" name="Malate transport via proton symport (3 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4123 or b4138)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p" stoichiometry="3"/>
- <speciesReference species="M_mal_DASH_L_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="3"/>
- <speciesReference species="M_mal_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALt3pp" name="L-malate transport out via proton antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_h_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mal_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MALtex" name="Malate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mal_DASH_L_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MAN1PT2" name="mannose-1-phosphate guanylyltransferase (GDP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2049</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.7.7.22</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gdp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_man1p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gdpmann_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MAN6PI" name="mannose-6-phosphate isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1613</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_man6p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_f6p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MAN6Pt6_2pp" name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3666</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pi_c" stoichiometry="2"/>
- <speciesReference species="M_man6p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_man6p_c"/>
- <speciesReference species="M_pi_p" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <reaction id="R_MANAO" name="Mannonate oxidoreductase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4323</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.57</p>
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- </notes>
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- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
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- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MANGLYCptspp" name="2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0731 and b2415 and b2416)</p>
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- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MANGLYCtex" name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MANPGH" name="2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0732</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MANptspp" name="D-mannose transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1817 and b1818 and b1819 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_man_p"/>
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- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MANtex" name="D-mannose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_man_e"/>
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- <listOfProducts>
- <speciesReference species="M_man_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCITD" name="2-methylcitrate dehydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0334</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.79</p>
- </body>
- </notes>
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- <speciesReference species="M_2mcit_c"/>
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- <speciesReference species="M_2mcacn_c"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCITL2" name="methylisocitrate lyase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0331</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.3.30</p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCITS" name="2-methylcitrate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0333</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.3.31</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_oaa_c"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCOATA" name="Malonyl-CoA-ACP transacylase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b1092)</p>
- <p>SUBSYSTEM: Membrane Lipid Metabolism</p>
- <p>EC Number: 2.3.1.39</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_malcoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_coa_c"/>
- <speciesReference species="M_malACP_c"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCPST" name="3-mercaptopyruvate sulfurtransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2521</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: 2.8.1.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cyan_c"/>
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- </listOfReactants>
- <listOfProducts>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0084 or b0635 or b0149 or b3396)</p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MCTP1Bpp" name="murein crosslinking transpeptidase 1B:(A2pm->A2pm) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0149 or b3396)</p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_murein5p5p_p"/>
- </listOfReactants>
- <listOfProducts>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0084 or b0635 or b3396 or b0149)</p>
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- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0632 or b3182 or b0839 or b2010)</p>
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- </body>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0632 or b3182 or b0839 or b2010)</p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
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- </body>
- </notes>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDCP3pp" name="murein D,D-carboxypeptidase (murein5p5p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0632 or b3182 or b0839 or b2010)</p>
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- <p>EC Number: 3.4.16.4</p>
- </body>
- </notes>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0632 or b3182 or b0839 or b2010)</p>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDCP5pp" name="murein D,D-carboxypeptidase (murein5p3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0632 or b3182 or b0839 or b2010)</p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.16.4</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5p3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_p"/>
- <speciesReference species="M_murein4p3p_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDEP1pp" name="murein D,D-endopeptidase (murein4px4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3182 or b2328 or b2134)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein4px4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein4p4p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDEP2pp" name="murein D,D-endopeptidase (murein3px4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3182 or b2328 or b2134)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein3px4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein4p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDEP3pp" name="murein D,D-endopeptidase (murein5px4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3182 or b2328 or b2134)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5px4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein5p4p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDDEP4pp" name="murein D,D-endopeptidase (murein4px4px4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3182 or b2328 or b2134)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein4px4px4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein4px4p4p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDH" name="malate dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3236</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 1.1.1.37</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_oaa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDH2" name="Malate dehydrogenase (ubiquinone 8 as acceptor)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2210</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 1.1.99.16</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_q8_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_oaa_c"/>
- <speciesReference species="M_q8h2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MDH3" name="Malate dehydrogenase (menaquinone 8 as acceptor)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2210</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 1.1.99.16</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_mqn8_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_oaa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ME1" name="malic enzyme (NAD)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1479</p>
- <p>SUBSYSTEM: Anaplerotic Reactions</p>
- <p>EC Number: 1.1.1.38</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ME2" name="malic enzyme (NADP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2463</p>
- <p>SUBSYSTEM: Anaplerotic Reactions</p>
- <p>EC Number: 1.1.1.40</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_pyr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MECDPDH5" name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2895 and b2515) or (b0684 and b2515))</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2mecdp_c"/>
- <speciesReference species="M_flxr_c" stoichiometry="2"/>
- <speciesReference species="M_h_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_flxso_c" stoichiometry="2"/>
- <speciesReference species="M_h2mb4p_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MECDPS" name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2746</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2p4c2me_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2mecdp_c"/>
- <speciesReference species="M_cmp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MELIBt2pp" name="melibiose transport in via symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4120</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_melib_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_melib_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MELIBt3ipp" name="melibiose transport in via antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1528</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_melib_c"/>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_melib_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MELIBtex" name="melibiose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_melib_e"/>
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- <listOfProducts>
- <speciesReference species="M_melib_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MEOHtex" name="Methanol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b0929 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_meoh_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_meoh_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MEOHtrpp" name="Methanol reversible transport via diffusion (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_meoh_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_meoh_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MEPCT" name="2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2747</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2me4p_c"/>
- <speciesReference species="M_ctp_c"/>
- <speciesReference species="M_h_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_4c2me_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_METAT" name="methionine adenosyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2942</p>
- <p>SUBSYSTEM: Methionine Metabolism</p>
- <p>EC Number: 2.5.1.6</p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MGSA" name="methylglyoxal synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0963</p>
- <p>SUBSYSTEM: Methylglyoxal Metabolism</p>
- <p>EC Number: 4.2.3.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dhap_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mthgxl_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MI1PP" name="myo-inositol 1-phosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2533</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 3.1.3.25</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_mi1p_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_inost_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MICITDr" name="2-methylisocitrate dehydratase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0118</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.99</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2mcacn_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_micit_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MINCYCtex" name="Minocycline transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mincyc_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mincyc_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MINCYCtpp" name="Minocycline transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_mincyc_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mincyc_e"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MINOHPtexi" name="myo-inositol phosphate transport via diffusion (extracellular to periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_minohp_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_minohp_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDCP1App" name="murein L,D-carboxypeptidase (murein5px4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.17.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5px4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alaala_p"/>
- <speciesReference species="M_murein3px4p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDCP1Bpp" name="murein L,D-carboxypeptidase (murein4p4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.17.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein4p4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_p"/>
- <speciesReference species="M_murein4p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDCP2App" name="murein L,D-carboxypeptidase (murein5p5p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.17.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5p5p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alaala_p"/>
- <speciesReference species="M_murein5p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDCP2Bpp" name="murein L,D-carboxypeptidase (murein4p3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.17.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein4p3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ala_DASH_D_p"/>
- <speciesReference species="M_murein3p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDCP3App" name="murein L,D-carboxypeptidase (murein5px3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: 3.4.17.13</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5px3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_alaala_p"/>
- <speciesReference species="M_murein3px3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDEP1pp" name="murein L,D-endopeptidase (murein3px3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein3px3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein3p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLDEP2pp" name="murein L,D-endopeptidase (murein5px3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_murein5px3p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_murein5p3p_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTG1" name="Maltodextrin glucosidase (maltotriose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0403</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malttr_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_malt_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTG2" name="Maltodextrin glucosidase (maltotetraose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0403</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_maltttr_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_malttr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTG3" name="Maltodextrin glucosidase (maltopentaose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0403</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_maltpt_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_maltttr_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTG4" name="Maltodextrin glucosidase (maltohexaose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0403</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malthx_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_maltpt_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTG5" name="Maltodextrin glucosidase (maltoheptaose)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0403</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_malthp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c"/>
- <speciesReference species="M_malthx_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTGY1pp" name="murein lytic transglycosylase (murein4p4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2558 or b2963 or b4392 or b2813 or b2701 or b1193)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_murein4p4p_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_anhgm4p_p" stoichiometry="2"/>
- </listOfProducts>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1193 or b2558 or b2963 or b4392 or b2813 or b2701)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_murein4p3p_p"/>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTGY3pp" name="murein lytic transglycosylase (murein3p3p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1193 or b2963 or b2558 or b4392 or b2813 or b2701)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_murein3p3p_p"/>
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- <listOfProducts>
- <speciesReference species="M_anhgm3p_p" stoichiometry="2"/>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTGY4pp" name="murein lytic transglycosylase (murein4px4p4p) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2701 or b1193 or b2963 or b2558 or b4392 or b2813)</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_murein4px4p4p_p"/>
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- <listOfProducts>
- <speciesReference species="M_anhgm4p_p"/>
- <speciesReference species="M_murein4px4p_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTP1" name="Maltodextrin phosphorylase (maltopentaose)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3417</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_maltpt_c"/>
- <speciesReference species="M_pi_c"/>
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- <listOfProducts>
- <speciesReference species="M_g1p_c"/>
- <speciesReference species="M_maltttr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTP2" name="Maltodextrin phosphorylase (maltohexaose)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3417</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malthx_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_g1p_c"/>
- <speciesReference species="M_maltpt_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MLTP3" name="Maltodextrin phosphorylase (maltoheptaose)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3417</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_malthp_c"/>
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- <listOfProducts>
- <speciesReference species="M_g1p_c"/>
- <speciesReference species="M_malthx_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MMCD" name="Methylmalonyl-CoA decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2919</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mmcoa_DASH_S_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_ppcoa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MMETt2pp" name="S-methylmethionine permease (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0260</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_mmet_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mmet_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MMETtex" name="S-methyl-L-methionine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mmet_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mmet_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MMM" name="Methylmalonyl-CoA mutase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2917</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.4.99.2</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_succoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mmcoa_DASH_S_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MN2t3pp" name="manganese (Mn+2) transport out via proton antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3915 or b0752)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_mn2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MN2tpp" name="manganese transport in via permease (no H+)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3040</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_mn2_p"/>
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- <listOfProducts>
- <speciesReference species="M_mn2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MN6PP" name="mannose 6-phosphate phosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0822</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_man_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MNLptspp" name="mannitol transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3599 and b2415 and b2416)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pep_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mnl1p_c"/>
- <speciesReference species="M_pyr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MNLtex" name="mannitol transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mnl_e"/>
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- <listOfProducts>
- <speciesReference species="M_mnl_p"/>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- <reaction id="R_MNNH" name="D-mannonate hydrolyase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4322</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mana_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2ddglcn_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MNt2pp" name="manganese (Mn+2) transport in via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2392</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_mn2_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- </notes>
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- <speciesReference species="M_mn2_e"/>
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- <speciesReference species="M_mn2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </reaction>
- <reaction id="R_MOADSUx" name="MoaD sulfuration (nadh, assumed)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2530 and b0784)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_iscssh_c"/>
- <speciesReference species="M_moadamp_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3633</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3633</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3624</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_MOBDabcpp" name="molybdate transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0763 and b0764 and b0765) or (b2422 and b2424 and b2423 and b3917) or (b2422 and b2425 and b2424 and b2423))</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <reaction id="R_MOBDtex" name="molybdate transport via diffusion (extracellular to periplasm)">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2877</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_mococdp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0827</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3857 or (b3857 and b3856))</p>
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- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0134</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.1.2.11</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_2dhp_c"/>
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- </reaction>
- <reaction id="R_MOX" name="malate oxidase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 1.1.3.3</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mal_DASH_L_c"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0009</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b3396 and b1069) or (b0149 and b1069) or (b1069 and b2519))</p>
- <p>SUBSYSTEM: Murein Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <p>EC Number: </p>
- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1008 or b1539)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0159</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 3.2.2.16</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0529</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 3.5.4.9</p>
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- </kineticLaw>
- </reaction>
- <reaction id="R_MTHFD" name="methylenetetrahydrofolate dehydrogenase (NADP)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0529</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 1.5.1.5</p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MTHFR2" name="5,10-methylenetetrahydrofolate reductase (NADH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3941</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 1.5.1.20</p>
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- </notes>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Methionine Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_MTRPOX" name="N-methyltryptophan oxidase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1059</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: 1.5.3.2</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_fald_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_N2Otex" name="nitrious oxide transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_n2o_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </reaction>
- <reaction id="R_N2Otpp" name="nitrious oxide transport (diffusion)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_n2o_p"/>
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- <speciesReference species="M_n2o_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NACODA" name="N-acetylornithine deacetylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3957</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acg5sa_c"/>
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- <listOfProducts>
- <speciesReference species="M_ac_c"/>
- <speciesReference species="M_glu5sa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NACtex" name="Nicotinic acid transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nac_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_nac_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NACtpp" name="Nicotinic acid uptake (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nac_p"/>
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- <speciesReference species="M_nac_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3996 or b2411)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.6.1.22</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1109</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.5.3</p>
- </body>
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- <listOfReactants>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.5.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.5.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2276 and b2277 and b2278 and b2279 and b2280 and b2281 and b2282 and b2283 and b2284 and b2285 and b2286 and b2287 and b2288)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.5.3</p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1109</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1109</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2615</p>
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- <p>EC Number: 2.7.1.23</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.2.2.5</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3028</p>
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- <p>EC Number: 1.6.99.6</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3028</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.99.6</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3028</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.6.99.6</p>
- </body>
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- <speciesReference species="M_2dmmql8_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- <reaction id="R_NADS1" name="NAD synthase (nh3)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1740</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 6.3.1.5</p>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <reaction id="R_NADTRHD" name="NAD transhydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3962 or (b1602 and b1603))</p>
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- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </reaction>
- <reaction id="R_NAMNPP" name="nicotinic acid mononucleotide pyrophosphorylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0931</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.4.2.11</p>
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- <speciesReference species="M_nac_c"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_NAt3_1p5pp" name="sodium proton antiporter (H:NA is 1.5) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1186</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_na1_c" stoichiometry="2"/>
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- <speciesReference species="M_h_c" stoichiometry="3"/>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0019</p>
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- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0842 or b1216)</p>
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- <p>EC Number: </p>
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- <ci> FLUX_VALUE </ci>
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- </reaction>
- <reaction id="R_NAtex" name="sodium transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
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- </body>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2518 or b0474)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2518 or b0474)</p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.7.4.6</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0474 or b2518)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.7.4.6</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0451 or s0001)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2710 and b2711)</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3469</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3915 or b0752)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
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- </reaction>
- <reaction id="R_NI2tpp" name="nickel (+2) transport in via permease (no H+)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3816</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <reaction id="R_NI2uabcpp" name="nickel transport via ABC system (uptake, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b3476 and b3477 and b3478 and b3479 and b3480) or b4242)</p>
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- <p>EC Number: </p>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4390 or b0639)</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0751</p>
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- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NNDPR" name="nicotinate-nucleotide diphosphorylase (carboxylating)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0109</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.4.2.19</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_prpp_c"/>
- <speciesReference species="M_quln_c"/>
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- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nicrnt_c"/>
- <speciesReference species="M_ppi_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO2t2rpp" name="nitrite transport in via proton symport, reversible (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3367 or b1223)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_no2_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO2tex" name="nitrite transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no2_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_no2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3R1bpp" name="Nitrate reductase (Ubiquinol-8)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2203 and b2206) and b2202 and b2205 and b2204)</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 1.7.99.4</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_q8h2_c"/>
- <speciesReference species="M_no3_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_q8_c"/>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_no2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3R1pp" name="Nitrate reductase (Ubiquinol-8) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1465 and b1466 and b1467 and b1468) or (b1224 and b1225 and b1226 and b1227))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.7.99.4</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_no3_c"/>
- <speciesReference species="M_q8h2_c"/>
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- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_no2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3R2bpp" name="Nitrate reductase (Menaquinol-8) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2203 and b2206) and b2202)</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 1.7.99.4</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_no3_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_mqn8_c"/>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_no2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3R2pp" name="Nitrate reductase (Menaquinol-8) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1465 and b1466 and b1467 and b1468) or (b1224 and b1225 and b1226 and b1227))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_mql8_c"/>
- <speciesReference species="M_no3_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_mqn8_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3t7pp" name="nitrate transport in via nitrite antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1223 or b1469)</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no2_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_no3_c"/>
- <speciesReference species="M_no2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NO3tex" name="nitrate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b0241 or b0929 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no3_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_no3_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NODOx" name="nitric oxide dioxygenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2552</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 1.14.12.17</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_no_c" stoichiometry="2"/>
- <speciesReference species="M_o2_c" stoichiometry="2"/>
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- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nad_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NODOy" name="nitric oxide dioxygenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2552</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: 1.14.12.17</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_no_c" stoichiometry="2"/>
- <speciesReference species="M_o2_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NOVBCNtex" name="Novobiocin transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_novbcn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_novbcn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NOVBCNtpp" name="Novobiocin transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_novbcn_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_no_e"/>
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- <listOfProducts>
- <speciesReference species="M_no_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <listOfProducts>
- <speciesReference species="M_no_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2291 or b2744 or b4374)</p>
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- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_duri_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2744</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- </body>
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- <listOfReactants>
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- <listOfProducts>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2744</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_imp_c"/>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD11pp" name="5'-nucleotidase (IMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD12" name="5'-nucleotidase (dIMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2291 or b2744)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dimp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_din_c"/>
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- <kineticLaw>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD12pp" name="5'-nucleotidase (dIMP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
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- <listOfProducts>
- <speciesReference species="M_din_p"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD1pp" name="5'-nucleotidase (dUMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dump_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_duri_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD2" name="5'-nucleotidase (UMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2744 or b4374)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_ump_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_uri_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD2pp" name="5'-nucleotidase (UMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_p"/>
- <speciesReference species="M_ump_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_p"/>
- <speciesReference species="M_uri_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD3" name="5'-nucleotidase (dCMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2744 or b2291)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dcmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dcyt_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD3pp" name="5'-nucleotidase (dCMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dcmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dcyt_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD4" name="5'-nucleotidase (CMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2744</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cytd_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD4pp" name="5'-nucleotidase (CMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_cmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cytd_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD5" name="5'-nucleotidase (dTMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2291 or b2744 or b4374)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dtmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_thymd_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD5pp" name="5'-nucleotidase (dTMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dtmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_p"/>
- <speciesReference species="M_thymd_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD6" name="5'-nucleotidase (dAMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2291 or b2744)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_damp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dad_DASH_2_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD6pp" name="5'-nucleotidase (dAMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_damp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dad_DASH_2_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD7" name="5'-nucleotidase (AMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2744</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_amp_c"/>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adn_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD7pp" name="5'-nucleotidase (AMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_amp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adn_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD8" name="5'-nucleotidase (dGMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2291 or b2744)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dgmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dgsn_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD8pp" name="5'-nucleotidase (dGMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dgmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dgsn_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD9" name="5'-nucleotidase (GMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2744</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gmp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gsn_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTD9pp" name="5'-nucleotidase (GMP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0480 or b4055)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gmp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gsn_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP1" name="nucleoside-triphosphatase (ATP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0650 or b4161)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP10" name="nucleoside-triphosphatase (ITP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4161 or b4394)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_itp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_idp_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP11" name="nucleoside-triphosphatase (dITP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4394</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ditp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_didp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP12" name="nucleoside-triphosphatase (XTP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4394</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_xtp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_xdp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP3" name="nucleoside-triphosphatase (GTP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4161</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gtp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gdp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP3pp" name="nucleoside-triphosphatase (GTP) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0980</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gtp_p"/>
- <speciesReference species="M_h2o_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gdp_p"/>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_pi_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTP5" name="nucleoside-triphosphatase (CTP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4161</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ctp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cdp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP1" name="Nucleoside triphosphate pyrophosphorylase (dgtp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0099 or b2781)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dgtp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dgmp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP10" name="Nucleoside triphosphate pyrophosphorylase (ditp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2954</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.19</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ditp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dimp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP11" name="Nucleoside triphosphate pyrophosphorylase (xtp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2954</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.19</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_xtp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- <speciesReference species="M_xmp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP2" name="Nucleoside triphosphate pyrophosphorylase (gtp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0099 or b2781)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gtp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gmp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP3" name="Nucleoside triphosphate pyrophosphorylase (dctp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2781 or b2251 or b1759)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dctp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dcmp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP4" name="Nucleoside triphosphate pyrophosphorylase (ctp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1759 or b2781)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ctp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cmp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP5" name="Nucleoside triphosphate pyrophosphorylase (datp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2781 or b1865)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_datp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_damp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP6" name="Nucleoside triphosphate pyrophosphorylase (atp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2781</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_amp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP7" name="Nucleoside triphosphate pyrophosphorylase (dttp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2781 or b2251)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_dttp_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dtmp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP8" name="Nucleoside triphosphate pyrophosphorylase (utp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2781</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_utp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_ppi_c"/>
- <speciesReference species="M_ump_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_NTPP9" name="Nucleoside triphosphate pyrophosphorylase (itp)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2954</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.6.1.19</p>
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- </notes>
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- <speciesReference species="M_imp_c"/>
- <speciesReference species="M_ppi_c"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_NTPTP1" name="Nucleoside triphosphate tripolyhydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0160</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.5.1</p>
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- <listOfReactants>
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- <speciesReference species="M_pppi_c"/>
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- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_NTPTP2" name="Nucleoside triphosphate tripolyhydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0160</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 3.1.5.1</p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </reaction>
- <reaction id="R_NTRIR2x" name="nitrite Reductase (NADH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3365 and b3366)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="5"/>
- <speciesReference species="M_nadh_c" stoichiometry="3"/>
- <speciesReference species="M_no2_c"/>
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- <listOfProducts>
- <speciesReference species="M_h2o_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_NTRIR3pp" name="nitrite Reductase (Ubiquinole-8, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4070 and b4071 and b4072 and b4073)</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
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- <reaction id="R_NTRIR4pp" name="nitrite Reductase (Menaquinole-8, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4070 and b4071 and b4072 and b4073)</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_mql8_c" stoichiometry="3"/>
- <speciesReference species="M_h_p" stoichiometry="2"/>
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- <listOfProducts>
- <speciesReference species="M_mqn8_c" stoichiometry="3"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <reaction id="R_O16A4COLIPAabctex" name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3200 and b3201 and b3199 and b4261 and b4262)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_o16a4colipa_p"/>
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- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_O16A4Lpp" name="O16 anitgen (x4) ligase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3622</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_colipa_p"/>
- <speciesReference species="M_o16a4und_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_o16a4colipa_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_O16AP1pp" name="O16 antigen polymerase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2035 and b2027)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_o16aund_p" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_o16a2und_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_O16AP2pp" name="O16 antigen polymerase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2035 and b2027)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_o16a2und_p"/>
- <speciesReference species="M_o16aund_p"/>
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- <speciesReference species="M_o16a3und_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2035 and b2027)</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2033</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
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- <speciesReference species="M_ragund_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_aragund_c"/>
- <speciesReference species="M_coa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2037</p>
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- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_o16aund_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2034</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2032</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
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- <p>EC Number: </p>
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- </notes>
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- <speciesReference species="M_o2s_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
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- <speciesReference species="M_o2_e"/>
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- <listOfProducts>
- <speciesReference species="M_o2_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1850</p>
- <p>SUBSYSTEM: Pyruvate Metabolism</p>
- <p>EC Number: 4.1.1.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (((b0902 and b0903) and b2579) or (b0902 and b0903) or (b0902 and b3114))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4254 or b0273)</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 2.1.3.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2344</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2344</p>
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- <p>EC Number: </p>
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- </reaction>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3187</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4386</p>
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- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0180</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 4.2.1.59</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1091</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0907</p>
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- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3833</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1281</p>
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- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_ump_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OMPHHX" name="2-octaprenyl-6-methoxyphenol hydroxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2907</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2omph_c"/>
- <speciesReference species="M_o2_c" stoichiometry="0.5"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2ombzl_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OMPHHX3" name="2-octaprenyl-6-methoxyphenol hydroxylase (anaerobic)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2omph_c"/>
- <speciesReference species="M_atp_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c" stoichiometry="3"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2ombzl_c"/>
- <speciesReference species="M_adp_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="3"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_pi_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OP4ENH" name="2-oxopent-4-enoate hydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0350</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.2.1.80</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_op4en_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_4h2opntn_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPHBDC" name="Octaprenyl-hydroxybenzoate decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3843 and b2311)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_3ophb_c"/>
- <speciesReference species="M_h_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2oph_c"/>
- <speciesReference species="M_co2_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPHHX" name="2-Octaprenylphenol hydroxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3835</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2oph_c"/>
- <speciesReference species="M_o2_c" stoichiometry="0.5"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2ohph_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPHHX3" name="2-Octaprenylphenol hydroxylase (anaerobic)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2oph_c"/>
- <speciesReference species="M_atp_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c" stoichiometry="3"/>
- <speciesReference species="M_nad_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2ohph_c"/>
- <speciesReference species="M_adp_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="3"/>
- <speciesReference species="M_nadh_c"/>
- <speciesReference species="M_pi_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPMEACPD" name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0180</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 4.2.1.59</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_hpmeACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_epmeACP_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPMEACPR" name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1093</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.1.1.100</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
- <speciesReference species="M_opmeACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_hpmeACP_c"/>
- <speciesReference species="M_nadp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OPMEACPS" name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2323</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.3.1.41</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gmeACP_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_malACP_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ACP_c"/>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_opmeACP_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ORNDC" name="Ornithine Decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2965 or b0693)</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 4.1.1.17</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_orn_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_ptrc_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ORNabcpp" name="ornithine transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2310 and b2307 and b2306 and b2308)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_orn_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_orn_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ORNtex" name="ornithine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_orn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_orn_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OROTt2_2pp" name="Orotate transport via proton symport (2 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3528</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p" stoichiometry="2"/>
- <speciesReference species="M_orot_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_orot_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OROTtex" name="Orotate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_orot_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_orot_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_ORPT" name="orotate phosphoribosyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3642</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 2.4.2.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_orot5p_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_orot_c"/>
- <speciesReference species="M_prpp_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OXAMTC" name="oxamate transcarbamoylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: 2.1.3.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_oxur_c"/>
- <speciesReference species="M_pi_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_cbp_c"/>
- <speciesReference species="M_oxam_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OXCDC" name="Oxalyl-CoA decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2373</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.1.8</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_oxalcoa_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_forcoa_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_OXCOAHDH" name="oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1387</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2oxpaccoa_c"/>
- <speciesReference species="M_h2o_c" stoichiometry="2"/>
- <speciesReference species="M_nadp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_3oxdhscoa_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
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- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1394 and b1397)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1014</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 1.5.1.12</p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
- <listOfParameters>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0386</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 1.5.1.2</p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PA120abcpp" name="phosphatidate transport via ABC system (n-C12:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PA140abcpp" name="phosphatidate transport via ABC system (n-C14:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PA141abcpp" name="phosphatidate transport via ABC system (n-C14:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PA160abcpp" name="phosphatidate transport via ABC system (n-C16:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PA161abcpp" name="phosphatidate transport via ABC system (n-C16:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_pa161_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PA180abcpp" name="phosphatidate transport via ABC system (n-C18:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_pa180_c"/>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PA181abcpp" name="phosphatidate transport via ABC system (n-C18:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_pa181_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </reaction>
- <reaction id="R_PACALDt2rpp" name="phenylacetaldehyde reversible transport via proton symport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <speciesReference species="M_pacald_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pacald_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1388 and b1389 and b1390 and b1391 and b1392)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1398</p>
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- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0133</p>
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- <p>EC Number: 6.3.2.1</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
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- <p>EC Number: 3.1.3.4</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.3.4</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.3.4</p>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PAPA160pp" name="Phosphatidate phosphatase (periplasmic, n-C16:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.3.4</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- <reaction id="R_PAPA161pp" name="Phosphatidate phosphatase (periplasmic, n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </reaction>
- <reaction id="R_PAPA180" name="Phosphatidate phosphatase (n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </reaction>
- <reaction id="R_PAPA180pp" name="Phosphatidate phosphatase (periplasmic, n-C18:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- </reaction>
- <reaction id="R_PAPA181" name="Phosphatidate phosphatase (n-C18:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 3.1.3.4</p>
- </body>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1278</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2762 and b2582) or (b2762 and b3781))</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
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- </body>
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- <notes>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1489</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0114 and b0115 and b0116)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1638</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.4.3.5</p>
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- <p>GENE_ASSOCIATION: (b0052 and b2564)</p>
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- <p>GENE_ASSOCIATION: b0766</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </reaction>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1386</p>
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- <notes>
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- <notes>
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- <p>GENE_ASSOCIATION: b3546</p>
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- <notes>
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- <notes>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0902 and b0903) or (b0902 and b3114) or (b3951 and b3952) or ((b0902 and b0903) and b2579))</p>
- <p>SUBSYSTEM: Pyruvate Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PG141abcpp" name="phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PG160abcpp" name="phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PG161abcpp" name="phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PG180abcpp" name="phosphatidylglycerol transport via ABC system (n-C18:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PG181abcpp" name="phosphatidylglycerol transport via ABC system (n-C18:1, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PGAMT" name="phosphoglucosamine mutase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3176</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 5.4.2.10</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gam1p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gam6p_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PGCD" name="phosphoglycerate dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2913</p>
- <p>SUBSYSTEM: Glycine and Serine Metabolism</p>
- <p>EC Number: 1.1.1.95</p>
- </body>
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- <listOfProducts>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PGI" name="glucose-6-phosphate isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4025</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2926</p>
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- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0767</p>
- <p>SUBSYSTEM: Pentose Phosphate Pathway</p>
- <p>EC Number: 3.1.1.31</p>
- </body>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3385</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3612 or b4395 or b0755)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: </p>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
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- <p>GENE_ASSOCIATION: b0914</p>
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- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PGP180abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0914</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PGPP120" name="phosphatidylglycerol phosphate phosphatase (n-C14:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1278 or b0418)</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
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- </reaction>
- <reaction id="R_PGPP140" name="phosphatidylglycerol phosphate phosphatase (n-C14:0)" reversible="false">
- <notes>
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- <p>GENE_ASSOCIATION: (b1278 or b0418)</p>
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- <notes>
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- <p>GENE_ASSOCIATION: (b0418 or b1278)</p>
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- </reaction>
- <reaction id="R_PGPP141" name="phosphatidylglycerol phosphate phosphatase (n-C14:1)" reversible="false">
- <notes>
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- <reaction id="R_PGPP160" name="phosphatidylglycerol phosphate phosphatase (n-C16:0)" reversible="false">
- <notes>
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- <p>GENE_ASSOCIATION: (b0418 or b1278)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.7.8.5</p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PGSA161" name="Phosphatidylglycerol synthase (n-C16:1)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
- <p>EC Number: 2.7.8.5</p>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1912</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2201 and b2200 and b2199 and b2198 and b2197)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_pheme_c"/>
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- <speciesReference species="M_adp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PHEMEtiex" name="protoheme transport irreversible out via diffusion (periplasm to extracellular)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_pheme_p"/>
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- <listOfProducts>
- <speciesReference species="M_pheme_e"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4054 or b0928 or b3770)</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 2.6.1.58</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_akg_c"/>
- <speciesReference species="M_phe_DASH_L_c"/>
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- <listOfProducts>
- <speciesReference species="M_glu_DASH_L_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1713 and b1714)</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.20</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
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- <listOfProducts>
- <speciesReference species="M_amp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1473 or b0112 or b0576)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0980</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2987 or b3493)</p>
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- <p>EC Number: </p>
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- <ci> FLUX_VALUE </ci>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3726 and b3725 and b3727 and b3728)</p>
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- <p>EC Number: </p>
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- </notes>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3821</p>
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- <p>EC Number: 3.1.1.32</p>
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- <ci> FLUX_VALUE </ci>
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- <p>GENE_ASSOCIATION: b3821</p>
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- <p>EC Number: 3.1.1.32</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3821</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3821</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3821</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2048</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.4.2.8</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3412</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2103</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.7.4.7</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3974</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.7.1.33</p>
- </body>
- </notes>
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- <speciesReference species="M_pnto_DASH_R_c"/>
- </listOfReactants>
- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3258</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_na1_p"/>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1010</p>
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- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>EC Number: 3.6.1.1</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PPALtpp" name="propanal transport via channel (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1015</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b0929 or b2215 or b0241)</p>
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- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0369</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 4.2.1.24</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3956</p>
- <p>SUBSYSTEM: Anaplerotic Reactions</p>
- <p>EC Number: 4.1.1.31</p>
- </body>
- </notes>
- <listOfReactants>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3639</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 4.1.1.36</p>
- </body>
- </notes>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PPCK" name="phosphoenolpyruvate carboxykinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3403</p>
- <p>SUBSYSTEM: Anaplerotic Reactions</p>
- <p>EC Number: 4.1.1.49</p>
- </body>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2920</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3650</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.1.7.2</p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PPK2r" name="polyphosphate kinase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2501</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 2.7.4.1</p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2501</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3380 or b4383)</p>
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4383</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3639</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2600</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2538 and b2539 and b2540 and b2542)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2536</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
- <reaction id="R_PPPNtex" name="3-phenylpropionate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PPS" name="phosphoenolpyruvate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1702</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 2.7.9.2</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_pyr_c"/>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0383</p>
- <p>SUBSYSTEM: Unassigned</p>
- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PPTtex" name="Phosphonate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_ppt_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PRAGSr" name="phosphoribosylglycinamide synthase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4005</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.4.13</p>
- </body>
- </notes>
- <listOfReactants>
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- <speciesReference species="M_gly_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PRAIS" name="phosphoribosylaminoimidazole synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2499</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.3.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_fpram_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PRAIi" name="phosphoribosylanthranilate isomerase (irreversible)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1262</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 5.3.1.24</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_pran_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2cpr5p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PRAMPC" name="phosphoribosyl-AMP cyclohydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2026</p>
- <p>SUBSYSTEM: Histidine Metabolism</p>
- <p>EC Number: 3.5.4.19</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_prbamp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_prfp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PRASCSi" name="phosphoribosylaminoimidazolesuccinocarboxamide synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2476</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.2.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5aizc_c"/>
- <speciesReference species="M_asp_DASH_L_c"/>
- <speciesReference species="M_atp_c"/>
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- <listOfProducts>
- <speciesReference species="M_25aics_c"/>
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- <ci> FLUX_VALUE </ci>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2026</p>
- <p>SUBSYSTEM: Histidine Metabolism</p>
- <p>EC Number: 3.6.1.31</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2557</p>
- <p>SUBSYSTEM: Purine and Pyrimidine Biosynthesis</p>
- <p>EC Number: 6.3.5.3</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2024</p>
- <p>SUBSYSTEM: Histidine Metabolism</p>
- <p>EC Number: 5.3.1.16</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1014</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 1.5.99.8</p>
- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3544 and b3543 and b3542 and b3541 and b3540)</p>
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- </body>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
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- <speciesReference species="M_progly_e"/>
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- <speciesReference species="M_progly_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0194</p>
- <p>SUBSYSTEM: tRNA Charging</p>
- <p>EC Number: 6.1.1.15</p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
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- <reaction id="R_PROabcpp" name="L-proline transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2677 and b2678 and b2679)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </notes>
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- <speciesReference species="M_pro_DASH_L_p"/>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4111</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1015</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1207</p>
- <p>SUBSYSTEM: Histidine Metabolism</p>
- <p>EC Number: 2.7.6.1</p>
- </body>
- </notes>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
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- <reaction id="R_PSCLYSt2pp" name="psicoselysine transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3370</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0241 or b0929)</p>
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- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_PSCVT" name="3-phosphoshikimate 1-carboxyvinyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0908</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: 2.5.1.19</p>
- </body>
- </notes>
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- </listOfParameters>
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- </reaction>
- <reaction id="R_PSD120" name="Phosphatidylserine decarboxylase (n-C12:0)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4160</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4160</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4160</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4160</p>
- <p>SUBSYSTEM: Glycerophospholipid Metabolism</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4160</p>
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- </body>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4388</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2407 or b4384)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.4.2.1</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2407 or b4384)</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2407 or b4384)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2407</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1638</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 1.4.3.5</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2418</p>
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- <p>GENE_ASSOCIATION: (b2215 or b0929 or b1377 or b0241)</p>
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- <p>GENE_ASSOCIATION: </p>
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- </body>
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- <notes>
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- <p>GENE_ASSOCIATION: b2418</p>
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- <notes>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3029</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3029</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_QUIN2tex" name="Quinate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_quin_e"/>
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- <listOfProducts>
- <speciesReference species="M_quin_p"/>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_QUIN2tpp" name="Quinate transport (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_quin_p"/>
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- <listOfProducts>
- <speciesReference species="M_quin_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_QUINDH" name="Quinate dehydrogenase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1692</p>
- <p>SUBSYSTEM: Tyrosine, Tryptophan, and Phenylalanine Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_nad_c"/>
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- <listOfProducts>
- <speciesReference species="M_3dhq_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_QULNS" name="quinolinate synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0750</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_dhap_c"/>
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- <speciesReference species="M_h2o_c" stoichiometry="2"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4094</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0822</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfProducts>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_R5PPpp" name="ribose 5-phosphate phosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4055</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_r5p_e"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0025</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.7.1.26</p>
- </body>
- </notes>
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- <listOfProducts>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RBFSa" name="riboflavin synthase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1662</p>
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- <p>EC Number: 2.5.1.9</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0415</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3752</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0063</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1394</p>
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- </reaction>
- <reaction id="R_RFAMPtex" name="Rifampin transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: s0001</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_rfamp_e"/>
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- <listOfProducts>
- <speciesReference species="M_rfamp_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RFAMPtpp" name="Rifampin transport via TolC system" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_h_p"/>
- <speciesReference species="M_rfamp_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_rfamp_e"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RHAT1" name="rhamnosyltransferase I (LPS core biosynthesis)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3629</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_dtdprmn_c"/>
- <speciesReference species="M_kphphhlipa_c"/>
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- <listOfProducts>
- <speciesReference species="M_dtdp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_icolipa_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RHCCE" name="S-ribosylhomocysteine cleavage enzyme" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2687</p>
- <p>SUBSYSTEM: Methionine Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rhcys_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dhptd_c"/>
- <speciesReference species="M_hcys_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RIBabcpp" name="D-ribose transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b4231 and b4227 and b4485 and b4230) or (b3749 and b3751 and b3750 and b3748) or (b4087 and b4088 and b4086))</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_rib_DASH_D_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RIBtex" name="ribose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rib_DASH_D_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_rib_DASH_D_p"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RMI" name="L-rhamnose isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3903</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.14</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rmn_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_rml_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RMK" name="rhamnulokinase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3904</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_rml_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_rml1p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RMNtex" name="L-rhamnose transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b0241 or b0929 or b1377)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rmn_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_rmn_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RMNtpp" name="L-rhamnose transport via proton symport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3907</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_p"/>
- <speciesReference species="M_rmn_p"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_rmn_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RMPA" name="Rhamnulose-1-phosphate aldolase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3902</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 4.1.2.19</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_rml1p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dhap_c"/>
- <speciesReference species="M_lald_DASH_L_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNDR1" name="ribonucleoside-diphosphate reductase (ADP)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (((b2234 and b2235) and b2582) or ((b2234 and b2235) and b3781))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 1.17.4.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_trdrd_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dadp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNDR1b" name="ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1064 and (b2675 and b2676)) or (b3610 and (b2675 and b2676)) or (b1654 and (b2675 and b2676)) or (b0849 and (b2675 and b2676)))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_adp_c"/>
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- <listOfProducts>
- <speciesReference species="M_dadp_c"/>
- <speciesReference species="M_grxox_c"/>
- <speciesReference species="M_h2o_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (((b2234 and b2235) and b3781) or ((b2234 and b2235) and b2582))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 1.17.4.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_gdp_c"/>
- <speciesReference species="M_trdrd_c"/>
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- <listOfProducts>
- <speciesReference species="M_dgdp_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNDR2b" name="ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0849 and (b2675 and b2676)) or (b3610 and (b2675 and b2676)) or (b1064 and (b2675 and b2676)) or (b1654 and (b2675 and b2676)))</p>
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- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_gdp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (((b2234 and b2235) and b3781) or ((b2234 and b2235) and b2582))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 1.17.4.1</p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_cdp_c"/>
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- <listOfProducts>
- <speciesReference species="M_dcdp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- <reaction id="R_RNDR3b" name="ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0849 and (b2675 and b2676)) or (b3610 and (b2675 and b2676)) or (b1654 and (b2675 and b2676)) or (b1064 and (b2675 and b2676)))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (((b2234 and b2235) and b3781) or ((b2234 and b2235) and b2582))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- <listOfReactants>
- <speciesReference species="M_trdrd_c"/>
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- <listOfProducts>
- <speciesReference species="M_dudp_c"/>
- <speciesReference species="M_h2o_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
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- <reaction id="R_RNDR4b" name="ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0849 and (b2675 and b2676)) or (b1064 and (b2675 and b2676)) or (b3610 and (b2675 and b2676)) or (b1654 and (b2675 and b2676)))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_grxrd_c"/>
- <speciesReference species="M_udp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dudp_c"/>
- <speciesReference species="M_grxox_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNTR1c2" name="ribonucleoside-triphosphate reductase (ATP) (flavodoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0684 and b3924 and b4238 and b4237) or (b2895 and b3924 and b4238 and b4237) or (b0684 and b4238) or (b2895 and b4238))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_flxr_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_datp_c"/>
- <speciesReference species="M_flxso_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNTR2c2" name="ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0684 and b3924 and b4238 and b4237) or (b2895 and b3924 and b4238 and b4237) or (b0684 and b4238) or (b2895 and b4238))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_flxr_c" stoichiometry="2"/>
- <speciesReference species="M_gtp_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dgtp_c"/>
- <speciesReference species="M_flxso_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNTR3c2" name="ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0684 and b3924 and b4238 and b4237) or (b2895 and b3924 and b4238 and b4237) or (b0684 and b4238) or (b2895 and b4238))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ctp_c"/>
- <speciesReference species="M_flxr_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dctp_c"/>
- <speciesReference species="M_flxso_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RNTR4c2" name="ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0684 and b3924 and b4238 and b4237) or (b2895 and b3924 and b4238 and b4237) or (b0684 and b4238) or (b2895 and b4238))</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_flxr_c" stoichiometry="2"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_utp_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_dutp_c"/>
- <speciesReference species="M_flxso_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RPE" name="ribulose 5-phosphate 3-epimerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4301 or b3386)</p>
- <p>SUBSYSTEM: Pentose Phosphate Pathway</p>
- <p>EC Number: 5.1.3.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_ru5p_DASH_D_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_xu5p_DASH_D_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RPI" name="ribose-5-phosphate isomerase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2914 or b4090)</p>
- <p>SUBSYSTEM: Pentose Phosphate Pathway</p>
- <p>EC Number: 5.3.1.6</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_r5p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_ru5p_DASH_D_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_RZ5PP" name="alpha-ribazole 5-phosphate phosphatase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0638</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_5prdmbz_c"/>
- <speciesReference species="M_h2o_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_rdmbzi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S2FE2SR" name="SUF [2Fe-2S] regeneration" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1683 and b1682 and b1681 and b1679 and b1680)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_2fe1s_c"/>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_sufbcd_c"/>
- <speciesReference species="M_sufsesh_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_h_c" stoichiometry="5"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s_c"/>
- <speciesReference species="M_sufse_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S2FE2SS" name="SUF [2Fe-2S] Synthesis" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3807 and b1683 and b1682 and b1681 and b1679 and b1680)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_sufbcd_c"/>
- <speciesReference species="M_sufsesh_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_h_c" stoichiometry="7"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s_c"/>
- <speciesReference species="M_sufse_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S2FE2SS2" name="SUF [2Fe-2S] Synthesis II" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3807 and b1683 and b1682 and b1681 and b1679 and b1680)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_fe2_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s_c"/>
- <speciesReference species="M_sufsesh_c" stoichiometry="2"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_adp_c"/>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_h_c" stoichiometry="7"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s2_c"/>
- <speciesReference species="M_sufse_c" stoichiometry="2"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S2FE2ST" name="SUF [2Fe-2S] Transfer" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1684 and b1683 and b1682 and b1681)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="4"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_2fe2s_c"/>
- <speciesReference species="M_sufbcd_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S4FE4SR" name="SUF [4Fe-4S] Reduction" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1683 and b1682 and b1681)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_fadh2_c"/>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_sufbcd_DASH_2fe2s2_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_fad_c"/>
- <speciesReference species="M_sufbcd_DASH_4fe4s_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S4FE4ST" name="SUF [4Fe-4S] Transfer" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1684 and b1683 and b1682 and b1681)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="4"/>
- <speciesReference species="M_sufbcd_DASH_4fe4s_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_4fe4s_c"/>
- <speciesReference species="M_sufbcd_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_S7PI" name="sedoheptulose 7-phosphate isomerase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0222</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_s7p_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_gmhep7p_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SADH" name="Succinylarginine dihydrolase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1745</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: 2.6.1.69</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c" stoichiometry="2"/>
- <speciesReference species="M_h2o_c" stoichiometry="2"/>
- <speciesReference species="M_sucarg_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_co2_c"/>
- <speciesReference species="M_nh4_c" stoichiometry="2"/>
- <speciesReference species="M_sucorn_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SADT2" name="Sulfate adenyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2751 and b2752)</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_gtp_c"/>
- <speciesReference species="M_h2o_c"/>
- <speciesReference species="M_so4_c"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_aps_c"/>
- <speciesReference species="M_gdp_c"/>
- <speciesReference species="M_pi_c"/>
- <speciesReference species="M_ppi_c"/>
- </listOfProducts>
- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: (b1679 and b1680)</p>
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- <p>GENE_ASSOCIATION: b2472</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: (b2796 or b3116)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3089</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <p>GENE_ASSOCIATION: (b2422 and b2425 and b2424 and b2423)</p>
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- <p>GENE_ASSOCIATION: s0001</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1206</p>
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- <p>EC Number: </p>
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- </listOfParameters>
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- </reaction>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1748</p>
- <p>SUBSYSTEM: Arginine and Proline Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1584</p>
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- <p>EC Number: 2.3.1.57</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1584</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b1126 and b1125 and b1124 and b1123) or (b1440 and b1441 and b1442 and b1443))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1599 and b1600)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2261</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3528</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCCt2_3pp" name="Succintate transport via proton symport (3 H) (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4123 or b4138)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCCt3pp" name="succinate transport out via proton antiport (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCCtex" name="succinate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_succ_e"/>
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- <listOfProducts>
- <speciesReference species="M_succ_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCDi" name="succinate dehydrogenase (irreversible)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0721 and b0722 and b0723 and b0724)</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.3.99.1</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_q8_c"/>
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- <listOfProducts>
- <speciesReference species="M_fum_c"/>
- <speciesReference species="M_q8h2_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCFUMtpp" name="succinate:fumarate antiporter (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4123 or b0621 or b4138)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCMALtpp" name="succinate:malate antiporter (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4138 or b4123 or b0621)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCOAS" name="succinyl-CoA synthetase (ADP-forming)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0728 and b0729)</p>
- <p>SUBSYSTEM: Citric Acid Cycle</p>
- <p>EC Number: 6.2.1.5</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_atp_c"/>
- <speciesReference species="M_coa_c"/>
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- <listOfProducts>
- <speciesReference species="M_adp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
- <parameter id="UPPER_BOUND" value="1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_sucr_e"/>
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- <listOfProducts>
- <speciesReference species="M_sucr_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="-1000" units="mmol_per_gDW_per_hr"/>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCTARTtpp" name="succinate:D-tartrate antiporter (periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4123</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <speciesReference species="M_tartr_DASH_D_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SUCptspp" name="sucrose transport via PEP:Pyr (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2417 and b2429 and b2415 and b2416)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_pep_c"/>
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- <listOfProducts>
- <speciesReference species="M_pyr_c"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_SULFACabcpp" name="sulfoacetate transport via ABC system (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0936 and b0933 and b0934)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_sulfac_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_sulfac_e"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="M_sulfac_p"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
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- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2763 and b2764)</p>
- <p>SUBSYSTEM: Cysteine Metabolism</p>
- <p>EC Number: 1.8.2.2</p>
- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2422 and b2425 and b2424 and b2423) or (b0763 and b0764 and b0765) or (b2422 and b2424 and b2423 and b3917))</p>
- <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0954</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
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- <speciesReference species="M_tdec2eACP_c"/>
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- <speciesReference species="M_cdec3eACP_c"/>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1521</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.1.1.58</p>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2464 or b0008)</p>
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- <p>EC Number: 2.2.1.2</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3061 and b3062)</p>
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- <p>EC Number: 4.2.1.32</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0241 or b0929)</p>
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- <p>EC Number: </p>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3063</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
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- <listOfReactants>
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- <listOfParameters>
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- <reaction id="R_TARTRtex" name="Tartrate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4123</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </reaction>
- <reaction id="R_TAUDO" name="Taurine dioxygenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0368</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 1.14.11.17</p>
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- </notes>
- <listOfReactants>
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- <listOfProducts>
- <speciesReference species="M_aacald_c"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0365 and b0366 and b0367)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
- <listOfReactants>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </reaction>
- <reaction id="R_TAURtex" name="taurine transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <speciesReference species="M_taur_e"/>
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- <listOfProducts>
- <speciesReference species="M_taur_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </reaction>
- <reaction id="R_TCYNTtex" name="Thiocyanate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </notes>
- <listOfReactants>
- <speciesReference species="M_tcynt_e"/>
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- <speciesReference species="M_tcynt_p"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1134</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 3.6.1.15</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h2o_c"/>
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- <listOfProducts>
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- <speciesReference species="M_thmmp_c"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3790</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3791</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.6.1.33</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfReactants>
- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2038</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- </body>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2040</p>
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- </body>
- </notes>
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- <notes>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
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- <p>EC Number: 2.3.1.117</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2551</p>
- <p>SUBSYSTEM: Folate Metabolism</p>
- <p>EC Number: 2.1.2.10</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2480 and b3781) or (b2480 and b2582) or b1710)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2393 or b2964)</p>
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- <p>GENE_ASSOCIATION: (b0068 and b0067 and b0066)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3116</p>
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- <p>GENE_ASSOCIATION: b3089</p>
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- <p>GENE_ASSOCIATION: </p>
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- <p>GENE_ASSOCIATION: (b2530 and b3992 and b3990 and b0423 and b4407)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2935 or b2465)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0894 and b0895 and b0896) or (b1587 and b1588 and b1589 and b1590))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3993</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.5.1.3</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3919</p>
- <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
- <p>EC Number: 5.3.1.1</p>
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- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0613</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: </p>
- </body>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_TRDR" name="thioredoxin reductase (NADPH)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b3781 and b0888) or (b0888 and b2582))</p>
- <p>SUBSYSTEM: Oxidative Phosphorylation</p>
- <p>EC Number: 1.8.1.9</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_h_c"/>
- <speciesReference species="M_nadph_c"/>
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- <speciesReference species="M_nadp_c"/>
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- <ci> FLUX_VALUE </ci>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4239</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.2.1.93</p>
- </body>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1897</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.1.3.12</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1896</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.4.1.15</p>
- </body>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- </reaction>
- <reaction id="R_TREH" name="alpha,alpha-trehalase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3519</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.2.1.28</p>
- </body>
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- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_c" stoichiometry="2"/>
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- <kineticLaw>
- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
- <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_TREHpp" name="alpha,alpha-trehalase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1197</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.2.1.28</p>
- </body>
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- <listOfProducts>
- <speciesReference species="M_glc_DASH_D_p" stoichiometry="2"/>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <reaction id="R_TREptspp" name="trehalose transport via PEP:Pyr PTS (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2417 and b2415 and b2416 and b4240)</p>
- <p>SUBSYSTEM: Transport, Inner Membrane</p>
- <p>EC Number: </p>
- </body>
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- <listOfReactants>
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- <listOfProducts>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
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- <listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </body>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3708</p>
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- <p>EC Number: 4.1.99.1</p>
- </body>
- </notes>
- <listOfReactants>
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- <listOfProducts>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3384</p>
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- </body>
- </notes>
- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0509 or b3125)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b2422 and b2425 and b2424 and b2423) or (b2422 and b2424 and b2423 and b3917))</p>
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- <p>EC Number: </p>
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- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2344</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- </listOfParameters>
- </kineticLaw>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2344</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- <speciesReference species="M_ttdcea_p"/>
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- </kineticLaw>
- </reaction>
- <reaction id="R_TTRCYCtex" name="Tetracycline transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1377 or b2215 or b0929 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: ((b0463 and b0462 and b3035) or (b0463 and b2470 and b3035))</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0763 and b0764 and b0765)</p>
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- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b1377 or b0241 or b0929)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3991</p>
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- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1386</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4055</p>
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- </body>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b2215 or b0241 or b0929 or b1377)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1473 or b1907 or b0112 or b0576)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0179</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0085</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.3.2.13</p>
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- </notes>
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- </listOfParameters>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0480</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.6.1.45</p>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UACGAMPpp" name="UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0480</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.6.1.45</p>
- </body>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UACMAMO" name="UDP-N-acetyl-D-mannosamine oxidoreductase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3787</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: </p>
- </body>
- </notes>
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- <listOfProducts>
- <speciesReference species="M_h_c" stoichiometry="3"/>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="mmol_per_gDW_per_hr"/>
- </listOfParameters>
- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3786</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 5.1.3.14</p>
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- </notes>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UAGAAT" name="UDP-N-acetylglucosamine acyltransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b1094 and b0181)</p>
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- </body>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UAGCVT" name="UDP-N-acetylglucosamine 1-carboxyvinyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3189</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.5.1.7</p>
- </body>
- </notes>
- <listOfReactants>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UAGDP" name="UDP-N-acetylglucosamine diphosphorylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3730</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 2.7.7.23</p>
- </body>
- </notes>
- <listOfReactants>
- <speciesReference species="M_acgam1p_c"/>
- <speciesReference species="M_h_c"/>
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- <listOfProducts>
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- </reaction>
- <reaction id="R_UAGPT3" name="UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0090</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0088</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 6.3.2.9</p>
- </body>
- </notes>
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- <notes>
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- <p>GENE_ASSOCIATION: b0091</p>
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- </body>
- </notes>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3972</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 1.1.1.158</p>
- </body>
- </notes>
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- </listOfParameters>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0841 or b1278 or b3057)</p>
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- <p>EC Number: 3.6.1.27</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0174</p>
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- <p>EC Number: </p>
- </body>
- </notes>
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- <notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: </p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0759</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.1.3.2</p>
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- <reaction id="R_UDPGALM" name="UDPgalactopyranose mutase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2036</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
- <p>EC Number: 5.4.99.9</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0480</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 3.6.1.45</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </reaction>
- <reaction id="R_UDPGD" name="UDPglucose 6-dehydrogenase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2028</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- </notes>
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- </reaction>
- <reaction id="R_UDPGDC" name="UDP-glucuronate C-4'' decarboxylase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2255</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <listOfParameters>
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- </listOfParameters>
- </kineticLaw>
- </reaction>
- <reaction id="R_UDPGLCURtex" name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0480</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
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- </reaction>
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- <notes>
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- <p>EC Number: </p>
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- <reaction id="R_UDPKAAT" name="UDP-4''-ketopentose:UDP-4-amino-4-deoxy-L-arabinose aminotransferase">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2253</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
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- <listOfProducts>
- <speciesReference species="M_akg_c"/>
- <speciesReference species="M_udpLa4n_c"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0480</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0758</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.7.12</p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0505</p>
- <p>SUBSYSTEM: Nitrogen Metabolism</p>
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- </body>
- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0086</p>
- <p>SUBSYSTEM: Cell Envelope Biosynthesis</p>
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- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0096</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2255</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b4544 and b2258)</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4233</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1192</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4233</p>
- <p>SUBSYSTEM: Murein Recycling</p>
- <p>EC Number: </p>
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- <listOfReactants>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0910 or b0171)</p>
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- <p>EC Number: 2.7.4.14</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0929 or b1377 or b2215 or b0241)</p>
- <p>SUBSYSTEM: Transport, Outer Membrane Porin</p>
- <p>EC Number: </p>
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- </kineticLaw>
- </reaction>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2256</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2254</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
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- <reaction id="R_UPP3MT" name="uroporphyrinogen methyltransferase" reversible="false">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3803 or b3368)</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 2.1.1.107</p>
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- <math xmlns="http://www.w3.org/1998/Math/MathML">
- <ci> FLUX_VALUE </ci>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3804</p>
- <p>SUBSYSTEM: Cofactor and Prosthetic Group Biosynthesis</p>
- <p>EC Number: 4.2.1.75</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3997</p>
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- <p>EC Number: 4.1.1.37</p>
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- </notes>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2498</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
- <p>EC Number: 2.4.2.9</p>
- </body>
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- <listOfReactants>
- <speciesReference species="M_prpp_c"/>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b1011</p>
- <p>SUBSYSTEM: Nucleotide Salvage Pathway</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2497</p>
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- <notes>
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- <p>GENE_ASSOCIATION: b1006</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b2066</p>
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- <p>GENE_ASSOCIATION: (b2393 or b2964)</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0411</p>
- <p>SUBSYSTEM: Transport, Outer Membrane</p>
- <p>EC Number: </p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0524</p>
- <p>SUBSYSTEM: Lipopolysaccharide Biosynthesis / Recycling</p>
- <p>EC Number: </p>
- </body>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3770</p>
- <p>SUBSYSTEM: Valine, Leucine, and Isoleucine Metabolism</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b4258</p>
- <p>SUBSYSTEM: tRNA Charging</p>
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- </body>
- </notes>
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- <p>GENE_ASSOCIATION: (b3454 and b3455 and b3457 and b3460 and b3456)</p>
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- <p>GENE_ASSOCIATION: (b0401 or (b2683 and b2682))</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0241 or b0929 or b1377 or b2215)</p>
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- </body>
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- <p>GENE_ASSOCIATION: b3572</p>
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- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0827</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b0030</p>
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- <p>EC Number: 3.2.2.8</p>
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- <p>GENE_ASSOCIATION: b2406</p>
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- <p>EC Number: </p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3565</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.5</p>
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- <speciesReference species="M_xylu_DASH_D_c"/>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: b3565</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 5.3.1.5</p>
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- <speciesReference species="M_fru_c"/>
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- <kineticLaw>
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- <ci> FLUX_VALUE </ci>
- </math>
- <listOfParameters>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0063 or b3564)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.17</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b0063 or b3580)</p>
- <p>SUBSYSTEM: Alternate Carbon Metabolism</p>
- <p>EC Number: 2.7.1.53</p>
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- <body xmlns="http://www.w3.org/1999/xhtml">
- <p>GENE_ASSOCIATION: (b3577 and b3578 and b3579)</p>
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- <p>GENE_ASSOCIATION: (b3566 and b3567 and b3568)</p>
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- <p>GENE_ASSOCIATION: b3469</p>
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- <p>GENE_ASSOCIATION: (b1857 and b1859 and b1858)</p>
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+ <model id="iJO1366" fbc:strict="true">
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr">
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+ <unit exponent="1" kind="mole" multiplier="1" scale="-3" />
+ <unit exponent="-1" kind="gram" multiplier="1" scale="0" />
+ <unit exponent="-1" kind="second" multiplier="3600" scale="0" />
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+ <fbc:listOfObjectives fbc:activeObjective="obj">
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+ <parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0" />
+ <parameter constant="true" id="R_EX_cbl1_e_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-0.01" />
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+ <parameter constant="true" id="R_ATPM_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.15" />
+ </listOfParameters>
+ <listOfCompartments>
+ <compartment constant="true" id="p" name="Periplasm" />
+ <compartment constant="true" id="c" name="Cytoplasm" />
+ <compartment constant="true" id="e" name="Extracellular" />
+ </listOfCompartments>
+ <listOfSpecies>
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_bglycogen_c" name="branching glycogen" fbc:charge="0" fbc:chemicalFormula="C6H10O5" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_btal_c" name="Butanal" fbc:charge="0" fbc:chemicalFormula="C4H8O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_btcoa_c" name="Butanoyl-CoA" fbc:charge="-4" fbc:chemicalFormula="C25H38N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_btn_c" name="Biotin" fbc:charge="-1" fbc:chemicalFormula="C10H15N2O3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_btnso_c" name="d-biotin d-sulfoxide" fbc:charge="-1" fbc:chemicalFormula="C10H15N2O4S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_bwco_c" name="tungsten bispterin cofactor" fbc:charge="-4" fbc:chemicalFormula="C20H20N10O13P2S4W" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ca2_c" name="Calcium" fbc:charge="2" fbc:chemicalFormula="Ca" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_camp_c" name="cAMP" fbc:charge="-1" fbc:chemicalFormula="C10H11N5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cbasp_c" name="N-Carbamoyl-L-aspartate" fbc:charge="-2" fbc:chemicalFormula="C5H6N2O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cbi_c" name="Cobinamide" fbc:charge="0" fbc:chemicalFormula="C48H72CoN11O8" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cbl1_c" name="Cob(I)alamin" fbc:charge="-1" fbc:chemicalFormula="C62H88CoN13O14P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cbm_c" name="Carbamate" fbc:charge="-1" fbc:chemicalFormula="CH2NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cbp_c" name="Carbamoyl phosphate" fbc:charge="-2" fbc:chemicalFormula="CH2NO5P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cd2_c" name="Cadmium" fbc:charge="2" fbc:chemicalFormula="Cd" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cddec5eACP_c" name="cis-dodec-5-enoyl-[acyl-carrier protein] (n-C12:1)" fbc:charge="-1" fbc:chemicalFormula="C23H41N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdec3eACP_c" name="cis-dec-3-enoyl-[acyl-carrier protein] (n-C10:1)" fbc:charge="-1" fbc:chemicalFormula="C21H37N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdg_c" name="7-deaza-7-carboxyguanine" fbc:charge="-1" fbc:chemicalFormula="C7H5N4O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdp_c" name="CDP" fbc:charge="-3" fbc:chemicalFormula="C9H12N3O11P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdddecg_c" name="CDP-1,2-didodecanoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C36H63N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdhdec9eg_c" name="CDP-1,2-dihexadec-9-enoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C44H75N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdhdecg_c" name="CDP-1,2-dihexadecanoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C44H79N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdodec11eg_c" name="CDP-1,2-dioctadec-11-enoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C48H83N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdodecg_c" name="CDP-1,2-dioctadecanoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C48H87N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdtdec7eg_c" name="CDP-1,2-ditetradec-7-enoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C40H67N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cdpdtdecg_c" name="CDP-1,2-ditetradecanoylglycerol" fbc:charge="-2" fbc:chemicalFormula="C40H71N3O15P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cechddd_c" name="cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol" fbc:charge="-1" fbc:chemicalFormula="C9H11O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cenchddd_c" name="cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol" fbc:charge="-1" fbc:chemicalFormula="C9H9O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cgly_c" name="Cys-Gly" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_chol_c" name="Choline" fbc:charge="1" fbc:chemicalFormula="C5H14NO" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_chor_c" name="chorismate" fbc:charge="-2" fbc:chemicalFormula="C10H8O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_chtbs6p_c" name="diacetylchitobiose-6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C16H27N2O14P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cinnm_c" name="trans-Cinnamate" fbc:charge="-1" fbc:chemicalFormula="C9H7O2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cit_c" name="Citrate" fbc:charge="-3" fbc:chemicalFormula="C6H5O7" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_citr__L_c" name="L-Citrulline" fbc:charge="0" fbc:chemicalFormula="C6H13N3O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ckdo_c" name="CMP-3-deoxy-D-manno-octulosonate" fbc:charge="-2" fbc:chemicalFormula="C17H24N3O15P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cl_c" name="Chloride" fbc:charge="-1" fbc:chemicalFormula="Cl" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cmp_c" name="CMP" fbc:charge="-2" fbc:chemicalFormula="C9H12N3O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_co2_c" name="CO2" fbc:charge="0" fbc:chemicalFormula="CO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_coa_c" name="Coenzyme A" fbc:charge="-4" fbc:chemicalFormula="C21H32N7O16P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cobalt2_c" name="Co2+" fbc:charge="2" fbc:chemicalFormula="Co" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_colipa_c" name="core oligosaccharide lipid A" fbc:charge="-11" fbc:chemicalFormula="C176H303N2O100P4" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cpgn_c" name="coprogen" fbc:charge="-1" fbc:chemicalFormula="C35H52N6O13Fe" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cpmp_c" name="cyclic pyranopterin monophosphate" fbc:charge="-1" fbc:chemicalFormula="C10H13N5O8P" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_crnDcoa_c" name="D-carnitinyl-CoA" fbc:charge="-3" fbc:chemicalFormula="C28H46N8O18P3S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_csn_c" name="Cytosine" fbc:charge="0" fbc:chemicalFormula="C4H5N3O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ctbt_c" name="crotonobetaine" fbc:charge="0" fbc:chemicalFormula="C7H13NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ctbtcoa_c" name="crotonobetainyl-CoA" fbc:charge="-3" fbc:chemicalFormula="C28H44N8O17P3S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cu_c" name="Cu+" fbc:charge="1" fbc:chemicalFormula="Cu" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cu2_c" name="Cu2+" fbc:charge="2" fbc:chemicalFormula="Cu" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cyan_c" name="Hydrogen cyanide" fbc:charge="0" fbc:chemicalFormula="CHN" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cynt_c" name="Cyanate" fbc:charge="-1" fbc:chemicalFormula="CNO" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cys__D_c" name="D-Cysteine" fbc:charge="0" fbc:chemicalFormula="C3H7NO2S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cys__L_c" name="L-Cysteine" fbc:charge="0" fbc:chemicalFormula="C3H7NO2S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cyst__L_c" name="L-Cystathionine" fbc:charge="0" fbc:chemicalFormula="C7H14N2O4S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cystrna_c" name="L-Cysteinyl-tRNA(Cys)" fbc:charge="1" fbc:chemicalFormula="C3H6NOSR" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cytd_c" name="Cytidine" fbc:charge="0" fbc:chemicalFormula="C9H13N3O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dad__2_c" name="Deoxyadenosine" fbc:charge="0" fbc:chemicalFormula="C10H13N5O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dad__5_c" name="5'-Deoxyadenosine" fbc:charge="0" fbc:chemicalFormula="C10H13N5O3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dcaACP_c" name="Decanoyl-ACP (n-C10:0ACP)" fbc:charge="-1" fbc:chemicalFormula="C21H39N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dcacoa_c" name="Decanoyl-CoA (n-C10:0CoA)" fbc:charge="-4" fbc:chemicalFormula="C31H50N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dcamp_c" name="N6-(1,2-Dicarboxyethyl)-AMP" fbc:charge="-4" fbc:chemicalFormula="C14H14N5O11P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dcdp_c" name="dCDP" fbc:charge="-3" fbc:chemicalFormula="C9H12N3O10P2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ddcaACP_c" name="Dodecanoyl-ACP (n-C12:0ACP)" fbc:charge="-1" fbc:chemicalFormula="C23H43N2O8PRS" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ddcap_c" name="Dodecanoly-phosphate (n-C12:0)" fbc:charge="-1" fbc:chemicalFormula="C12H24O5P1" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dgdp_c" name="dGDP" fbc:charge="-3" fbc:chemicalFormula="C10H12N5O10P2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dgsn_c" name="Deoxyguanosine" fbc:charge="0" fbc:chemicalFormula="C10H13N5O4" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dha_c" name="Dihydroxyacetone" fbc:charge="0" fbc:chemicalFormula="C3H6O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhap_c" name="Dihydroxyacetone phosphate" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhcinnm_c" name="2,3-dihydroxicinnamic acid" fbc:charge="-1" fbc:chemicalFormula="C9H7O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhf_c" name="7,8-Dihydrofolate" fbc:charge="-2" fbc:chemicalFormula="C19H19N7O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhgly_c" name="dehydroglycine" fbc:charge="-1" fbc:chemicalFormula="C2H2NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhmpt_c" name="Dihydromonapterin" fbc:charge="0" fbc:chemicalFormula="C9H13N5O4" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_etoh_c" name="Ethanol" fbc:charge="0" fbc:chemicalFormula="C2H6O" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_for_c" name="Formate" fbc:charge="-1" fbc:chemicalFormula="CH1O2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_frulysp_c" name="fructoselysine Phosphate" fbc:charge="-1" fbc:chemicalFormula="C12H24N2O10P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_fruur_c" name="D-Fructuronate" fbc:charge="-1" fbc:chemicalFormula="C6H9O7" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_fum_c" name="Fumarate" fbc:charge="-2" fbc:chemicalFormula="C4H2O4" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_gly_c" name="Glycine" fbc:charge="0" fbc:chemicalFormula="C2H5NO2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_glyb_c" name="Glycine betaine" fbc:charge="0" fbc:chemicalFormula="C5H11NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_glyc_c" name="Glycerol" fbc:charge="0" fbc:chemicalFormula="C3H8O3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_glycogen_c" name="glycogen" fbc:charge="0" fbc:chemicalFormula="C6H10O5" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_grxox_c" name="glutaredoxin (oxidized)" fbc:charge="0" fbc:chemicalFormula="X" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_hco3_c" name="Bicarbonate" fbc:charge="-1" fbc:chemicalFormula="CHO3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_hqn_c" name="Hydroquinone" fbc:charge="0" fbc:chemicalFormula="C6H6O2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_indole_c" name="Indole" fbc:charge="0" fbc:chemicalFormula="C8H7N" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_k_c" name="potassium" fbc:charge="1" fbc:chemicalFormula="K" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_kdo_c" name="3-Deoxy-D-manno-2-octulosonate" fbc:charge="-1" fbc:chemicalFormula="C8H13O8" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_malACP_c" name="Malonyl-[acyl-carrier protein]" fbc:charge="-2" fbc:chemicalFormula="C14H22N2O10PRS" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_malt_c" name="Maltose" fbc:charge="0" fbc:chemicalFormula="C12H22O11" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_maltttr_c" name="Maltotetraose" fbc:charge="0" fbc:chemicalFormula="C24H42O21" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_man_c" name="D-Mannose" fbc:charge="0" fbc:chemicalFormula="C6H12O6" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_melib_c" name="Melibiose" fbc:charge="0" fbc:chemicalFormula="C12H22O11" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_meoh_c" name="Methanol" fbc:charge="0" fbc:chemicalFormula="CH4O1" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_mercppyr_c" name="Mercaptopyruvate" fbc:charge="-1" fbc:chemicalFormula="C3H3O3S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_mg2_c" name="magnesium" fbc:charge="2" fbc:chemicalFormula="Mg" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_mn2_c" name="Mn2+" fbc:charge="2" fbc:chemicalFormula="Mn" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_mobd_c" name="Molybdate" fbc:charge="-2" fbc:chemicalFormula="MoO4" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_mptamp_c" name="adenylated molybdopterin" fbc:charge="-2" fbc:chemicalFormula="C20H22N10O12P2S2Cu" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_n2o_c" name="Nitrous oxide" fbc:charge="0" fbc:chemicalFormula="N2O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_n8aspmd_c" name="N8-Acetylspermidine" fbc:charge="2" fbc:chemicalFormula="C9H23N3O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_na1_c" name="Sodium" fbc:charge="1" fbc:chemicalFormula="Na" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_na15dap_c" name="N-3-aminopropyl-1,5-diaminopentane" fbc:charge="3" fbc:chemicalFormula="C8H24N3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nac_c" name="Nicotinate" fbc:charge="-1" fbc:chemicalFormula="C6H4NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nad_c" name="Nicotinamide adenine dinucleotide" fbc:charge="-1" fbc:chemicalFormula="C21H26N7O14P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" fbc:charge="-2" fbc:chemicalFormula="C21H27N7O14P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadp_c" name="Nicotinamide adenine dinucleotide phosphate" fbc:charge="-3" fbc:chemicalFormula="C21H25N7O17P3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nh4_c" name="Ammonium" fbc:charge="1" fbc:chemicalFormula="H4N" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ni2_c" name="nickel" fbc:charge="2" fbc:chemicalFormula="Ni" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nicrnt_c" name="Nicotinate D-ribonucleotide" fbc:charge="-2" fbc:chemicalFormula="C11H12NO9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nmn_c" name="NMN" fbc:charge="-1" fbc:chemicalFormula="C11H14N2O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_no_c" name="Nitric oxide" fbc:charge="0" fbc:chemicalFormula="NO" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_no2_c" name="Nitrite" fbc:charge="-1" fbc:chemicalFormula="NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_no3_c" name="Nitrate" fbc:charge="-1" fbc:chemicalFormula="NO3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_o2s_c" name="Superoxide anion" fbc:charge="-1" fbc:chemicalFormula="O2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_oaa_c" name="Oxaloacetate" fbc:charge="-2" fbc:chemicalFormula="C4H2O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_oc2coa_c" name="trans-Oct-2-enoyl-CoA" fbc:charge="-4" fbc:chemicalFormula="C29H44N7O17P3S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_odecoa_c" name="Octadecenoyl-CoA (n-C18:1CoA)" fbc:charge="-4" fbc:chemicalFormula="C39H64N7O17P3S" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_op4en_c" name="2-Oxopent-4-enoate" fbc:charge="-1" fbc:chemicalFormula="C5H5O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_opmeACP_c" name="3-Oxo-pimeloyl-[acyl-carrier protein] methyl ester" fbc:charge="-1" fbc:chemicalFormula="C19H31N2O11PRS" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ragund_c" name="rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate" fbc:charge="-2" fbc:chemicalFormula="C69H113N1O16P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rbflvrd_c" name="Reduced riboflavin" fbc:charge="0" fbc:chemicalFormula="C17H22N4O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rbl__L_c" name="L-Ribulose" fbc:charge="0" fbc:chemicalFormula="C5H10O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rdmbzi_c" name="N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole" fbc:charge="0" fbc:chemicalFormula="C14H18N2O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rephaccoa_c" name="Ring 1,2-epoxyphenylacetyl-CoA" fbc:charge="-4" fbc:chemicalFormula="C29H38N7O18P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rhcys_c" name="S-Ribosyl-L-homocysteine" fbc:charge="0" fbc:chemicalFormula="C9H17NO6S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rib__D_c" name="D-Ribose" fbc:charge="0" fbc:chemicalFormula="C5H10O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ribflv_c" name="Riboflavin" fbc:charge="0" fbc:chemicalFormula="C17H20N4O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rml_c" name="L-Rhamnulose" fbc:charge="0" fbc:chemicalFormula="C6H12O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rml1p_c" name="L-Rhamnulose 1-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_rmn_c" name="L-Rhamnose" fbc:charge="0" fbc:chemicalFormula="C6H12O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ru5p__D_c" name="D-Ribulose 5-phosphate" fbc:charge="-2" fbc:chemicalFormula="C5H9O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ru5p__L_c" name="L-Ribulose 5-phosphate" fbc:charge="-2" fbc:chemicalFormula="C5H9O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_s17bp_c" name="Sedoheptulose 1,7-bisphosphate" fbc:charge="-4" fbc:chemicalFormula="C7H12O13P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_s7p_c" name="Sedoheptulose 7-phosphate" fbc:charge="-2" fbc:chemicalFormula="C7H13O10P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sarcs_c" name="Sarcosine" fbc:charge="0" fbc:chemicalFormula="C3H7NO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sbt6p_c" name="D-Sorbitol 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H13O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sbzcoa_c" name="O-Succinylbenzoyl-CoA" fbc:charge="-5" fbc:chemicalFormula="C32H39N7O20P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_scl_c" name="sirohydrochlorin" fbc:charge="-7" fbc:chemicalFormula="C42H39N4O16" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sectrna_c" name="L-Selenocysteinyl-tRNA(Sec)" fbc:charge="1" fbc:chemicalFormula="C3H6NOSeR" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sel_c" name="Selenate" fbc:charge="-2" fbc:chemicalFormula="O4Se" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_seln_c" name="Selenide" fbc:charge="-1" fbc:chemicalFormula="HSe" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_selnp_c" name="Selenophosphate" fbc:charge="-1" fbc:chemicalFormula="H2O3PSe" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ser__D_c" name="D-Serine" fbc:charge="0" fbc:chemicalFormula="C3H7NO3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ser__L_c" name="L-Serine" fbc:charge="0" fbc:chemicalFormula="C3H7NO3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_seramp_c" name="L-seryl-AMP" fbc:charge="0" fbc:chemicalFormula="C13H19N6O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sertrna_c" name="L-Seryl-tRNA(Ser)" fbc:charge="1" fbc:chemicalFormula="C3H6NO2R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sertrna[sec]_c" name="L-Seryl-tRNA(Sec)" fbc:charge="1" fbc:chemicalFormula="C3H6NO2R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sheme_c" name="Siroheme" fbc:charge="-8" fbc:chemicalFormula="C42H36FeN4O16" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_skm_c" name="Shikimate" fbc:charge="-1" fbc:chemicalFormula="C7H9O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_skm5p_c" name="Shikimate 5-phosphate" fbc:charge="-3" fbc:chemicalFormula="C7H8O8P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sl26da_c" name="N-Succinyl-LL-2,6-diaminoheptanedioate" fbc:charge="-2" fbc:chemicalFormula="C11H16N2O7" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sl2a6o_c" name="N-Succinyl-2-L-amino-6-oxoheptanedioate" fbc:charge="-3" fbc:chemicalFormula="C11H12NO8" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_slnt_c" name="selenite" fbc:charge="-2" fbc:chemicalFormula="O3Se" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_so2_c" name="sulfur dioxide" fbc:charge="0" fbc:chemicalFormula="O2S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_so3_c" name="Sulfite" fbc:charge="-2" fbc:chemicalFormula="O3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_so4_c" name="Sulfate" fbc:charge="-2" fbc:chemicalFormula="O4S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_spmd_c" name="Spermidine" fbc:charge="3" fbc:chemicalFormula="C7H22N3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_stcoa_c" name="Stearoyl-CoA (n-C18:0CoA)" fbc:charge="-4" fbc:chemicalFormula="C39H66N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_suc6p_c" name="Sucrose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C12H21O14P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucarg_c" name="N2-Succinyl-L-arginine" fbc:charge="-1" fbc:chemicalFormula="C10H17N4O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucbz_c" name="o-Succinylbenzoate" fbc:charge="-2" fbc:chemicalFormula="C11H8O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_succ_c" name="Succinate" fbc:charge="-2" fbc:chemicalFormula="C4H4O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_succoa_c" name="Succinyl-CoA" fbc:charge="-5" fbc:chemicalFormula="C25H35N7O19P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucglu_c" name="N2-Succinyl-L-glutamate" fbc:charge="-3" fbc:chemicalFormula="C9H10NO7" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucgsa_c" name="N2-Succinyl-L-glutamate 5-semialdehyde" fbc:charge="-2" fbc:chemicalFormula="C9H11NO6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_suchms_c" name="O-Succinyl-L-homoserine" fbc:charge="-1" fbc:chemicalFormula="C8H12NO6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucorn_c" name="N2-Succinyl-L-ornithine" fbc:charge="-1" fbc:chemicalFormula="C9H15N2O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sucsal_c" name="Succinic semialdehyde" fbc:charge="-1" fbc:chemicalFormula="C4H5O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufbcd_c" name="SufBCD scaffold complex" fbc:charge="0" fbc:chemicalFormula="H8O2S6R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufbcd__2fe2s_c" name="SufBCD with bound [2Fe-2S] cluster" fbc:charge="-2" fbc:chemicalFormula="H4O2S8Fe2R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufbcd__2fe2s2_c" name="SufBCD with two bound [2Fe-2S] clusters" fbc:charge="-4" fbc:chemicalFormula="O2S10Fe4R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufbcd__4fe4s_c" name="SufBCD with bound [4Fe-4S] cluster" fbc:charge="-2" fbc:chemicalFormula="H4O2S10Fe4R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufse_c" name="SufSE sulfur acceptor complex" fbc:charge="0" fbc:chemicalFormula="HSR" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sufsesh_c" name="SufSE with bound sulfur" fbc:charge="0" fbc:chemicalFormula="HS2R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_sulfac_c" name="sulfoacetate" fbc:charge="-2" fbc:chemicalFormula="C2H2O5S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_t3c11vaceACP_c" name="trans-3-cis-11-vacceoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C29H51N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_t3c5ddeceACP_c" name="trans-3-cis-5-dodecenoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C23H39N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_t3c7mrseACP_c" name="trans-3-cis-7-myristoleoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C25H43N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_t3c9palmeACP_c" name="trans-3-cis-9-palmitoleoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C27H47N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tag6p__D_c" name="D-Tagatose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tagdp__D_c" name="D-Tagatose 1,6-biphosphate" fbc:charge="-4" fbc:chemicalFormula="C6H10O12P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tagur_c" name="D-Tagaturonate" fbc:charge="-1" fbc:chemicalFormula="C6H9O7" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tartr__D_c" name="D-tartrate" fbc:charge="-2" fbc:chemicalFormula="C4H4O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tartr__L_c" name="L-tartrate" fbc:charge="-2" fbc:chemicalFormula="C4H4O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_taur_c" name="Taurine" fbc:charge="0" fbc:chemicalFormula="C2H7NO3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tcynt_c" name="Thiocyanate" fbc:charge="-1" fbc:chemicalFormula="CNS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_td2coa_c" name="trans-Tetradec-2-enoyl-CoA" fbc:charge="-4" fbc:chemicalFormula="C35H56N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tdcoa_c" name="Tetradecanoyl-CoA (n-C14:0CoA)" fbc:charge="-4" fbc:chemicalFormula="C35H58N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tddec2eACP_c" name="trans-Dodec-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C23H41N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tdeACP_c" name="cis-tetradec-7-enoyl-[acyl-carrier protein] (n-C14:1)" fbc:charge="-1" fbc:chemicalFormula="C25H45N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tdec2eACP_c" name="trans-Dec-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C21H37N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tdecoa_c" name="Tetradecenoyl-CoA (n-C14:1CoA)" fbc:charge="-4" fbc:chemicalFormula="C35H56N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thdp_c" name="2,3,4,5-Tetrahydrodipicolinate" fbc:charge="-2" fbc:chemicalFormula="C7H7NO4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thex2eACP_c" name="trans-Hex-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C17H29N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thf_c" name="5,6,7,8-Tetrahydrofolate" fbc:charge="-2" fbc:chemicalFormula="C19H21N7O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thm_c" name="Thiamin" fbc:charge="1" fbc:chemicalFormula="C12H17N4OS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thmmp_c" name="Thiamin monophosphate" fbc:charge="-1" fbc:chemicalFormula="C12H16N4O4PS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thmnp_c" name="Tetrahydromonapterin" fbc:charge="0" fbc:chemicalFormula="C9H15N5O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thmpp_c" name="Thiamine diphosphate" fbc:charge="-2" fbc:chemicalFormula="C12H16N4O7P2S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thptdn_c" name="5,6,7,8-tetrahydropteridine" fbc:charge="2" fbc:chemicalFormula="C6H10N4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thr__L_c" name="L-Threonine" fbc:charge="0" fbc:chemicalFormula="C4H9NO3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thrtrna_c" name="L-Threonyl-tRNA(Thr)" fbc:charge="1" fbc:chemicalFormula="C4H8NO2R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thym_c" name="Thymine" fbc:charge="0" fbc:chemicalFormula="C5H6N2O2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_thymd_c" name="Thymidine" fbc:charge="0" fbc:chemicalFormula="C10H14N2O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tma_c" name="trimethylamine" fbc:charge="1" fbc:chemicalFormula="C3H10N" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tmao_c" name="Trimethylamine N-oxide" fbc:charge="0" fbc:chemicalFormula="C3H9NO" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tmrs2eACP_c" name="trans-Tetradec-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C25H45N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_toct2eACP_c" name="trans-Oct-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C19H33N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_toctd2eACP_c" name="trans-octadec-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C29H53N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tpalm2eACP_c" name="trans-Hexadec-2-enoyl-[acyl-carrier protein]" fbc:charge="-1" fbc:chemicalFormula="C27H49N2O8PRS" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trdox_c" name="Oxidized thioredoxin" fbc:charge="0" fbc:chemicalFormula="X" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trdrd_c" name="Reduced thioredoxin" fbc:charge="0" fbc:chemicalFormula="XH2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tre_c" name="Trehalose" fbc:charge="0" fbc:chemicalFormula="C12H22O11" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_tre6p_c" name="alpha,alpha'-Trehalose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C12H21O14P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaala_c" name="tRNA(Ala)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaarg_c" name="tRNA(Arg)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaasn_c" name="tRNA(Asn)" fbc:charge="0" fbc:chemicalFormula="C10H17O10PR2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaasp_c" name="tRNA(Asp)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnacys_c" name="tRNA(Cys)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnagln_c" name="tRNA(Gln)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaglu_c" name="tRNA (Glu)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnagly_c" name="tRNA(Gly)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnahis_c" name="tRNA(His)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaile_c" name="tRNA(Ile)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaleu_c" name="tRNA(Leu)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnalys_c" name="tRNA(Lys)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnamet_c" name="tRNA(Met)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnaphe_c" name="tRNA(Phe)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnapro_c" name="tRNA(Pro)" fbc:charge="0" fbc:chemicalFormula="R" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_trnasecys_c" name="tRNA(SeCys)" fbc:charge="0" fbc:chemicalFormula="R" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_cl_e" name="Chloride" fbc:charge="-1" fbc:chemicalFormula="Cl" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_fusa_e" name="fusidic acid" fbc:charge="0" fbc:chemicalFormula="C31H48O5" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_glyb_e" name="Glycine betaine" fbc:charge="0" fbc:chemicalFormula="C5H11NO2" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_e" name="H2O" fbc:charge="0" fbc:chemicalFormula="H2O" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_h2s_e" name="Hydrogen sulfide" fbc:charge="0" fbc:chemicalFormula="H2S" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_hg2_e" name="Hg2+" fbc:charge="2" fbc:chemicalFormula="Hg" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_hxa_e" name="Hexanoate (n-C6:0)" fbc:charge="-1" fbc:chemicalFormula="C6H11O2" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_indole_e" name="Indole" fbc:charge="0" fbc:chemicalFormula="C8H7N" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_k_e" name="potassium" fbc:charge="1" fbc:chemicalFormula="K" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_meoh_e" name="Methanol" fbc:charge="0" fbc:chemicalFormula="CH4O1" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_mg2_e" name="magnesium" fbc:charge="2" fbc:chemicalFormula="Mg" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_mincyc_e" name="minocycline" fbc:charge="0" fbc:chemicalFormula="C23H27N3O7" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_na1_e" name="Sodium" fbc:charge="1" fbc:chemicalFormula="Na" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_nh4_e" name="Ammonium" fbc:charge="1" fbc:chemicalFormula="H4N" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ni2_e" name="nickel" fbc:charge="2" fbc:chemicalFormula="Ni" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_nmn_e" name="NMN" fbc:charge="-1" fbc:chemicalFormula="C11H14N2O8P" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_no_e" name="Nitric oxide" fbc:charge="0" fbc:chemicalFormula="NO" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_no2_e" name="Nitrite" fbc:charge="-1" fbc:chemicalFormula="NO2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_no3_e" name="Nitrate" fbc:charge="-1" fbc:chemicalFormula="NO3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_novbcn_e" name="novobiocin" fbc:charge="0" fbc:chemicalFormula="C31H36N2O11" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_o16a4colipa_e" name="(O16 antigen)x4 core oligosaccharide lipid A" fbc:charge="-11" fbc:chemicalFormula="C312H523N6O200P4" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_o2_e" name="O2" fbc:charge="0" fbc:chemicalFormula="O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_o2s_e" name="Superoxide anion" fbc:charge="-1" fbc:chemicalFormula="O2" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_peamn_e" name="Phenethylamine" fbc:charge="1" fbc:chemicalFormula="C8H12N" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ppal_e" name="Propanal" fbc:charge="0" fbc:chemicalFormula="C3H6O" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_pppn_e" name="Phenylpropanoate" fbc:charge="-1" fbc:chemicalFormula="C9H9O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ppt_e" name="Phosphonate" fbc:charge="-2" fbc:chemicalFormula="HO3P" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ptrc_e" name="Putrescine" fbc:charge="2" fbc:chemicalFormula="C4H14N2" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_pyr_e" name="Pyruvate" fbc:charge="-1" fbc:chemicalFormula="C3H3O3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_quin_e" name="Quinate" fbc:charge="0" fbc:chemicalFormula="C7H12O6" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_r5p_e" name="alpha-D-Ribose 5-phosphate" fbc:charge="-2" fbc:chemicalFormula="C5H9O8P" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_rfamp_e" name="rifampin" fbc:charge="0" fbc:chemicalFormula="C43H58N4O12" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_sel_e" name="Selenate" fbc:charge="-2" fbc:chemicalFormula="O4Se" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ser__D_e" name="D-Serine" fbc:charge="0" fbc:chemicalFormula="C3H7NO3" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_skm_e" name="Shikimate" fbc:charge="-1" fbc:chemicalFormula="C7H9O5" />
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+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_DM_MTHTHF" name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mththf_c" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_DM_OXAM" name="Sink needed to allow oxamate to leave system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_oxam_c" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_Ec_biomass_iJO1366_WT_53p95M" name="E. coli biomass objective function (iJO1366) - WT - with 53.95 GAM estimate" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe161_c" stoichiometry="0.009618" />
+ <speciesReference constant="true" species="M_murein4p4p_p" stoichiometry="0.005381" />
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="0.004439" />
+ <speciesReference constant="true" species="M_pe161_p" stoichiometry="0.024732" />
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+ <speciesReference constant="true" species="M_chor_c" stoichiometry="0.000223" />
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+ <speciesReference constant="true" species="M_bmocogdp_c" stoichiometry="0.000116" />
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+ <speciesReference constant="true" species="M_datp_c" stoichiometry="0.024805" />
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+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="0.749831" />
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+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_Ec_biomass_iJO1366_core_53p95M" name="E. coli biomass objective function (iJO1366) - core - with 53.95 GAM estimate" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="0.000223" />
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+ <speciesReference constant="true" species="M_ca2_c" stoichiometry="0.005205" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="0.773903" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="53.945662" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="53.95" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="53.95" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_EX_12ppd__R_e" name="(R)-Propane-1,2-diol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__R_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_12ppd__S_e" name="(S)-Propane-1,2-diol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__S_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_14glucan_e" name="1,4-alpha-D-glucan exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_14glucan_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_15dap_e" name="1,5-Diaminopentane exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_15dap_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_23camp_e" name="2',3'-Cyclic AMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23camp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_23ccmp_e" name="2',3'-Cyclic CMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23ccmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_23cgmp_e" name="2',3'-Cyclic GMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23cgmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_23cump_e" name="2',3'-Cyclic UMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23cump_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_23dappa_e" name="2,3-diaminopropionate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dappa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_26dap__M_e" name="meso-2,6-Diaminoheptanedioate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_26dap__M_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_2ddglcn_e" name="2-Dehydro-3-deoxy-D-gluconate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ddglcn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_34dhpac_e" name="3,4-Dihydroxyphenylacetaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_34dhpac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_3amp_e" name="3'-AMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3amp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_3cmp_e" name="3'-cmp exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3cmp_e" stoichiometry="1" />
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+ </reaction>
+ <reaction fast="false" id="R_EX_3gmp_e" name="3'-GMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3gmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_3hcinnm_e" name="3-hydroxycinnamic acid exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcinnm_e" stoichiometry="1" />
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+ </reaction>
+ <reaction fast="false" id="R_EX_3hpp_e" name="3-Hydroxypropanoate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hpp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_3hpppn_e" name="3-(3-hydroxy-phenyl)propionate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hpppn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_3ump_e" name="3'-UMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3ump_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_4abut_e" name="4-Aminobutanoate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4abut_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_4hoxpacd_e" name="4-Hydroxyphenylacetaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4hoxpacd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_5dglcn_e" name="5-Dehydro-D-gluconate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dglcn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_5mtr_e" name="5-Methylthio-D-ribose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5mtr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_LalaDglu_e" name="L-alanine-D-glutamate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDglu_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_LalaDgluMdap_e" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdap_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_LalaDgluMdapDala_e" name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_LalaLglu_e" name="L-alanine-L-glutamate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaLglu_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ac_e" name="Acetate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acac_e" name="Acetoacetate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acald_e" name="Acetaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acald_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acgal_e" name="N-Acetyl-D-galactosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgal_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acgal1p_e" name="N-Acetyl-D-galactosamine 1-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgal1p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acgam_e" name="N-Acetyl-D-glucosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acgam1p_e" name="N-Acetyl-D-glucosamine 1-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgam1p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acmana_e" name="N-Acetyl-D-mannosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmana_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acmum_e" name="N-Acetylmuramate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmum_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acnam_e" name="N-Acetylneuraminate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acnam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acolipa_e" name="4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acolipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acser_e" name="O-Acetyl-L-serine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acser_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ade_e" name="Adenine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ade_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_adn_e" name="Adenosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_adocbl_e" name="Adenosylcobalamin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adocbl_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ag_e" name="silver exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ag_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_agm_e" name="Agmatine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_agm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_akg_e" name="2-Oxoglutarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ala__B_e" name="beta-Alanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__B_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ala__D_e" name="D-Alanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ala__L_e" name="L-Alanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_alaala_e" name="D-Alanyl-D-alanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_alaala_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_all__D_e" name="D-Allose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_all__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_alltn_e" name="Allantoin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_alltn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_amp_e" name="AMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_amp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_anhgm_e" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_anhgm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_arab__L_e" name="L-Arabinose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arab__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_arbt_e" name="Arbutin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_arbtn_e" name="aerobactin minus Fe3 exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbtn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_arbtn__fe3_e" name="Aerobactin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbtn__fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_arg__L_e" name="L-Arginine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arg__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ascb__L_e" name="L-Ascorbate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ascb__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_asn__L_e" name="L-Asparagine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asn__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_aso3_e" name="arsenite exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_aso3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_asp__L_e" name="L-Aspartate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_btn_e" name="Biotin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_btn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_but_e" name="Butyrate (n-C4:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_but_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_butso3_e" name="butanesulfonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_butso3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ca2_e" name="Calcium exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ca2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cbi_e" name="Cobinamide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbi_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cbl1_e" name="Cob(I)alamin exchange" reversible="true" fbc:lowerFluxBound="R_EX_cbl1_e_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbl1_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cd2_e" name="Cadmium exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cd2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cgly_e" name="Cys-Gly exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cgly_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_chol_e" name="Choline exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chol_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_chtbs_e" name="chitobiose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chtbs_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cit_e" name="Citrate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cit_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cl_e" name="Chloride exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cl_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cm_e" name="Chloramphenicol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cmp_e" name="CMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_co2_e" name="CO2 exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cobalt2_e" name="Co2+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cobalt2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_colipa_e" name="core oligosaccharide lipid A exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_colipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_colipap_e" name="core oligosaccharide lipid A diphosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_colipap_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cpgn_e" name="coprogen exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cpgn__un_e" name="coprogen unloaded (no Fe(III)) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn__un_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_crn_e" name="L-Carnitine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_crn__D_e" name="D-carnitine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_csn_e" name="Cytosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_csn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cu_e" name="Cu+ exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cu2_e" name="Cu2+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cyan_e" name="Hydrogen cyanide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cyan_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cynt_e" name="Cyanate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cynt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cys__D_e" name="D-Cysteine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cys__L_e" name="L-Cysteine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_cytd_e" name="Cytidine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cytd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dad__2_e" name="Deoxyadenosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dad__2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_damp_e" name="dAMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_damp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dca_e" name="Decanoate (n-C10:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dca_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dcmp_e" name="dCMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dcyt_e" name="Deoxycytidine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcyt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ddca_e" name="Dodecanoate (n-C12:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ddca_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dgmp_e" name="dGMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dgsn_e" name="Deoxyguanosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgsn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dha_e" name="Dihydroxyacetone exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dha_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dimp_e" name="dIMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dimp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_din_e" name="Deoxyinosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_din_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dms_e" name="Dimethyl sulfide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dms_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dmso_e" name="Dimethyl sulfoxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dmso_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dopa_e" name="Dopamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dopa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_doxrbcn_e" name="doxorubicin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_doxrbcn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dtmp_e" name="dTMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_dump_e" name="dUMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dump_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_duri_e" name="Deoxyuridine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_duri_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_eca4colipa_e" name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_eca4colipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_enlipa_e" name="phosphoethanolamine KDO(2)-lipid (A) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_enlipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_enter_e" name="Enterochelin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_enter_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_etha_e" name="Ethanolamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etha_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ethso3_e" name="ethanesulfonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ethso3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_etoh_e" name="Ethanol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_f6p_e" name="D-fructose 6-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_f6p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fald_e" name="Formaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fald_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe2_e" name="Fe2+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe3_e" name="Fe3+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe3dcit_e" name="Fe(III)dicitrate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3dcit_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe3dhbzs_e" name="ferric 2,3-dihydroxybenzoylserine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3dhbzs_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe3hox_e" name="Fe(III)hydroxamate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fe3hox__un_e" name="Fe(III)hydoxamate, unloaded exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox__un_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fecrm_e" name="Ferrichrome exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fecrm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fecrm__un_e" name="Ferrichrome minus Fe(III) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fecrm__un_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_feenter_e" name="Fe-enterobactin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feenter_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_feoxam_e" name="ferroxamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_feoxam__un_e" name="ferroxamine minus Fe(3) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam__un_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_for_e" name="Formate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fru_e" name="D-Fructose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fru_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_frulys_e" name="fructoselysine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_frulys_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fruur_e" name="D-Fructuronate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fruur_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fuc__L_e" name="L-Fucose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fuc__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fum_e" name="Fumarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fusa_e" name="fusidic acid exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fusa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g1p_e" name="D-Glucose 1-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g1p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g3pc_e" name="sn-Glycero-3-phosphocholine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g3pe_e" name="sn-Glycero-3-phosphoethanolamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pe_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g3pg_e" name="Glycerophosphoglycerol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pg_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g3pi_e" name="sn-Glycero-3-phospho-1-inositol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pi_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g3ps_e" name="Glycerophosphoserine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3ps_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_g6p_e" name="D-Glucose 6-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gal_e" name="D-Galactose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gal__bD_e" name="beta D-Galactose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal__bD_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gal1p_e" name="alpha-D-Galactose 1-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal1p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_galct__D_e" name="D-Galactarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galct__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_galctn__D_e" name="D-Galactonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galctn__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_galctn__L_e" name="L-Galactonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galctn__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_galt_e" name="Galactitol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_galur_e" name="D-Galacturonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galur_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gam_e" name="D-Glucosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gam6p_e" name="D-Glucosamine 6-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gam6p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gbbtn_e" name="gamma-butyrobetaine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gbbtn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gdp_e" name="GDP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glc_e" name="D-Glucose exchange" reversible="true" fbc:lowerFluxBound="R_EX_glc_e_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glcn_e" name="D-Gluconate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glcr_e" name="D-Glucarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glcur_e" name="D-Glucuronate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glcur1p_e" name="D-Glucuronate 1-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur1p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gln__L_e" name="L-Glutamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gln__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glu__L_e" name="L-Glutamate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gly_e" name="Glycine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gly_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyald_e" name="D-Glyceraldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyald_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyb_e" name="Glycine betaine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyb_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyc_e" name="Glycerol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyc__R_e" name="(R)-Glycerate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc__R_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyc2p_e" name="Glycerol 2-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc2p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyc3p_e" name="Glycerol 3-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glyclt_e" name="Glycolate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gmp_e" name="GMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gsn_e" name="Guanosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gsn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gthox_e" name="Oxidized glutathione exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthox_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gthrd_e" name="Reduced glutathione exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gtp_e" name="GTP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gtp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gua_e" name="Guanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gua_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h_e" name="H+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h2_e" name="H2 exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h2o_e" name="H2O exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h2o2_e" name="Hydrogen peroxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h2s_e" name="Hydrogen sulfide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2s_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hacolipa_e" name="hepta-acylated core oligosaccharide lipid A (E. coli) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hacolipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_halipa_e" name="hepta-acylated KDO(2)-lipid (A) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_halipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hdca_e" name="Hexadecanoate (n-C16:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdca_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hdcea_e" name="hexadecenoate (n-C16:1) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hg2_e" name="Hg2+ exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hg2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_his__L_e" name="L-Histidine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_his__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hom__L_e" name="L-Homoserine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hom__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hxa_e" name="Hexanoate (n-C6:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_hxan_e" name="Hypoxanthine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxan_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_idon__L_e" name="L-Idonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_idon__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ile__L_e" name="L-Isoleucine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ile__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_imp_e" name="IMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_imp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_indole_e" name="Indole exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_indole_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_inost_e" name="myo-Inositol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_inost_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ins_e" name="Inosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ins_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_isetac_e" name="Isethionic acid exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_isetac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_k_e" name="K+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_k_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_kdo2lipid4_e" name="KDO(2)-lipid IV(A) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdo2lipid4_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lac__L_e" name="L-Lactate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lcts_e" name="Lactose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lcts_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_leu__L_e" name="L-Leucine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_leu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lipa_e" name="KDO(2)-lipid (A) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lipa_cold_e" name="cold adapted KDO(2)-lipid (A) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipa_cold_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lipoate_e" name="Lipoate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipoate_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lys__L_e" name="L-Lysine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lys__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lyx__L_e" name="L-Lyxose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lyx__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mal__D_e" name="D-Malate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mal__L_e" name="L-Malate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_malt_e" name="Maltose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_malthx_e" name="Maltohexaose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malthx_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_maltpt_e" name="Maltopentaose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_maltpt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_malttr_e" name="Maltotriose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malttr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_maltttr_e" name="Maltotetraose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_maltttr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_man_e" name="D-Mannose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_man6p_e" name="D-Mannose 6-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man6p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_manglyc_e" name="2(alpha-D-Mannosyl)-D-glycerate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_manglyc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_melib_e" name="Melibiose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_melib_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_meoh_e" name="methanol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_meoh_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_met__D_e" name="D-Methionine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_met__L_e" name="L-Methionine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_metsox__R__L_e" name="L-methionine-R-sulfoxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_metsox__R__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_metsox__S__L_e" name="L-Methionine S-oxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_metsox__S__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mg2_e" name="Mg exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mg2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mincyc_e" name="minocycline exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mincyc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_minohp_e" name="myo-Inositol hexakisphosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_minohp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mmet_e" name="S-Methyl-L-methionine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mmet_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mn2_e" name="Mn2+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mn2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mnl_e" name="D-Mannitol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mnl_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mobd_e" name="Molybdate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mobd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mso3_e" name="methanesulfonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mso3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_n2o_e" name="Nitrous oxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_n2o_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_na1_e" name="Sodium exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_nac_e" name="Nicotinate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_nh4_e" name="Ammonia exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nh4_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ni2_e" name="Ni2+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ni2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_nmn_e" name="NMN exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nmn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_no_e" name="Nitric oxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_no2_e" name="Nitrite exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_no3_e" name="Nitrate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_novbcn_e" name="novobiocin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_novbcn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_o16a4colipa_e" name="(O16 antigen)x4 core oligosaccharide lipid A exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16a4colipa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_o2_e" name="O2 exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_o2s_e" name="Superoxide anion exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2s_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ocdca_e" name="octadecanoate (n-C18:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdca_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ocdcea_e" name="octadecenoate (n-C18:1) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_octa_e" name="octanoate (n-C8:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_orn_e" name="Ornithine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_orn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_orot_e" name="Orotate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_orot_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pacald_e" name="Phenylacetaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pacald_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_peamn_e" name="Phenethylamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_peamn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_phe__L_e" name="L-Phenylalanine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_phe__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pheme_e" name="Protoheme exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pheme_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pi_e" name="Phosphate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pnto__R_e" name="(R)-Pantothenate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pnto__R_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ppa_e" name="Propionate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppa_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ppal_e" name="Propanal exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppal_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pppn_e" name="Phenylpropanoate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pppn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ppt_e" name="Phosphonate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pro__L_e" name="L-Proline exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pro__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_progly_e" name="L-Prolinylglycine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_progly_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_psclys_e" name="psicoselysine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_psclys_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pser__L_e" name="O-Phospho-L-serine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pser__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ptrc_e" name="Putrescine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ptrc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pydam_e" name="Pyridoxamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pydx_e" name="Pyridoxal exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pydxn_e" name="Pyridoxine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydxn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pyr_e" name="Pyruvate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_quin_e" name="Quinate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_quin_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_r5p_e" name="alpha-D-Ribose 5-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_rfamp_e" name="rifampin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rfamp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_rib__D_e" name="D-Ribose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rib__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_rmn_e" name="L-Rhamnose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rmn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_sbt__D_e" name="D-Sorbitol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sbt__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_sel_e" name="Selenate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sel_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ser__D_e" name="D-Serine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ser__L_e" name="L-Serine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_skm_e" name="Shikimate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_skm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_slnt_e" name="selenite exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_slnt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_so2_e" name="sulfur dioxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_so3_e" name="Sulfite exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so3_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_so4_e" name="Sulfate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so4_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_spmd_e" name="Spermidine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_spmd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_succ_e" name="Succinate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_sucr_e" name="Sucrose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sucr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_sulfac_e" name="sulfoacetate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sulfac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tartr__D_e" name="D-tartrate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tartr__L_e" name="L-tartrate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_taur_e" name="Taurine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_taur_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tcynt_e" name="Thiocyanate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tcynt_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_thm_e" name="Thiamin exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thm_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_thr__L_e" name="L-Threonine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_thrp_e" name="L-Threonine O-3-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thrp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_thym_e" name="Thymine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thym_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_thymd_e" name="Thymidine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thymd_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tma_e" name="Trimethylamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tma_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tmao_e" name="Trimethylamine N-oxide exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tmao_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tre_e" name="Trehalose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tre_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_trp__L_e" name="L-Tryptophan exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trp__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tsul_e" name="Thiosulfate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tsul_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ttdca_e" name="tetradecanoate (n-C14:0) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttdca_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ttdcea_e" name="tetradecenoate (n-C14:1) exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ttrcyc_e" name="tetracycline exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttrcyc_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tungs_e" name="tungstate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tungs_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tym_e" name="Tyramine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tym_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tyr__L_e" name="L-Tyrosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tyr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_tyrp_e" name="Phosphotyrosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tyrp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_uacgam_e" name="UDP-N-acetyl-D-glucosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_udpacgal_e" name="UDP-N-acetyl-D-galactosamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpacgal_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_udpg_e" name="UDPglucose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_udpgal_e" name="UDPgalactose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpgal_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_udpglcur_e" name="UDP-D-glucuronate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpglcur_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ump_e" name="UMP exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ump_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_ura_e" name="Uracil exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ura_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_urea_e" name="Urea exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_urea_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_uri_e" name="Uridine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uri_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_val__L_e" name="L-Valine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_val__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_xan_e" name="Xanthine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xan_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_xmp_e" name="Xanthosine 5'-phosphate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xmp_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_xtsn_e" name="Xanthosine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xtsn_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_xyl__D_e" name="D-Xylose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xyl__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_xylu__L_e" name="L-Xylulose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xylu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_zn2_e" name="Zinc exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_zn2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_12DGR120tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr120_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR140tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr140_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR141tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr141_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR160tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr160_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR161tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr161_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR180tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr180_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12DGR181tipp" name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr181_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12PPDRtex" name="(R)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__R_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__R_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_12PPDRtpp" name="(R)-Propane-1,2-diol facilitated transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__R_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__R_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_12PPDStex" name="(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__S_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__S_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_12PPDStpp" name="(S)-Propane-1,2-diol facilitated transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12ppd__S_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__S_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_14GLUCANabcpp" name="1,4-alpha-D-glucan transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_14glucan_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_14glucan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_14GLUCANtexi" name="1,4-alpha-D-glucan transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_14glucan_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_14glucan_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23CAMPtex" name="23cAMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23camp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23camp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23CCMPtex" name="23cCMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23ccmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23ccmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23CGMPtex" name="23cGMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23cgmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23cgmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23CUMPtex" name="23cUMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23cump_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23cump_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23DAPPAt2pp" name="2,3-diaminopropionate transport in via proton symport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dappa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dappa_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_23DAPPAtex" name="2,3-diaminopropionate transport via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dappa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23dappa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23PDE2pp" name="2',3'-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23cump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ump_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23PDE4pp" name="2',3'-cyclic-nucleotide phosphodiesterase (CMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23ccmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3cmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23PDE7pp" name="2',3'-cyclic-nucleotide phosphodiesterase (AMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23camp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3amp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_23PDE9pp" name="2',3'-cyclic-nucleotide phosphodiesterase (GMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23cgmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3gmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_26DAHtex" name="meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_26dap__M_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_26dap__M_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA120tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C12:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ddecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ddecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA140tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2tdecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2tdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA141tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2tdec7eg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2tdec7eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA160tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2hdecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2hdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA161tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2hdec9eg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2hdec9eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA180tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2odecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2odecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPA181tipp" name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2odec11eg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2odec11eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE120tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE140tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE141tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE160tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE161tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE180tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPE181tipp" name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT120" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT140" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT141" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pe141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT160" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT161" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT180" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPEAT181" name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG120tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG140tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG141tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG160tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG161tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG180tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPG181tipp" name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT120" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT140" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT141" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT160" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT161" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT180" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2AGPGAT181" name="2-acyl-glycerophospho-glycerol acyltransferase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2DGULRGx" name="2-Dehydro-L-gulonate reductase to gluconate (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dhguln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2DGULRGy" name="2-Dehydro-L-gulonate reductase to gluconate (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dhguln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2DGULRx" name="2-dehydro-L-gulonate reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dhguln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idon__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2DGULRy" name="2-dehydro-L-gulonate reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dhguln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idon__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_2MAHMP" name="2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mahmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ampm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0446" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1134" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_34dhpactex" name="dihydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_34dhpac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_34dhpac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3AMACHYD" name="3-aminoacrylate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3amac_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_msa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1009" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3AMPtex" name="3AMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3amp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3amp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3CMPtex" name="3CMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3cmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3cmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3GMPtex" name="3GMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3gmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3gmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD100" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hdecACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdec2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD120" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hddecACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tddec2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD121" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcddec5eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c5ddeceACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD140" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hmrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tmrs2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD141" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcmrs7eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c7mrseACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD160" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hpalmACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tpalm2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD161" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcpalm9eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c9palmeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD180" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hoctaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_toctd2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD181" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcvac11eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c11vaceACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD40" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3haACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD60" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hhexACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thex2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HAD80" name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hoctACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_toct2eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HCINNMH" name="3-hydroxycinnamate hydroxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hcinnm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhcinnm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0347" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HPPPNH" name="3-(3-hydroxy-phenyl)propionate hydroxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpppn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhpppn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0347" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HPPtex" name="3-hydroxypropionate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hpp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hpp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3HPPtpp" name="3-hydroxypropionate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpp_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_3KGK" name="3-keto-L-gulonate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhguln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhgulnp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3580" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3NTD2pp" name="3'-nucleotidase (UMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uri_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3NTD4pp" name="3'-nucleotidase (CMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3cmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3NTD7pp" name="3'-nucleotidase (AMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3amp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3NTD9pp" name="3'-nucleotidase (GMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3gmp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4213" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR100" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3odecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hdecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR120" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3oddecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hddecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR121" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocddec5eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hcddec5eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR140" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3omrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hmrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR141" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocmrs7eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hcmrs7eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR160" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3opalmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hpalmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR161" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocpalm9eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hcpalm9eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR180" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ooctdACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hoctaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR181" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocvac11eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hcvac11eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR40" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_actACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3haACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR60" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3ohexACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hhexACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAR80" name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C8:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ooctACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hoctACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS100" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3odecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS120" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3oddecACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS121" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cdec3eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocddec5eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS140" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3omrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS141" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cddec5eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocmrs7eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS160" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3opalmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS161" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocpalm9eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS180" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ooctdACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS181" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ocvac11eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS60" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_butACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ohexACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OAS80" name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hexACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ooctACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3OXCOAT" name="3-oxoadipyl-CoA thiolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_oxadpcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1397" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3PEPTabcpp" name="tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdap_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1329" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1244" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1245" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1246" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1247" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3PEPTtex" name="LalaDgluMdap (tripeptide) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdap_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_3UMPtex" name="3UMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3ump_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3ump_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_42A12BOOXpp" name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dopa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_34dhpac_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_4HOXPACDtex" name="4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4hoxpacd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4hoxpacd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_4HTHRS" name="4-Hydroxy-L-threonine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phthr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4hthr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0004" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_4PCP" name="tetrapeptide L,D-carboxypeptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1192" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_4PCPpp" name="tetrapeptide L,D-carboxypeptidase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_4PEPTabcpp" name="tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1243" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1244" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1245" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1246" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1247" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_4PEPTtex" name="LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5DGLCNR" name="5-dehydro-D-gluconate reductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4266" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5DGLCNt2rpp" name="5-Dehydro-D-gluconate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5dglcn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4265" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5DGLCNtex" name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dglcn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5dglcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5DOAN" name="5'-deoxyadenosine nuclosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__5_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5drib_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0159" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5MTRtex" name="5-Methylthio-D-ribose transport via proton diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5mtr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5mtr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_5MTRtpp" name="5-Methylthio-D-ribose transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5mtr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mtr_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_A5PISO" name="arabinose-5-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ara5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3197" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2708" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS1" name="acyl-[acyl-carrier-protein] synthetase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS2" name="acyl-[acyl-carrier-protein] synthetase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS3" name="acyl-[acyl-carrier-protein] synthetase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS4" name="acyl-[acyl-carrier-protein] synthetase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS5" name="acyl-[acyl-carrier-protein] synthetase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS6" name="acyl-[acyl-carrier-protein] synthetase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS7" name="acyl-[acyl-carrier-protein] synthetase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS8" name="acyl-[acyl-carrier-protein] synthetase (n-C10:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dca_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACPS9" name="acyl-[acyl-carrier-protein] synthetase (n-C8:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2836" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AACTOOR" name="Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aact_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_AADDGT" name="dTDP-N-4-acetamido-4,6-dideoxy-D-galactose transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_unagamu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4aaddg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_unagamuf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4481" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AAMYL" name="alpha-amylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_14glucan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1927" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AAMYLpp" name="alpha-amylase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_14glucan_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malthx_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3571" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AB6PGH" name="Arbutin 6-phosphate glucohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbt6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hqn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2901" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ABTA" name="4-aminobutyrate transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucsal_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2662" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1302" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ABUTD" name="Aminobutyraldehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abutn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1444" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ABUTt2pp" name="4-aminobutyrate transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abut_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2663" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ABUTtex" name="4-aminobutyrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4abut_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4abut_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACCT" name="acetyl-CoA:acetoacetyl-CoA transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acac_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aacoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2221" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2222" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT1r" name="acetyl-CoA C-acetyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aacoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2224" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT2r" name="acetyl-CoA C-acyltransferase (butanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3ohcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT3r" name="acetyl-CoA C-acyltransferase (hexanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3oocoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT4r" name="acetyl-CoA C-acyltransferase (octanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_occoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3odcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT5r" name="acetyl-CoA C-acyltransferase (decanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3oddcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT6r" name="acetyl-CoA C-acyltransferase (dodecanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3otdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT7r" name="acetyl-CoA C-acyltransferase (tetradecanoyl-CoA) (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3ohdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACT8r" name="acetyl-CoA acyltransferase (hexadecanoyl-CoA), (r)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3oodcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pmtcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2342" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3845" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACt2pp" name="acetoacetate transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acac_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acac_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2223" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACACtex" name="acetoacetate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACALD" name="acetaldehyde dehydrogenase (acetylating)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0351" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACALDtex" name="acetaldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acald_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACALDtpp" name="acetaldehyde reversible transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acald_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACANTHAT" name="acetyl-CoA:anthranilate acetyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anth_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acanth_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1463" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACBIPGT" name="Adenosyl cobinamide phosphate guanyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adocbip_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_agdpcbi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1993" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACCOAC" name="acetyl-CoA carboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hco3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0185" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2316" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3255" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3256" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACCOAL" name="acetate-CoA ligase (ADP-forming)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4069" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAL1PPpp" name="N-acetyl-D-galactosamine 1-phosphatase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgal1p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgal_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ACGAL1Ptex" name="N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgal1p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgal1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGALtex" name="N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgal_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAM1PPpp" name="N-acetyl-D-glucosamine 1-phosphatase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam1p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ACGAM1Ptex" name="N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgam1p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAMK" name="N-acetylglucosamine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1119" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAMT" name="UDP-N-acetylglucosamine:undecaprenylphosphate N-acetylglucosamine -1-phosphate transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udcpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_unaga_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3784" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAptspp" name="N-Acetyl-D-glucosamine transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1101" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0679" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGAtex" name="N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acgam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGK" name="acetylglutamate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acg5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3959" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACGS" name="N-acetylglutamate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acglu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2818" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACHBS" name="2-aceto-2-hydroxybutanoate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2obut_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ahbut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3670" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3671" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0077" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0078" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACKr" name="acetate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3115" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2296" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1849" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACLS" name="acetolactate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alac__S_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3670" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3671" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0077" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0078" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACM6PH" name="N-acetylmuramate 6-phosphate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmum6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2428" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACMAMUT" name="UDP-N-acetyl-D-mannosaminuronic acid transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_unaga_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uacmamu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_unagamu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3794" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACMANAptspp" name="N-acetyl-D-mannosamine transport via PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmana_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmanap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACMANAtex" name="N-acetyl-D-mannosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmana_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acmana_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACMUMptspp" name="N-acetylmuramate transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmum_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmum6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2429" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACMUMtex" name="N-acetylmuramate transport via diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmum_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acmum_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACNAMt2pp" name="N-acetylneuraminate proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acnam_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acnam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3224" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACNAMtex" name="N-acetylneuraminate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acnam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acnam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4311" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACNML" name="N-Acetylneuraminate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acnam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmana_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3225" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD1f" name="acyl-CoA dehydrogenase (butanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_b2coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD2f" name="acyl-CoA dehydrogenase (hexanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hx2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD3f" name="acyl-CoA dehydrogenase (octanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_occoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_oc2coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD4f" name="acyl-CoA dehydrogenase (decanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dc2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD5f" name="acyl-CoA dehydrogenase (dodecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dd2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD6f" name="acyl-CoA dehydrogenase (tetradecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_td2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD7f" name="acyl-CoA dehydrogenase (hexadecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pmtcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdd2coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOAD8f" name="acyl-CoA dehydrogenase (octadecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_stcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_od2coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0221" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOATA" name="Acetyl-CoA ACP transacylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1091" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACODA" name="acetylornithine deacetylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acorn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3957" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOLIPAabctex" name="arabinose modified core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acolipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acolipa_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONIs" name="aconitate isomerase (spontaneous)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acon__T_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acon__C_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONMT" name="Trans-aconitate methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acon__T_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_aconm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1519" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONTa" name="aconitase (half-reaction A, Citrate hydro-lyase)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acon__C_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0118" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1276" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONTb" name="aconitase (half-reaction B, Isocitrate hydro-lyase)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acon__C_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0118" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1276" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACOTA" name="acetylornithine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acorn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acg5sa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1748" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3359" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT120" name="acyl-(acyl carrier protein):phosphate acyltransferase (C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT140" name="acyl-(acyl carrier protein):phosphate acyltransferase (C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdcap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT141" name="acyl-(acyl carrier protein):phosphate acyltransferase (C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdceap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT160" name="acyl-(acyl carrier protein):phosphate acyltransferase (C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT161" name="acyl-(acyl carrier protein):phosphate acyltransferase (C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdceap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT180" name="acyl-(acyl carrier protein):phosphate acyltransferase (C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPPAT181" name="acyl-(acyl carrier protein):phosphate acyltransferase (C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdceap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1090" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACPS1" name="acyl-carrier protein synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apoACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3475" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2563" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACS" name="acetyl-CoA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4069" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACSERtex" name="O-Acetyl-L-serine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acser_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acser_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACSERtpp" name="O-Acetyl-L-serine export via facilitated transport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acser_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acser_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2578" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1533" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACt2rpp" name="acetate reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ac_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ACt4pp" name="Na+/Acetate symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ac_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4067" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACtex" name="Acetate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADA" name="Adenosine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1623" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADCL" name="4-aminobenzoate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4adcho_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1096" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADCS" name="4-amino-4-deoxychorismate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4adcho_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3360" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1812" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADD" name="adenine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3665" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADEt2rpp" name="adenine transport via proton symport (reversible) (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ade_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3654" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3714" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADEtex" name="adenine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ade_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADK1" name="adenylate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADK3" name="adentylate kinase (GTP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADK4" name="adentylate kinase (ITP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_itp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADMDC" name="adenosylmethionine decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ametam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0120" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNCYC" name="adenylate cyclase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_camp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3806" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNK1" name="adenosine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNUC" name="adenosine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0030" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNt2pp" name="adenosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNt2rpp" name="adenosine transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADNtex" name="adenosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADOCBIK" name="Adenosyl cobinamide kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adocbi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adocbip_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1993" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADOCBLS" name="Adenosylcobalamin 5'-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rdmbzi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_agdpcbi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adocbl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1992" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADOCBLabcpp" name="Adenosylcobalamin transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adocbl_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adocbl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1711" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1709" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0158" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADOCBLtonex" name="Adenosylcobalimin transport via ton system (extermal)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adocbl_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adocbl_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3966" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADPRDP" name="ADPribose diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adprib_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3397" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3034" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADPT" name="adenine phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADSK" name="adenylyl-sulfate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aps_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_paps_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2750" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADSL1r" name="adenylsuccinate lyase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1131" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADSL2r" name="adenylosuccinate lyase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_25aics_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aicar_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1131" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ADSS" name="adenylosuccinate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcamp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4177" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGDC" name="N-acetylglucosamine-6-phosphate deacetylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0677" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM3PA" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0110" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM3PApp" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdap_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2435" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4169" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM3PH" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide beta -1,4-N-acetylglucosaminidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhm3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1107" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM3Pt2pp" name="GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0433" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM4PA" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0110" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM4PApp" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2435" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4169" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM4PCP" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1192" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM4PCPpp" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_AGM4PH" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhm4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1107" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGM4Pt2pp" name="GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0433" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGMH" name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1107" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGMHE" name="ADP-D-glycero-D-manno-heptose epimerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adphep__DD_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adphep__LD_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3619" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGMT" name="agmatinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_agm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_urea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2937" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGMt2pp" name="GlcNAc-anhMurNAc transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0433" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGMtex" name="agmatine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_agm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_agm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT120" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1ddecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT140" name="1-tetradecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT141" name="1-tetradec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdec7eg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT160" name="1-hexadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1hdecg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT161" name="1-hexadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1hdec9eg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT180" name="1-octadecanoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1odecg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPAT181" name="1-octadec-7-enoyl-sn-glycerol 3-phosphate O-acyltransferase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1odec11eg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3018" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGPR" name="N-acetyl-g-glutamyl-phosphate reductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acg5sa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acg5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3958" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AGt3" name="silver transport out via proton antiport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ag_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ag_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0572" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0573" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0574" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0575" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AHCYSNS" name="S-adenosylhomocysteine nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rhcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0159" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AICART" name="phosphoribosylaminoimidazolecarboxamide formyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aicar_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fprica_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4006" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AIRC2" name="phosphoribosylaminoimidazole carboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_air_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hco3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5caiz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0522" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AIRC3" name="phosphoribosylaminoimidazole carboxylase (mutase rxn)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5aizc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5caiz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0523" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AKGDH" name="2-Oxogluterate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0116" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0726" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0727" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AKGt2rpp" name="2-oxoglutarate reversible transport via symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2587" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AKGtex" name="alpha-ketoglutarate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAALAD" name="D-alanine-D-alanine dipeptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1488" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAALAabcpp" name="D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alaala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1487" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1486" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1485" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1484" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1483" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3544" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3543" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3542" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3541" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3540" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAALAr" name="D-alanine-D-alanine ligase (reversible)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alaala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0381" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0092" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAALAtex" name="D-alanyl-D-alanine (DalaDala) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_alaala_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAGLUE" name="L-alanyl-gamma-glutamate epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaLglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1325" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAR" name="alanine racemase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1190" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4053" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALATA_D2" name="D-alanine transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyam5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0870" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALATA_L" name="L-alanine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2290" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2379" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALATA_L2" name="alanine transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyam5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0870" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALATRS" name="Alanyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnaala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alatrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2697" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAabcpp" name="L-alanine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3460" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAt2pp" name="L-alanine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4208" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAt2rpp" name="L-alanine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ALAt4pp" name="L-alanine transport in via sodium symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0007" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALAtex" name="L-alanine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALCD19" name="alcohol dehydrogenase (glycerol)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0356" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALCD2x" name="alcohol dehydrogenase (ethanol)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1478" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0356" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALDD19xr" name="aldehyde dehydrogenase (phenylacetaldehyde, NAD)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pacald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1385" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALDD2x" name="aldehyde dehydrogenase (acetaldehyde, NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1300" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALDD2y" name="aldehyde dehydrogenase (acetaldehyde, NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3588" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALDD3y" name="aldehyde dehydrogenase (propanal, NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppal_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3588" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALDD4" name="aldehyde dehydrogenase (butanal, NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btal_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_but_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ALLK" name="Allose kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_all__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_all6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4084" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLPI" name="Allose 6-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_all6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_allul6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4090" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLTAMH" name="allantoate amidohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_alltt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_urdglyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0516" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLTN" name="allantoinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alltn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alltt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0512" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLTNt2rpp" name="allantoin transport in via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alltn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alltn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0511" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLTNtex" name="allantoin transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_alltn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alltn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLULPE" name="Allulose 6-phosphate epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_allul6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4085" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLabcpp" name="D-allose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_all__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_all__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4087" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4088" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4086" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALLtex" name="Allose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_all__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_all__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALPATE160pp" name="apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alpp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lpp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0657" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1677" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALPATG160pp" name="apolipoprotein N-acyltransferase (phosphatidylglycerol, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_alpp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpg160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lpp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0657" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1677" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALR2" name="aldose reductase (methylglyoxal)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acetol_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3012" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0207" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3001" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALR4x" name="aldose reductase (acetol)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acetol_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__R_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALTRH" name="altronate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_altrn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddglcn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3091" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AM3PA" name="anhydrous-N-Acetylmuramyl-tripeptide amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0110" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AM4PA" name="anhydrous-N-Acetylmuramyl-tetrapeptide amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0110" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AM4PCP" name="anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhm3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1192" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMALT1" name="Amylomaltase (maltotriose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malttr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3416" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMALT2" name="Amylomaltase (maltotetraose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3416" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMALT3" name="Amylomaltase (maltopentaose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3416" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMALT4" name="Amylomaltase (maltohexaose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3416" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMANAPEr" name="N-acetylmannosamine 6-phosphate epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmanap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3223" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMANK" name="N-acetyl-D-mannosamine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acmana_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmanap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3222" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMAOTr" name="adenosylmethionine-8-amino-7-oxononanoate transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_8aonn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_amob_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dann_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0774" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMMQLT8" name="S-adenosylmethione:2-demthylmenaquinole methyltransferase (menaquinone 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3833" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMPMS2" name="4-amino-2-methyl-5-phosphomethylpyrimidine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_air_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4ampm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3994" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMPN" name="AMP nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1982" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMPTASECG" name="alanyl aminopeptidase (cys-gly)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cgly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0237" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0932" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4260" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2523" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMPTASEPG" name="aminopeptidase (pro-gly)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_progly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4260" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0237" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2523" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0932" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AMPtex" name="AMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_amp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_amp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ANHGMtex" name="GlcNAc-anhMurNAc transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_anhgm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ANHMK" name="1,6-anhydrous-N-Acetylmuramate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acmum6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1640" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ANPRT" name="anthranilate phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anth_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pran_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1263" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ANS" name="anthranilate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anth_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1263" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1264" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AOBUTDs" name="L-2-amino-3-oxobutanoate decarboxylation (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2aobut_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_aact_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AOXSr2" name="8-amino-7-oxononanoate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pimACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_8aonn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0776" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AP4AH" name="Ap4A hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ap4a_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0049" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AP4AS" name="Ap4A synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ap4a_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4129" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AP5AH" name="Ap5A hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ap5a_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0049" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APCS" name="aminopropylcadaverine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ametam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_15dap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mta_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na15dap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0121" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT120" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1ddecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT140" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttdcap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT141" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdec7eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT160" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1hdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT161" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1hdec9eg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT180" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_1odecg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APG3PAT181" name="acyl-phosphate:glycerol-3-phosphate acyltransferase (C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1odec11eg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH120" name="acylphosphatase (C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH140" name="acylphosphatase (C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH141" name="acylphosphatase (C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH160" name="acylphosphatase (C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH161" name="acylphosphatase (C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH180" name="acylphosphatase (C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APH181" name="acylphosphatase (C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdceap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0968" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APPLDHr" name="aminopropanol dehydrogenase reversible" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_aact_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_appl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_APRAUR" name="5-amino-6-(5-phosphoribosylamino)uracil reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5apru_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5aprbu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0414" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARAI" name="L-arabinose isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arab__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rbl__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0062" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNR1" name="aerobactin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbtn__fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNR2" name="aerobactin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbtn__fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNR3" name="aerobactin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbtn__fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNabcpp" name="aerobactin transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn__fe3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn__fe3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNexs" name="aerobactin Fe-loading reaction (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn__fe3_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNtex" name="aerobactin secretion (to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn_e" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNtonex" name="aerobactin transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn__fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbtn__fe3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTNtpp" name="aerobactin secretion (to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbtn_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ARBTptspp" name="arbutin transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arbt6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3722" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2715" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBTtex" name="arbutin transport via diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arbt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arbt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBabcpp" name="L-arabinose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1901" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1900" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4460" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBt2rpp" name="L-arabinose transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2841" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBt3ipp" name="L-arabinose transport via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arab__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARBtex" name="L-arabinose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arab__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arab__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGAGMt7pp" name="Arginine/agmatine antiport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_agm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_agm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4115" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGDC" name="arginine decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_agm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4117" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGDCpp" name="arginine decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_agm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2938" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGORNt7pp" name="arginine/ornithine antiporter (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1605" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGSL" name="argininosuccinate lyase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_argsuc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3960" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGSS" name="argininosuccinate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_citr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_argsuc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3172" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGTRS" name="Arginyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnaarg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_argtrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1876" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGabcpp" name="L-arginine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2310" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2308" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0863" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0860" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0861" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0864" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0862" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGt3pp" name="L-arginine transport out via proton antiport (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2923" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ARGtex" name="L-arginine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_arg__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_arg__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASAD" name="aspartate-semialdehyde dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aspsa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4pasp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3433" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASCBPL" name="L-ascorbate 6-phosphate lactonase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ascb6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhgulnp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4192" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASCBptspp" name="L-ascorbate transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ascb__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ascb6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4195" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4194" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4193" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASCBtex" name="L-ascorbate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ascb__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ascb__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNN" name="L-asparaginase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1767" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0828" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNNpp" name="L-asparaginase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asn__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2957" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNS1" name="asparagine synthase (glutamine-hydrolysing)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0674" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNS2" name="asparagine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNTRS" name="Asparaginyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnaasn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asntrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0930" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNabcpp" name="L-asparagine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asn__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ASNt2rpp" name="L-asparagine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asn__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asn__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1453" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASNtex" name="L-asparagine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asn__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asn__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASO3t8pp" name="arsenite efflux via ATP hydrolysis (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aso3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aso3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3502" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASO3tex" name="arsenite transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_aso3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_aso3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASP1DC" name="aspartate 1-decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__B_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0131" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPCT" name="aspartate carbamoyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbasp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4244" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4245" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4245" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPK" name="aspartate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4pasp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0002" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3940" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4024" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPO3" name="L-aspartate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iasp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2574" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPO4" name="L-aspartate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iasp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2574" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPO5" name="L-aspartate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iasp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2574" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPO6" name="L-aspartate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iasp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2574" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPT" name="L-aspartase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4139" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPTA" name="aspartate transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0928" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPTRS" name="Aspartyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnaasp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asptrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1866" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPabcpp" name="L-aspartate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0655" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0654" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0653" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0652" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPt2_2pp" name="Aspartate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPt2_3pp" name="L-asparate transport via proton symport (3 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPt2pp" name="L-aspartate transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4077" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASPt2rpp" name="L-aspartate transport in via proton symport (periplasm) reversible" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ASPtex" name="L-aspartate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ASR" name="arsenate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_aso4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aso3_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3503" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AST" name="Arginine succinyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_arg__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sucarg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1747" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ATHRDHr" name="L-allo-threonine dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_athr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2aobut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1539" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ATPHs" name="ATP amine hydrolysis (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_itp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ATPM" name="ATP maintenance requirement" reversible="false" fbc:lowerFluxBound="R_ATPM_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ATPPRT" name="ATP phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_prbatp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2019" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ATPS4rpp" name="ATP synthase (four protons for one ATP) (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3736" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3737" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3738" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3731" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3732" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3734" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3735" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3739" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3736" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3737" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3738" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3731" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3732" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3734" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3735" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BALAt2pp" name="beta-alanine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__B_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__B_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4208" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BALAtex" name="beta-alanine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__B_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__B_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BETALDHx" name="betaine-aldehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_betald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0312" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BETALDHy" name="betaine-aldehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_betald_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_glyb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0312" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BMOCOS" name="bis-molybdenum cofactor synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_moco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mptamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bmoco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0827" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BMOGDS1" name="bis-molybdopterin guanine dinucleotide synthase (single GDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bmoco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bmoco1gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3856" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BMOGDS2" name="bis-molybdopterin guanine dinucleotide synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bmoco1gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bmocogdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3856" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BPNT" name="3',5'-bisphosphate nucleotidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4214" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BSORx" name="Biotin sulfoxide reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btnso_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3551" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BSORy" name="Biotin sulfoxide reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btnso_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3551" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BTNt2ipp" name="Biotin transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_btn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_BTNtex" name="Biotin transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_btn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_btn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BTS5" name="Biotin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_btn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__5_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe1s_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0775" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BUTCT" name="Acetyl-CoA:butyrate-CoA transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2221" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2222" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BUTSO3abcpp" name="butanesulfonate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_butso3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_butso3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0936" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0933" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0934" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0365" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0366" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0367" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BUTSO3tex" name="butanesulfonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_butso3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_butso3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BUTt2rpp" name="Butyrate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2223" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BUTtex" name="Butyrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_but_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_but_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BWCOGDS1" name="tungsten bispterin guanine dinucleotide synthase (single GDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bwco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bwco1gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3856" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BWCOGDS2" name="tungsten bispterin guanine dinucleotide synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_bwco1gdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bwcogdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3856" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_BWCOS" name="tungsten bispterin cofactor synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_wco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mptamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bwco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0827" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CA2t3pp" name="calcium (Ca+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ca2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ca2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1216" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CA2tex" name="calcium (Ca+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ca2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ca2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CADVtpp" name="Lysine/Cadaverine antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_15dap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_15dap_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4132" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CAT" name="catalase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1732" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3942" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CAt6pp" name="calcium / sodium antiporter (1:1)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ca2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ca2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3196" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBIAT" name="Cobinamide adenyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adocbi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1270" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBItonex" name="Cobinamide transport via ton system (extermal)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbi_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cbi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3966" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBIuabcpp" name="Cobinamide transport via ABC system (uptake, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1711" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1709" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0158" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBL1abcpp" name="Cob(1)alamin transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbl1_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cbl1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1711" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1709" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0158" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBL1tonex" name="Cob(1)alamin transport via ton system (extermal)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbl1_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbl1_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3966" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBLAT" name="cob(I)alamin adenosyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbl1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adocbl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1270" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBMD" name="carbamate deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cbm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBMKr" name="Carbamate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cbp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0521" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2874" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CBPS" name="carbamoyl-phosphate synthase (glutamine-hydrolysing)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hco3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cbp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0033" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CCGS" name="7-cyano-7-carbaguanine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cdg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_preq0_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0444" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CD2abcpp" name="Cadmium (Cd+2) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cd2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cd2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CD2t3pp" name="cadmium (Cd+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cd2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cd2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0752" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CD2tex" name="cadmium (Cd+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cd2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cd2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CD2tpp" name="cadmium (+2) transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cd2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cd2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA120" name="CDP-Diacylglycerol pyrophostatase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdddecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA140" name="CDP-Diacylglycerol pyrophostatase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA141" name="CDP-Diacylglycerol pyrophostatase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdec7eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA160" name="CDP-Diacylglycerol pyrophostatase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA161" name="CDP-Diacylglycerol pyrophostatase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdec9eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA180" name="CDP-Diacylglycerol pyrophostatase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDAPPA181" name="CDP-Diacylglycerol pyrophostatase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodec11eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDGR" name="7-cyano-7-deazaguanine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_preq0_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_preq1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2794" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CDGS" name="7-deaza-7-carboxyguanine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cph4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cdg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CDPMEK" name="4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4c2me_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2p4c2me_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1208" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CFAS160E" name="cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1661" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CFAS160G" name="cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cpg160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1661" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CFAS180E" name="cyclopropane fatty acid synthase (Phosphatidylethanolamine, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cpe180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1661" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CFAS180G" name="cyclopropane fatty acid synthase (Phosphatidylglycerol, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1661" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CGLYabcpp" name="L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cgly_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cgly_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3544" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3543" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3542" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3541" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3540" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CGLYtex" name="L-Cysteinylglycine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cgly_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cgly_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHLabcpp" name="choline transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2128" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2129" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2130" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2131" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHLt2pp" name="choline transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0314" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1801" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHLtex" name="choline transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chol_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_chol_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHOLD" name="choline dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_betald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0311" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHORM" name="chorismate mutase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pphn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2599" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2600" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHORS" name="chorismate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3psme_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2329" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHRPL" name="Chorismate pyruvate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4hbz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4039" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHTBSptspp" name="chitobiose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chtbs_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chtbs6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CHTBStex" name="chitobiose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chtbs_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_chtbs_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CINNDO" name="Cinnamate dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cinnm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cenchddd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2538" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2539" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2540" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2542" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CITL" name="Citrate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0615" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0616" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0617" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0614" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CITt3pp" name="citrate transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CITt7pp" name="Citrate transport via succinate antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0612" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CITtex" name="citrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cit_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cit_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLIPAabctex" name="cold lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_cold_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipa_cold_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH120pp" name="cardiolipin hydrolase (periplasm, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH140pp" name="cardiolipin hydrolase (periplasm, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_clpn140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH141pp" name="cardiolipin hydrolase (periplasm, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH160pp" name="cardiolipin hydrolase (periplasm, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_clpn160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH161pp" name="cardiolipin hydrolase (periplasm, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_clpn161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH180pp" name="cardiolipin hydrolase (periplasm, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa180_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNH181pp" name="cardiolipin hydrolase (periplasm, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa181_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS120pp" name="cardiolipin synthase (periplasmic, n-C12:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn120_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS140pp" name="cardiolipin synthase (periplasmic, n-C14:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS141pp" name="cardiolipin synthase (periplasmic, n-C14:1)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS160pp" name="cardiolipin synthase (periplasmic, n-C16:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_clpn160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS161pp" name="cardiolipin synthase (periplasmic, n-C16:1)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS180pp" name="cardiolipin synthase (periplasmic, n-C18:0)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLPNS181pp" name="cardiolipin synthase (periplasmic, n-C18:1)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_clpn181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1249" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLt3_2pp" name="chloride transport out via proton antiport (2:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cl_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cl_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0155" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1592" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CLtex" name="chloride (Cl-1) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cl_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cl_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CMPN" name="CMP nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_csn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CMPtex" name="CMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CMtex" name="Chloramphenicol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CMtpp" name="Chloramphenicol transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cm_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cm_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CO2tex" name="CO2 transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CO2tpp" name="CO2 transporter via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COBALT2abcpp" name="Cobalt (Co+2) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cobalt2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cobalt2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COBALT2t3pp" name="cobalt (Co+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cobalt2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cobalt2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0752" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COBALT2tex" name="cobalt (Co+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cobalt2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cobalt2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COBALT2tpp" name="cobalt transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cobalt2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cobalt2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3816" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COLIPAKpp" name="Lipid A core kinase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udcpp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipap_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2174" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COLIPAPabctex" name="core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipap_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_colipap_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COLIPAabcpp" name="core oligosaccharide lipid A transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_COLIPAabctex" name="core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_colipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPGNR1" name="coprogen(Fe(III)) reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_c" stoichiometry="2" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CPGNR2" name="coprogen(Fe(III)) reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_c" stoichiometry="2" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CPGNR3" name="coprogen(Fe(III)) reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_c" stoichiometry="2" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CPGNUtex" name="coprogen unloaded secretion (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpgn__un_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CPGNUtpp" name="coprogen unloaded secretion" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn__un_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CPGNabcpp" name="coprogen transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpgn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPGNexs" name="coprogen Fe-loading reaction (spontaneaous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpgn__un_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpgn_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPGNtonex" name="Coprogen transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpgn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1102" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPH4S" name="6-carboxy-5,6,7,8-tetrahydropterin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahdt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cph4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2765" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPMPS" name="cyclic pyranopterin monophosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cpmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0783" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPPPGO" name="coproporphyrinogen oxidase (O2 required)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cpppg3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pppg9_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2436" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CPPPGO2" name="Oxygen Independent coproporphyrinogen-III oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_cpppg3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_dad__5_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pppg9_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3867" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNBTCT" name="gamma-butyrobetainyl-CoA: carnitine CoA transferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bbtcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gbbtn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crncoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0038" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNCAL2" name="Carnitine-CoA Ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crncoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0037" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNCAR" name="carnitine-CoA racemase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crncoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crnDcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNCBCT" name="crotonobetainyl-CoA: carnitine CoA transferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctbtcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ctbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crncoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0038" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNCDH" name="Carnityl-CoA dehydratse" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crncoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctbtcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNDCAL2" name="D-Carnitine-CoA Ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crnDcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0037" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNDabcpp" name="D-carnitine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2677" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2678" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2679" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNDt2rpp" name="D-carnitine outward transport (H+ antiport)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4111" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNDtex" name="D-carnitine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crn__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNabcpp" name="L-carnitine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2677" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2678" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2679" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNt2rpp" name="L-carnitine outward transport (H+ antiport)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4111" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNt7pp" name="Carnitine/butyrobetaine antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gbbtn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gbbtn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNt8pp" name="L-carnitine/D-carnitine antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_crn__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CRNtex" name="L-carnitine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_crn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_crn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CS" name="citrate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0720" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CSND" name="Cytosine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_csn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0337" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CSNt2pp" name="cytosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_csn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_csn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0336" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CSNtex" name="cytosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_csn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_csn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTBTCAL2" name="Crotonobetaine-CoA Ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctbtcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0037" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTBTabcpp" name="crotonobetaine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctbt_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ctbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2677" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2678" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2679" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTBTt2rpp" name="cronobetaine outward transport (H+ antiport)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctbt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ctbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4111" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTECOAI6" name="3-cis-2-trans-enoyl-CoA isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdecoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_td2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTECOAI7" name="3-cis-2-trans-enoyl-CoA isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdd2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTECOAI8" name="3-cis-2-trans-enoyl-CoA isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_odecoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_od2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CTPS2" name="CTP synthase (glutamine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2780" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CU1Opp" name="Cuprous Oxidase (Cu+1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu_p" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0123" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CU1abcpp" name="Copper (Cu +1) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0484" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CU2abcpp" name="Copper (Cu+2) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CU2tex" name="copper (Cu+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CU2tpp" name="copper transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CUt3" name="copper transport out via proton antiport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0572" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0573" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0574" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0575" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CUtex" name="copper (Cu+1) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cu_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cu_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYANST" name="Cyanide sulfurtransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tsul_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cyan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tcynt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3425" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYANSTpp" name="Cyanide sulfurtransferase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cyan_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tsul_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tcynt_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_so3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1308" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYANtex" name="Cyanide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cyan_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cyan_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYNTAH" name="Cyanate aminohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_cynt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hco3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0340" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYNTt2pp" name="Cyanate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cynt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cynt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0341" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYNTtex" name="Cyanate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cynt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cynt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSDDS" name="D-cysteine desulfhydrase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1919" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSDS" name="Cysteine Desulfhydrase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3708" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3008" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSDabcpp" name="D-cysteine uptake via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CYSDtex" name="D-cysteine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSS" name="cysteine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acser_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2414" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2421" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSSADS" name="L-cysteine sulfinic acid desulfurase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3sala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2810" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSTL" name="cystathionine b-lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cyst__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hcys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1622" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3008" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSTRS" name="Cysteinyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnacys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cystrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0526" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSabc2pp" name="L-cysteine export via ABC system (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0886" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0887" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYSabcpp" name="L-cysteine uptake via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CYStex" name="L-cysteine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYStpp" name="L-cysteine export via facilitated transport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cys__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2578" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1533" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTBD2pp" name="cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0978" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0979" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTBDpp" name="cytochrome oxidase bd (ubiquinol-8: 2 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0978" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0979" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0734" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTBO3_4pp" name="cytochrome oxidase bo3 (ubiquinol-8: 4 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0429" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0430" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0431" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0432" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTD" name="cytidine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2143" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTDH" name="Cytidine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_csn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2162" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0651" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0030" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTDK2" name="cytidine kinase (GTP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2066" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTDt2pp" name="cytidine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTDt2rpp" name="cytidine transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTDtex" name="cytidine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cytd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cytd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTK1" name="cytidylate kinase (CMP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0910" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTK2" name="cytidylate kinase (dCMP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0910" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_D__LACt2pp" name="D-lactate transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3603" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2975" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_D__LACtex" name="D-lactate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lac__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAAD" name="D-Amino acid dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1189" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DADA" name="Deoxyadenosine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_din_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1623" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DADK" name="deoxyadenylate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_damp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DADNt2pp" name="deoxyadenosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dad__2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DADNtex" name="deoxyadenosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dad__2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dad__2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK120" name="diacylglycerol kinase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK140" name="diacylglycerol kinase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK141" name="diacylglycerol kinase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK160" name="diacylglycerol kinase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK161" name="diacylglycerol kinase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_12dgr161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK180" name="diacylglycerol kinase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAGK181" name="diacylglycerol kinase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4042" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DALAt2pp" name="D-alanine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4208" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DALAtex" name="D-Alanine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ala__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAMPtex" name="dAMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_damp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_damp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAPAL" name="2,3-diaminopropionate amonnia lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dappa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2871" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAPDC" name="diaminopimelate decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_26dap__M_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2838" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAPE" name="diaminopimelate epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_26dap__LL_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_26dap__M_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3809" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DAPabcpp" name="M-diaminopimelic acid ABC transport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_26dap__M_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_26dap__M_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_DAPtex" name="1,5-Diaminopentane transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_15dap_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_15dap_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN120" name="CDP-diacylglycerol synthetase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdddecg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN140" name="CDP-diacylglycerol synthetase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdecg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN141" name="CDP-diacylglycerol synthetase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdec7eg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN160" name="CDP-diacylglycerol synthetase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdecg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN161" name="CDP-diacylglycerol synthetase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdec9eg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN180" name="CDP-diacylglycerol synthetase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodecg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DASYN181" name="CDP-diacylglycerol synthetase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodec11eg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0175" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DATPHs" name="dATP amine hydrolysis (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_datp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ditp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DB4PS" name="3,4-Dihydroxy-2-butanone-4-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_db4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3041" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DBTS" name="dethiobiotin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dann_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtbt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0778" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DC6PH" name="diacetylchitobiose-6-phosphate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chtbs6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1734" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCAtex" name="Decanoate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dca_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCMPtex" name="dCMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCTPD" name="dCTP deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dutp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2065" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCYTD" name="deoxycytidine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcyt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_duri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2143" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCYTt2pp" name="deoxycytidine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcyt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcyt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DCYTtex" name="deoxycytidine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcyt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcyt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDCAtexi" name="Fatty acid (dodecanoate) transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ddca_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDGALK" name="2-dehydro-3-deoxygalactonokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dh3dgal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dh3dgal6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3693" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDGLCNt2rpp" name="2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddglcn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ddglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3909" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDGLCNtex" name="2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ddglcn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ddglcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDGLK" name="2-dehydro-3-deoxygluconokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ddglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddg6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3526" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDPA" name="3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dda7p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2601" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0754" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1704" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DDPGALA" name="2-dehydro-3-deoxy-6-phosphogalactonate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dh3dgal6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4477" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DGK1" name="deoxyguanylate kinase (dGMP:ATP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3648" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DGMPtex" name="dGMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dgmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DGSNt2pp" name="deoxyguanosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgsn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgsn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DGSNtex" name="deoxyguanosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgsn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dgsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHACOAH" name="2,3-dehydroadipyl-CoA hydratase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hadpcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1393" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHAD1" name="dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dhmb_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mob_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3771" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHAD2" name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dhmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mop_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3771" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHAPT" name="Dihydroxyacetone phosphotransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dha_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1198" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHAtex" name="Dihydroxyacetone transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dha_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dha_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHAtpp" name="Dihydroxyacetone transport via facilitated diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dha_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dha_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_DHBD" name="2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23ddhb_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0596" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHBS" name="2,3-dihydroxybenzoate adenylate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhb_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhba_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0594" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHBSH" name="2,3-dihydroxybenzoylserine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhbzs_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhb_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_DHCIND" name="2,3-dihydroxycinnamate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cenchddd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhcinnm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2541" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHCINDO" name="2,3-dihydroxycinnamate 1,2-dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhcinnm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hkntd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0348" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHDPRy" name="dihydrodipicolinate reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dhdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0031" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHDPS" name="dihydrodipicolinate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aspsa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_23dhdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2478" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHFR" name="dihydrofolate reductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1606" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0048" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHFS" name="dihydrofolate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2315" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHMPTR" name="Dihydromonapterin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhmpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thmnp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1606" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHNAOT4" name="1,4-dihydroxy-2-naphthoate octaprenyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhna_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3930" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHNCOAS" name="1,4-dihydroxy-2-napthoyl-CoA synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sbzcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_14dhncoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2262" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHNCOAT" name="1,4-dihydroxy-2-napthoyl-CoA thioesterase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_14dhncoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0736" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHNPA2r" name="dihydroneopterin aldolase reversible" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhnpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gcald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6hmhpt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3058" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHNPTE" name="Dihydroneopterin epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhnpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhmpt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3058" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHORD2" name="dihydoorotic acid dehydrogenase (quinone8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhor__S_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orot_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHORD5" name="dihydroorotic acid (menaquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhor__S_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orot_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHORDfum" name="Fumarate dependent DHORD" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhor__S_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orot_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_DHORTS" name="dihydroorotase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhor__S_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbasp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1062" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPPD" name="2,3-dihydroxyphenylpropionate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cechddd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhpppn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2541" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPPDA2" name="diaminohydroxyphosphoribosylaminopryrimidine deaminase (25drapp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25drapp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5apru_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0414" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPS2" name="dihydropteroate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4abz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6hmhptpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhpt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3177" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPTDCs2" name="4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhptd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mdhdhf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPTDNR" name="dihydropteridine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_dhptdn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thptdn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0578" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPTDNRN" name="dihydropteridine reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhptdn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thptdn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0578" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHPTPE" name="dihydroneopterin triphosphate 2'-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ahdt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhmptp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2303" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHQS" name="3-dehydroquinate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dda7p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhq_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3389" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DHQTi" name="3-dehydroquinate dehydratase, irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3dhq_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhsk_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1693" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DIMPtex" name="dIMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dimp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dimp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DINSt2pp" name="deoxyinosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_din_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_din_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DINStex" name="deoxyinosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_din_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_din_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DKGLCNR1" name="2,5-diketo-D-gluconate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25dkglcn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dhguln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0207" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3012" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DKGLCNR2x" name="2,5-diketo-D-gluconate reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25dkglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DKGLCNR2y" name="2,5-diketo-D-gluconate reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25dkglcn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMATT" name="dimethylallyltranstransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0421" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMPPS" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2mb4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMQMT" name="3-Dimethylubiquinonol 3-methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2omhmbl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2232" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOR1" name="Dimethyl sulfoxide reductase (Menaquinol 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmso_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dms_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1587" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1588" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1589" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1590" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0894" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0896" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOR1pp" name="Dimethyl sulfoxide reductase (Menaquinol 8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmso_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dms_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1872" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1873" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOR2" name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmso_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dms_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0894" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0896" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOR2pp" name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmso_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dms_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1872" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1873" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOtex" name="Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dmso_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dmso_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMSOtpp" name="Dimethyl sulfoxide transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dmso_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dmso_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DMStex" name="Dimethyl sulfide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dms_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dms_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DNMPPA" name="Dihydroneopterin monophosphate dephosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhpmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhnpt_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_DNTPPA" name="Dihydroneopterin triphosphate pyrophosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahdt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhpmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0099" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1865" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DOGULNR" name="2,3 dioxo-L-gulonate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23doguln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3dhguln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3575" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DOPAtex" name="dopamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dopa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dopa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DOXRBCNtex" name="Doxorubicin transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_doxrbcn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_doxrbcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DOXRBCNtpp" name="Doxorubicin transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_doxrbcn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_doxrbcn_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DPCOAK" name="dephospho-CoA kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dpcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0103" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DPR" name="2-dehydropantoate 2-reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dhp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pant__R_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3774" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DRPA" name="deoxyribose-phosphate aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dr5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4381" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSBAO1" name="DsbA protein reoxidation reaction (aerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dsbard_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dsbaox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3860" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1185" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSBAO2" name="DsbA protein reoxidation reaction (anaerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbard_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbaox_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3860" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1185" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSBCGT" name="DsbC:glutathione thiotransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_dsbcox_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbcrd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2893" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSBDR" name="DsbD reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dsbdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbdrd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4136" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4136" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSBGGT" name="DsbG:glutathione thiotransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dsbgox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbgrd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0604" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSERDHr" name="D-serine dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2amsa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1539" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSERt2pp" name="D-serine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4208" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DSERtex" name="D-serine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DTARTD" name="D(-)-tartrate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4122" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DTMPK" name="dTMP kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1098" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DTMPtex" name="dTMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DUMPtex" name="dUMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dump_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dump_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DURADx" name="dihydrouracil dehydrogenase (NAD)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_56dura_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2147" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2146" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DURIK1" name="deoxyuridine kinase (ATP:Deoxyuridine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_duri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1238" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DURIPP" name="deoxyuridine phosphorylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_duri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4382" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DURIt2pp" name="deoxyuridine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_duri_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_duri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DURItex" name="deoxyuridine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_duri_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_duri_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DUTPDP" name="dUTP diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dutp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3640" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2251" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DXPRIi" name="1-deoxy-D-xylulose reductoisomerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dxyl5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2me4p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0173" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DXPS" name="1-deoxy-D-xylulose 5-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dxyl5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0420" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_DXYLK" name="1-Deoxy-D-xylulose kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dxyl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dxyl5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3564" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_E4PD" name="Erythrose 4-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4per_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2927" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1779" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR100x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdec2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR100y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdec2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR120x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tddec2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR120y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tddec2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR121x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_t3c5ddeceACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cddec5eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR121y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_t3c5ddeceACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cddec5eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR140x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tmrs2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR140y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tmrs2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR141x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_t3c7mrseACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR141y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_t3c7mrseACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR160x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tpalm2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR160y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tpalm2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR161x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_t3c9palmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR161y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c9palmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR180x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_toctd2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR180y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_toctd2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR181x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c11vaceACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR181y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_t3c11vaceACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR40x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_butACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR40y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_but2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_butACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR60x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thex2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hexACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR60y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thex2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hexACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR80x" name="enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_toct2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EAR80y" name="enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_toct2eACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECA4COLIPAabctex" name="enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca4colipa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca4colipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECA4OALpp" name="enterobacterial common antigen (x4) O-antigen ligase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_eca4und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca4colipa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3622" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECAP1pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_unagamuf_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca2und_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3793" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3785" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECAP2pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_eca2und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_unagamuf_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca3und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3793" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3785" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECAP3pp" name="enterobacterial common antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_eca3und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_unagamuf_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eca4und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3793" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3785" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECAtpp" name="enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_unagamuf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_unagamuf_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3792" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH1" name="3-hydroxyacyl-CoA dehydratase (3-hydroxybutanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hbcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_b2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH2" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyhexanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hhcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hx2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH3" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hocoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oc2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH4" name="3-hydroxyacyl-CoA dehydratase (3-hydroxydecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dc2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH5" name="3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hddcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dd2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH6" name="3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3htdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_td2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH7" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hhdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdd2coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ECOAH8" name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hodcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_od2coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDA" name="2-dehydro-3-deoxy-phosphogluconate aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ddg6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1850" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDD" name="6-phosphogluconate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddg6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1851" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDTXS1" name="Endotoxin Synthesis (lauroyl transferase)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdo2lipid4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo2lipid4L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1054" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDTXS2" name="Endotoxin Synthesis (myristoyl transferase)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdo2lipid4L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1855" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDTXS3" name="Endotoxin Synthesis (palmitoleoyl ACP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdo2lipid4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo2lipid4p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2378" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EDTXS4" name="Endotoxin Synthesis (myristoyl transferase)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo2lipid4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_cold_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1855" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EGMEACPR" name="Enoylglutaryl-[ACP] methyl ester reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_egmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENLIPAabctex" name="phosphoethanolamine lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enlipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enlipa_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENO" name="enolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENTCS" name="enterochelin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_seramp_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_23dhba_c" stoichiometry="3" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="9" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="6" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0583" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENTERES" name="Enterochelin Esterase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_23dhbzs_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENTERES2" name="Enterochelin Esterase (Fe containing)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_feenter_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhbzs_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EPMEACPR" name="Enoylpimeloyl-[ACP] methyl ester reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_epmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETHAAL" name="Ethanolamine ammonia-lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etha_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2440" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2441" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETHAt2pp" name="ethanolamine transport in via proton symport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_etha_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etha_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ETHAtex" name="ethanolamine transport via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etha_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etha_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETHSO3abcpp" name="ethanesulfonate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ethso3_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ethso3_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0936" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0933" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0934" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETHSO3tex" name="ethanesulfonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ethso3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ethso3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETOHtex" name="ethanol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etoh_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETOHtrpp" name="ethanol reversible transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etoh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_F6PA" name="fructose 6-phosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dha_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0825" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3946" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_F6PP" name="D-fructose 6-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fru_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0822" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_F6Pt6_2pp" name="Fructose-6-phosphate transport via phosphate antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_f6p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3666" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_F6Ptex" name="fructose 6-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_f6p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA100ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA120ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA140ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA141ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA160ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA161ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FA80ACPHi" name="fatty-acyl-ACP hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0404" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE100" name="fatty-acid-CoA thioesterase (decanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE120" name="fatty-acid-CoA thioesterase (dodecanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE140" name="fatty-acid-CoA thioesterase (tetradecanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE141" name="fatty-acid-CoA thioesterase (tetradecenoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdecoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE160" name="fatty-acid-CoA thioesterase (hexadecanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pmtcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE161" name="fatty-acid-CoA thioesterase (hexadecenoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE180" name="fatty-acid-CoA thioesterase (octadecanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_stcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE181" name="fatty-acid-CoA thioesterase (octadecenoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_odecoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE60" name="fatty-acid-CoA thioesterase (hexanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAE80" name="fatty-acid-CoA thioesterase (octanoate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_occoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_octa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0452" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL100t2pp" name="fatty-acid-CoA ligase (decanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcacoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL120t2pp" name="fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcacoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL140t2pp" name="fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL141t2pp" name="fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdecoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL160t2pp" name="fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pmtcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL161t2pp" name="fatty-acid-CoA ligase (hexadecenoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL180t2pp" name="fatty-acid-CoA ligase (octadecanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_stcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL181t2pp" name="fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_odecoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL60t2pp" name="fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FACOAL80t2pp" name="fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_occoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1805" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FADRx" name="FAD reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FADRx2" name="FAD reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2764" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FALDH2" name="formaldehyde dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hmgth_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_Sfglutth_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0356" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FALDtex" name="formaldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fald_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fald_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FALDtpp" name="formaldehyde transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fald_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FALGTHLs" name="formaldehyde glutathione ligase (spontaneous)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hmgth_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2097" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1773" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2925" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FBA3" name="Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_s17bp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2925" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FBP" name="fructose-bisphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3925" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4232" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2930" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FCI" name="L-fucose isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fuc__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fcl__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2802" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FCLK" name="L-fuculokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fcl__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fc1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2803" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FCLPA" name="L-fuculose 1-phosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fc1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lald__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2738" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2800" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FCLT" name="Ferrochelatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppp9_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pheme_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0475" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDH4pp" name="formate dehydrogenase (quinone-8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3892" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3893" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3894" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1475" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1476" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDH5pp" name="Formate Dehydrogenase (menaquinone-8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_for_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1475" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1476" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3892" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3893" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3894" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDMO" name="FMNH2-dependent monooxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_isetac_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gcald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0935" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDMO2" name="FMNH2-dependent monooxygenase (methanesulfonate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mso3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0935" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDMO3" name="FMNH2-dependent monooxygenase (ethanesulfonate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ethso3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0935" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDMO4" name="FMNH2-dependent monooxygenase (butanesulfonate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_butso3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_btal_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0935" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FDMO6" name="FMNH2-dependent monooxygenase (sulfoacetate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sulfac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0935" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE2abcpp" name="iron (II) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3409" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE2t2pp" name="iron (II) transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2392" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE2t3pp" name="iron (Fe+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE2tex" name="iron (II) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE2tpp" name="iron (+2) transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3DCITabcpp" name="iron transport from ferric-dicitrate via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3dcit_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4290" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4289" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4288" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4287" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3DCITtonex" name="ferric-dicitrate transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3dcit_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3dcit_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4291" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3DHBZR" name="release of Fe(III) from ferric 2,3-dihydroxybenzoylserine" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3dhbzs_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhbzs_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3DHBZSabcpp" name="ferric 2,3-dihydroxybenzoylserine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3dhbzs_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3dhbzs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0592" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0588" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0590" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0589" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3DHBZStonex" name="ferric 2,3-dihydroxybenzoylserine transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3dhbzs_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3dhbzs_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0805" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2155" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXR1" name="Fe(III)hydroxamate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3hox__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXR2" name="Fe(III)hydroxamate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3hox__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXR3" name="Fe(III)hydroxamate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3hox__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXUtex" name="Fe(III)hydroxamate unloaded secretion" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox__un_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox__un_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXUtpp" name="Fe(III)hydroxamate unloaded secretion (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox__un_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox__un_e" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXabcpp" name="ferric-dicitrate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3hox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXexs" name="Fe(III) hydroxamate Fe-loading reaction (spontaneaous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox__un_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3hox_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3HOXtonex" name="Fe(III)hydroxamine transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3hox_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3hox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0150" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3Ri" name="Fe(III) reduction" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FE3abcpp" name="iron (III) transport via ABC system (periplasm to cytoplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FE3tex" name="iron (III) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FECRMR1" name="Ferrichrome reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fecrm_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FECRMR2" name="Ferrichrome reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fecrm_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FECRMR3" name="Ferrichrome reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fecrm_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm__un_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FECRMUtex" name="ferrichrome (minus Fe) secretion (to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm__un_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm__un_e" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FECRMUtpp" name="ferrichrome (minus Fe) secretion (to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm__un_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm__un_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FECRMabcpp" name="ferrichrome transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FECRMexs" name="ferrichrome Fe(III)-loading reaction (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm__un_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FECRMtonex" name="ferrichrome transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fecrm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fecrm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0150" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERR1" name="Fe-enterobactin reduction (Fe(III)-unloading)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feenter_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERR2" name="Fe-enterobactin reduction (Fe(III)-unloading)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feenter_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERR3" name="Fe-enterobactin reduction (Fe(III)-unloading)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feenter_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERabcpp" name="Fe-enterobactin transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feenter_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feenter_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0592" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0588" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0590" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0589" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERexs" name="enterobactin Fe(III) binding (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enter_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_feenter_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERtex" name="enterochelin transport (secretion periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enter_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enter_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERtonex" name="Fe-enterobactin transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feenter_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feenter_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0584" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEENTERtpp" name="enterochelin transport (secretion)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_enter_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enter_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0591" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMR1" name="ferroxamine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4367" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMR2" name="ferroxamine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4367" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMR3" name="ferroxamine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4367" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMUtex" name="ferroxamine (minus Fe3) secretion (to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_feoxam__un_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMUtpp" name="ferroxamine (minus Fe3) secretion (to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam__un_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMabcpp" name="ferroxamine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_feoxam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMexs" name="ferroxamine Fe3-loading reaction (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_feoxam__un_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_feoxam_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEOXAMtonex" name="ferroxamine transport via ton system (extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_feoxam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0150" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1252" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3005" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3006" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FEROpp" name="ferroxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_fe2_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe3_p" stoichiometry="4" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0123" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FESD1s" name="iron-sulfur cluster damage (peroxide, spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_3fe4s_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FESD2s" name="iron-sulfur cluster damage (nitrous oxide, spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_no_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_n2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fe3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_3fe4s_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FESR" name="iron-sulfur cluster repair" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3fe4s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4209" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FFSD" name="beta-fructofuranosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_suc6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fru_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FHL" name="Formate-hydrogen lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4079" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2481" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2482" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2483" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2484" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2485" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2486" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2487" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2488" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2489" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2490" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4079" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2719" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2720" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2721" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2722" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2723" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2724" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FLDR2" name="flavodoxin reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FLVR" name="flavin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2764" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FLVRx" name="flavin reductase (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rbflvrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FMETTRS" name="Methionyl-tRNA formyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mettrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmettrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3288" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FMNAT" name="FMN adenylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0025" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FMNRx" name="FMN reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0937" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FMNRx2" name="FMN reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmnh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3844" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0937" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2764" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FOMETRi" name="Aminomethyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5fthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_methf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORCT" name="Formyl-CoA Transferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_oxa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_forcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_oxalcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2374" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORt2pp" name="formate transport via proton symport (uptake only, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0904" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2492" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORtex" name="formate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_for_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORtppi" name="formate transport via diffusion (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_for_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0904" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2492" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRD2" name="fumarate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4152" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4154" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRD3" name="fumarate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4152" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4154" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUK" name="fructose-1-phosphate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_f1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2168" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRULYSDG" name="Fructoselysine phosphate deglycase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frulysp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3371" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRULYSE" name="fructoselysine 3-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_psclys_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_frulys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRULYSK" name="Fructoselysine Kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_frulys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frulysp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3374" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRULYSt2pp" name="Fructoselysine transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frulys_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frulys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3370" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRULYStex" name="fructoselysine transporter via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_frulys_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_frulys_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUURt2rpp" name="D-fructuronate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fruur_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fruur_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4321" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUURtex" name="D-fructuronate transport via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fruur_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fruur_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUpts2pp" name="Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fru_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUptspp" name="D-fructose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fru_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2167" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2169" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUtex" name="D-fructose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fru_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fru_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FTHFD" name="formyltetrahydrofolate deformylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1232" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FTHFLi" name="formate-tetrahydrofolate ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_FUCtex" name="L-fucose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fuc__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fuc__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUCtpp" name="L-fucose transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fuc__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fuc__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2801" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUM" name="fumarase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1612" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4122" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1611" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUMt2_2pp" name="Fumarate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fum_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUMt2_3pp" name="Fumarate transport via proton symport (3 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_fum_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0621" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUMtex" name="Fumarate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUSAtex" name="Fusidic acid transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fusa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fusa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUSAtpp" name="Fusidic acid transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fusa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fusa_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G1PACT" name="glucosamine-1-phosphate N-acetyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3730" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G1PPpp" name="Glucose-1-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1002" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G1PTT" name="glucose-1-phosphate thymidylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dttp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdpglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2039" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3789" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G1Ptex" name="D-glucose 1-phosphate transport via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g1p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G1SAT" name="glutamate-1-semialdehyde aminotransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu1sa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5aop_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0154" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G2PP" name="glycerol-2-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc2p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2533" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G2PPpp" name="glycerol 2-phosphate phosphatase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc2p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT120" name="glycerol-3-phosphate acyltransferase (C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1ddecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT140" name="glycerol-3-phosphate acyltransferase (C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_myrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT141" name="glycerol-3-phosphate acyltransferase (C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdec7eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT160" name="glycerol-3-phosphate acyltransferase (C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_palmACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1hdecg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT161" name="glycerol-3-phosphate acyltransferase (C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1hdec9eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT180" name="glycerol-3-phosphate acyltransferase (C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcaACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_1odecg3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PAT181" name="glycerol-3-phosphate acyltransferase (C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1odec11eg3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4041" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PCabcpp" name="sn-glycerol-3-phosphocholine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PCtex" name="glycero-3-phosphocholine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PD2" name="glycerol-3-phosphate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3608" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PD5" name="glycerol-3-phosphate dehydrogenase (ubiquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2242" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2243" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3426" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PD6" name="glycerol-3-phosphate dehydrogenase (menaquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2242" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2243" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PD7" name="glycerol-3-phosphate dehydrogenase (demethylmenaquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2242" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2243" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PEabcpp" name="sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PEtex" name="glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pe_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PGabcpp" name="sn-glycerol-3-phosphoglycerol transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PGtex" name="glycerophoglycerol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pg_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PIabcpp" name="sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pi_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PItex" name="glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pi_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PSabcpp" name="sn-glycerol-3-phosphoserine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3ps_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3ps_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PStex" name="glycerophosphserine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3ps_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3ps_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G3PT" name="glycerol-3-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0822" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G5SADs" name="L-glutamate 5-semialdehyde dehydratase (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu5sa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1pyr5c_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G5SD" name="glutamate-5-semialdehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu5sa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0243" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6PDA" name="glucosamine-6-phosphate deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0678" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6PDH2r" name="glucose 6-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1852" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6PP" name="glucose-6-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0822" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6Pt6_2pp" name="Glucose-6-phosphate transport via phosphate antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_g6p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3666" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6Ptex" name="glucose 6-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAL1PPpp" name="D-galactose 1-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal1p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1002" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAL1Ptex" name="D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal1p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALBDtex" name="beta D-galactose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal__bD_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal__bD_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTD" name="galactarate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galct__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5dh4dglc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3128" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTLO" name="L-galactonate oxidoreductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galctn__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tagur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4358" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTND" name="galactonate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galctn__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dh3dgal_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4478" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTNLt2pp" name="L-galactonate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galctn__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galctn__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4356" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTNLtex" name="L-galactonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galctn__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galctn__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTNt2pp" name="D-galactonate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galctn__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galctn__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3691" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTNtex" name="D-galactonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galctn__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galctn__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTt2rpp" name="D-galactarte transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galct__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galct__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3127" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALCTtex" name="D-galactarte transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galct__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galct__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALKr" name="galactokinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2045" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0757" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALM2pp" name="aldose-1-epimerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal__bD_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0756" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALS3" name="a-galactosidase (melibiose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_melib_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4119" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALT1" name="galactosyltransferase I (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gagicolipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3628" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALTptspp" name="Galactitol transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galt_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galt1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2093" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2092" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALTtex" name="Galactitol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALURt2rpp" name="D-galacturonate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galur_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALURtex" name="D-galacturonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galur_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_galur_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALUi" name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1236" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALabcpp" name="D-galactose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2150" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2148" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4231" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4227" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4485" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4230" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALt2pp" name="D-galactose transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2943" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GALtex" name="D-galactose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAM6Pt6_2pp" name="D-Glucosamine 6-phosphate transport via phosphate antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gam6p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3666" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAMAN6Ptex" name="D-glucosamine 6-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gam6p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gam6p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAMptspp" name="D-glucosamine transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAMtex" name="D-glucosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GARFT" name="phosphoribosylglycinamide formyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gar_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2500" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GART" name="GAR transformylase-T" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gar_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fgam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1849" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GBBTNtex" name="gamma-butyrobetaine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gbbtn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gbbtn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GCALDD" name="Glycolaldehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gcald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1415" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDMANE" name="GDP-4-dehydro-6-deoxy-D-mannose epimerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdpddman_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gdpofuc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2052" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDPDPK" name="GDP diphosphokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppgpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2784" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3650" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDPMNH" name="GDP-mannose mannosyl hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdpmann_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2051" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDPMNP" name="GDP-mannose phyrophosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdpmann_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_man1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2467" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDPTPDP" name="guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdptp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3650" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GDPtex" name="GDP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gdp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GF6PTA" name="glutamine-fructose-6-phosphate transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3729" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GGGABADr" name="gamma-glutamyl-gamma aminobutyric acid dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ggbutal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gg4abut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1300" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GGGABAH" name="gamma-glutamyl-gamma-aminobutyric acid hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gg4abut_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1298" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GGPTRCO" name="gamma glutamyl putrescine oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ggptrc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ggbutal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1301" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GGPTRCS" name="gamma glutamyl putrescine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ggptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1297" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GHBDHx" name="gamma-hydroxybutyrate dehydrogenase (NADH)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sucsal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ghb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3882" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GHMT2r" name="glycine hydroxymethyltransferase, reversible" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GK1" name="guanylate kinase (GMP:ATP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3648" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLBRAN2" name="1,4-alpha-glucan branching enzyme (glycogen -> bglycogen)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glycogen_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_bglycogen_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3432" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCATr" name="D-glucose O-acetyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acglc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0459" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCDpp" name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0124" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0837" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCNt2rpp" name="D-gluconate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glcn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glcn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4321" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4476" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4265" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCNtex" name="D-gluconate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCP" name="glycogen phosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glycogen_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3428" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3417" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCP2" name="glycogen phosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_bglycogen_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3428" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCRAL" name="5-dehydro-4-deoxyglucarate aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dh4dglc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2h3oppan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3126" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCRD" name="glucarate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5dh4dglc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2788" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2787" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCRt2rpp" name="D-glucarate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glcr_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3127" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2789" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCRtex" name="D-glucarate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCS1" name="glycogen synthase (ADPGlc)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_adpglc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glycogen_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3429" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCTR1" name="glucosyltransferase I (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_icolipa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3631" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCTR2" name="glucosyltransferase II (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gagicolipa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ggagicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3627" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCTR3" name="glucosyltransferase III (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ggagicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gggagicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3626" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCUR1Ptex" name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur1p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcur1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCURt2rpp" name="D-glucuronate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glcur_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3909" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3093" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCURtex" name="D-glucuronat transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcur_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCabcpp" name="D-glucose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2150" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2148" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCptspp" name="D-glucose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1621" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1101" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCt2pp" name="D-glucose transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2943" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCtex" name="glucose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCtexi" name="D-glucose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLDBRAN2" name="glycogen debranching enzyme (bglycogen -> glycogen)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_bglycogen_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glycogen_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3431" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLGC" name="glucose-1-phosphate adenylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adpglc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3430" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNS" name="glutamine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3870" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1297" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNTRS" name="Glutaminyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnagln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glntrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0680" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNabcpp" name="L-glutamine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0811" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0810" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0809" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNtex" name="L-glutamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gln__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gln__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLTPD" name="Galactitol-1-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_galt1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tag6p__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2091" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLU5K" name="glutamate 5-kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0242" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUABUTt7pp" name="4-aminobutyrate/glutamate antiport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abut_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1492" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUCYS" name="gamma-glutamylcysteine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glucys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2688" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUDC" name="Glutamate Decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3517" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1493" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUDy" name="glutamate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1761" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUN" name="glutaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1812" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0485" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1524" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUNpp" name="glutaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2957" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUPRT" name="glutamine phosphoribosyldiphosphate amidotransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pram_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2312" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUR" name="glutamate racemase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3967" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUSy" name="glutamate synthase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3212" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3213" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUTRR" name="glutamyl-tRNA reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glutrna_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_trnaglu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu1sa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1210" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUTRS" name="Glutamyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnaglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glutrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2400" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUabcpp" name="L-glutamate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0655" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0654" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0653" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0652" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUt2rpp" name="L-glutamate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4077" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUt4pp" name="Na+/glutamate symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3653" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUtex" name="L-glutamate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLXCL" name="glyoxalate carboligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2h3oppan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0507" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYALDtex" name="Glyceraldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyald_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyald_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYALDtpp" name="Glyceraldehyde facilitated diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyald_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3927" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYAT" name="glycine C-acetyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2aobut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3617" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYBabcpp" name="Glycine betaine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyb_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2128" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2129" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2130" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2131" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYBt2pp" name="Glycine betaine transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyb_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1801" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4111" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYBtex" name="Glycine betaine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyb_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyb_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYC2Pabcpp" name="sn-Glycerol 2-phosphate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc2p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc2p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYC2Ptex" name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc2p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc2p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYC3Pabcpp" name="sn-Glycerol 3-phosphate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3452" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3453" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3450" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3451" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYC3Pt6pp" name="Glycerol-3-phosphate : phosphate antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2240" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYC3Ptex" name="Glycerol-3-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCAt2rpp" name="D-glycerate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2789" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3127" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCAtex" name="D-glycerate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc__R_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc__R_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCDx" name="Glycerol dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dha_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCK" name="glycerate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0514" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCK2" name="glycerate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3124" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCL" name="Glycine Cleavage System" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2904" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2903" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2905" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0116" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCLTDx" name="Glycolate dehydrogenase (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1033" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCLTDy" name="Glycolate dehydrogenase (NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCLTt2rpp" name="glycolate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyclt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3603" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2975" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCLTt4pp" name="glycolate transport via sodium symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4067" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCLTtex" name="glycolate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCTO2" name="Glycolate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2979" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4467" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4468" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCTO3" name="Glycolate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2979" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4467" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4468" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCTO4" name="Glycolate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2979" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4467" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4468" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCtex" name="glycerol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYCtpp" name="glycerol transport via channel (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3927" />
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYK" name="glycerol kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3926" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYOX" name="hydroxyacylglutathione hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lgt__S_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0212" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYOX3" name="glyoxalase III" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_GLYTRS" name="Glycyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnagly_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glytrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3559" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3560" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYt2pp" name="glycine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4208" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1801" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYt2rpp" name="glycine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_GLYt4pp" name="glycine transport in via sodium symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0007" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLYtex" name="Glycine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gly_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gly_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMAND" name="GDP-D-mannose dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gdpmann_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdpddman_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2053" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMHEPAT" name="D-glycero-D-manno-hepose 1-phosphate adenyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmhep1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adphep__DD_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3052" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMHEPK" name="D-glycero-D-manno-heptose 7-phosphate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmhep7p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmhep17bp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3052" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMHEPPA" name="D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmhep17bp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmhep1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0200" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMPR" name="GMP reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0104" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMPS2" name="GMP synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2507" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GMPtex" name="GMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GND" name="phosphogluconate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GNK" name="gluconokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4268" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3437" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GOFUCR" name="GDP-4-oxo-L-fucose reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdpofuc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gdpfuc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2052" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GP4GH" name="Gp4G hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gp4g_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0049" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA1" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3449" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA1pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphocholine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_chol_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA2" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etha_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3449" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA2pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_etha_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA3" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3ps_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3449" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA3pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g3ps_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA4" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3449" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA4pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoglycerol)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA5" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_inost_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3449" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GPDDA5pp" name="Glycerophosphodiester phosphodiesterase (Glycerophosphoinositol)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pi_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_inost_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GRTT" name="geranyltranstransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_grdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0421" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GRXR" name="glutaredoxin reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GSNK" name="guanosine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0477" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GSNt2pp" name="guanosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GSNtex" name="guanosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gsn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GSPMDA" name="Glutathionylspermidine amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtspmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2988" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GSPMDS" name="Glutathionylspermidine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtspmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2988" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHOXtex" name="glutathione (ox) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthox_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthox_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHOr" name="glutathione oxidoreductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3500" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHPi" name="glutathione peridoxase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gthox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1710" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHRDHpp" name="glutathione hydralase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cgly_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3447" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHRDabc2pp" name="glutathione export via ABC system (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0886" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0887" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHRDabcpp" name="Reduced glutathione via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0829" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0830" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0831" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0832" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHRDtex" name="glutathione transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTHS" name="glutathione synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glucys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2947" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPCI" name="GTP cyclohydrolase I" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ahdt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2153" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPCII2" name="GTP cyclohydrolase II (25drapp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25drapp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1277" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPDPDP" name="guanosine-5'-triphosphate,3'-diphosphate diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdptp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppgpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPDPK" name="GTP diphosphokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdptp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2784" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPHs" name="GTP amine hydrolysis (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xtp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GTPtex" name="GTP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gtp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gtp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUACYC" name="guanylate cyclase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_35cgmp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_GUAD" name="guanine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2883" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUAPRT" name="guanine phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0125" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUAt2pp" name="guanine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gua_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3654" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUAtex" name="Guanine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gua_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gua_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUAtpp" name="Guanine transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gua_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_GUI1" name="glucuronate isomerase (D-glucuronate)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fruur_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3092" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUI2" name="glucuronate isomerase (D-galacturonate)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_galur_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tagur_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3092" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GUR1PPpp" name="Glucuronate 1-phosphate phosphatase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glcur1p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glcur_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_H2O2tex" name="hydrogen peroxide transport via diffusion (external)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2Otex" name="H2O transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0957" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3875" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1319" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2Otpp" name="H2O transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0875" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2SO" name="Hydrogen sulfide oxidation" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_so4_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_H2St1pp" name="h2s transport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2s_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2Stex" name="h2s transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2s_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2s_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2tex" name="hydrogen transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2tpp" name="hydrogen transport diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD1" name="3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aacoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hbcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD2" name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ohcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hhcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD3" name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3oocoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hocoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD4" name="3-hydroxyacyl-CoA dehydrogenase (3-oxodecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3odcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hdcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD5" name="3-hydroxyacyl-CoA dehydrogenase (3-oxododecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3oddcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hddcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD6" name="3-hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3otdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3htdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD7" name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ohdcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hhdcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HACD8" name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3oodcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hodcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3846" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2341" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HADPCOADH3" name="3-hydroxyadipyl-CoA dehydrogenase (NAD+)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hadpcoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oxadpcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1395" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HBZOPT" name="Hydroxybenzoate octaprenyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4hbz_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ophb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HCINNMt2rpp" name="3-hydroxycinnamic acid transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hcinnm_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hcinnm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0353" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HCINNMtex" name="3-hydroxycinnamic acid transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hcinnm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hcinnm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HCO3E" name="HCO3 equilibration reaction" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hco3_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0126" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0339" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HCYSMT" name="homocysteine S-methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hcys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0261" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HCYSMT2" name="Homocysteine Methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hcys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mmet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0261" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HDCAtexi" name="Hexadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdca_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HDCEAtexi" name="Hexadecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEMEOS" name="Heme O synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pheme_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_frdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hemeO_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0428" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPK1" name="LPS heptose kinase I (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hhlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_phhlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3630" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPK2" name="LPS heptose kinase II (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hphhlipa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phphhlipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3625" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPT1" name="heptosyltransferase I (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adphep__LD_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3621" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPT2" name="heptosyltransferase II (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adphep__LD_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hhlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3620" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPT3" name="heptosyltransferase III (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_phhlipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adphep__LD_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hphhlipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3632" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEPT4" name="heptosyltransferase IV (LPS core synthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gggagicolipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adphep__LD_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_colipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3623" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HETZK" name="hydroxyethylthiazole kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4mhetz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4mpetz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2104" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEX1" name="hexokinase (D-glucose:ATP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2388" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEX4" name="hexokinase (D-mannose:ATP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_HEX7" name="hexokinase (D-fructose:ATP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fru_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0394" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HEXt2rpp" name="hexanoate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2223" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HG2abcpp" name="Mercury (Hg+2) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hg2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hg2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HG2t3pp" name="mercury (Hg+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hg2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hg2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HG2tex" name="mercury (Hg+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hg2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hg2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HISTD" name="histidinol dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_histd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_his__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2020" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HISTP" name="histidinol-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hisp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_histd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2022" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HISTRS" name="Histidyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_his__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnahis_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_histrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2514" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HISabcpp" name="L-histidine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_his__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_his__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2309" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2308" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HISt2rpp" name="L-histidine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_his__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_his__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0112" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HIStex" name="L-histidine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_his__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_his__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HKNDDH" name="2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hkndd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_op4en_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0349" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HKNTDH" name="2-hydroxy-6-ketononotrienedioate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hkntd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_op4en_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0349" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HMBS" name="hydroxymethylbilane synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppbng_c" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hmbil_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="4" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3805" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HMPK1" name="hydroxymethylpyrimidine kinase (ATP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ahmmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ampm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2103" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HOMt2pp" name="L-homoserineserine efflux via proton symport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hom__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hom__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0813" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3824" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HOMtex" name="L-homoserine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hom__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hom__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HOPNTAL" name="4-hydroxy-2-oxopentanoate aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4h2opntn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0352" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPPK2" name="6-hydroxymethyl-dihydropterin pyrophosphokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_6hmhpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_6hmhptpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0142" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPPPNDO" name="2,3-dihydroxypheylpropionate 1,2-dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhpppn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hkndd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0348" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPPPNt2rpp" name="3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpppn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpppn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0353" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPPPNtex" name="3-(3-hydroxyphenyl)propionate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hpppn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3hpppn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPYRI" name="hydroxypyruvate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hpyr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2h3oppan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0508" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPYRRx" name="Hydroxypyruvate reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hpyr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HPYRRy" name="Hydroxypyruvate reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hpyr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3553" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HSDy" name="homoserine dehydrogenase (NADPH)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hom__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aspsa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3940" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0002" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HSK" name="homoserine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hom__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phom_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0003" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HSST" name="homoserine O-succinyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hom__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_suchms_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4013" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HSTPT" name="histidinol-phosphate transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imacp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hisp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2021" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HXAND" name="hypoxanthine dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2866" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2867" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2868" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HXAtex" name="Hexanoate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HXCT" name="Acetyl-CoA:hexanoate-CoA transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2221" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2222" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HXPRT" name="hypoxanthine phosphoribosyltransferase (Hypoxanthine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0125" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HYD1pp" name="hydrogenase (ubiquinone-8: 2 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0972" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0973" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0974" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2994" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2995" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2997" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2719" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2720" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2721" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2722" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2723" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2724" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HYD2pp" name="Hydrogenase (menaquinone8: 2 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0972" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0973" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0974" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2994" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2995" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2997" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HYD3pp" name="Hydrogenase (Demethylmenaquinone-8: 2 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0972" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0973" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0974" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2994" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2995" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2997" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HYPOE" name="hypothetical enyme" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyam5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydam_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_HYXNtex" name="Hypoxanthine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxan_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_HYXNtpp" name="Hypoxanthine transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hxan_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_Htex" name="proton transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I2FE2SR" name="ISC [2Fe-2S] regeneration" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_iscu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe1s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscu__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I2FE2SS" name="ISC [2Fe-2S] Synthesis" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_iscu__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="6" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3807" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I2FE2SS2" name="ISC [2Fe-2S] Synthesis II" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_iscu__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="6" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscu__2fe2s2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3807" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I2FE2ST" name="ISC [2Fe-2S] Transfer" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_iscu__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe2s_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2528" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I4FE4SR" name="ISC [4Fe-4S] Reduction" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscu__2fe2s2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscu__4fe4s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_I4FE4ST" name="ISC [4Fe-4S] Transfer" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_iscu__4fe4s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2528" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2529" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICDHyr" name="isocitrate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1136" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICHORS" name="isochorismate synthase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ichor_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2265" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICHORSi" name="Isochorismate Synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_chor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ichor_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0593" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICHORT" name="isochorismatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ichor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23ddhb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0595" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICL" name="Isocitrate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4015" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICYSDS" name="ISC Cysteine desulfuration" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IDOND" name="L-idonate 5-dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idon__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4267" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IDOND2" name="L-indonate 5-dehydrogenase (NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5dglcn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idon__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4267" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IDONt2rpp" name="L-idonate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_idon__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_idon__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4265" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IDONtex" name="L-idonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_idon__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_idon__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IG3PS" name="Imidazole-glycerol-3-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prlp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_eig3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aicar_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2023" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2025" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IGPDH" name="imidazoleglycerol-phosphate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_eig3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imacp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2022" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IGPS" name="indole-3-glycerol-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2cpr5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ig3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1262" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ILETA" name="isoleucine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ile__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mop_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3770" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ILETRS" name="Isoleucyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ile__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnaile_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iletrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0026" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ILEabcpp" name="L-isoleucine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ile__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ile__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3460" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ILEt2rpp" name="L-isoleucine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ile__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ile__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0401" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ILEtex" name="L-isoleucine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ile__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ile__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IMPC" name="IMP cyclohydrolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fprica_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4006" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IMPD" name="IMP dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2508" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IMPtex" name="IMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_imp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_imp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INDOLEt2pp" name="Indole transport via proton symport, irreversible (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3265" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3266" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INDOLEt2rpp" name="Indole transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3161" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INDOLEtex" name="Indole transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_indole_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_indole_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INOSTt4pp" name="Na+/myo-inositol symporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_inost_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_inost_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3679" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INSH" name="Inosine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0030" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INSK" name="insosine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0477" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INSTtex" name="inositol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_inost_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_inost_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INSt2pp" name="inosine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INSt2rpp" name="inosine transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_INStex" name="inosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ins_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ins_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPDDI" name="isopentenyl-diphosphate D-isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dmpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2889" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPDPS" name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2mb4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPMD" name="3-isopropylmalate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3c2hmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3c4mop_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0073" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPPMIa" name="3-isopropylmalate dehydratase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3c2hmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ippm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0071" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0072" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPPMIb" name="2-isopropylmalate hydratase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ippm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3c3hmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0071" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0072" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_IPPS" name="2-isopropylmalate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mob_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3c3hmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0074" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ISETACabcpp" name="isethionate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_isetac_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_isetac_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0365" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0366" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0367" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0936" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0933" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0934" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ISETACtex" name="isethionate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_isetac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_isetac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_K2L4Aabcpp" name="KDO(2)-lipid IV A transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo2lipid4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_kdo2lipid4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_K2L4Aabctex" name="KDO(2)-lipid IV A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo2lipid4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_kdo2lipid4_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KARA1" name="ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_23dhmb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alac__S_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3774" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KARA2" name="ketol-acid reductoisomerase (2-Acetolactate)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ahbut_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_23dhmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3774" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KAS14" name="beta-ketoacyl-ACP synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1095" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KAS15" name="beta-ketoacyl-ACP synthase (2)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1091" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KDOCT2" name="3-deoxy-manno-octulosonate cytidylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdo_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ckdo_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0918" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KDOPP" name="3-deoxy-manno-octulosonate-8-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo8p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3198" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KDOPS" name="3-deoxy -D-manno-octulosonic -acid 8-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ara5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdo8p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1215" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_KG6PDC" name="3-keto-L-gulonate 6-phosphate decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhgulnp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xu5p__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4196" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3581" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Kabcpp" name="Potassium ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_k_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_k_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0698" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0697" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0696" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0698" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0697" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0696" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4513" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Kt2pp" name="potassium transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_k_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_k_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3290" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3849" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1250" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3290" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1363" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3747" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Kt3pp" name="potassium transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_k_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_k_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1216" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0842" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3350" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0047" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Ktex" name="potassium transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_k_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_k_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_L__LACD2" name="L-Lactate dehydrogenase (ubiquinone)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3605" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0308" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_L__LACD3" name="L-Lactate dehydrogenase (menaquinone)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3605" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0308" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_L__LACt2rpp" name="L-lactate reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3603" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2975" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_L__LACtex" name="L-lactate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lac__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LA4NTpp" name="4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uLa4n_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acolipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2257" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LACZ" name="b-galactosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LACZpp" name="b-galactosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2132" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LADGMDH" name="L-alanyl-gamma-D-glutamyl-meso-diaminopimelate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_26dap__M_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1326" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALADGLUtex" name="L-alanyl-D-glutamate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDglu_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaDglu_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALADGLUtpp" name="L-alanyl-D-glutamate transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDglu_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1634" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3496" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4130" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0709" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALALGLUtex" name="L-alanyl-L-glutamate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaLglu_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_LalaLglu_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALALGLUtpp" name="L-alanyl-L-glutamate transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaLglu_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaLglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1634" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3496" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4130" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0709" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALDO2x" name="D-Lactaldehyde:NAD+ 1-oxidoreductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lald__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3945" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LALDO3" name="L-Lactaldehyde:NADP+ 1-oxidoreductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lald__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_LALGP" name="L-alanyl-gamma-L-glutamate peptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaLglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0237" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LCADi" name="lactaldehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lald__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1415" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LCARR" name="lacaldehyde reductase (R-propane-1,2-diol forming)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lald__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__R_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_LCARS" name="lacaldehyde reductase (S-propane-1,2-diol forming)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lald__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12ppd__S_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2799" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LCTSt3ipp" name="Lactose transport via proton aniport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2170" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0070" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1528" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LCTStex" name="Lactose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lcts_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lcts_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LCTStpp" name="Lactose transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lcts_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0343" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2133" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1380" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LDH_D2" name="D-lactate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2133" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LEUTAi" name="leucine transaminase (irreversible)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4mop_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_leu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3770" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4054" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LEUTRS" name="Leucyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_leu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnaleu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_leutrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0642" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LEUabcpp" name="L-leucine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_leu__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_leu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3460" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3458" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LEUt2rpp" name="L-leucine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_leu__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_leu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0401" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LEUtex" name="L-leucine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_leu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_leu__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LGTHL" name="lactoylglutathione lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lgt__S_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1651" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPACabcpp" name="lipid (cold) A transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_cold_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipa_cold_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPAHT2ex" name="core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hdca_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hacolipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0622" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPAHTex" name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_halipa_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0622" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPAMPL" name="Lipoyl-adenylate protein ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipoamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipopb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPATPT" name="Lipoate-ATP adenylate transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipoate_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipoamp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPAabcpp" name="lipid A transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPAabctex" name="lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPOCT" name="Lipoyl(octanoyl) transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octapb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0630" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPOS" name="Lipoate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octapb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_lipopb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__5_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0628" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LIPOt2pp" name="Lipoate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipoate_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipoate_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_LIPOtex" name="lipoate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipoate_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipoate_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPADSS" name="Lipid A disaccaride synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipidX_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u23ga_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lipidAds_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0182" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A120pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1ddecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A140pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdecg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A141pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdec7eg3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A160pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1hdecg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A161pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1hdec9eg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A180pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1odecg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1A181pp" name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1odec11eg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E120pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpe120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E140pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpe140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E141pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpe141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E160pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E161pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E180pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1E181pp" name="Lysophospholipase L1 (2-acylglycerophosphoethanolamine, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G120pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G140pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpg140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G141pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_1agpg141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G160pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G161pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G180pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL1G181pp" name="Lysophospholipase L1 (2-acylglycerophosphoglycerol, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0494" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A120" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A140" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2tdecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A141" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2tdec7eg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A160" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2hdecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A161" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2hdec9eg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A180" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2odecg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2A181" name="Lysophospholipase L2 (2-acylglycerophosphotidate, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2odec11eg3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE120" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apg120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE140" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apg140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE141" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apg141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE160" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE161" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE180" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apg180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATE181" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoethanolamine, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_apg181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG120" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG140" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG141" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG160" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG161" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG180" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2ATG181" name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_apg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E120" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E140" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E141" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E160" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2agpe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E161" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E180" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2E181" name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G120" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G140" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G141" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G160" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G161" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G180" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdca_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LPLIPAL2G181" name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3825" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LSERDHr" name="L-serine dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2amsa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1539" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYSDC" name="lysine decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_15dap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0186" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4131" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYSTRS" name="Lysyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnalys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lystrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4129" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2890" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYSabcpp" name="L-lysine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2310" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2308" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYSt2pp" name="L-lysine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2156" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYSt3pp" name="L-lysine transport out via proton antiport (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lys__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2923" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYStex" name="L-lysine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lys__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lys__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYXI" name="Lyxose isomerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lyx__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xylu__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3903" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYXt2pp" name="L-Lyxose transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lyx__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lyx__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3907" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LYXtex" name="L-Lyxose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lyx__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lyx__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_M1PD" name="mannitol-1-phosphate 5-dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mnl1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3600" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MACPD" name="Malonyl-ACP decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALCOAMT" name="Malonyl-CoA methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malcoame_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0777" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALDDH" name="malate decarboxylating oxidoreductase (decarboxylating)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1800" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALDt2_2pp" name="D-Malate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mal__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALDtex" name="D-Malate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALS" name="malate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4014" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2976" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTATr" name="maltose O-acetyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acmalt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0459" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTHXabcpp" name="maltohexaose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTHXtexi" name="maltohexaose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malthx_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malthx_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTPTabcpp" name="maltopentaose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltpt_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTPTtexi" name="maltopentaoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_maltpt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_maltpt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTTRabcpp" name="Maltotriose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malttr_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malttr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTTRtexi" name="Maltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malttr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malttr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTTTRabcpp" name="maltotetraose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTTTRtexi" name="maltotetraoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_maltttr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_maltttr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTabcpp" name="maltose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4034" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4033" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4032" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4035" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTptspp" name="maltose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malt6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1621" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALTtexi" name="maltoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALt2_2pp" name="Malate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mal__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALt2_3pp" name="Malate transport via proton symport (3 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_mal__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALt3pp" name="L-malate transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mal__L_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MALtex" name="Malate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MAN1PT2" name="mannose-1-phosphate guanylyltransferase (GDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gdpmann_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2049" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MAN6PI" name="mannose-6-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1613" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MAN6Pt6_2pp" name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_man6p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3666" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MAN6Ptex" name="Mannose 6-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man6p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_man6p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANAO" name="Mannonate oxidoreductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mana_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fruur_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANGLYCptspp" name="2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_manglyc_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man6pglyc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0731" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANGLYCtex" name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_manglyc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_manglyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANPGH" name="2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man6pglyc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0732" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANptspp" name="D-mannose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MANtex" name="D-mannose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_man_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCITD" name="2-methylcitrate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2mcit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mcacn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0334" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCITL2" name="methylisocitrate lyase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_micit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0331" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCITS" name="2-methylcitrate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mcit_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0333" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCOATA" name="Malonyl-CoA-ACP transacylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_malcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1092" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCPST" name="3-mercaptopyruvate sulfurtransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mercppyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cyan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tcynt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2521" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCTP1App" name="murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0084" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0635" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3396" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCTP1Bpp" name="murein crosslinking transpeptidase 1B:(A2pm->A2pm) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5px3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3396" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MCTP2App" name="murein crosslinking transpeptidase 1A:(A2pm->D-ala) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein5p5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5px4px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0084" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0635" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3396" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0149" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDCP1pp" name="murein D,D-carboxypeptidase (murein5px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0632" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0839" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2010" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDCP2pp" name="murein D,D-carboxypeptidase (murein5px4px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px4px4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4px4px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0632" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0839" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2010" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDCP3pp" name="murein D,D-carboxypeptidase (murein5p5p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5p4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0632" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0839" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2010" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDCP4pp" name="murein D,D-carboxypeptidase (murein5p4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4p4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0632" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0839" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2010" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDCP5pp" name="murein D,D-carboxypeptidase (murein5p3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein4p3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0632" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0839" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2010" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDEP1pp" name="murein D,D-endopeptidase (murein4px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein4px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4p4p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2328" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2134" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDEP2pp" name="murein D,D-endopeptidase (murein3px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein3px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4p3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2328" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2134" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDEP3pp" name="murein D,D-endopeptidase (murein5px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5p4p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2328" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2134" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDDEP4pp" name="murein D,D-endopeptidase (murein4px4px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein4px4px4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4px4p4p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3182" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2328" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2134" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDH" name="malate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3236" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDH2" name="Malate dehydrogenase (ubiquinone 8 as acceptor)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2210" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDH3" name="Malate dehydrogenase (menaquinone 8 as acceptor)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2210" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ME1" name="malic enzyme (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1479" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ME2" name="malic enzyme (NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2463" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MECDPDH5" name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_2mecdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2mb4p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2515" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2515" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MECDPS" name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2p4c2me_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2mecdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2746" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MELIBt2pp" name="melibiose transport in via symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_melib_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_melib_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4120" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MELIBt3ipp" name="melibiose transport in via antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_melib_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_melib_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MELIBtex" name="melibiose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_melib_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_melib_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MEOHtex" name="Methanol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_meoh_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_meoh_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MEOHtrpp" name="Methanol reversible transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_meoh_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_meoh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MEPCT" name="2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2me4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4c2me_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2747" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METAT" name="methionine adenosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2942" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METDabcpp" name="D-methionine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_met__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0198" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0197" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METDtex" name="D-methionine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_met__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METOX1s" name="methionine oxidation (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__S__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METOX2s" name="methionine oxidation 2 (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__R__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METS" name="methionine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hcys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4019" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3829" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METSOX1abcpp" name="L-methionine S-oxide transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__S__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__S__L_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_METSOX1tex" name="L-methionine S-oxide diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_metsox__S__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_metsox__S__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METSOX2abcpp" name="L-methionine R-oxide transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__R__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_metsox__R__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_METSOX2tex" name="L-methionine R-oxide diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_metsox__R__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_metsox__R__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METSOXR1" name="L-methionine-S-oxide reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__S__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4219" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4219" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3551" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3551" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METSOXR2" name="L-methionine-R-sulfoxide reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_metsox__R__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1778" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1778" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METTRS" name="Methionyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnamet_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mettrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2114" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METabcpp" name="L-methionine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_met__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0198" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0197" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_METtex" name="L-methionine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_met__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_met__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MG2t3_2pp" name="magnesium (Mg+2) transport in/out via proton antiport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mg2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mg2_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MG2tex" name="magnesium (Mg+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mg2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mg2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MG2tpp" name="magnesium (+2) transport in via diffusion" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mg2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mg2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3816" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MG2uabcpp" name="Magnesium (Mg+2) ABC transporter (ubtake, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mg2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mg2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4242" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MGSA" name="methylglyoxal synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mthgxl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0963" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MI1PP" name="myo-inositol 1-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mi1p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_inost_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2533" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MICITDr" name="2-methylisocitrate dehydratase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mcacn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_micit_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0118" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MINCYCtex" name="Minocycline transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mincyc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mincyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MINCYCtpp" name="Minocycline transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mincyc_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mincyc_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MINOHPtexi" name="myo-inositol phosphate transport via diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_minohp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_minohp_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDCP1App" name="murein L,D-carboxypeptidase (murein5px4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein3px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDCP1Bpp" name="murein L,D-carboxypeptidase (murein4p4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein4p4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein4p3p_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDCP2App" name="murein L,D-carboxypeptidase (murein5p5p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5p3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDCP2Bpp" name="murein L,D-carboxypeptidase (murein4p3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein4p3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein3p3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDCP3App" name="murein L,D-carboxypeptidase (murein5px3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein3px3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDEP1pp" name="murein L,D-endopeptidase (murein3px3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein3px3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein3p3p_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLDEP2pp" name="murein L,D-endopeptidase (murein5px3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5px3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein5p3p_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MLTG1" name="Maltodextrin glucosidase (maltotriose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malttr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTG2" name="Maltodextrin glucosidase (maltotetraose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malttr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTG3" name="Maltodextrin glucosidase (maltopentaose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTG4" name="Maltodextrin glucosidase (maltohexaose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTG5" name="Maltodextrin glucosidase (maltoheptaose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTGY1pp" name="murein lytic transglycosylase (murein4p4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein4p4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2558" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2963" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4392" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2813" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1193" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTGY2pp" name="murein lytic transglycosylase (murein4p3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein4p3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1193" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2558" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2963" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4392" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2813" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTGY3pp" name="murein lytic transglycosylase (murein3p3p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein3p3p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_anhgm3p_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1193" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2963" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2558" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4392" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2813" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2701" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTGY4pp" name="murein lytic transglycosylase (murein4px4p4p) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_murein4px4p4p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_murein4px4p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_anhgm4p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2701" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1193" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2963" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2558" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4392" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2813" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTP1" name="Maltodextrin phosphorylase (maltopentaose)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_maltttr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3417" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTP2" name="Maltodextrin phosphorylase (maltohexaose)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_maltpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3417" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MLTP3" name="Maltodextrin phosphorylase (maltoheptaose)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malthx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3417" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MMCD" name="Methylmalonyl-CoA decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mmcoa__S_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2919" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MMETt2pp" name="S-methylmethionine permease (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mmet_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mmet_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0260" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MMETtex" name="S-methyl-L-methionine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mmet_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mmet_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MMM" name="Methylmalonyl-CoA mutase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mmcoa__S_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2917" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MN2t3pp" name="manganese (Mn+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mn2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mn2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0752" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MN2tpp" name="manganese transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mn2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mn2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MN6PP" name="mannose 6-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_man_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0822" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MNLptspp" name="mannitol transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mnl_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mnl1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3599" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MNLtex" name="mannitol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mnl_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mnl_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MNNH" name="D-mannonate hydrolyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mana_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ddglcn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4322" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MNt2pp" name="manganese (Mn+2) transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mn2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mn2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2392" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MNtex" name="Manganese (Mn+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mn2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mn2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOADSUx" name="MoaD sulfuration (nadh, assumed)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_moadamp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moadcosh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0784" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOAT" name="3-deoxy-D-manno-octulosonic acid transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipidA_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ckdo_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kdolipid4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3633" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOAT2" name="3-deoxy-D-manno-octulosonic acid transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_kdolipid4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ckdo_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_kdo2lipid4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3633" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOAT3C" name="3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ckdo_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phphhlipa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kphphhlipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3624" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOBDabcpp" name="molybdate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mobd_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mobd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0764" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0765" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3917" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOBDtex" name="molybdate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mobd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mobd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOCDS" name="molybdopterin cytidine dinucleotide synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moco_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mococdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2877" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOCOS" name="molybdenum cofactor synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mobd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mptamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0827" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOGDS" name="molybdopterin guanine dinucleotide synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mocogdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3856" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOHMT" name="3-methyl-2-oxobutanoate hydroxymethyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mob_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dhp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0134" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MOX" name="malate oxidase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_MPTAT" name="molybdopterin adenylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mptamp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0009" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MPTG" name="murein polymerizing transglycosylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uaagmda_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_udcpdp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3396" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2519" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MPTG2" name="murein polymerizing transglycosylase 2 (three linked units)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uaagmda_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udcpdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_murein5p5p5p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3396" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0149" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1069" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2519" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MPTS" name="molybdopterin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cpmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moadcosh_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mpt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="5" />
+ <speciesReference constant="true" species="M_moadcoo_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0784" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0785" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MPTSS" name="molybdopterin synthase sulfurylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moadcoo_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_moadamp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0826" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MSAR" name="malonic semialdehyde reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_msa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1008" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1539" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MSO3abcpp" name="methanesulfonate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mso3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mso3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0936" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0933" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0934" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MSO3tex" name="methanesulfonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mso3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mso3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTAN" name="methylthioadenosine nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mta_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mtr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0159" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTHFC" name="methenyltetrahydrofolate cyclohydrolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_methf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0529" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTHFD" name="methylenetetrahydrofolate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_methf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0529" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTHFR2" name="5,10-methylenetetrahydrofolate reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5mthf_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3941" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTHTHFSs" name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran synthesis (spontaneous)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mdhdhf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mththf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MTRPOX" name="N-methyltryptophan oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_Nmtrp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_N2Otex" name="nitrious oxide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_n2o_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_n2o_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_N2Otpp" name="nitrious oxide transport (diffusion)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_n2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_n2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NACODA" name="N-acetylornithine deacetylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acg5sa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu5sa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3957" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NACtex" name="Nicotinic acid transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NACtpp" name="Nicotinic acid uptake (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nac_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nac_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NADDP" name="NAD diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2411" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH10" name="NADH dehydrogenase (menaquinone-8 & 0 protons)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1109" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH16pp" name="NADH dehydrogenase (ubiquinone-8 & 3 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2276" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2277" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2279" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2280" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2281" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2282" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2283" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2284" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2285" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2286" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2287" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2288" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH17pp" name="NADH dehydrogenase (menaquinone-8 & 3 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2276" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2277" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2279" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2280" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2281" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2282" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2283" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2284" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2285" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2286" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2287" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2288" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH18pp" name="NADH dehydrogenase (demethylmenaquinone-8 & 3 protons) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2276" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2277" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2279" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2280" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2281" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2282" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2283" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2284" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2285" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2286" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2287" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2288" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH5" name="NADH dehydrogenase (ubiquinone-8 )" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1109" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH9" name="NADH dehydrogenase (demethylmenaquinone-8 & 0 protons)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1109" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADK" name="NAD kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2615" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADN" name="NAD nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ncam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adprib_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NADPHQR2" name="NADPH Quinone Reductase (Ubiquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3028" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADPHQR3" name="NADPH Quinone Reductase (Menaquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3028" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADPHQR4" name="NADPH Quinone Reductase (2-Demethylmenaquinone-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3028" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADPPPS" name="NADP phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NADS1" name="NAD synthase (nh3)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dnad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1740" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADTRHD" name="NAD transhydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3962" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1602" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1603" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NAMNPP" name="nicotinic acid mononucleotide pyrophosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nac_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nicrnt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0931" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NAt3_1p5pp" name="sodium proton antiporter (H:NA is 1.5) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1186" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NAt3_2pp" name="sodium proton antiporter (H:NA is 2) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0019" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NAt3pp" name="sodium transport out via proton antiport (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0842" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1216" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NAtex" name="sodium transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK1" name="nucleoside-diphosphate kinase (ATP:GDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK2" name="nucleoside-diphosphate kinase (ATP:UDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK3" name="nucleoside-diphosphate kinase (ATP:CDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK4" name="nucleoside-diphosphate kinase (ATP:dTDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dttp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK5" name="nucleoside-diphosphate kinase (ATP:dGDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgtp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK6" name="nucleoside-diphosphate kinase (ATP:dUDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dudp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dutp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK7" name="nucleoside-diphosphate kinase (ATP:dCDP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dcdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NDPK8" name="nucleoside-diphosphate kinase (ATP:dADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_datp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2518" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NH4tex" name="ammonia transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nh4_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NH4tpp" name="ammonia reversible transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0451" />
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NHFRBO" name="NADH:flavorubredoxin oxidoreductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_n2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2710" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2711" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NI2abcpp" name="Nickle (Ni+2) ABC transporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NI2t3pp" name="nickle (Ni+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0752" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NI2tex" name="nickel transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ni2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ni2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NI2tpp" name="nickel (+2) transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ni2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ni2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3816" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NI2uabcpp" name="nickel transport via ABC system (uptake, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ni2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3476" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3477" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3478" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3479" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3480" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4242" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NMNAT" name="nicotinamide-nucleotide adenylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4390" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0639" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NMNDA" name="nicotinamide-nucleotide amidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nicrnt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NMNN" name="NMN nucleosidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ncam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NMNPtpp" name="NMN permease (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nmn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nmn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0751" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NMNt7pp" name="NMN transport via NMN glycohydrolase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nmn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ncam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_NMNtex" name="NMN transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nmn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nmn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NNAM" name="nicotinamidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ncam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1768" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NNATr" name="nicotinate-nucleotide adenylyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nicrnt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dnad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0639" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NNDMBRT" name="Nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dmbzid_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nicrnt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_5prdmbz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nac_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1991" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NNDPR" name="nicotinate-nucleotide diphosphorylase (carboxylating)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_quln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nicrnt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0109" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO2t2rpp" name="nitrite transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3367" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1223" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO2tex" name="nitrite transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3R1bpp" name="Nitrate reductase (Ubiquinol-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no3_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2203" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2206" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2202" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2205" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2204" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3R1pp" name="Nitrate reductase (Ubiquinol-8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_no3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1465" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1466" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1467" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1468" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1224" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1225" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1226" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1227" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3R2bpp" name="Nitrate reductase (Menaquinol-8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no3_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2203" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2206" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2202" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3R2pp" name="Nitrate reductase (Menaquinol-8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_no3_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1465" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1466" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1467" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1468" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1224" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1225" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1226" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1227" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3t7pp" name="nitrate transport in via nitrite antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no3_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_no3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1223" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1469" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NO3tex" name="nitrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_no3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NODOx" name="nitric oxide dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no3_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2552" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NODOy" name="nitric oxide dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_no_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_no3_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2552" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NOVBCNtex" name="Novobiocin transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_novbcn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_novbcn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NOVBCNtpp" name="Novobiocin transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_novbcn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_novbcn_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NOtex" name="nitric oxide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_no_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NOtpp" name="NO transport (diffusion)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_no_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_no_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD1" name="5'-nucleotidase (dUMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_duri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4374" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD10" name="5'-nucleotidase (XMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtsn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD10pp" name="5'-nucleotidase (XMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xmp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD11" name="5'-nucleotidase (IMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD11pp" name="5'-nucleotidase (IMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD12" name="5'-nucleotidase (dIMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dimp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_din_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD12pp" name="5'-nucleotidase (dIMP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dimp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_din_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD1pp" name="5'-nucleotidase (dUMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dump_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_duri_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD2" name="5'-nucleotidase (UMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4374" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD2pp" name="5'-nucleotidase (UMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uri_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD3" name="5'-nucleotidase (dCMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcyt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD3pp" name="5'-nucleotidase (dCMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcyt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD4" name="5'-nucleotidase (CMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD4pp" name="5'-nucleotidase (CMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cytd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD5" name="5'-nucleotidase (dTMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thymd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4374" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD5pp" name="5'-nucleotidase (dTMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtmp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thymd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD6" name="5'-nucleotidase (dAMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_damp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD6pp" name="5'-nucleotidase (dAMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_damp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dad__2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD7" name="5'-nucleotidase (AMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD7pp" name="5'-nucleotidase (AMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD8" name="5'-nucleotidase (dGMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgsn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2291" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD8pp" name="5'-nucleotidase (dGMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgmp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD9" name="5'-nucleotidase (GMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTD9pp" name="5'-nucleotidase (GMP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gmp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP1" name="nucleoside-triphosphatase (ATP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0650" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4161" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP10" name="nucleoside-triphosphatase (ITP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_itp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_idp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4161" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4394" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP11" name="nucleoside-triphosphatase (dITP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ditp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_didp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4394" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP12" name="nucleoside-triphosphatase (XTP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4394" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP3" name="nucleoside-triphosphatase (GTP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4161" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP3pp" name="nucleoside-triphosphatase (GTP) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0980" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTP5" name="nucleoside-triphosphatase (CTP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4161" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP1" name="Nucleoside triphosphate pyrophosphorylase (dgtp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0099" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP10" name="Nucleoside triphosphate pyrophosphorylase (ditp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ditp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dimp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2954" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP11" name="Nucleoside triphosphate pyrophosphorylase (xtp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2954" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP2" name="Nucleoside triphosphate pyrophosphorylase (gtp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0099" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP3" name="Nucleoside triphosphate pyrophosphorylase (dctp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dctp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2251" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1759" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP4" name="Nucleoside triphosphate pyrophosphorylase (ctp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1759" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP5" name="Nucleoside triphosphate pyrophosphorylase (datp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_datp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_damp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1865" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP6" name="Nucleoside triphosphate pyrophosphorylase (atp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP7" name="Nucleoside triphosphate pyrophosphorylase (dttp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dttp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2251" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP8" name="Nucleoside triphosphate pyrophosphorylase (utp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2781" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPP9" name="Nucleoside triphosphate pyrophosphorylase (itp)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_itp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_imp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2954" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPTP1" name="Nucleoside triphosphate tripolyhydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dgsn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTPTP2" name="Nucleoside triphosphate tripolyhydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gsn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTRIR2x" name="nitrite Reductase (NADH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="5" />
+ <speciesReference constant="true" species="M_no2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="3" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3365" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3366" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTRIR3pp" name="nitrite Reductase (Ubiquinole-8, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4070" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4071" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4072" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4073" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NTRIR4pp" name="nitrite Reductase (Menaquinole-8, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_no2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4070" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4071" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4072" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4073" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16A4COLIPAabctex" name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16a4colipa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o16a4colipa_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4261" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4262" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16A4Lpp" name="O16 anitgen (x4) ligase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16a4und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_colipa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16a4colipa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3622" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16AP1pp" name="O16 antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16aund_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16a2und_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2035" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2027" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16AP2pp" name="O16 antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16a2und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16aund_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16a3und_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2035" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2027" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16AP3pp" name="O16 antigen polymerase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16a3und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16aund_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16a4und_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2035" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2027" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16AT" name="rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ragund_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_aragund_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2033" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16AUNDtpp" name="O16 antigen (flippase, cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o16aund_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o16aund_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2037" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16GALFT" name="galactofuranosyltransferase (LPS O16 antigen biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpgalfur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_garagund_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gfgaragund_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2034" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16GLCT1" name="glucosyltransferase I (LPS O16 antigen biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aragund_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_garagund_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2032" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O16GLCT2" name="glucosyltransferase II (LPS O16 antigen biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gfgaragund_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o16aund_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_O2Stex" name="superoxide anion transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2s_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2s_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O2tex" name="oxygen transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O2tpp" name="o2 transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OAADC" name="oxaloacetate decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1850" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OBTFL" name="2-Oxobutanoate formate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2obut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2579" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3114" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCBT" name="ornithine carbamoyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cbp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_citr__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4254" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0273" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCDCAtexi" name="Octadecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdca_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCDCEAtexi" name="Octadecenoate (n-C18:1) transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ocdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCTAtex" name="Octanoate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_octa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCTDPS" name="Octaprenyl pyrophosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_frdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="5" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="5" />
+ <speciesReference constant="true" species="M_octdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3187" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OCTNLL" name="Octanoate non-lipoylated apo domain ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_octa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_octapb_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OGMEACPD" name="3-Oxo-glutaryl-[ACP] methyl ester dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hgmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_egmeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OGMEACPR" name="3-Oxo-glutaryl-[ACP] methyl ester reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ogmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hgmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OGMEACPS" name="3-Oxo-glutaryl-[ACP] methyl ester synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malcoame_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ogmeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1091" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OHPBAT" name="O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ohpb_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phthr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0907" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OHPHM" name="2-octaprenyl-6-hydroxyphenol methylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ohph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2omph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2232" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMBZLM" name="2-Octaprenyl-6-methoxy-benzoquinol methylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2ombzl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ommbl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3833" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMCDC" name="2-Oxo-4-methyl-3-carboxypentanoate decarboxylation" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3c4mop_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4mop_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMMBLHX" name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_2ommbl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2omhmbl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0662" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMMBLHX3" name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (anaerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2ommbl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2omhmbl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_OMPDC" name="orotidine-5'-phosphate decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orot5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1281" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMPHHX" name="2-octaprenyl-6-methoxyphenol hydroxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_2omph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ombzl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2907" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OMPHHX3" name="2-octaprenyl-6-methoxyphenol hydroxylase (anaerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2omph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_2ombzl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_OP4ENH" name="2-oxopent-4-enoate hydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_op4en_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4h2opntn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0350" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OPHBDC" name="Octaprenyl-hydroxybenzoate decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ophb_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2oph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3843" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2311" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OPHHX" name="2-Octaprenylphenol hydroxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_2oph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ohph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3835" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OPHHX3" name="2-Octaprenylphenol hydroxylase (anaerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2oph_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ohph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_OPMEACPD" name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hpmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_epmeACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0180" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OPMEACPR" name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_opmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hpmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1093" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OPMEACPS" name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_malACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_opmeACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2323" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ORNDC" name="Ornithine Decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2965" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0693" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ORNabcpp" name="ornithine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2310" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2307" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2306" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2308" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ORNtex" name="ornithine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_orn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OROTt2_2pp" name="Orotate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_orot_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orot_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OROTtex" name="Orotate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_orot_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orot_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ORPT" name="orotate phosphoribosyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orot5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orot_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3642" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OXAMTC" name="oxamate transcarbamoylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oxur_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cbp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oxam_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_OXCDC" name="Oxalyl-CoA decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_oxalcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_forcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2373" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OXCOAHDH" name="oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_2oxpaccoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_3oxdhscoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1387" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_OXDHCOAT" name="3-oxo-5,6-dehydrosuberyl-CoA thiolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3oxdhscoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_23dhacoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1394" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1397" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_P5CD" name="1-pyrroline-5-carboxylate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_1pyr5c_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1014" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_P5CR" name="pyrroline-5-carboxylate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_1pyr5c_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA120abcpp" name="phosphatidate transport via ABC system (n-C12:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA140abcpp" name="phosphatidate transport via ABC system (n-C14:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA141abcpp" name="phosphatidate transport via ABC system (n-C14:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA160abcpp" name="phosphatidate transport via ABC system (n-C16:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pa160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA161abcpp" name="phosphatidate transport via ABC system (n-C16:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA180abcpp" name="phosphatidate transport via ABC system (n-C18:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PA181abcpp" name="phosphatidate transport via ABC system (n-C18:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PACALDt2rpp" name="phenylacetaldehyde reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pacald_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pacald_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PACALDtex" name="phenethylacetaldehyde transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pacald_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pacald_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PACCOAE" name="ring 1,2-phenylacetyl-CoA epoxidase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phaccoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rephaccoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1388" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1389" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1390" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1391" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1392" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PACCOAL" name="phenylacetate-CoA ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phaccoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1398" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PANTS" name="pantothenate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pant__R_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__B_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pnto__R_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0133" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA120" name="Phosphatidate phosphatase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA120pp" name="Phosphatidate phosphatase (periplasmic, n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA140" name="Phosphatidate phosphatase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA140pp" name="Phosphatidate phosphatase (periplasmic, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA141" name="Phosphatidate phosphatase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA141pp" name="Phosphatidate phosphatase (periplasmic, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_12dgr141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA160" name="Phosphatidate phosphatase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA160pp" name="Phosphatidate phosphatase (periplasmic, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA161" name="Phosphatidate phosphatase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA161pp" name="Phosphatidate phosphatase (periplasmic, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA180" name="Phosphatidate phosphatase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA180pp" name="Phosphatidate phosphatase (periplasmic, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA181" name="Phosphatidate phosphatase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPA181pp" name="Phosphatidate phosphatase (periplasmic, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPPT3" name="phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udcpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ugmda_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uagmda_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0087" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPSR" name="phosphoadenylyl-sulfate reductase (thioredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_paps_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PAPSR2" name="phosphoadenylyl-sulfate reductase (glutaredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_paps_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2762" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDE1" name="3',5'-cyclic-nucleotide phosphodiesterase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_camp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1489" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDE4" name="3',5'-cyclic-nucleotide phosphodiesterase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_35cgmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1489" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDH" name="pyruvate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0114" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0115" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0116" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDX5PO2" name="pyridoxine 5'-phosphate oxidase (anaerboic" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pdx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PDX5POi" name="pyridoxine 5'-phosphate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pdx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1638" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDX5PS" name="Pyridoxine 5'-phosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dxyl5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phthr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pdx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0052" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2564" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDXPP" name="Pyridoxine 5-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pdx5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydxn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0766" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE120abcpp" name="phosphatidylethanolamine transport via ABC system (n-C12:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pe120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE140abcpp" name="phosphatidylethanolamine transport via ABC system (n-C14:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE141abcpp" name="phosphatidylethanolamine transport via ABC system (n-C14:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE160abcpp" name="phosphatidylethanolamine transport via ABC system (n-C16:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pe160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE161abcpp" name="phosphatidylethanolamine transport via ABC system (n-C16:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pe161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE180abcpp" name="phosphatidylethanolamine transport via ABC system (n-C18:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PE181abcpp" name="phosphatidylethanolamine transport via ABC system (n-C18:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PEAMNOpp" name="Phenethylamine oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_peamn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pacald_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PEAMNtex" name="phenethylamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_peamn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_peamn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PERD" name="Erythronate 4-phosphate (4per) dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4per_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ohpb_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2320" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PETNT161pp" name="phosphoethanolamine transferase (c-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enlipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3546" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PETNT181pp" name="phosphoethanolamine transferase (c-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_enlipa_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_12dgr181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3546" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFK" name="phosphofructokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1723" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFK_2" name="Phosphofructokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tag6p__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tagdp__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFK_3" name="phosphofructokinase (s7p)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_s17bp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFL" name="pyruvate formate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3114" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3951" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3952" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2579" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG120abcpp" name="phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG140abcpp" name="phosphatidylglycerol transport via ABC system (n-C14:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG141abcpp" name="phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG160abcpp" name="phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG161abcpp" name="phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG180abcpp" name="phosphatidylglycerol transport via ABC system (n-C18:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg180_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PG181abcpp" name="phosphatidylglycerol transport via ABC system (n-C18:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGAMT" name="phosphoglucosamine mutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gam1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gam6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3176" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGCD" name="phosphoglycerate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3php_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2913" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4025" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGK" name="phosphoglycerate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2926" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGL" name="6-phosphogluconolactonase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0767" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGLYCP" name="Phosphoglycolate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2pglyc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glyclt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3385" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGM" name="phosphoglycerate mutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3612" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4395" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0755" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGMT" name="phosphoglucomutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2690" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0688" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP120abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C12:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp120_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP140abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C14:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP141abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C14:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP160abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C16:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pgp160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP161abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C16:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP180abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGP181abcpp" name="phosphatidylglycerophosphate transport via ABC system (n-C18:1, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0914" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP120" name="phosphatidylglycerol phosphate phosphatase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP120pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP140" name="phosphatidylglycerol phosphate phosphatase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP140pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pgp140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP141" name="phosphatidylglycerol phosphate phosphatase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp141_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP141pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pgp141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP160" name="phosphatidylglycerol phosphate phosphatase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pgp160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP160pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP161" name="phosphatidylglycerol phosphate phosphatase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp161_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP161pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pgp161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP180" name="phosphatidylglycerol phosphate phosphatase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP180pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP181" name="phosphatidylglycerol phosphate phosphatase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGPP181pp" name="phosphatidylglycerol phosphate phosphatase (periplasm, n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0418" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA120" name="Phosphatidylglycerol synthase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdddecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA140" name="Phosphatidylglycerol synthase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp140_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA141" name="Phosphatidylglycerol synthase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdec7eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA160" name="Phosphatidylglycerol synthase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA161" name="Phosphatidylglycerol synthase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdec9eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pgp161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA180" name="Phosphatidylglycerol synthase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGSA181" name="Phosphatidylglycerol synthase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cdpdodec11eg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pgp181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1912" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHEMEabcpp" name="protoheme transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pheme_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pheme_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2201" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2200" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2199" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2198" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2197" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHEMEtiex" name="protoheme transport irreversible out via diffusion (periplasm to extracellular)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pheme_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pheme_e" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PHETA1" name="phenylalanine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phe__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phpyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4054" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0928" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3770" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHETRS" name="Phenylalanyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnaphe_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phe__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phetrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1713" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1714" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHEt2rpp" name="L-phenylalanine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phe__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phe__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1473" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0112" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0576" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHEtex" name="L-phenylalanine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_phe__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_phe__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PHYTSpp" name="Phytase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_minohp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="6" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_inost_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="6" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0980" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PIt2rpp" name="phosphate reversible transport via symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2987" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3493" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PItex" name="phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PIuabcpp" name="phosphate transport via ABC system (uptake, periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3726" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3725" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3727" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3728" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A120pp" name="Phospholipase A1 (phosphatidate, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2ddecg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A140pp" name="Phospholipase A1 (phosphatidate, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2tdecg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A141pp" name="Phospholipase A1 (phosphatidate, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2tdec7eg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A160pp" name="Phospholipase A1 (phosphatidate, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2hdecg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A161pp" name="Phospholipase A1 (phosphatidate, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2hdec9eg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A180pp" name="Phospholipase A1 (phosphatidate, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2odecg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1A181pp" name="Phospholipase A1 (phosphatidate, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2odec11eg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E120pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe120_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E140pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E141pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2agpe141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E160pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E161pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E180pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1E181pp" name="Phospholipase A1 (phosphatidylethanolamine, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpe181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G120pp" name="Phospholipase A1 (phosphatidylglycerol, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G140pp" name="Phospholipase A1 (phosphatidylglycerol, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G141pp" name="Phospholipase A1 (phosphatidylglycerol, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg141_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G160pp" name="Phospholipase A1 (phosphatidylglycerol, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G161pp" name="Phospholipase A1 (phosphatidylglycerol, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G180pp" name="Phospholipase A1 (phosphatidylglycerol, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA1G181pp" name="Phospholipase A1 (phosphatidylglycerol, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2agpg181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A120pp" name="Phospholipase A2 (phosphatidate, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1ddecg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A140pp" name="Phospholipase A2 (phosphatidate, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdecg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A141pp" name="Phospholipase A2 (phosphatidate, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1tdec7eg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A160pp" name="Phospholipase A2 (phosphatidate, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_1hdecg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A161pp" name="Phospholipase A2 (phosphatidate, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pa161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_1hdec9eg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A180pp" name="Phospholipase A2 (phosphatidate, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1odecg3p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2A181pp" name="Phospholipase A2 (phosphatidate, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pa181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1odec11eg3p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E120pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe120_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E140pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe140_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E141pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E160pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe160_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E161pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pe161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe161_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E180pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2E181pp" name="Phospholipase A2 (phosphatidylethanolamine, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpe181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G120pp" name="Phospholipase A2 (phosphatidylglycerol, n-C12:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg120_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ddca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G140pp" name="Phospholipase A2 (phosphatidylglycerol, n-C14:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg140_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg140_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G141pp" name="Phospholipase A2 (phosphatidylglycerol, n-C14:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg141_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg141_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G160pp" name="Phospholipase A2 (phosphatidylglycerol, n-C16:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg160_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg160_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G161pp" name="Phospholipase A2 (phosphatidylglycerol, n-C16:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pg161_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg161_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_hdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G180pp" name="Phospholipase A2 (phosphatidylglycerol, n-C18:0) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg180_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ocdca_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg180_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PLIPA2G181pp" name="Phospholipase A2 (phosphatidylglycerol, n-C18:1) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pg181_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ocdcea_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_1agpg181_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3821" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PMANM" name="phosphomannomutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_man1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_man6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2048" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PMDPHT" name="pyrimidine phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5aprbu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4r5au_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PMEACPE" name="Pimeloyl-[ACP] methyl ester esterase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pmeACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_meoh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pimACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3412" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PMPK" name="phosphomethylpyrimidine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4ampm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mahmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2103" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PNTK" name="pantothenate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pnto__R_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ppan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3974" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PNTOt4pp" name="Pantothenate sodium symporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pnto__R_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pnto__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3258" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PNTOtex" name="Pantothenate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pnto__R_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pnto__R_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_POAACR" name="peroxyaminoacrylate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_poaac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3amac_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1010" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_POR5" name="pyruvate synthase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1378" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1378" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_POX" name="pyruvate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0871" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPA" name="inorganic diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4226" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2502" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPA2" name="inorganic triphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2502" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2744" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPAKr" name="Propionate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3115" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPALtex" name="propanal transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppal_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPALtpp" name="propanal transport via channel (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppal_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppal_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PPAt4pp" name="Na+/Propionate symporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppa_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1015" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPAtex" name="propionate transport via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppa_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppa_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPBNGS" name="porphobilinogen synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5aop_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppbng_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0369" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPC" name="phosphoenolpyruvate carboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3956" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPCDC" name="phosphopantothenoylcysteine decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ppcys_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pan4p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3639" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPCK" name="phosphoenolpyruvate carboxykinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPCSCT" name="Propanoyl-CoA: succinate CoA-transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2920" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPGPPDP" name="guanosine-3',5'-bis(diphosphate) 3'-diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppgpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3650" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPK2r" name="polyphosphate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2501" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPKr" name="polyphosphate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2501" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPM" name="phosphopentomutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3380" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4383" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPM2" name="phosphopentomutase 2 (deoxyribose)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2dr5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4383" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPNCL2" name="phosphopantothenate-cysteine ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ppan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4ppcys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3639" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPND" name="prephenate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pphn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_34hpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2600" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPNDH" name="prephenate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pphn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phpyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2599" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPPGO" name="protoporphyrinogen oxidase (aerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1.5" />
+ <speciesReference constant="true" species="M_pppg9_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_ppp9_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3850" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPPGO3" name="protoporphyrinogen oxidase (anaerobic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_pppg9_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_ppp9_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3850" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPPNDO" name="Phenylpropanoate Dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cechddd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2538" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2539" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2540" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2542" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPPNt2rpp" name="3-phenylpropionate transport via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pppn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2536" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPPNtex" name="3-phenylpropionate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pppn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pppn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPS" name="phosphoenolpyruvate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1702" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPTHpp" name="Phosphonate hydrogenase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0383" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPTtex" name="Phosphonate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRAGSr" name="phosphoribosylglycinamide synthase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pram_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gar_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4005" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRAIS" name="phosphoribosylaminoimidazole synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fpram_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_air_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2499" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRAIi" name="phosphoribosylanthranilate isomerase (irreversible)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pran_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2cpr5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1262" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRAMPC" name="phosphoribosyl-AMP cyclohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_prbamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_prfp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2026" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRASCSi" name="phosphoribosylaminoimidazolesuccinocarboxamide synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_5aizc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_25aics_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2476" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRATPP" name="phosphoribosyl-ATP pyrophosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_prbatp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_prbamp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2026" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRFGS" name="phosphoribosylformylglycinamidine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fpram_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2557" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRMICI" name="1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prfp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_prlp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2024" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROD2" name="Proline dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_1pyr5c_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1014" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROGLYabcpp" name="L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_progly_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_progly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3544" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3543" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3542" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3541" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3540" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROGLYtex" name="L-Prolinylglycine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_progly_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_progly_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROTRS" name="Prolyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnapro_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_protrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0194" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROabcpp" name="L-proline transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pro__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2677" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2678" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2679" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROt2rpp" name="L-proline reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pro__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4111" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROt4pp" name="Na+/Proline-L symporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pro__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1015" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PROtex" name="L-proline transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pro__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pro__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PRPPS" name="phosphoribosylpyrophosphate synthetase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1207" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSCLYSt2pp" name="psicoselysine transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_psclys_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_psclys_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3370" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSCLYStex" name="psicoselysine transporter via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_psclys_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_psclys_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSCVT" name="3-phosphoshikimate 1-carboxyvinyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_skm5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3psme_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0908" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD120" name="Phosphatidylserine decarboxylase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps120_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe120_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD140" name="Phosphatidylserine decarboxylase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps140_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD141" name="Phosphatidylserine decarboxylase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ps141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pe141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD160" name="Phosphatidylserine decarboxylase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ps160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe160_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD161" name="Phosphatidylserine decarboxylase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ps161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe161_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD180" name="Phosphatidylserine decarboxylase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps180_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSD181" name="Phosphatidylserine decarboxylase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps181_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pe181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4160" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSERT" name="phosphoserine transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3php_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0907" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSERtex" name="phospho-L-serine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pser__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pser__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSP_L" name="phosphoserine phosphatase (L-serine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pser__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4388" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSP_Lpp" name="phospho-L-serine phosphatase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pser__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA120" name="Phosphatidylserine syntase (n-C12:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdddecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps120_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA140" name="Phosphatidylserine syntase (n-C14:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps140_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA141" name="Phosphatidylserine syntase (n-C14:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdtdec7eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ps141_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA160" name="Phosphatidylserine syntase (n-C16:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ps160_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA161" name="Phosphatidylserine syntase (n-C16:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdhdec9eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ps161_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA180" name="Phosphatidylserine syntase (n-C18:0)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodecg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps180_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PSSA181" name="Phosphatidylserine syntase (n-C18:1)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdpdodec11eg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ps181_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2585" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTA2" name="Phosphate acetyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ppcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2297" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTAr" name="phosphotransacetylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2297" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2458" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTHRpp" name="phospho-L-threonine phosphatase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thrp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTPATi" name="pantetheine-phosphate adenylyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pan4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dpcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3634" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTRCORNt7pp" name="putrescine/ornithine antiporter (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ptrc_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_orn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_orn_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0692" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTRCTA" name="Putrescine Transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4abutn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3073" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTRCabcpp" name="putrescine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0854" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0855" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0856" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0857" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1126" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1125" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1124" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1123" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1440" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1441" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1442" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1443" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTRCt2pp" name="putrescine transport in via proton symport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1296" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0692" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTRCtex" name="putrescine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ptrc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ptrc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP1" name="purine-nucleoside phosphorylase (Adenosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP2" name="purine-nucleoside phosphorylase (Deoxyadenosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dad__2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP3" name="purine-nucleoside phosphorylase (Guanosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gsn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2407" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP4" name="purine-nucleoside phosphorylase (Deoxyguanosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgsn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gua_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2407" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP5" name="purine-nucleoside phosphorylase (Inosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ins_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2407" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP6" name="purine-nucleoside phosphorylase (Deoxyinosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_din_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hxan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2407" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4384" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PUNP7" name="purine-nucleoside phosphorylase (Xanthosine)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xtsn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2407" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYAM5PO" name="pyridoxamine 5'-phosphate oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyam5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1638" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDAMK" name="pyridoxamine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyam5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2418" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDAMtex" name="pyridoxamine transport via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDAMtpp" name="pyridoxamine import" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydam_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydam_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PYDXK" name="pyridoxal kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1636" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2418" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDXNK" name="pyridoxine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydxn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pdx5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2418" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDXNtex" name="pyridoxine transport via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydxn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydxn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDXNtpp" name="pyridoxine import" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydxn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydxn_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PYDXPP" name="Pyridoxal 5-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydx5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pydx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0446" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3826" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0766" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDXtex" name="pyridoxal transport via diffusion (extracellular)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydx_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYDXtpp" name="pyridoxal import" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pydx_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pydx_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PYK" name="pyruvate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1854" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1676" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYNP2r" name="pyrimidine-nucleoside phosphorylase (uracil)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3831" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYROX" name="pyrimidine oxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uracp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1012" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1007" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYRt2rpp" name="pyruvate reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_PYRtex" name="pyruvate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_QMO2" name="quinol monooxygenase (Ubiquinol-8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2s_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_QMO3" name="quinol monooxygenase (menaquinol 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2s_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_QUIN2tex" name="Quinate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_quin_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_quin_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_QUIN2tpp" name="Quinate transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_quin_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_quin_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_QUINDH" name="Quinate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_quin_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3dhq_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1692" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_QULNS" name="quinolinate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_iasp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_quln_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0750" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_R15BPK" name="ribose-1,5-bisphosphokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r15bp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4094" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_R1PK" name="ribose 1-phosphokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r15bp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_R5PP" name="ribose 5-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0822" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_R5PPpp" name="ribose 5-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_r5p_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_R5Ptex" name="Ribose 5-phosphate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBFK" name="riboflavin kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fmn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0025" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBFSa" name="riboflavin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_db4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4r5au_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dmlz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1662" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBFSb" name="riboflavin synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dmlz_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ribflv_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4r5au_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0415" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBK" name="ribokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3752" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBK_L1" name="L-ribulokinase (L-ribulose)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rbl__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ru5p__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0063" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RBP4E" name="L-ribulose-phosphate 4-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ru5p__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4198" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3583" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0061" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_REPHACCOAI" name="ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rephaccoa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2oxpaccoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1394" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RFAMPtex" name="Rifampin transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rfamp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rfamp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RFAMPtpp" name="Rifampin transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rfamp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rfamp_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RHAT1" name="rhamnosyltransferase I (LPS core biosynthesis)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtdprmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_kphphhlipa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_icolipa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3629" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RHCCE" name="S-ribosylhomocysteine cleavage enzyme" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rhcys_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_hcys__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhptd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2687" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RIBabcpp" name="D-ribose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4231" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4227" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4485" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4230" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3749" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3751" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3750" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3748" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4087" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4088" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4086" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RIBtex" name="ribose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rib__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rib__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RMI" name="L-rhamnose isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rmn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rml_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3903" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RMK" name="rhamnulokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rml_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rml1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3904" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RMNtex" name="L-rhamnose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rmn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rmn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RMNtpp" name="L-rhamnose transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rmn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_rmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3907" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RMPA" name="Rhamnulose-1-phosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_rml1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_lald__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3902" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR1" name="ribonucleoside-diphosphate reductase (ADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR1b" name="ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR2" name="ribonucleoside-diphosphate reductase (GDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR2b" name="ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR3" name="ribonucleoside-diphosphate reductase (CDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR3b" name="ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dcdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR4" name="ribonucleoside-diphosphate reductase (UDP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dudp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2234" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2235" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNDR4b" name="ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dudp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_grxox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0849" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1064" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3610" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1654" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2675" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2676" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNTR1c2" name="ribonucleoside-triphosphate reductase (ATP) (flavodoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_datp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNTR2c2" name="ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dgtp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNTR3c2" name="ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dctp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RNTR4c2" name="ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxr_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dutp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_flxso_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3924" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4237" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4238" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RPE" name="ribulose 5-phosphate 3-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4301" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3386" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RPI" name="ribose-5-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2914" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4090" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RZ5PP" name="alpha-ribazole 5-phosphate phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5prdmbz_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rdmbzi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0638" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S2FE2SR" name="SUF [2Fe-2S] regeneration" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufsesh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2fe1s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sufse_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="5" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1679" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1680" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S2FE2SS" name="SUF [2Fe-2S] Synthesis" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sufsesh_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sufse_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sufbcd__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="7" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3807" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1679" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1680" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S2FE2SS2" name="SUF [2Fe-2S] Synthesis II" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sufsesh_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sufbcd__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sufse_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sufbcd__2fe2s2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="7" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3807" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1679" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1680" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S2FE2ST" name="SUF [2Fe-2S] Transfer" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sufbcd__2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2fe2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S4FE4SR" name="SUF [4Fe-4S] Reduction" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sufbcd__2fe2s2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fadh2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd__4fe4s_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S4FE4ST" name="SUF [4Fe-4S] Transfer" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_sufbcd__4fe4s_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_4fe4s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sufbcd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1684" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1682" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1681" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_S7PI" name="sedoheptulose 7-phosphate isomerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gmhep7p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0222" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SADH" name="Succinylarginine dihydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sucarg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucorn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1745" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SADT2" name="Sulfate adenyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_so4_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aps_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2751" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2752" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SARCOX" name="sarcosine oxidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sarcs_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1059" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SBTPD" name="sorbitol-6-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sbt6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2705" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SBTptspp" name="D-sorbitol transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sbt__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sbt6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2702" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2704" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2703" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SBTtex" name="D-sorbitol transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sbt__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sbt__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SCYSDS" name="SUF Cysteine desulfuration" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sufse_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sufsesh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1679" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1680" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SDPDS" name="succinyl-diaminopimelate desuccinylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sl26da_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_26dap__LL_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2472" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SDPTA" name="succinyldiaminopimelate transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sl26da_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sl2a6o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3359" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SELCYSS" name="selenocysteine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sertrna[sec]_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_selnp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sectrna_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3591" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SELGTHR" name="selenate glutathione reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_slnt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dgslnt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gthox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_SELGTHR2" name="selenate glutathione reductase II" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dgslnt_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gslnt_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_SELGTHR3" name="selenate glutathione reductase III" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gslnt_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_seln_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_SELNPS" name="Selenophosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_seln_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_selnp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1764" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SELR" name="selenate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sel_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_slnt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1587" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1588" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1589" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1590" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SELtex" name="selenate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sel_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sel_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SELtpp" name="selenate transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_sel_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sel_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SEPHCHCS" name="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ichor_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2sephchc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2264" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERASr" name="(L-seryl)adenylate synthase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_seramp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0586" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERAT" name="serine O-acetyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acser_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3607" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERD_D" name="D-serine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2366" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERD_L" name="L-serine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4471" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1814" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2797" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3708" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERTRS" name="Seryl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnaser_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sertrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0893" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERTRS2" name="Seryl-tRNA synthetase (selenocystein)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnasecys_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sertrna[sec]_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0893" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERt2rpp" name="L-serine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2796" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3116" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERt4pp" name="L-serine via sodium symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ser__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3089" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SERtex" name="L-serine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ser__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SFGTHi" name="S-Formylglutathione hydralase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_Sfglutth_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_gthrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2154" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0355" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SGDS" name="Succinylglutamate desuccinylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1744" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SGSAD" name="Succinylglutamic semialdehyde dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucgsa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucglu_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1746" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHCHCS3" name="2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2sephchc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2shchc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2263" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHCHD2" name="sirohydrochlorin dehydrogenase (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dscl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_scl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3368" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHCHF" name="sirohydrochlorin ferrochelatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fe2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_scl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_sheme_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3368" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHK3Dr" name="shikimate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3dhsk_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_skm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1692" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3281" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHKK" name="shikimate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_skm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_skm5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3390" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0388" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SHSL1" name="O-succinylhomoserine lyase (L-cysteine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_suchms_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cys__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cyst__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3939" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SKMt2pp" name="shikimate transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_skm_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_skm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1981" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SKMtex" name="shikimate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_skm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_skm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SLNTtex" name="selenite transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_slnt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_slnt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SLNTtpp" name="selenite transport via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_slnt_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_slnt_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SO2tex" name="SO2 transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SO2tpp" name="SO2 transport via diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SO3tex" name="sulfite transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so3_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SO4t2pp" name="sulfate transport in via proton symport (periplasm to cytoplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_so4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1206" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SO4tex" name="sulfate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so4_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so4_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SOTA" name="Succinylornithine transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sucorn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucgsa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1748" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMDAT1" name="Spermidine acetyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_N1aspmd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1584" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMDAT2" name="Spermidine acetyltransferase (N8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_n8aspmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1584" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMDabcpp" name="spermidine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1126" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1125" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1124" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1123" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1440" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1441" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1442" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1443" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMDt3pp" name="spermidine transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1599" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1600" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMDtex" name="spermidine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_spmd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_spmd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPMS" name="spermidine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ametam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ptrc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_spmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5mta_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0121" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPODM" name="superoxide dismutase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2s_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3908" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1656" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SPODMpp" name="superoxide dismutase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2s_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1646" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SSALx" name="succinate-semialdehyde dehydrogenase (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucsal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1525" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SSALy" name="succinate-semialdehyde dehydrogenase (NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucsal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2661" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1525" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCASPtpp" name="succinate:aspartate antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_asp__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_asp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0621" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCBZL" name="o-succinylbenzoate-CoA ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucbz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sbzcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2260" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCBZS" name="O-succinylbenzoate-CoA synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2shchc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucbz_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2261" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCCt2_2pp" name="succinate transport via proton symport (2 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCCt2_3pp" name="Succintate transport via proton symport (3 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCCt3pp" name="succinate transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_SUCCtex" name="succinate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCDi" name="succinate dehydrogenase (irreversible)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0721" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0722" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0723" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0724" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCFUMtpp" name="succinate:fumarate antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0621" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCMALtpp" name="succinate:malate antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4138" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0621" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCOAS" name="succinyl-CoA synthetase (ADP-forming)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0728" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0729" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCRtex" name="sucrose transport transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sucr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sucr_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCTARTtpp" name="succinate:D-tartrate antiporter (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_0_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tartr__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tartr__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCptspp" name="sucrose transport via PEP:Pyr (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sucr_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_suc6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2429" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SULFACabcpp" name="sulfoacetate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sulfac_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_sulfac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0936" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0933" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0934" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SULFACtex" name="sulfoaceate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_sulfac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sulfac_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SULRi" name="sulfite reductase (NADPH2)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="5" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_h2s_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="3" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2764" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SULabcpp" name="sulfate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_so4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_so4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0764" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0765" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3917" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_T2DECAI" name="trans-2-decenoyl-ACP isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tdec2eACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_cdec3eACP_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0954" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TAGURr" name="tagaturonate reductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_altrn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tagur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1521" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TALA" name="transaldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2464" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0008" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TARTD" name="L(+)-tartrate dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3061" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3062" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TARTRDtex" name="D-tartrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tartr__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TARTRt7pp" name="Tartrate/succinate antiporter (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tartr__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tartr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3063" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TARTRtex" name="Tartrate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tartr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tartr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TARTt2_3pp" name="D-tartrate transport via proton symport (3 H) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="3" />
+ <speciesReference constant="true" species="M_tartr__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_tartr__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4123" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TAUDO" name="Taurine dioxygenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_taur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_so3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_aacald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0368" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TAURabcpp" name="taurine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_taur_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_taur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0365" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0366" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0367" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TAURtex" name="taurine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_taur_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_taur_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TCYNTtex" name="Thiocyanate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tcynt_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tcynt_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDP" name="thiamin pyrophosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thmpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thmmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1134" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDPADGAT" name="dTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4addg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdp4aaddg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3790" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDPAGTA" name="dTDP-4-amino-4,6-dideoxy-D-glucose transaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4d6dg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4addg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3791" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDPDRE" name="dTDP-4-dehydrorhamnose 3,5-epimerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtdp4d6dg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdp4d6dm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2038" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDPDRR" name="dTDP-4-dehydrorhamnose reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4d6dm_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtdprmn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDPGDH" name="dTDPglucose 4,6-dehydratase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dtdpglu_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtdp4d6dg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3788" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2041" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDSK" name="Tetraacyldisaccharide 4'kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lipidAds_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipidA_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0915" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDSR1" name="thiol:disulfide reductase (DsbC)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dsbcox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dsbdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbcrd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2893" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4136" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TDSR2" name="thiol:disulfide reductase (DsbG)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dsbgox_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbdrd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dsbdox_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dsbgrd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4136" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0604" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TGBPA" name="Tagatose-bisphosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tagdp__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3132" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3137" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2095" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2096" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THD2pp" name="NAD(P) transhydrogenase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1602" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1603" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THDPS" name="tetrahydrodipicolinate succinylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_sl2a6o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0166" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THFAT" name="Tetrahydrofolate aminomethyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_methf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_5fthf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THIORDXi" name="hydrogen peroxide reductase (thioredoxin)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2480" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1710" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THMDt2pp" name="thymidine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thymd_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thymd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THMDt2rpp" name="thymidine transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thymd_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thymd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THMDtex" name="thymidine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thymd_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thymd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THMabcpp" name="thiamine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thm_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0068" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0067" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0066" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THMtex" name="Thiamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thm_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thm_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRA2i" name="L-allo-Threonine Aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_athr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0870" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRAi" name="Threonine aldolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2551" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0870" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRD" name="L-threonine dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2aobut_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3616" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRD_L" name="L-threonine deaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_2obut_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3117" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3772" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRPtex" name="phospho-L-threonine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thrp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thrp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRS" name="threonine synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_phom_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0004" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRTRS" name="Threonyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnathr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thrtrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1719" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRabcpp" name="L-threonine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3460" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRt2pp" name="L-threonine efflux transport via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0813" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3823" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRt2rpp" name="L-threonine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3116" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRt4pp" name="L-threonine via sodium symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_na1_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_na1_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3089" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THRtex" name="L-threonine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THYMt3pp" name="thymine transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thym_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thym_p" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_THYMtex" name="thymine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thym_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thym_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THZPSN3" name="thiazole phosphate synthesis" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dxyl5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhgly_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscssh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4mpetz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_iscs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2530" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3992" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3990" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0423" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4407" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TKT1" name="transketolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2935" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2465" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TKT2" name="transketolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2935" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2465" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAOR1" name="Trimethylamine N-oxide reductase (menaquinol 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tmao_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tma_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0894" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0896" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1587" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1588" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1589" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1590" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAOR1pp" name="Trimethylamine N-oxide reductase (menaquinol 8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tmao_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mqn8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tma_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0997" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1872" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1873" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAOR2" name="Trimethylamine N-oxide reductase (demethylmenaquinol 8)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tmao_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tma_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0894" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0895" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0896" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAOR2pp" name="Trimethylamine N-oxide reductase (demethylmenaquinol 8) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmql8_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tmao_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tma_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dmmq8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0996" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0997" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1872" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1873" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAOtex" name="Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tmao_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tmao_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMAtex" name="Trimethylamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tma_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tma_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMDK1" name="thymidine kinase (ATP:thymidine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thymd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dtmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1238" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMDPP" name="thymidine phosphorylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thymd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thym_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2dr1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4382" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMDS" name="thymidylate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_mlthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dtmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2827" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMK" name="thiamine kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thm_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_thmmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1106" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMPK" name="thiamine-phosphate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_thmmp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thmpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0417" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TMPPP" name="thiamine-phosphate diphosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_4mpetz_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2mahmp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thmmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3993" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TPI" name="triose-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3919" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TPRDCOAS" name="triphosphoribosyl-dephospho-CoA synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dpcoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ade_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2tpr3dpcoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0613" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRDR" name="thioredoxin reductase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trdox_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_trdrd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3781" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0888" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0888" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2582" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRE6PH" name="trehalose-6-phosphate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4239" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRE6PP" name="trehalose-phosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1897" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRE6PS" name="alpha,alpha-trehalose-phosphate synthase (UDP-forming)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1896" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TREH" name="alpha,alpha-trehalase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3519" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TREHpp" name="alpha,alpha-trehalase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tre_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glc__D_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1197" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TREptspp" name="trehalose transport via PEP:Pyr PTS (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tre_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tre6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4240" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TREtex" name="trehalose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tre_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tre_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPAS2" name="Tryptophanase (L-tryptophan)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3708" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPS1" name="tryptophan synthase (indoleglycerol phosphate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3ig3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1260" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1261" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPS2" name="tryptophan synthase (indole)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ser__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1260" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1261" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPS3" name="tryptophan synthase (indoleglycerol phosphate)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3ig3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_indole_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1260" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1261" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPTRS" name="Tryptophanyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trnatrp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trptrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3384" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPt2rpp" name="L-tryptophan reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_trp__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3161" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3709" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1473" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0112" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRPtex" name="L-tryptophan transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trp__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_trp__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TRSARr" name="tartronate semialdehyde reductase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_2h3oppan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glyc__R_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0509" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3125" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TSULabcpp" name="thiosulfate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tsul_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tsul_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2425" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2422" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2424" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2423" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3917" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TSULtex" name="thiosulfate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tsul_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tsul_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TTDCAtexi" name="Tetradecanoate transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttdca_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdca_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TTDCEAtexi" name="Tetradecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttdcea_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttdcea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2344" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TTRCYCtex" name="Tetracycline transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ttrcyc_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ttrcyc_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TTRCYCtpp" name="Tetracycline transport via TolC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttrcyc_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ttrcyc_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0462" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0463" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2470" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3035" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TUNGSabcpp" name="tungstate transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tungs_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tungs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0763" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0764" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0765" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TUNGStex" name="tungstate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tungs_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tungs_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYMtex" name="tyramine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tym_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tym_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRL" name="tyrosine lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_met__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4crsol_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dad__5_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dhgly_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3991" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYROXDApp" name="Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tym_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_4hoxpacd_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1386" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRPpp" name="phospho-L-tyrosine phosphatase (periplasmic)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyrp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4055" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRPtex" name="phopho-L-tyrosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tyrp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tyrp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRTA" name="tyrosine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_34hpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4054" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0928" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRTRS" name="tyrosyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnatyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyrtrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1637" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRt2rpp" name="L-tyrosine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_tyr__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1473" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1907" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0112" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0576" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TYRtex" name="L-tyrosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tyr__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_tyr__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ThDPAT" name="ThDP adenylyl transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thmpp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_athtp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_U23GAAT" name="UDP-3-O-(3-hydroxymyristoyl)glucosamine acyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3hmrsACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u3hga_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u23ga_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0179" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAAGDS" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_26dap__M_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uamag_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ugmd_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0085" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UACGALPpp" name="UDP-N-acetyl-D-galactosamine pyrophosphohydrolase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpacgal_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgal1p_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UACGAMPpp" name="UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UACGAMtex" name="UDP-N-acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uacgam_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UACMAMO" name="UDP-N-acetyl-D-mannosamine oxidoreductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uacmam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_uacmamu_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3787" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAG2E" name="UDP-N-acetylglucosamine 2-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uacmam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3786" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAGAAT" name="UDP-N-acetylglucosamine acyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3hmrsACP_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ACP_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u3aga_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1094" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0181" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAGCVT" name="UDP-N-acetylglucosamine 1-carboxyvinyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uaccg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3189" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAGDP" name="UDP-N-acetylglucosamine diphosphorylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_utp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acgam1p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3730" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAGPT3" name="UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uacgam_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uagmda_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uaagmda_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0090" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAMAGS" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uama_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uamag_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0088" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAMAS" name="UDP-N-acetylmuramoyl-L-alanine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uamr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uama_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0091" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UAPGR" name="UDP-N-acetylenolpyruvoylglucosamine reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uaccg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uamr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3972" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDCPDP" name="undecaprenyl-diphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0841" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3057" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDCPDPS" name="Undecaprenyl diphosphate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_frdp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ipdp_c" stoichiometry="8" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="8" />
+ <speciesReference constant="true" species="M_udcpdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0174" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDCPDPpp" name="undecaprenyl-diphosphatase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udcpdp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udcpp_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3057" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0841" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDCPPtppi" name="undecaprenyl phosphate transport (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udcpp_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udcpp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_UDPACGALtex" name="UDP-N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpacgal_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpacgal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPG4E" name="UDPglucose 4-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpgal_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0759" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGALM" name="UDPgalactopyranose mutase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpgal_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpgalfur_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2036" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGALPpp" name="UDPgalactose pyrophosphohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpgal_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_gal1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGALtex" name="UDPgalactose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpgal_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpgal_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGD" name="UDPglucose 6-dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpglcur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2028" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGDC" name="UDP-glucuronate C-4'' decarboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpglcur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpLa4o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2255" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGLCURtex" name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpglcur_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpglcur_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGPpp" name="UDPglucose pyrophosphohydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_g1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPGtex" name="UDPglucose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpg_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpg_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UDPKAAT" name="UDP-4''-ketopentose:UDP-4-amino-4-deoxy-L-arabinose aminotransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpLa4o_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpLa4n_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2253" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UGLCURPpp" name="UDP-D-glucuronate pyrophosphohydrolase (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpglcur_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="2" />
+ <speciesReference constant="true" species="M_glcur1p_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0480" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UGLT" name="UDPglucose--hexose-1-phosphate uridylyltransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gal1p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udpgal_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g1p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0758" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UGLYCH" name="Ureidoglycolate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_urdglyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0505" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UGMDDS" name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_alaala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ugmd_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ugmda_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0086" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UHGADA" name="UDP-3-O-acetylglucosamine deacetylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u3aga_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u3hga_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0096" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ULA4NFT" name="UDP-L-Ara4N formyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udpLa4n_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_10fthf_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpLa4fn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_thf_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2255" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ULA4Ntppi" name="transport (cytoplasm to periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uLa4n_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uLa4n_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4544" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2258" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UM3PL" name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_LalaDgluMdap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uamr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ugmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4233" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UM4PCP" name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_um4p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ugmd_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1192" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UM4PL" name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate-D-alanine ligase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_LalaDgluMdapDala_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uamr_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_um4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4233" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UMPK" name="UMP kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0910" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0171" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UMPtex" name="UMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ump_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ump_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPLA4FNF" name="undecaprenyl phosphate-L-Ara4FN formylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uLa4fn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uLa4n_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2256" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPLA4FNT" name="undecaprenyl phosphate-L-Ara4FN transferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_udcpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_udpLa4fn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_udp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uLa4fn_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2254" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPP3MT" name="uroporphyrinogen methyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uppg3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amet_c" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_dscl_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ahcys_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3803" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3368" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPP3S" name="uroporphyrinogen-III synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_hmbil_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uppg3_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3804" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPPDC1" name="uroporphyrinogen decarboxylase (uroporphyrinogen III)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uppg3_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_cpppg3_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3997" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UPPRT" name="uracil phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2498" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URACPAH" name="peroxyureidoacrylate hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uracp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_poaac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cbm_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1011" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URAt2pp" name="uracil transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2497" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URAt2rpp" name="uracil transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1006" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URAtex" name="uracil transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ura_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ura_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URDGLYCD" name="ureidoglycolate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_urdglyc_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_oxur_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0517" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UREAtex" name="Urea transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_urea_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_urea_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_UREAtpp" name="Urea transport via facilitate diffusion (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_urea_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_urea_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3927" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URIC" name="uricase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_urate_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_alltn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h2o2_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_URIH" name="Uridine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ura_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2162" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0651" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0030" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URIK2" name="uridine kinase (GTP:Uridine)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gtp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2066" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URIt2pp" name="uridine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uri_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2393" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2964" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URIt2rpp" name="uridine transport in via proton symport, reversible (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_uri_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_URItex" name="uridine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_uri_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_uri_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0411" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_USHD" name="UDP-sugar hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_u23ga_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_ump_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lipidX_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0524" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VALTA" name="valine transaminase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3mob_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3770" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VALTRS" name="Valyl-tRNA synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_trnaval_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_valtrna_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4258" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VALabcpp" name="L-valine transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3454" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3455" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3457" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3460" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3456" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VALt2rpp" name="L-valine reversible transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0401" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2683" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2682" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VALtex" name="L-valine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_val__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_val__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_VPAMTr" name="Valine-pyruvate aminotransferase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_3mob_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ala__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_val__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3572" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_WCOS" name="tungsten pterin cofactor synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_tungs_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mptamp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cu2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_wco_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0827" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_X5PL3E" name="L-xylulose 5-phosphate 3-epimerase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xu5p__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ru5p__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4197" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XAND" name="xanthine dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_urate_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2866" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2867" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2868" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XANt2pp" name="xanthine transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3654" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2882" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XANtex" name="xanthine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xan_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xan_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XANtpp" name="xanthine reversible transport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xan_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_XMPtex" name="XMP transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xmp_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xmp_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XPPT" name="xanthine phosphoribosyltransferase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_prpp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ppi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xmp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0238" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XTSNH" name="Xanthosine hydrolase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtsn_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xan_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_rib__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0030" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XTSNt2rpp" name="Xanthosine transport via proton symport (periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xtsn_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xtsn_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2406" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XTSNtex" name="xanthosine transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xtsn_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xtsn_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLI1" name="xylose isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xyl__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xylu__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3565" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLI2" name="xylose isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fru_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3565" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLK" name="xylulokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xylu__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0063" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3564" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLK2" name="L-xylulokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xylu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xu5p__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0063" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3580" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLUt2pp" name="L-xylulose transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xylu__L_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xylu__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3577" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3578" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3579" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLUtex" name="L-xylulose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xylu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xylu__L_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLabcpp" name="D-xylose transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xyl__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xyl__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3566" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3567" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3568" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLt2pp" name="D-xylose transport in via proton symport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xyl__D_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xyl__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4031" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_XYLtex" name="D-xylose transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_xyl__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xyl__D_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ZN2abcpp" name="Zinc (Zn+2) ABC transporter, efflux (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_zn2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_zn2_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3469" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ZN2t3pp" name="zinc (Zn+2) transport out via proton antiport (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_p" stoichiometry="1" />
+ <speciesReference constant="true" species="M_zn2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_zn2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3915" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0752" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ZN2tpp" name="zinc transport in via permease (no H+)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_zn2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_zn2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3040" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ZNabcpp" name="zinc (Zn+2) transport via ABC system (periplasm)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_zn2_p" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_zn2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1857" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1859" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1858" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Zn2tex" name="zinc (Zn+2) transport via diffusion (extracellular to periplasm)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_zn2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_zn2_p" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0929" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1377" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2215" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/cobra/test/data/mini.json b/cobra/test/data/mini.json
new file mode 100644
index 0000000..265095b
--- /dev/null
+++ b/cobra/test/data/mini.json
@@ -0,0 +1 @@
+{"reactions": [{"subsystem": "Oxidative Phosphorylation", "name": "ATP maintenance requirement", "upper_bound": 999999.0, "lower_bound": 8.39, "notes": {}, "metabolites": {"h2o_c": -1.0, "pi_c": 1.0, "h_c": 1.0, "atp_c": -1.0, "adp_c": 1.0}, "objective_coefficient": 1, "variable_kind": "continuous", "id": "ATPM", "gene_reaction_rule": ""}, {"subsystem": "Glycolysis/Gluconeogenesis", "name": "enolase", "upper_bound": 999999.0, "lower_bound": -999999.0, "notes": {}, "metabolites": {"pep_c" [...]
\ No newline at end of file
diff --git a/cobra/test/data/mini.mat b/cobra/test/data/mini.mat
new file mode 100644
index 0000000..264b307
Binary files /dev/null and b/cobra/test/data/mini.mat differ
diff --git a/cobra/test/data/mini.pickle b/cobra/test/data/mini.pickle
new file mode 100644
index 0000000..c7dc9b8
Binary files /dev/null and b/cobra/test/data/mini.pickle differ
diff --git a/cobra/test/data/mini_cobra.xml b/cobra/test/data/mini_cobra.xml
new file mode 100644
index 0000000..3fe6a59
--- /dev/null
+++ b/cobra/test/data/mini_cobra.xml
@@ -0,0 +1,634 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+ <model id="mini_textbook">
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr">
+ <listOfUnits>
+ <unit kind="mole" scale="-3"/>
+ <unit kind="gram" exponent="-1"/>
+ <unit kind="second" exponent="-1" multiplier="0.000277777777777778"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="c" name="Cytoplasm" size="1"/>
+ <compartment id="e" name="Extracellular" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="M_atp_c" name="ATP" compartment="c" charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_c" name="H+" compartment="c" charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_adp_c" name="ADP" compartment="c" charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h2o_c" name="H2O" compartment="c" charge="0">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pi_c" name="Phosphate" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_2pg_c" name="D-Glycerate 2-phosphate" compartment="c" charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pep_c" name="Phosphoenolpyruvate" compartment="c" charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_glc__D_e" name="D-Glucose" compartment="e" charge="0">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_e" name="H+" compartment="e" charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_g3p_c" name="Glyceraldehyde 3-phosphate" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_dhap_c" name="Dihydroxyacetone phosphate" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_fdp_c" name="D-Fructose 1,6-bisphosphate" compartment="c" charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" compartment="c" charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_nad_c" name="Nicotinamide adenine dinucleotide" compartment="c" charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_g6p_c" name="D-Glucose 6-phosphate" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pyr_c" name="Pyruvate" compartment="c" charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h2o_e" name="H2O" compartment="e" charge="0">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_f6p_c" name="D-Fructose 6-phosphate" compartment="c" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_3pg_c" name="3-Phospho-D-glycerate" compartment="c" charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pi_e" name="Phosphate" compartment="e" charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_lac__D_c" name="D-Lactate" compartment="c" charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ <species id="M_lac__D_e" name="D-Lactate" compartment="e" charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ <species id="M_glc__D_e_boundary" name="D-Glucose" compartment="e" boundaryCondition="true" charge="0">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_e_boundary" name="H+" compartment="e" boundaryCondition="true" charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_lac__D_e_boundary" name="D-Lactate" compartment="e" boundaryCondition="true" charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R_ATPM" name="ATP maintenance requirement" reversible="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: Oxidative Phosphorylation</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_atp_c" stoichiometry="1"/>
+ <speciesReference species="M_h2o_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ <speciesReference species="M_adp_c" stoichiometry="1"/>
+ <speciesReference species="M_pi_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="8.39" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="1" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_ENO" name="enolase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2779)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h2o_c" stoichiometry="1"/>
+ <speciesReference species="M_pep_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_glc__D_e_boundary" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-10" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_EX_h_e" name="H+ exchange" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_h_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_e_boundary" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2925) or (b1773) or (b2097)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_fdp_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g3p_c" stoichiometry="1"/>
+ <speciesReference species="M_dhap_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b1779)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pi_c" stoichiometry="1"/>
+ <speciesReference species="M_g3p_c" stoichiometry="1"/>
+ <speciesReference species="M_nad_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_nadh_c" stoichiometry="1"/>
+ <speciesReference species="M_13dpg_c" stoichiometry="1"/>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: ((b2417 and b1621 and b2415 and b2416) or (b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416))</p>
+ <p>SUBSYSTEM: Transport, Extracellular</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1"/>
+ <speciesReference species="M_pep_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g6p_c" stoichiometry="1"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_H2Ot" name="H2O transport via diffusion" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b0875)</p>
+ <p>SUBSYSTEM: Transport, Extracellular</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_h2o_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h2o_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PFK" name="phosphofructokinase" reversible="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3916) or (b1723)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_f6p_c" stoichiometry="1"/>
+ <speciesReference species="M_atp_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1"/>
+ <speciesReference species="M_fdp_c" stoichiometry="1"/>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b4025)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_g6p_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_f6p_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PGK" name="phosphoglycerate kinase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2926)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_3pg_c" stoichiometry="1"/>
+ <speciesReference species="M_atp_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1"/>
+ <speciesReference species="M_13dpg_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PGM" name="phosphoglycerate mutase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b4395) or (b3612) or (b0755)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_3pg_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PIt2r" name="phosphate reversible transport via symport" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2987) or (b3493)</p>
+ <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pi_e" stoichiometry="1"/>
+ <speciesReference species="M_h_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_pi_c" stoichiometry="1"/>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_PYK" name="pyruvate kinase" reversible="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b1854) or (b1676)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pep_c" stoichiometry="1"/>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ <speciesReference species="M_adp_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_pyr_c" stoichiometry="1"/>
+ <speciesReference species="M_atp_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_TPI" name="triose-phosphate isomerase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3919)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_dhap_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g3p_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2133 or b1380)</p>
+ <p>SUBSYSTEM: Pyruvate Metabolism</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_c" stoichiometry="1"/>
+ <speciesReference species="M_nad_c" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_nadh_c" stoichiometry="1"/>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_lac__D_e_boundary" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="R_D_LACt2" name="D_LACt2" reversible="true">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3603 or b2975)</p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_e" stoichiometry="1"/>
+ <speciesReference species="M_h_e" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1"/>
+ <speciesReference species="M_lac__D_c" stoichiometry="1"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> FLUX_VALUE </ci>
+ </math>
+ <listOfParameters>
+ <parameter id="LOWER_BOUND" value="-999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="OBJECTIVE_COEFFICIENT" value="0" units="dimensionless"/>
+ <parameter id="UPPER_BOUND" value="999999" units="mmol_per_gDW_per_hr"/>
+ <parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
+ </listOfParameters>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/cobra/test/data/mini_fbc1.xml b/cobra/test/data/mini_fbc1.xml
new file mode 100644
index 0000000..66e9030
--- /dev/null
+++ b/cobra/test/data/mini_fbc1.xml
@@ -0,0 +1,561 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" level="3" version="1" fbc:required="false">
+ <model id="mini_textbook" substanceUnits="substance" timeUnits="dimensionless" volumeUnits="volume" areaUnits="area" lengthUnits="metre" extentUnits="substance">
+ <annotation>
+ <listOfGeneAssociations xmlns="http://www.sbml.org/sbml/level3/version1/fbc/version1">
+ <geneAssociation id="ga_1" reaction="R_ENO">
+ <gene reference="b2779"/>
+ </geneAssociation>
+ <geneAssociation id="ga_2" reaction="R_FBA">
+ <or>
+ <gene reference="b2925"/>
+ <gene reference="b1773"/>
+ <gene reference="b2097"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_3" reaction="R_GAPD">
+ <gene reference="b1779"/>
+ </geneAssociation>
+ <geneAssociation id="ga_4" reaction="R_GLCpts">
+ <or>
+ <and>
+ <gene reference="b2417"/>
+ <gene reference="b1621"/>
+ <gene reference="b2415"/>
+ <gene reference="b2416"/>
+ </and>
+ <and>
+ <gene reference="b2417"/>
+ <gene reference="b1101"/>
+ <gene reference="b2415"/>
+ <gene reference="b2416"/>
+ </and>
+ <and>
+ <gene reference="b1817"/>
+ <gene reference="b1818"/>
+ <gene reference="b1819"/>
+ <gene reference="b2415"/>
+ <gene reference="b2416"/>
+ </and>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_5" reaction="R_H2Ot">
+ <gene reference="b0875"/>
+ </geneAssociation>
+ <geneAssociation id="ga_6" reaction="R_PFK">
+ <or>
+ <gene reference="b3916"/>
+ <gene reference="b1723"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_7" reaction="R_PGI">
+ <gene reference="b4025"/>
+ </geneAssociation>
+ <geneAssociation id="ga_8" reaction="R_PGK">
+ <gene reference="b2926"/>
+ </geneAssociation>
+ <geneAssociation id="ga_9" reaction="R_PGM">
+ <or>
+ <gene reference="b4395"/>
+ <gene reference="b3612"/>
+ <gene reference="b0755"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_10" reaction="R_PIt2r">
+ <or>
+ <gene reference="b2987"/>
+ <gene reference="b3493"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_11" reaction="R_PYK">
+ <or>
+ <gene reference="b1854"/>
+ <gene reference="b1676"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_12" reaction="R_TPI">
+ <gene reference="b3919"/>
+ </geneAssociation>
+ <geneAssociation id="ga_13" reaction="R_LDH_D">
+ <or>
+ <gene reference="b2133"/>
+ <gene reference="b1380"/>
+ </or>
+ </geneAssociation>
+ <geneAssociation id="ga_14" reaction="R_D_LACt2">
+ <or>
+ <gene reference="b3603"/>
+ <gene reference="b2975"/>
+ </or>
+ </geneAssociation>
+ </listOfGeneAssociations>
+ </annotation>
+ <listOfCompartments>
+ <compartment id="c" name="Cytoplasm" spatialDimensions="3" size="1" constant="true"/>
+ <compartment id="e" name="Extracellular" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="M_atp_c" name="ATP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_c" name="H+" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_adp_c" name="ADP" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h2o_c" name="H2O" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pi_c" name="Phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_2pg_c" name="D-Glycerate 2-phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pep_c" name="Phosphoenolpyruvate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_glc__D_e" name="D-Glucose" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_e" name="H+" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_g3p_c" name="Glyceraldehyde 3-phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_dhap_c" name="Dihydroxyacetone phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_fdp_c" name="D-Fructose 1,6-bisphosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-4">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_nad_c" name="Nicotinamide adenine dinucleotide" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_g6p_c" name="D-Glucose 6-phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pyr_c" name="Pyruvate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h2o_e" name="H2O" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_f6p_c" name="D-Fructose 6-phosphate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_3pg_c" name="3-Phospho-D-glycerate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_pi_e" name="Phosphate" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-2">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_lac__D_c" name="D-Lactate" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C3H5O3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ <species id="M_lac__D_e" name="D-Lactate" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-1" fbc:chemicalFormula="C3H5O3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ <species id="M_glc__D_e_boundary" name="D-Glucose" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_h_e_boundary" name="H+" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="1">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml"/>
+ </notes>
+ </species>
+ <species id="M_lac__D_e_boundary" name="D-Lactate" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="-1" fbc:chemicalFormula="C3H5O3">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: C3H5O3</p>
+ </html>
+ </notes>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="R_ATPM" name="ATP maintenance requirement" reversible="false" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: Oxidative Phosphorylation</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_ENO" name="enolase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2779)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_glc__D_e_boundary" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_EX_h_e" name="H+ exchange" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_e_boundary" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2925) or (b1773) or (b2097)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b1779)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: ((b2417 and b1621 and b2415 and b2416) or (b2417 and b1101 and b2415 and b2416) or (b1817 and b1818 and b1819 and b2415 and b2416))</p>
+ <p>SUBSYSTEM: Transport, Extracellular</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_glc__D_e" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_H2Ot" name="H2O transport via diffusion" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b0875)</p>
+ <p>SUBSYSTEM: Transport, Extracellular</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_h2o_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PFK" name="phosphofructokinase" reversible="false" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3916) or (b1723)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_fdp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b4025)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PGK" name="phosphoglycerate kinase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2926)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_13dpg_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PGM" name="phosphoglycerate mutase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b4395) or (b3612) or (b0755)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PIt2r" name="phosphate reversible transport via symport" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2987) or (b3493)</p>
+ <p>SUBSYSTEM: Inorganic Ion Transport and Metabolism</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pi_e" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_PYK" name="pyruvate kinase" reversible="false" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b1854) or (b1676)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_TPI" name="triose-phosphate isomerase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3919)</p>
+ <p>SUBSYSTEM: Glycolysis/Gluconeogenesis</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b2133 or b1380)</p>
+ <p>SUBSYSTEM: Pyruvate Metabolism</p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: </p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_lac__D_e_boundary" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="R_D_LACt2" name="D_LACt2" reversible="true" fast="false">
+ <notes>
+ <html xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: (b3603 or b2975)</p>
+ <p>SUBSYSTEM: </p>
+ </html>
+ </notes>
+ <listOfReactants>
+ <speciesReference species="M_lac__D_e" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_h_e" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
+ <speciesReference species="M_lac__D_c" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ <fbc:listOfFluxBounds>
+ <fbc:fluxBound fbc:reaction="R_ATPM" fbc:operation="greaterEqual" fbc:value="8.39"/>
+ <fbc:fluxBound fbc:reaction="R_ATPM" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_ENO" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_ENO" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_EX_glc__D_e" fbc:operation="greaterEqual" fbc:value="-10"/>
+ <fbc:fluxBound fbc:reaction="R_EX_glc__D_e" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_EX_h_e" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_EX_h_e" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_FBA" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_FBA" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_GAPD" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_GAPD" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_GLCpts" fbc:operation="greaterEqual" fbc:value="0"/>
+ <fbc:fluxBound fbc:reaction="R_GLCpts" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_H2Ot" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_H2Ot" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PFK" fbc:operation="greaterEqual" fbc:value="0"/>
+ <fbc:fluxBound fbc:reaction="R_PFK" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGI" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGI" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGK" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGK" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGM" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_PGM" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PIt2r" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_PIt2r" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_PYK" fbc:operation="greaterEqual" fbc:value="0"/>
+ <fbc:fluxBound fbc:reaction="R_PYK" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_TPI" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_TPI" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_LDH_D" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_LDH_D" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_EX_lac__D_e" fbc:operation="greaterEqual" fbc:value="0"/>
+ <fbc:fluxBound fbc:reaction="R_EX_lac__D_e" fbc:operation="lessEqual" fbc:value="999999"/>
+ <fbc:fluxBound fbc:reaction="R_D_LACt2" fbc:operation="greaterEqual" fbc:value="-999999"/>
+ <fbc:fluxBound fbc:reaction="R_D_LACt2" fbc:operation="lessEqual" fbc:value="999999"/>
+ </fbc:listOfFluxBounds>
+ <fbc:listOfObjectives fbc:activeObjective="obj">
+ <fbc:objective fbc:id="obj" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:reaction="R_ATPM" fbc:coefficient="1"/>
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ </model>
+</sbml>
diff --git a/cobra/test/data/mini_fbc2.xml b/cobra/test/data/mini_fbc2.xml
new file mode 100644
index 0000000..526a88b
--- /dev/null
+++ b/cobra/test/data/mini_fbc2.xml
@@ -0,0 +1,337 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
+ <model id="mini_textbook" fbc:strict="true">
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="-3" />
+ <unit exponent="-1" kind="gram" multiplier="1" scale="0" />
+ <unit exponent="-1" kind="second" multiplier="3600" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <fbc:listOfObjectives fbc:activeObjective="obj">
+ <fbc:objective fbc:id="obj" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:coefficient="1" fbc:reaction="R_ATPM" />
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ <listOfParameters>
+ <parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-999999" />
+ <parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="999999" />
+ <parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0" />
+ <parameter constant="true" id="R_ATPM_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="8.39" />
+ <parameter constant="true" id="R_EX_glc__D_e_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-10" />
+ </listOfParameters>
+ <listOfCompartments>
+ <compartment constant="true" id="c" name="Cytoplasm" />
+ <compartment constant="true" id="e" name="Extracellular" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_atp_c" name="ATP" fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_h_c" name="H+" fbc:charge="1" fbc:chemicalFormula="H" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_adp_c" name="ADP" fbc:charge="-3" fbc:chemicalFormula="C10H12N5O10P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_c" name="H2O" fbc:charge="0" fbc:chemicalFormula="H2O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_pi_c" name="Phosphate" fbc:charge="-2" fbc:chemicalFormula="HO4P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_2pg_c" name="D-Glycerate 2-phosphate" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_pep_c" name="Phosphoenolpyruvate" fbc:charge="-3" fbc:chemicalFormula="C3H2O6P" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_glc__D_e" name="D-Glucose" fbc:charge="0" fbc:chemicalFormula="C6H12O6" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_h_e" name="H+" fbc:charge="1" fbc:chemicalFormula="H" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_g3p_c" name="Glyceraldehyde 3-phosphate" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhap_c" name="Dihydroxyacetone phosphate" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_fdp_c" name="D-Fructose 1,6-bisphosphate" fbc:charge="-4" fbc:chemicalFormula="C6H10O12P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" fbc:charge="-2" fbc:chemicalFormula="C21H27N7O14P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" fbc:charge="-4" fbc:chemicalFormula="C3H4O10P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nad_c" name="Nicotinamide adenine dinucleotide" fbc:charge="-1" fbc:chemicalFormula="C21H26N7O14P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_g6p_c" name="D-Glucose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_pyr_c" name="Pyruvate" fbc:charge="-1" fbc:chemicalFormula="C3H3O3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_e" name="H2O" fbc:charge="0" fbc:chemicalFormula="H2O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_f6p_c" name="D-Fructose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_3pg_c" name="3-Phospho-D-glycerate" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_pi_e" name="Phosphate" fbc:charge="-2" fbc:chemicalFormula="HO4P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_c" name="D-Lactate" fbc:charge="-1" fbc:chemicalFormula="C3H5O3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_e" name="D-Lactate" fbc:charge="-1" fbc:chemicalFormula="C3H5O3" />
+ </listOfSpecies>
+ <fbc:listOfGeneProducts>
+ <fbc:geneProduct fbc:id="G_b2779" fbc:label="b2779" fbc:name="eno" />
+ <fbc:geneProduct fbc:id="G_b1773" fbc:label="b1773" fbc:name="ydjI" />
+ <fbc:geneProduct fbc:id="G_b2097" fbc:label="b2097" fbc:name="fbaB" />
+ <fbc:geneProduct fbc:id="G_b2925" fbc:label="b2925" fbc:name="fbaA" />
+ <fbc:geneProduct fbc:id="G_b1779" fbc:label="b1779" fbc:name="gapA" />
+ <fbc:geneProduct fbc:id="G_b2415" fbc:label="b2415" fbc:name="ptsH" />
+ <fbc:geneProduct fbc:id="G_b1819" fbc:label="b1819" fbc:name="manZ" />
+ <fbc:geneProduct fbc:id="G_b1818" fbc:label="b1818" fbc:name="manY" />
+ <fbc:geneProduct fbc:id="G_b1621" fbc:label="b1621" fbc:name="malX" />
+ <fbc:geneProduct fbc:id="G_b2417" fbc:label="b2417" fbc:name="crr" />
+ <fbc:geneProduct fbc:id="G_b1101" fbc:label="b1101" fbc:name="ptsG" />
+ <fbc:geneProduct fbc:id="G_b2416" fbc:label="b2416" fbc:name="ptsI" />
+ <fbc:geneProduct fbc:id="G_b1817" fbc:label="b1817" fbc:name="manX" />
+ <fbc:geneProduct fbc:id="G_b0875" fbc:label="b0875" fbc:name="aqpZ" />
+ <fbc:geneProduct fbc:id="G_b3916" fbc:label="b3916" fbc:name="pfkA" />
+ <fbc:geneProduct fbc:id="G_b1723" fbc:label="b1723" fbc:name="pfkB" />
+ <fbc:geneProduct fbc:id="G_b4025" fbc:label="b4025" fbc:name="pgi" />
+ <fbc:geneProduct fbc:id="G_b2926" fbc:label="b2926" fbc:name="pgk" />
+ <fbc:geneProduct fbc:id="G_b3612" fbc:label="b3612" fbc:name="gpmM" />
+ <fbc:geneProduct fbc:id="G_b4395" fbc:label="b4395" fbc:name="ytjC" />
+ <fbc:geneProduct fbc:id="G_b0755" fbc:label="b0755" fbc:name="gpmA" />
+ <fbc:geneProduct fbc:id="G_b3493" fbc:label="b3493" fbc:name="pitA" />
+ <fbc:geneProduct fbc:id="G_b2987" fbc:label="b2987" fbc:name="pitB" />
+ <fbc:geneProduct fbc:id="G_b1854" fbc:label="b1854" fbc:name="pykA" />
+ <fbc:geneProduct fbc:id="G_b1676" fbc:label="b1676" fbc:name="pykF" />
+ <fbc:geneProduct fbc:id="G_b3919" fbc:label="b3919" fbc:name="tpiA" />
+ <fbc:geneProduct fbc:id="G_b1380" fbc:label="b1380" fbc:name="ldhA" />
+ <fbc:geneProduct fbc:id="G_b2133" fbc:label="b2133" fbc:name="dld" />
+ <fbc:geneProduct fbc:id="G_b2975" fbc:label="b2975" fbc:name="glcA" />
+ <fbc:geneProduct fbc:id="G_b3603" fbc:label="b3603" fbc:name="lldP" />
+ </fbc:listOfGeneProducts>
+ <listOfReactions>
+ <reaction fast="false" id="R_ATPM" name="ATP maintenance requirement" reversible="false" fbc:lowerFluxBound="R_ATPM_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ENO" name="enolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h_e" name="H+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2925" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1773" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2097" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1621" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1101" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2Ot" name="H2O transport via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0875" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFK" name="phosphofructokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1723" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4025" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGK" name="phosphoglycerate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2926" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGM" name="phosphoglycerate mutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4395" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3612" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0755" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PIt2r" name="phosphate reversible transport via symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2987" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3493" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYK" name="pyruvate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1854" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1676" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TPI" name="triose-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3919" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2133" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1380" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_D_LACt2" name="D_LACt2" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3603" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2975" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/cobra/test/data/textbook.xml b/cobra/test/data/textbook.xml
new file mode 100644
index 0000000..2b58204
--- /dev/null
+++ b/cobra/test/data/textbook.xml
@@ -0,0 +1,1562 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
+ <model id="textbook" fbc:strict="true">
+ <listOfUnitDefinitions>
+ <unitDefinition id="mmol_per_gDW_per_hr">
+ <listOfUnits>
+ <unit exponent="1" kind="mole" multiplier="1" scale="-3" />
+ <unit exponent="-1" kind="gram" multiplier="1" scale="0" />
+ <unit exponent="-1" kind="second" multiplier="3600" scale="0" />
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <fbc:listOfObjectives fbc:activeObjective="obj">
+ <fbc:objective fbc:id="obj" fbc:type="maximize">
+ <fbc:listOfFluxObjectives>
+ <fbc:fluxObjective fbc:coefficient="1" fbc:reaction="R_Biomass_Ecoli_core" />
+ </fbc:listOfFluxObjectives>
+ </fbc:objective>
+ </fbc:listOfObjectives>
+ <listOfParameters>
+ <parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000" />
+ <parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000" />
+ <parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0" />
+ <parameter constant="true" id="R_ATPM_upper_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="8.39" />
+ <parameter constant="true" id="R_ATPM_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="8.39" />
+ <parameter constant="true" id="R_EX_glc__D_e_lower_bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="-10" />
+ </listOfParameters>
+ <listOfCompartments>
+ <compartment constant="true" id="c" name="Cytoplasm" />
+ <compartment constant="true" id="e" name="Extracellular" />
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_13dpg_c" name="3-Phospho-D-glyceroyl phosphate" fbc:charge="-4" fbc:chemicalFormula="C3H4O10P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_2pg_c" name="D-Glycerate 2-phosphate" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_3pg_c" name="3-Phospho-D-glycerate" fbc:charge="-3" fbc:chemicalFormula="C3H4O7P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_6pgc_c" name="6-Phospho-D-gluconate" fbc:charge="-3" fbc:chemicalFormula="C6H10O10P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_6pgl_c" name="6-phospho-D-glucono-1,5-lactone" fbc:charge="-2" fbc:chemicalFormula="C6H9O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_ac_c" name="Acetate" fbc:charge="-1" fbc:chemicalFormula="C2H3O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_ac_e" name="Acetate" fbc:charge="-1" fbc:chemicalFormula="C2H3O2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_acald_c" name="Acetaldehyde" fbc:charge="0" fbc:chemicalFormula="C2H4O" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_acald_e" name="Acetaldehyde" fbc:charge="0" fbc:chemicalFormula="C2H4O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_accoa_c" name="Acetyl-CoA" fbc:charge="-4" fbc:chemicalFormula="C23H34N7O17P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_acon__C_c" name="cis-Aconitate" fbc:charge="-3" fbc:chemicalFormula="C6H3O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_actp_c" name="Acetyl phosphate" fbc:charge="-2" fbc:chemicalFormula="C2H3O5P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_adp_c" name="ADP" fbc:charge="-3" fbc:chemicalFormula="C10H12N5O10P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_akg_c" name="2-Oxoglutarate" fbc:charge="-2" fbc:chemicalFormula="C5H4O5" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_akg_e" name="2-Oxoglutarate" fbc:charge="-2" fbc:chemicalFormula="C5H4O5" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_amp_c" name="AMP" fbc:charge="-2" fbc:chemicalFormula="C10H12N5O7P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_atp_c" name="ATP" fbc:charge="-4" fbc:chemicalFormula="C10H12N5O13P3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_cit_c" name="Citrate" fbc:charge="-3" fbc:chemicalFormula="C6H5O7" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_co2_c" name="CO2" fbc:charge="0" fbc:chemicalFormula="CO2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_co2_e" name="CO2" fbc:charge="0" fbc:chemicalFormula="CO2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_coa_c" name="Coenzyme A" fbc:charge="-4" fbc:chemicalFormula="C21H32N7O16P3S" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_dhap_c" name="Dihydroxyacetone phosphate" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_e4p_c" name="D-Erythrose 4-phosphate" fbc:charge="-2" fbc:chemicalFormula="C4H7O7P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_etoh_c" name="Ethanol" fbc:charge="0" fbc:chemicalFormula="C2H6O" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_etoh_e" name="Ethanol" fbc:charge="0" fbc:chemicalFormula="C2H6O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_f6p_c" name="D-Fructose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_fdp_c" name="D-Fructose 1,6-bisphosphate" fbc:charge="-4" fbc:chemicalFormula="C6H10O12P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_for_c" name="Formate" fbc:charge="-1" fbc:chemicalFormula="CH1O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_for_e" name="Formate" fbc:charge="-1" fbc:chemicalFormula="CH1O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_fru_e" name="D-Fructose" fbc:charge="0" fbc:chemicalFormula="C6H12O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_fum_c" name="Fumarate" fbc:charge="-2" fbc:chemicalFormula="C4H2O4" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_fum_e" name="Fumarate" fbc:charge="-2" fbc:chemicalFormula="C4H2O4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_g3p_c" name="Glyceraldehyde 3-phosphate" fbc:charge="-2" fbc:chemicalFormula="C3H5O6P" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_g6p_c" name="D-Glucose 6-phosphate" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_glc__D_e" name="D-Glucose" fbc:charge="0" fbc:chemicalFormula="C6H12O6" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_gln__L_c" name="L-Glutamine" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_gln__L_e" name="L-Glutamine" fbc:charge="0" fbc:chemicalFormula="C5H10N2O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_glu__L_c" name="L-Glutamate" fbc:charge="-1" fbc:chemicalFormula="C5H8NO4" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_glu__L_e" name="L-Glutamate" fbc:charge="-1" fbc:chemicalFormula="C5H8NO4" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_glx_c" name="Glyoxylate" fbc:charge="-1" fbc:chemicalFormula="C2H1O3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_c" name="H2O" fbc:charge="0" fbc:chemicalFormula="H2O" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_e" name="H2O" fbc:charge="0" fbc:chemicalFormula="H2O" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_h_c" name="H+" fbc:charge="1" fbc:chemicalFormula="H" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_c" name="D-Lactate" fbc:charge="-1" fbc:chemicalFormula="C3H5O3" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_lac__D_e" name="D-Lactate" fbc:charge="-1" fbc:chemicalFormula="C3H5O3" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadh_c" name="Nicotinamide adenine dinucleotide - reduced" fbc:charge="-2" fbc:chemicalFormula="C21H27N7O14P2" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadp_c" name="Nicotinamide adenine dinucleotide phosphate" fbc:charge="-3" fbc:chemicalFormula="C21H25N7O17P3" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_nadph_c" name="Nicotinamide adenine dinucleotide phosphate - reduced" fbc:charge="-4" fbc:chemicalFormula="C21H26N7O17P3" />
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+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_nh4_e" name="Ammonium" fbc:charge="1" fbc:chemicalFormula="H4N" />
+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_o2_c" name="O2" fbc:charge="0" fbc:chemicalFormula="O2" />
+ <species boundaryCondition="false" compartment="e" constant="false" hasOnlySubstanceUnits="false" id="M_o2_e" name="O2" fbc:charge="0" fbc:chemicalFormula="O2" />
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+ <species boundaryCondition="false" compartment="c" constant="false" hasOnlySubstanceUnits="false" id="M_pi_c" name="Phosphate" fbc:charge="-2" fbc:chemicalFormula="HO4P" />
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+ <fbc:geneProduct fbc:id="G_b0755" fbc:label="b0755" fbc:name="gpmA" />
+ <fbc:geneProduct fbc:id="G_b2987" fbc:label="b2987" fbc:name="pitB" />
+ <fbc:geneProduct fbc:id="G_b3493" fbc:label="b3493" fbc:name="pitA" />
+ <fbc:geneProduct fbc:id="G_b3956" fbc:label="b3956" />
+ <fbc:geneProduct fbc:id="G_b3403" fbc:label="b3403" />
+ <fbc:geneProduct fbc:id="G_b1702" fbc:label="b1702" />
+ <fbc:geneProduct fbc:id="G_b2297" fbc:label="b2297" />
+ <fbc:geneProduct fbc:id="G_b2458" fbc:label="b2458" />
+ <fbc:geneProduct fbc:id="G_b1854" fbc:label="b1854" fbc:name="pykA" />
+ <fbc:geneProduct fbc:id="G_b1676" fbc:label="b1676" fbc:name="pykF" />
+ <fbc:geneProduct fbc:id="G_b3386" fbc:label="b3386" />
+ <fbc:geneProduct fbc:id="G_b4301" fbc:label="b4301" />
+ <fbc:geneProduct fbc:id="G_b4090" fbc:label="b4090" />
+ <fbc:geneProduct fbc:id="G_b2914" fbc:label="b2914" />
+ <fbc:geneProduct fbc:id="G_b0722" fbc:label="b0722" />
+ <fbc:geneProduct fbc:id="G_b0724" fbc:label="b0724" />
+ <fbc:geneProduct fbc:id="G_b0723" fbc:label="b0723" />
+ <fbc:geneProduct fbc:id="G_b0721" fbc:label="b0721" />
+ <fbc:geneProduct fbc:id="G_b0729" fbc:label="b0729" />
+ <fbc:geneProduct fbc:id="G_b0728" fbc:label="b0728" />
+ <fbc:geneProduct fbc:id="G_b2464" fbc:label="b2464" />
+ <fbc:geneProduct fbc:id="G_b0008" fbc:label="b0008" />
+ <fbc:geneProduct fbc:id="G_b2935" fbc:label="b2935" />
+ <fbc:geneProduct fbc:id="G_b2465" fbc:label="b2465" />
+ <fbc:geneProduct fbc:id="G_b3919" fbc:label="b3919" fbc:name="tpiA" />
+ </fbc:listOfGeneProducts>
+ <listOfReactions>
+ <reaction fast="false" id="R_ACALD" name="acetaldehyde dehydrogenase (acetylating)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0351" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1241" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACALDt" name="acetaldehyde reversible transport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acald_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACKr" name="acetate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2296" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1849" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3115" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONTa" name="aconitase (half-reaction A, Citrate hydro-lyase)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acon__C_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0118" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1276" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACONTb" name="aconitase (half-reaction B, Isocitrate hydro-lyase)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acon__C_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0118" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1276" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ACt2r" name="acetate reversible transport via proton symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ac_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ac_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ADK1" name="adenylate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0474" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AKGDH" name="2-Oxoglutarate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0727" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0116" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0726" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_AKGt2r" name="2-oxoglutarate reversible transport via symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2587" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ALCD2x" name="alcohol dehydrogenase (ethanol)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_acald_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0356" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1241" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1478" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ATPM" name="ATP maintenance requirement" reversible="false" fbc:lowerFluxBound="R_ATPM_lower_bound" fbc:upperFluxBound="R_ATPM_upper_bound">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_ATPS4r" name="ATP synthase (four protons for one ATP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="4" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="3" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3739" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3737" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3736" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3738" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3735" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3734" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3732" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3731" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3737" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3736" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3738" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3735" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3734" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3732" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3731" />
+ </fbc:and>
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_Biomass_Ecoli_core" name="core E. coli biomass equation (Neidhardt Based with GAM, N metabolism)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="4.9414" />
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="0.8977" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="59.81" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="0.2557" />
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="3.7478" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="0.129" />
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="0.361" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1.7867" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="0.5191" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1.496" />
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="0.205" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="13.0279" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="2.8328" />
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="59.81" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="3.547" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="0.0709" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="4.1182" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="59.81" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="3.547" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="59.81" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="13.0279" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="59.81" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="3.7478" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_CO2t" name="CO2 transporter via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CS" name="citrate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_cit_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0720" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_CYTBD" name="cytochrome oxidase bd (ubiquinol-8: 2 protons)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="0.5" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="2" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0979" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0978" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0733" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0734" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_D_LACt2" name="D-lactate transport via proton symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2975" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3603" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ENO" name="enolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ETOHt2r" name="ethanol reversible transport via proton symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_etoh_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_etoh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_EX_ac_e" name="Acetate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ac_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_acald_e" name="Acetaldehyde exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_acald_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_akg_e" name="2-Oxoglutarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_akg_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_co2_e" name="CO2 exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_co2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_etoh_e" name="Ethanol exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_etoh_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_for_e" name="Formate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fru_e" name="D-Fructose exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fru_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_fum_e" name="Fumarate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glc__D_e" name="D-Glucose exchange" reversible="true" fbc:lowerFluxBound="R_EX_glc__D_e_lower_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_gln__L_e" name="L-Glutamine exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_gln__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_glu__L_e" name="L-Glutamate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h2o_e" name="H2O exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_h_e" name="H+ exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_lac__D_e" name="D-lactate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_lac__D_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_mal__L_e" name="L-Malate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_nh4_e" name="Ammonia exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nh4_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_o2_e" name="O2 exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pi_e" name="Phosphate exchange" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_pyr_e" name="Pyruvate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_EX_succ_e" name="Succinate exchange" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_e" stoichiometry="1" />
+ </listOfReactants>
+ </reaction>
+ <reaction fast="false" id="R_FBA" name="fructose-bisphosphate aldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2925" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1773" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2097" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FBP" name="fructose-bisphosphatase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4232" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3925" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORt2" name="formate transport in via proton symport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0904" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2492" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FORti" name="formate transport via diffusion" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_for_e" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0904" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2492" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRD7" name="fumarate reductase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b4151" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4154" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4153" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4152" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FRUpts2" name="Fructose transport via PEP:Pyr PTS (f6p generating)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fru_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUM" name="fumarase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1612" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1611" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4122" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_FUMt2_2" name="Fumarate transport via proton symport (2 H)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="2" />
+ <speciesReference constant="true" species="M_fum_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_G6PDH2r" name="glucose 6-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgl_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1852" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GAPD" name="glyceraldehyde-3-phosphate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1779" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLCpts" name="D-glucose transport via PEP:Pyr PTS" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glc__D_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1621" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1818" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1819" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1817" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2415" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2417" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2416" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1101" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNS" name="glutamine synthetase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3870" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1297" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLNabc" name="L-glutamine transport via ABC system" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0811" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0810" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0809" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUDy" name="glutamate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1761" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUN" name="glutaminase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1812" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1524" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0485" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUSy" name="glutamate synthase (NADPH)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_gln__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3212" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3213" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GLUt2r" name="L-glutamate transport via proton symport, reversible" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glu__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_glu__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4077" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_GND" name="phosphogluconate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2029" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_H2Ot" name="H2O transport via diffusion" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0875" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICDHyr" name="isocitrate dehydrogenase (NADP)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_akg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1136" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ICL" name="Isocitrate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_icit_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4015" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_LDH_D" name="D-lactate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_lac__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1380" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2133" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALS" name="malate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_glx_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2976" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4014" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MALt2_2" name="Malate transport via proton symport (2 H)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="2" />
+ <speciesReference constant="true" species="M_mal__L_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_MDH" name="malate dehydrogenase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3236" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ME1" name="malic enzyme (NAD)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1479" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_ME2" name="malic enzyme (NADP)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_mal__L_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2463" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADH16" name="NADH dehydrogenase (ubiquinone-8 & 3 protons)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="4" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="3" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2285" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2284" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2281" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2287" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2276" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2283" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2288" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2282" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2286" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2277" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2278" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2280" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2279" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NADTRHD" name="NAD transhydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1602" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1603" />
+ </fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3962" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_NH4t" name="ammonia reversible transport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nh4_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nh4_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0451" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_O2t" name="o2 transport (diffusion)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_o2_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_o2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_s0001" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PDH" name="pyruvate dehydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0114" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0116" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0115" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFK" name="phosphofructokinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_fdp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3916" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1723" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PFL" name="pyruvate formate lyase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_for_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b3951" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3952" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b2579" />
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3114" />
+ </fbc:and>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0902" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0903" />
+ </fbc:and>
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGI" name="glucose-6-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_g6p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b4025" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGK" name="phosphoglycerate kinase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_13dpg_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b2926" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGL" name="6-phosphogluconolactonase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgl_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_6pgc_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b0767" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PGM" name="phosphoglycerate mutase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_2pg_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_3pg_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b4395" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3612" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0755" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PIt2r" name="phosphate reversible transport via symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2987" />
+ <fbc:geneProductRef fbc:geneProduct="G_b3493" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPC" name="phosphoenolpyruvate carboxylase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3956" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPCK" name="phosphoenolpyruvate carboxykinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_oaa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_co2_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3403" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PPS" name="phosphoenolpyruvate synthase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h2o_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_amp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b1702" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PTAr" name="phosphotransacetylase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_accoa_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_actp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2297" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2458" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYK" name="pyruvate kinase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_pep_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b1854" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1676" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_PYRt2r" name="pyruvate reversible transport via proton symport" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_pyr_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pyr_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_RPE" name="ribulose 5-phosphate 3-epimerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b3386" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4301" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_RPI" name="ribose-5-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_ru5p__D_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2914" />
+ <fbc:geneProductRef fbc:geneProduct="G_b4090" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCCt2_2" name="succinate transport via proton symport (2 H)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="2" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3528" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCCt3" name="succinate transport out via proton antiport" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_succ_e" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="1" />
+ </listOfProducts>
+ </reaction>
+ <reaction fast="false" id="R_SUCDi" name="succinate dehydrogenase (irreversible)" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_fum_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_q8h2_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0722" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0721" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0723" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0724" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_SUCOAS" name="succinyl-CoA synthetase (ADP-forming)" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_atp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succ_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_coa_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_pi_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_adp_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_succoa_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b0728" />
+ <fbc:geneProductRef fbc:geneProduct="G_b0729" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TALA" name="transaldolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b0008" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2464" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_THD2" name="NAD(P) transhydrogenase" reversible="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_nadh_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_e" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nadp_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_nadph_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_h_c" stoichiometry="2" />
+ <speciesReference constant="true" species="M_nad_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:and>
+ <fbc:geneProductRef fbc:geneProduct="G_b1602" />
+ <fbc:geneProductRef fbc:geneProduct="G_b1603" />
+ </fbc:and>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TKT1" name="transketolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_r5p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_s7p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2935" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2465" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TKT2" name="transketolase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_e4p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_xu5p__D_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_f6p_c" stoichiometry="1" />
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:or>
+ <fbc:geneProductRef fbc:geneProduct="G_b2935" />
+ <fbc:geneProductRef fbc:geneProduct="G_b2465" />
+ </fbc:or>
+ </fbc:geneProductAssociation>
+ </reaction>
+ <reaction fast="false" id="R_TPI" name="triose-phosphate isomerase" reversible="true" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+ <listOfReactants>
+ <speciesReference constant="true" species="M_dhap_c" stoichiometry="1" />
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference constant="true" species="M_g3p_c" stoichiometry="1" />
+ </listOfProducts>
+ <fbc:geneProductAssociation>
+ <fbc:geneProductRef fbc:geneProduct="G_b3919" />
+ </fbc:geneProductAssociation>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
diff --git a/cobra/test/data/update_pickles.py b/cobra/test/data/update_pickles.py
index 151453a..ddbaf99 100755
--- a/cobra/test/data/update_pickles.py
+++ b/cobra/test/data/update_pickles.py
@@ -14,7 +14,7 @@ from cobra.io import read_sbml_model, read_legacy_sbml, write_sbml_model
from cobra.io import save_matlab_model, save_json_model
from cobra.test import create_test_model
-model_names = ['salmonella', 'iJO1366',]
+model_names = ['salmonella', 'iJO1366']
for model_name in model_names:
# read in old pickle and model from sbml
diff --git a/cobra/test/flux_analysis.py b/cobra/test/flux_analysis.py
index 745137f..b10e0aa 100644
--- a/cobra/test/flux_analysis.py
+++ b/cobra/test/flux_analysis.py
@@ -4,6 +4,8 @@ from warnings import warn
import sys
from os import name
+from six import iteritems
+
try:
import numpy
except:
@@ -16,14 +18,7 @@ if __name__ == "__main__":
from cobra.manipulation import initialize_growth_medium
from cobra.solvers import solver_dict, get_solver_name
from cobra.manipulation import modify, delete
- from cobra.flux_analysis.parsimonious import optimize_minimal_flux
- from cobra.flux_analysis.variability import flux_variability_analysis
- from cobra.flux_analysis.variability import find_blocked_reactions
- from cobra.flux_analysis.single_deletion import single_deletion
- from cobra.flux_analysis.loopless import construct_loopless_model
- from cobra.external.six import iteritems
- if numpy:
- from cobra.flux_analysis.double_deletion import double_deletion
+ from cobra.flux_analysis import *
sys.path.pop(0)
else:
from . import create_test_model
@@ -31,34 +26,28 @@ else:
from ..manipulation import initialize_growth_medium
from ..solvers import solver_dict, get_solver_name
from ..manipulation import modify, delete
- from ..flux_analysis.parsimonious import optimize_minimal_flux
- from ..flux_analysis.variability import flux_variability_analysis
- from ..flux_analysis.variability import find_blocked_reactions
- from ..flux_analysis.single_deletion import single_deletion
- from ..flux_analysis.loopless import construct_loopless_model
- from ..external.six import iteritems
- if numpy:
- from ..flux_analysis.double_deletion import double_deletion
+ from ..flux_analysis import *
class TestCobraFluxAnalysis(TestCase):
"""Test the simulation functions in cobra.flux_analysis"""
def setUp(self):
- self.model = create_test_model()
+ pass
def test_pFBA(self):
- model = self.model
+ model = create_test_model("textbook")
for solver in solver_dict:
optimize_minimal_flux(model, solver=solver)
abs_x = [abs(i) for i in model.solution.x]
- self.assertAlmostEqual(model.solution.f, 0.3800, places=3)
- self.assertAlmostEqual(sum(abs_x), 343.021, places=3)
+ self.assertEqual(model.solution.status, "optimal")
+ self.assertAlmostEqual(model.solution.f, 0.8739, places=3)
+ self.assertAlmostEqual(sum(abs_x), 518.4221, places=3)
def test_modify_reversible(self):
- model1 = self.model
+ model1 = create_test_model("textbook")
model1.optimize()
- model2 = create_test_model()
+ model2 = create_test_model("textbook")
modify.convert_to_irreversible(model2)
model2.optimize()
self.assertAlmostEqual(model1.solution.f, model2.solution.f, places=3)
@@ -68,18 +57,18 @@ class TestCobraFluxAnalysis(TestCase):
# Ensure revert_to_reversible is robust to solutions generated both
# before and after reversibility conversion, or not solved at all.
- model3 = create_test_model()
+ model3 = create_test_model("textbook")
model3.optimize()
modify.convert_to_irreversible(model3)
modify.revert_to_reversible(model3)
self.assertAlmostEqual(model1.solution.f, model3.solution.f, places=3)
- model4 = create_test_model()
+ model4 = create_test_model("textbook")
modify.convert_to_irreversible(model4)
modify.revert_to_reversible(model4)
def test_gene_knockout_computation(self):
- cobra_model = self.model
+ cobra_model = create_test_model()
# helper functions for running tests
delete_model_genes = delete.delete_model_genes
@@ -155,147 +144,159 @@ class TestCobraFluxAnalysis(TestCase):
test_computation(test_model, ["try:'"], set())
test_computation(test_model, ["try:'", "'except:1"], {"test1"})
- def test_single_deletion(self):
- cobra_model = self.model
- initialize_growth_medium(cobra_model, 'LB')
-
- # Expected growth rates for the salmonella model with deletions in LB
- the_loci = ['STM4081', 'STM0247', 'STM3867', 'STM2952']
- the_genes = tpiA, metN, atpA, eno = map(cobra_model.genes.get_by_id,
- the_loci)
- id_to_name = dict([(x.id, x.name) for x in the_genes])
- growth_dict = {'fba': {tpiA.id: 2.41, metN.id: 2.44,
- atpA.id: 1.87, eno.id: 1.81},
- 'moma': {tpiA.id: 1.62, metN.id: 2.4,
- atpA.id: 1.40, eno.id: 0.33}}
+ def test_single_gene_deletion(self):
+ cobra_model = create_test_model("textbook")
+ # expected knockouts for textbook model
+ growth_dict = {"fba": {"b0008": 0.87, "b0114": 0.80, "b0116": 0.78,
+ "b2276": 0.21, "b1779": 0.00},
+ "moma": {"b0008": 0.87, "b0114": 0.73, "b0116": 0.59,
+ "b2276": 0.11, "b1779": 0.00},
+ }
# MOMA requires cplex or gurobi
try:
get_solver_name(qp=True)
except:
growth_dict.pop('moma')
- for method, the_growth_rates in growth_dict.items():
- element_list = the_growth_rates.keys()
- results = single_deletion(cobra_model, element_list=element_list,
- method=method)
- rates = results[0]
- statuses = results[1]
-
- for the_gene in element_list:
- self.assertEqual(statuses[the_gene], 'optimal')
- self.assertAlmostEqual(rates[the_gene],
- the_growth_rates[the_gene],
- places=2)
+ for method, expected in growth_dict.items():
+ rates, statuses = single_gene_deletion(cobra_model,
+ gene_list=expected.keys(),
+ method=method)
+ for gene, expected_value in iteritems(expected):
+ self.assertEqual(statuses[gene], 'optimal')
+ self.assertAlmostEqual(rates[gene], expected_value, places=2)
def test_single_reaction_deletion(self):
- cobra_model = self.model
- results, status = single_deletion(
- cobra_model, element_list=cobra_model.reactions[100:110:2],
- element_type="reaction")
- self.assertEqual(len(results), 5)
- self.assertEqual(len(status), 5)
+ cobra_model = create_test_model("textbook")
+ expected_results = {'FBA': 0.70404, 'FBP': 0.87392, 'CS': 0,
+ 'FUM': 0.81430, 'GAPD': 0, 'GLUDy': 0.85139}
+
+ results, status = single_reaction_deletion(
+ cobra_model, reaction_list=expected_results.keys())
+ self.assertEqual(len(results), 6)
+ self.assertEqual(len(status), 6)
for status_value in status.values():
self.assertEqual(status_value, "optimal")
- expected_results = {'3OAS140': 0, '3OAS160': 0.38001,
- '3OAS180': 0.38001, '3OAS60': 0,
- '3PEPTabcpp': 0.38001}
for reaction, value in results.items():
self.assertAlmostEqual(value, expected_results[reaction], 5)
+ def compare_matrices(self, matrix1, matrix2, places=3):
+ nrows = len(matrix1)
+ ncols = len(matrix1[0])
+ self.assertEqual(nrows, len(matrix2))
+ self.assertEqual(ncols, len(matrix2[0]))
+ for i in range(nrows):
+ for j in range(ncols):
+ self.assertAlmostEqual(matrix1[i][j], matrix2[i][j],
+ places=places)
+
+ @skipIf(numpy is None, "double deletions require numpy")
+ def test_double_gene_deletion(self):
+ cobra_model = create_test_model("textbook")
+ genes = ["b0726", "b4025", "b0724", "b0720",
+ "b2935", "b2935", "b1276", "b1241"]
+ growth_list = [
+ [0.858, 0.857, 0.814, 0.000, 0.858, 0.858, 0.858, 0.858],
+ [0.857, 0.863, 0.739, 0.000, 0.863, 0.863, 0.863, 0.863],
+ [0.814, 0.739, 0.814, 0.000, 0.814, 0.814, 0.814, 0.814],
+ [0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000],
+ [0.858, 0.863, 0.814, 0.000, 0.874, 0.874, 0.874, 0.874],
+ [0.858, 0.863, 0.814, 0.000, 0.874, 0.874, 0.874, 0.874],
+ [0.858, 0.863, 0.814, 0.000, 0.874, 0.874, 0.874, 0.874],
+ [0.858, 0.863, 0.814, 0.000, 0.874, 0.874, 0.874, 0.874]]
+ solution = double_gene_deletion(cobra_model, gene_list1=genes)
+ self.assertEqual(solution["x"], genes)
+ self.assertEqual(solution["y"], genes)
+ self.compare_matrices(growth_list, solution["data"])
+ # test when lists differ slightly
+ solution = double_gene_deletion(cobra_model, gene_list1=genes[:-1],
+ gene_list2=genes,
+ number_of_processes=1)
+ self.assertEqual(solution["x"], genes[:-1])
+ self.assertEqual(solution["y"], genes)
+ self.compare_matrices(growth_list[:-1], solution["data"])
+
@skipIf(numpy is None, "double deletions require numpy")
- def test_double_deletion(self):
- cobra_model = self.model
- # turn into a double deletion unit test
- initialize_growth_medium(cobra_model, 'LB')
- # Expected growth rates for the salmonella model with deletions in LB
- the_loci = ['STM4081', 'STM0247', 'STM3867', 'STM2952']
- the_genes = list(map(cobra_model.genes.get_by_id, the_loci))
- growth_dict = {}
- growth_list = [[2.41, 2.389, 1.775, 1.81],
- [2.389, 2.437, 1.86, 1.79],
- [1.775, 1.86, 1.87, 1.3269],
- [1.81, 1.79, 1.3269, 1.81]]
- for the_gene, the_rates in zip(the_genes, growth_list):
- growth_dict[the_gene] = dict(zip(the_genes, the_rates))
-
- the_solution = double_deletion(cobra_model, element_list_1=the_genes,
- element_list_2=the_genes)
- # Potential problem if the data object doesn't have a tolist function
- s_data = the_solution['data'].tolist()
- s_x = the_solution['x']
- s_y = the_solution['y']
- for gene_x, rates_x in zip(s_x, s_data):
- for gene_y, the_rate in zip(s_y, rates_x):
- self.assertAlmostEqual(
- growth_dict[gene_x][gene_y], the_rate, places=2,
- msg="%.3f != %.3f for (%s, %s)" %
- (growth_dict[gene_x][gene_y], the_rate,
- gene_x.id, gene_y.id))
+ def test_double_reaction_deletion(self):
+ cobra_model = create_test_model("textbook")
+ reactions = ['FBA', 'ATPS4r', 'ENO', 'FRUpts2']
+ growth_list = [[0.704, 0.135, 0.000, 0.704],
+ [0.135, 0.374, 0.000, 0.374],
+ [0.000, 0.000, 0.000, 0.000],
+ [0.704, 0.374, 0.000, 0.874]]
+
+ solution = double_reaction_deletion(cobra_model,
+ reaction_list1=reactions,
+ number_of_processes=1)
+ self.assertEqual(solution["x"], reactions)
+ self.assertEqual(solution["y"], reactions)
+ self.compare_matrices(growth_list, solution["data"])
def test_flux_variability(self):
fva_results = {
- '5DGLCNtex': {'minimum': 0.0, 'maximum': 0.0},
- 'ABTA': {'minimum': 0.0, 'maximum': 0.0},
- '5DOAN': {'minimum': 0.0, 'maximum': 0.0},
- 'A5PISO': {'minimum': 0.00692, 'maximum': 0.00692},
- 'AACPS1': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS2': {'minimum': 0.0, 'maximum': 0.0},
- 'ACALDtex': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS3': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS4': {'minimum': 0.0, 'maximum': 0.0},
- 'ABUTD': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS5': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS6': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS7': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS8': {'minimum': 0.0, 'maximum': 0.0},
- 'AACPS9': {'minimum': 0.0, 'maximum': 0.0},
- 'AACTOOR': {'minimum': 0.0, 'maximum': 0.0},
- 'ABUTt2pp': {'minimum': 0.0, 'maximum': 0.0},
- '3OAS140': {'minimum': 0.50419, 'maximum': 0.50419},
- '3OAS141': {'minimum': 0.03748, 'maximum': 0.03748},
- '3OAS160': {'minimum': 0.41769, 'maximum': 0.41769},
- '3OAS161': {'minimum': 0.03748, 'maximum': 0.03748},
- '3OAS180': {'minimum': 0.01071, 'maximum': 0.01071},
- '3OAS181': {'minimum': 0.01606, 'maximum': 0.01606},
- 'ABUTtex': {'minimum': 0.0, 'maximum': 0.0},
- '3OAS60': {'minimum': 0.54399, 'maximum': 0.54399},
- '3OAS80': {'minimum': 0.54399, 'maximum': 0.54399},
- 'AAMYL': {'minimum': 0.0, 'maximum': 0.0},
- '3PEPTabcpp': {'minimum': 0.0, 'maximum': 0.0},
- '3PEPTtex': {'minimum': 0.0, 'maximum': 0.0},
- '3UMPtex': {'minimum': 0.0, 'maximum': 0.0},
- '4HOXPACDtex': {'minimum': 0.0, 'maximum': 0.0},
- 'ACACtex': {'minimum': 0.0, 'maximum': 0.0},
- '4PCP': {'minimum': 0.0, 'maximum': 0.0},
- '4PCPpp': {'minimum': 0.0, 'maximum': 0.0},
- 'AAMYLpp': {'minimum': 0.0, 'maximum': 0.0},
- '4PEPTabcpp': {'minimum': 0.0, 'maximum': 0.0},
- '4PEPTtex': {'minimum': 0.0, 'maximum': 0.0},
- '5DGLCNR': {'minimum': 0.0, 'maximum': 0.0},
- '5DGLCNt2rpp': {'minimum': 0.0, 'maximum': 0.0},
- 'ACALD': {'minimum': 3.35702, 'maximum': 7.49572}}
-
- infeasible_model = create_test_model()
- infeasible_model.reactions.get_by_id("EX_glyc_e").lower_bound = 0
+ 'ACALDt': {'minimum': 0.00000, 'maximum': 0.00000},
+ 'ACONTb': {'minimum': 6.00725, 'maximum': 6.00725},
+ 'AKGDH': {'minimum': 5.06438, 'maximum': 5.06438},
+ 'ATPM': {'minimum': 8.39000, 'maximum': 8.39000},
+ 'CO2t': {'minimum': -22.80983, 'maximum': -22.80983},
+ 'D_LACt2': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'EX_ac_e': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'EX_co2_e': {'minimum': 22.80983, 'maximum': 22.80983},
+ 'EX_fru_e': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'EX_gln__L_e': {'minimum': 0.00000, 'maximum': 0.00000},
+ 'EX_h_e': {'minimum': 17.53087, 'maximum': 17.53087},
+ 'EX_nh4_e': {'minimum': -4.76532, 'maximum': -4.76532},
+ 'EX_pyr_e': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'FBP': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'FRD7': {'minimum': 0.00000, 'maximum': 994.93562},
+ 'FUMt2_2': {'minimum': 0.00000, 'maximum': 0.00000},
+ 'GLCpts': {'minimum': 10.00000, 'maximum': 10.00000},
+ 'GLUDy': {'minimum': -4.54186, 'maximum': -4.54186},
+ 'GLUt2r': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'ICDHyr': {'minimum': 6.00725, 'maximum': 6.00725},
+ 'MALS': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'ME1': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'NADTRHD': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'PDH': {'minimum': 9.28253, 'maximum': 9.28253},
+ 'PGI': {'minimum': 4.86086, 'maximum': 4.86086},
+ 'PGM': {'minimum': -14.71614, 'maximum': -14.71614},
+ 'PPCK': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'PYK': {'minimum': 1.75818, 'maximum': 1.75818},
+ 'RPI': {'minimum': -2.28150, 'maximum': -2.28150},
+ 'SUCDi': {'minimum': 5.06438, 'maximum': 1000.00000},
+ 'THD2': {'minimum': 0.00000, 'maximum': -0.00000},
+ 'TPI': {'minimum': 7.47738, 'maximum': 7.47738},
+ }
+
+ infeasible_model = create_test_model("textbook")
+ infeasible_model.reactions.get_by_id("EX_glc__D_e").lower_bound = 0
for solver in solver_dict:
- cobra_model = create_test_model()
- initialize_growth_medium(cobra_model, 'LB')
+ # esolver is really slow
+ if solver == "esolver":
+ continue
+ cobra_model = create_test_model("textbook")
fva_out = flux_variability_analysis(
cobra_model, solver=solver,
- reaction_list=cobra_model.reactions[100:140:2])
- for the_reaction, the_range in iteritems(fva_out):
- for k, v in iteritems(the_range):
- self.assertAlmostEqual(fva_results[the_reaction][k], v,
- places=5)
+ reaction_list=cobra_model.reactions[1::3])
+ for name, result in iteritems(fva_out):
+ for k, v in iteritems(result):
+ self.assertAlmostEqual(fva_results[name][k], v, places=5)
+
# ensure that an infeasible model does not run FVA
self.assertRaises(ValueError, flux_variability_analysis,
infeasible_model, solver=solver)
def test_find_blocked_reactions(self):
- m = self.model
- result = find_blocked_reactions(m, reaction_list=m.reactions[:10])
- self.assertEqual(len(result), 1)
- self.assertEqual(result[0], '12PPDStex')
+ m = create_test_model("textbook")
+ result = find_blocked_reactions(m, m.reactions[40:46])
+ self.assertEqual(result, ['FRUpts2'])
+
+ result = find_blocked_reactions(m, m.reactions[42:48])
+ self.assertEqual(set(result), {'FUMt2_2', 'FRUpts2'})
+
+ result = find_blocked_reactions(m, m.reactions[30:50],
+ open_exchanges=True)
+ self.assertEqual(result, [])
def test_loopless(self):
try:
@@ -327,6 +328,84 @@ class TestCobraFluxAnalysis(TestCase):
self.assertEqual(feasible_sol.status, "optimal")
self.assertEqual(infeasible_sol.status, "infeasible")
+ def test_gapfilling(self):
+ try:
+ solver = get_solver_name(mip=True)
+ except:
+ self.skip("no MILP solver found")
+ m = Model()
+ m.add_metabolites(map(Metabolite, ["a", "b", "c"]))
+ r = Reaction("EX_A")
+ m.add_reaction(r)
+ r.add_metabolites({m.metabolites.a: 1})
+ r = Reaction("r1")
+ m.add_reaction(r)
+ r.add_metabolites({m.metabolites.b: -1, m.metabolites.c: 1})
+ r = Reaction("DM_C")
+ m.add_reaction(r)
+ r.add_metabolites({m.metabolites.c: -1})
+ r.objective_coefficient = 1
+
+ U = Model()
+ r = Reaction("a2b")
+ U.add_reaction(r)
+ r.build_reaction_from_string("a --> b", verbose=False)
+ r = Reaction("a2d")
+ U.add_reaction(r)
+ r.build_reaction_from_string("a --> d", verbose=False)
+
+ result = gapfilling.growMatch(m, U)[0]
+ self.assertEqual(len(result), 1)
+ self.assertEqual(result[0].id, "a2b")
+
+ # 2 rounds with exchange reactions
+ result = gapfilling.growMatch(m, None, ex_rxns=True, iterations=2)
+ self.assertEqual(len(result), 2)
+ self.assertEqual(len(result[0]), 1)
+ self.assertEqual(len(result[1]), 1)
+ self.assertEqual({i[0].id for i in result},
+ {"SMILEY_EX_b", "SMILEY_EX_c"})
+
+ def test_remove_genes(self):
+ m = Model("test")
+ m.add_reactions([Reaction("r" + str(i + 1)) for i in range(8)])
+ self.assertEqual(len(m.reactions), 8)
+ rxns = m.reactions
+ rxns.r1.gene_reaction_rule = "(a and b) or (c and a)"
+ rxns.r2.gene_reaction_rule = "(a and b and d and e)"
+ rxns.r3.gene_reaction_rule = "(a and b) or (b and c)"
+ rxns.r4.gene_reaction_rule = "(f and b) or (b and c)"
+ rxns.r5.gene_reaction_rule = "x"
+ rxns.r6.gene_reaction_rule = "y"
+ rxns.r7.gene_reaction_rule = "x or z"
+ rxns.r8.gene_reaction_rule = ""
+ self.assertIn("a", m.genes)
+ self.assertIn("x", m.genes)
+ delete.remove_genes(m, ["a"], remove_reactions=False)
+ self.assertNotIn("a", m.genes)
+ self.assertIn("x", m.genes)
+ self.assertEqual(rxns.r1.gene_reaction_rule, "")
+ self.assertEqual(rxns.r2.gene_reaction_rule, "")
+ self.assertEqual(rxns.r3.gene_reaction_rule, "b and c")
+ self.assertEqual(rxns.r4.gene_reaction_rule, "(f and b) or (b and c)")
+ self.assertEqual(rxns.r5.gene_reaction_rule, "x")
+ self.assertEqual(rxns.r6.gene_reaction_rule, "y")
+ self.assertEqual(rxns.r7.genes, {m.genes.x, m.genes.z})
+ self.assertEqual(rxns.r8.gene_reaction_rule, "")
+ delete.remove_genes(m, ["x"], remove_reactions=True)
+ self.assertEqual(len(m.reactions), 7)
+ self.assertNotIn("r5", m.reactions)
+ self.assertNotIn("x", m.genes)
+ self.assertEqual(rxns.r1.gene_reaction_rule, "")
+ self.assertEqual(rxns.r2.gene_reaction_rule, "")
+ self.assertEqual(rxns.r3.gene_reaction_rule, "b and c")
+ self.assertEqual(rxns.r4.gene_reaction_rule, "(f and b) or (b and c)")
+ self.assertEqual(rxns.r6.gene_reaction_rule, "y")
+ self.assertEqual(rxns.r7.gene_reaction_rule, "z")
+ self.assertEqual(rxns.r7.genes, {m.genes.z})
+ self.assertEqual(rxns.r8.gene_reaction_rule, "")
+
+
# make a test suite to run all of the tests
loader = TestLoader()
suite = loader.loadTestsFromModule(sys.modules[__name__])
diff --git a/cobra/test/io_tests.py b/cobra/test/io_tests.py
index e86d202..fe97398 100644
--- a/cobra/test/io_tests.py
+++ b/cobra/test/io_tests.py
@@ -9,16 +9,10 @@ import sys
if __name__ == "__main__":
from cobra import io
- from cobra.test import data_directory, create_test_model
- from cobra.test import ecoli_mat, ecoli_pickle, ecoli_json
- from cobra.test import salmonella_sbml, salmonella_pickle
- from cobra.test import salmonella_fbc_sbml
+ from cobra.test import data_directory
else:
from .. import io
- from . import data_directory, create_test_model
- from . import ecoli_mat, ecoli_pickle, ecoli_json
- from . import salmonella_sbml, salmonella_pickle
- from . import salmonella_fbc_sbml
+ from . import data_directory
libraries = ["scipy", "libsbml", "cPickle"]
for library in libraries:
@@ -27,6 +21,9 @@ for library in libraries:
except ImportError:
exec("%s = None" % library)
+with open(join(data_directory, "mini.pickle"), "rb") as infile:
+ mini_model = load(infile)
+
class TestCobraIO(object):
def compare_models(self, model1, model2):
@@ -50,8 +47,8 @@ class TestCobraIO(object):
getattr(model2.metabolites[-1], attr))
self.assertEqual(len(model1.reactions[0].metabolites),
len(model2.reactions[0].metabolites))
- self.assertEqual(len(model1.reactions[20].metabolites),
- len(model2.reactions[20].metabolites))
+ self.assertEqual(len(model1.reactions[14].metabolites),
+ len(model2.reactions[14].metabolites))
self.assertEqual(len(model1.reactions[-1].metabolites),
len(model2.reactions[-1].metabolites))
# ensure they have the same solution max
@@ -76,38 +73,47 @@ class TestCobraIO(object):
unlink(test_output_filename)
- at skipIf(not libsbml, "libsbml required")
-class TestCobraIOSBML(TestCase, TestCobraIO):
+class TestCobraIOSBMLfbc2(TestCase, TestCobraIO):
def setUp(self):
- self.test_model = create_test_model()
- self.test_file = salmonella_sbml
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini_fbc2.xml")
self.read_function = io.read_sbml_model
self.write_function = io.write_sbml_model
@skipIf(not libsbml, "libsbml required")
-class TestCobraIOSBMLfbc(TestCase, TestCobraIO):
+class TestCobraIOSBMLfbc1(TestCase, TestCobraIO):
def setUp(self):
- self.test_model = create_test_model()
- self.test_file = salmonella_fbc_sbml
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini_fbc1.xml")
self.read_function = io.read_sbml_model
- self.write_function = partial(io.write_sbml_model,
+ self.write_function = partial(io.write_legacy_sbml,
use_fbc_package=True)
+ at skipIf(not libsbml, "libsbml required")
+class TestCobraIOSBMLcobra(TestCase, TestCobraIO):
+ def setUp(self):
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini_cobra.xml")
+ self.read_function = io.read_sbml_model
+ self.write_function = partial(io.write_sbml_model,
+ use_fbc_package=False)
+
+
@skipIf(not scipy, "scipy required")
class TestCobraIOmat(TestCase, TestCobraIO):
def setUp(self):
- self.test_model = create_test_model(ecoli_pickle)
- self.test_file = ecoli_mat
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini.mat")
self.read_function = io.load_matlab_model
self.write_function = io.save_matlab_model
class TestCobraIOjson(TestCase, TestCobraIO):
def setUp(self):
- self.test_model = create_test_model(ecoli_pickle)
- self.test_file = ecoli_json
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini.json")
self.read_function = io.load_json_model
self.write_function = io.save_json_model
@@ -127,8 +133,8 @@ class TestCobraIOjson(TestCase, TestCobraIO):
class TestCobraIOPickle(TestCase, TestCobraIO):
def setUp(self):
- self.test_model = create_test_model()
- self.test_file = salmonella_pickle
+ self.test_model = mini_model
+ self.test_file = join(data_directory, "mini.pickle")
self.load = load
self.dump = dump
diff --git a/cobra/test/solvers.py b/cobra/test/solvers.py
index 2d62a09..ceed550 100644
--- a/cobra/test/solvers.py
+++ b/cobra/test/solvers.py
@@ -3,13 +3,11 @@ import sys
# deal with absolute imports by adding the appropriate directory to the path
if __name__ == "__main__":
sys.path.insert(0, "../..")
- from cobra.manipulation import initialize_growth_medium
from cobra.test import create_test_model
from cobra import Model, Reaction, Metabolite
from cobra import solvers
sys.path.pop(0) # remove the added directory to the path
else:
- from ..manipulation import initialize_growth_medium
from . import create_test_model
from .. import Model, Reaction, Metabolite
from .. import solvers
@@ -23,9 +21,8 @@ except:
class TestCobraSolver(object):
def setUp(self):
self.solver = solvers.solver_dict[self.solver_name]
- self.model = create_test_model()
- initialize_growth_medium(self.model, 'MgM')
- self.old_solution = 0.320064
+ self.model = create_test_model("textbook")
+ self.old_solution = 0.8739215
self.infeasible_model = Model()
metabolite_1 = Metabolite("met1")
reaction_1 = Reaction("rxn1")
@@ -107,7 +104,9 @@ class TestCobraSolver(object):
max_solution = solver.format_solution(maximize, self.model)
min_solution = solver.format_solution(minimize, self.model)
self.assertAlmostEqual(0, min_solution.f, places=4)
+ self.assertEqual(min_solution.status, "optimal")
self.assertAlmostEqual(self.old_solution, max_solution.f, places=4)
+ self.assertEqual(max_solution.status, "optimal")
# if we set minimize at creation, can we override it at solve
solver.solve_problem(minimize, objective_sense="maximize")
override_minimize = solver.format_solution(minimize, self.model)
@@ -214,10 +213,10 @@ class TestCobraSolver(object):
m = Model()
m.add_reactions([x, y])
# test that optimal values are at the vertices
- m.change_objective("x")
+ m.objective = "x"
self.assertAlmostEqual(solver.solve(m).f, 1.0)
self.assertAlmostEqual(solver.solve(m).x_dict["y"], 2.0)
- m.change_objective("y")
+ m.objective = "y"
self.assertAlmostEqual(solver.solve(m).f, 3.0)
self.assertAlmostEqual(solver.solve(m, objective_sense="minimize").f,
1.0)
@@ -244,6 +243,7 @@ class TestCobraSolver(object):
solver.set_quadratic_objective(lp, quadratic_obj)
solver.solve_problem(lp, objective_sense="minimize")
solution = solver.format_solution(lp, m)
+ self.assertEqual(solution.status, "optimal")
# Respecting linear objectives also makes the objective value 1.
self.assertAlmostEqual(solution.f, 1.)
self.assertAlmostEqual(solution.x_dict["y"], 1.)
@@ -253,10 +253,12 @@ class TestCobraSolver(object):
solver.change_variable_objective(lp, 1, 0.)
solver.solve_problem(lp, objective_sense="minimize")
solution = solver.format_solution(lp, m)
+ self.assertEqual(solution.status, "optimal")
self.assertAlmostEqual(solution.f, 2.)
# test quadratic from solve function
solution = solver.solve(m, quadratic_component=quadratic_obj,
objective_sense="minimize")
+ self.assertEqual(solution.status, "optimal")
self.assertAlmostEqual(solution.f, 1.)
c._bound = 6
z = Reaction("z")
@@ -268,10 +270,11 @@ class TestCobraSolver(object):
solution = solver.solve(m, quadratic_component=scipy.sparse.eye(3),
objective_sense="minimize")
# should be 12 not 24 because 1/2 (V^T Q V)
+ self.assertEqual(solution.status, "optimal")
self.assertAlmostEqual(solution.f, 6)
- self.assertAlmostEqual(solution.x_dict["x"], 2)
- self.assertAlmostEqual(solution.x_dict["y"], 2)
- self.assertAlmostEqual(solution.x_dict["z"], 2)
+ self.assertAlmostEqual(solution.x_dict["x"], 2, places=6)
+ self.assertAlmostEqual(solution.x_dict["y"], 2, places=6)
+ self.assertAlmostEqual(solution.x_dict["z"], 2, places=6)
for solver_name in solvers.solver_dict:
exec('class %sTester(TestCobraSolver, TestCase): None' % solver_name)
diff --git a/cobra/test/unit_tests.py b/cobra/test/unit_tests.py
index f6f7003..0b51faf 100644
--- a/cobra/test/unit_tests.py
+++ b/cobra/test/unit_tests.py
@@ -2,18 +2,15 @@ import sys
from unittest import TestCase, TestLoader, TextTestRunner, skipIf
from copy import copy, deepcopy
from pickle import loads, dumps, HIGHEST_PROTOCOL
+import warnings
if __name__ == "__main__":
sys.path.insert(0, "../..")
- from cobra.test import data_directory, create_test_model
- from cobra.test import ecoli_mat, ecoli_pickle
- from cobra.test import salmonella_sbml, salmonella_pickle
+ from cobra.test import create_test_model
from cobra import Object, Model, Metabolite, Reaction, DictList
sys.path.pop(0)
else:
- from . import data_directory, create_test_model
- from . import ecoli_mat, ecoli_pickle
- from . import salmonella_sbml, salmonella_pickle
+ from . import create_test_model
from .. import Object, Model, Metabolite, Reaction, DictList
# libraries which may or may not be installed
@@ -42,6 +39,9 @@ class TestDictList(TestCase):
self.assertEqual(self.list.index(self.obj), 0)
self.assertRaises(ValueError, self.list.index, "f")
self.assertRaises(ValueError, self.list.index, Object("f"))
+ # ensure trying to index with an object that is a different object
+ # also raises an error
+ self.assertRaises(ValueError, self.list.index, Object("test1"))
def testIndependent(self):
a = DictList([Object("o1"), Object("o2")])
@@ -58,9 +58,18 @@ class TestDictList(TestCase):
self.assertRaises(ValueError, self.list.append, Object("test1"))
self.assertEqual(self.list.index(obj2), 1)
self.assertEqual(self.list[1], obj2)
- self.assertEqual(self.list.get_by_id("test2"), obj2)
+ self.assertIs(self.list.get_by_id("test2"), obj2)
self.assertEqual(len(self.list), 2)
+ def testInsert(self):
+ obj2 = Object("a")
+ self.list.insert(0, obj2)
+ self.assertEqual(self.list.index(obj2), 0)
+ self.assertEqual(self.list.index("test1"), 1)
+ self.assertIs(self.list.get_by_id("a"), obj2)
+ self.assertEqual(len(self.list), 2)
+ self.assertRaises(ValueError, self.list.append, obj2)
+
def testExtend(self):
obj_list = [Object("test%d" % (i)) for i in range(2, 10)]
self.list.extend(obj_list)
@@ -171,14 +180,21 @@ class TestDictList(TestCase):
del obj_list[3]
self.assertNotIn("test5", obj_list)
self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
+ self.assertEqual(len(obj_list), 7)
del obj_list[3:5]
self.assertNotIn("test6", obj_list)
self.assertNotIn("test7", obj_list)
self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
+ self.assertEqual(len(obj_list), 5)
removed = obj_list.pop(1)
self.assertEqual(obj_list.index(obj_list[-1]), len(obj_list) - 1)
self.assertEqual(removed.id, "test3")
self.assertNotIn("test3", obj_list)
+ self.assertEqual(len(obj_list), 4)
+ removed = obj_list.pop()
+ self.assertEqual(removed.id, "test9")
+ self.assertNotIn(removed.id, obj_list)
+ self.assertEqual(len(obj_list), 3)
def testSet(self):
obj_list = DictList(Object("test%d" % (i)) for i in range(10))
@@ -198,7 +214,7 @@ class TestDictList(TestCase):
class CobraTestCase(TestCase):
def setUp(self):
- self.model = create_test_model()
+ self.model = create_test_model("textbook")
self.model_class = Model
@@ -256,8 +272,20 @@ class TestReactions(CobraTestCase):
reaction.subtract_metabolites(reaction.metabolites)
self.assertEqual(len(reaction.metabolites), 0)
+ def test_mass_balance(self):
+ model = self.model
+ reaction = model.reactions.get_by_id("PGI")
+ # should be balanced now
+ self.assertEqual(len(reaction.check_mass_balance()), 0)
+ # should not be balanced after adding a hydrogen
+ reaction.add_metabolites({model.metabolites.get_by_id("h_c"): 1})
+ imbalance = reaction.check_mass_balance()
+ self.assertIn("H", imbalance)
+ self.assertEqual(imbalance["H"], 1)
+
def test_build_from_string(self):
model = self.model
+ m = len(model.metabolites)
pgi = model.reactions.get_by_id("PGI")
pgi.reaction = "g6p_c --> f6p_c"
self.assertEqual(pgi.lower_bound, 0)
@@ -269,7 +297,15 @@ class TestReactions(CobraTestCase):
self.assertNotIn(model.metabolites.h2o_c, pgi._metabolites)
self.assertIn("foo", model.metabolites)
self.assertIn(model.metabolites.foo, pgi._metabolites)
- self.assertEqual(len(model.metabolites), 1803)
+ self.assertEqual(len(model.metabolites), m + 1)
+
+
+class TestCobraMetabolites(CobraTestCase):
+ def test_metabolite_formula(self):
+ met = Metabolite("water")
+ met.formula = "H2O"
+ self.assertEqual(met.elements, {"H": 2, "O": 1})
+ self.assertEqual(met.formula_weight, 18.01528)
class TestCobraModel(CobraTestCase):
@@ -321,7 +357,7 @@ class TestCobraModel(CobraTestCase):
other = model.copy()
for i in other.reactions:
i.id += "_other"
- other.reactions._generate_index()
+ other.repair()
model.add_reactions(other.reactions)
def test_model_remove_reaction(self):
@@ -412,7 +448,9 @@ class TestCobraModel(CobraTestCase):
def test_remove_gene(self):
target_gene = self.model.genes[0]
gene_reactions = list(target_gene.reactions)
- target_gene.remove_from_model()
+ with warnings.catch_warnings():
+ warnings.simplefilter("ignore")
+ target_gene.remove_from_model()
self.assertEqual(target_gene.model, None)
# make sure the reaction was removed from the model
self.assertNotIn(target_gene, self.model.genes)
@@ -473,42 +511,51 @@ class TestCobraModel(CobraTestCase):
'when running Model.add_reactions')
def test_change_objective(self):
- biomass = self.model.reactions.get_by_id("biomass_iRR1083_metals")
+ biomass = self.model.reactions.get_by_id("Biomass_Ecoli_core")
atpm = self.model.reactions.get_by_id("ATPM")
- self.model.change_objective(atpm.id)
+ self.model.objective = atpm.id
self.assertEqual(atpm.objective_coefficient, 1.)
self.assertEqual(biomass.objective_coefficient, 0.)
+ self.assertEqual(self.model.objective, {atpm: 1.})
# change it back using object itself
- self.model.change_objective(biomass)
+ self.model.objective = biomass
self.assertEqual(atpm.objective_coefficient, 0.)
self.assertEqual(biomass.objective_coefficient, 1.)
# set both to 1 with a list
- self.model.change_objective([atpm, biomass])
+ self.model.objective = [atpm, biomass]
self.assertEqual(atpm.objective_coefficient, 1.)
self.assertEqual(biomass.objective_coefficient, 1.)
# set both using a dict
- self.model.change_objective({atpm: 0.2, biomass: 0.3})
+ self.model.objective = {atpm: 0.2, biomass: 0.3}
self.assertEqual(atpm.objective_coefficient, 0.2)
self.assertEqual(biomass.objective_coefficient, 0.3)
+ # test setting by index
+ self.model.objective = self.model.reactions.index(atpm)
+ self.assertEqual(self.model.objective, {atpm: 1.})
+ # test by setting list of indexes
+ self.model.objective = map(self.model.reactions.index, [atpm, biomass])
+ self.assertEqual(self.model.objective, {atpm: 1., biomass: 1.})
@skipIf(scipy is None, "scipy required for ArrayBasedModel")
class TestCobraArrayModel(TestCobraModel):
def setUp(self):
- model = create_test_model().to_array_based_model()
+ model = create_test_model("textbook").to_array_based_model()
self.model_class = model.__class__
self.model = model
def test_array_based_model(self):
+ m = len(self.model.metabolites)
+ n = len(self.model.reactions)
assertEqual = self.assertEqual # alias
for matrix_type in ["scipy.dok_matrix", "scipy.lil_matrix"]:
- model = create_test_model().\
+ model = create_test_model("textbook").\
to_array_based_model(matrix_type=matrix_type)
- self.assertEqual(model.S[1605, 0], -1)
- self.assertEqual(model.S[43, 0], 0)
+ assertEqual(model.S[7, 0], -1)
+ assertEqual(model.S[43, 0], 0)
model.S[43, 0] = 1
- self.assertEqual(model.S[43, 0], 1)
- self.assertEqual(
+ assertEqual(model.S[43, 0], 1)
+ assertEqual(
model.reactions[0].metabolites[model.metabolites[43]], 1)
model.S[43, 0] = 0
assertEqual(model.lower_bounds[0], model.reactions[0].lower_bound)
@@ -524,20 +571,44 @@ class TestCobraArrayModel(TestCobraModel):
model.upper_bounds = [0] * len(model.reactions)
self.assertEqual(max(model.upper_bounds), 0)
+ # test something for all the attributes
+ model.lower_bounds[2] = -1
+ assertEqual(model.reactions[2].lower_bound, -1)
+ assertEqual(model.lower_bounds[2], -1)
+ model.objective_coefficients[2] = 1
+ assertEqual(model.reactions[2].objective_coefficient, 1)
+ assertEqual(model.objective_coefficients[2], 1)
+ model.b[2] = 1
+ assertEqual(model.metabolites[2]._bound, 1)
+ assertEqual(model.b[2], 1)
+ model.constraint_sense[2] = "L"
+ assertEqual(model.metabolites[2]._constraint_sense, "L")
+ assertEqual(model.constraint_sense[2], "L")
+
+ # test resize matrix on reaction removal
+ m, n = model.S.shape
+ model.remove_reactions([model.reactions[2]], remove_orphans=False)
+ self.assertEqual(len(model.metabolites), model.S.shape[0])
+ self.assertEqual(len(model.reactions), model.S.shape[1])
+ self.assertEqual(model.S.shape, (m, n - 1))
+
def test_array_based_model_add(self):
+ m = len(self.model.metabolites)
+ n = len(self.model.reactions)
for matrix_type in ["scipy.dok_matrix", "scipy.lil_matrix"]:
- model = create_test_model().\
+ model = create_test_model("textbook").\
to_array_based_model(matrix_type=matrix_type)
test_reaction = Reaction("test")
test_reaction.add_metabolites({model.metabolites[0]: 4})
test_reaction.lower_bound = -3.14
model.add_reaction(test_reaction)
- self.assertEqual(len(model.reactions), 2547)
- self.assertEqual(model.S.shape[1], 2547)
- self.assertEqual(len(model.lower_bounds), 2547)
- self.assertEqual(model.S[0, 2546], 4)
- self.assertEqual(model.S[1605, 0], -1)
- self.assertEqual(model.lower_bounds[2546], -3.14)
+ self.assertEqual(len(model.reactions), n + 1)
+ self.assertEqual(model.S.shape, (m, n + 1))
+ self.assertEqual(len(model.lower_bounds), n + 1)
+ self.assertEqual(len(model.upper_bounds), n + 1)
+ self.assertEqual(model.S[0, n], 4)
+ self.assertEqual(model.S[7, 0], -1)
+ self.assertEqual(model.lower_bounds[n], -3.14)
def test_array_based_select(self):
model = self.model
diff --git a/cobra/topology/reporter_metabolites.py b/cobra/topology/reporter_metabolites.py
index 9291626..e8f928e 100644
--- a/cobra/topology/reporter_metabolites.py
+++ b/cobra/topology/reporter_metabolites.py
@@ -134,32 +134,3 @@ def identify_reporter_metabolites(cobra_model, reaction_scores_dict,
return_dictionary['corrections'] = correction_dict
return(return_dictionary)
-
-def ppmap_identify_reporter_metabolites(keywords):
- """
- A function that receives a dict with all of the parameters for identify_reporter_metabolites
- Serves to make it possible to call the reporter metabolites function from ppmap.
- It only will be useful for parallel experiments not for breaking up a single experiment.
-
- """
- the_results = identify_reporter_metabolites(**keywords)
- return({'id': the_id, 'results': the_results })
-
-if __name__ == '__main__':
- from cPickle import load
- from time import time
- solver = 'glpk'
- from cobra.test import salmonella_pickle, salmonella_reaction_p_values_pickle
- with open(salmonella_pickle) as in_file:
- cobra_model = load(in_file)
- with open(salmonella_reaction_p_values_pickle) as in_file:
- reaction_p = load(in_file)
-
- the_reactions = map(cobra_model.reactions.get_by_id, reaction_p.keys())
- the_scores = reaction_p.values()
- reaction_scores_dict = dict(zip(the_reactions, the_scores))
-
- tmp_reps = identify_reporter_metabolites(cobra_model, reaction_scores_dict,
- background_correction=True)
-
- print 'Need to add in validation for the test'
diff --git a/documentation_builder/autodoc.bat b/documentation_builder/autodoc.bat
deleted file mode 100644
index 3c533f7..0000000
--- a/documentation_builder/autodoc.bat
+++ /dev/null
@@ -1,4 +0,0 @@
-del cobra.*.rst
-sphinx-apidoc -o . ..\cobra
-del *.oven*rst
-del modules.rst
diff --git a/documentation_builder/autodoc.sh b/documentation_builder/autodoc.sh
index 959bf60..e2474e0 100755
--- a/documentation_builder/autodoc.sh
+++ b/documentation_builder/autodoc.sh
@@ -1,10 +1,7 @@
rm cobra.rst cobra.*.rst
sphinx-apidoc -o . ../cobra ../cobra/oven ../cobra/external \
- ../cobra/test ../cobra/solvers/*_java.py ../cobra/test_all.py \
+ ../cobra/test ../cobra/solvers/ ../cobra/test_all.py \
../cobra/version.py ../cobra/solvers/legacy.py
rm modules.rst
ipython nbconvert --to=rst *.ipynb
-
-ipython nbconvert --to=python --template=pyscript.tpl *.ipynb
-ls -1 *py | grep -v ^conf.py$ | xargs -Ipy mv py ../examples
diff --git a/documentation_builder/building_model.ipynb b/documentation_builder/building_model.ipynb
index 176a808..0afc2af 100644
--- a/documentation_builder/building_model.ipynb
+++ b/documentation_builder/building_model.ipynb
@@ -1,267 +1,284 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:e4c839935bc077fef105bd09af17e9df5996674528ffafbc16a6a0554c0ea820"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Building a Model"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This simple example (available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/building_model.ipynb)) demonstrates how to create a model, create a reaction, and then add the reaction to the model.\n",
- "\n",
- "We'll use the '3OAS140' reaction from the STM_1.0 model:\n",
- "\n",
- "1.0 malACP[c] + 1.0 h[c] + 1.0 ddcaACP[c] $\\rightarrow$ 1.0 co2[c] + 1.0 ACP[c] + 1.0 3omrsACP[c]"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "First, create the model and reaction."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from cobra import Model, Reaction, Metabolite\n",
- "# Best practise: SBML compliant IDs\n",
- "cobra_model = Model('example_cobra_model')\n",
- "\n",
- "reaction = Reaction('3OAS140')\n",
- "reaction.name = '3 oxoacyl acyl carrier protein synthase n C140 '\n",
- "reaction.subsystem = 'Cell Envelope Biosynthesis'\n",
- "reaction.lower_bound = 0. # This is the default\n",
- "reaction.upper_bound = 1000. # This is the default\n",
- "reaction.objective_coefficient = 0. # this is the default\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We need to create metabolites as well. If we were using an existing model, we could use get_by_id to get the apporpriate Metabolite objects instead."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "ACP_c = Metabolite('ACP_c', formula='C11H21N2O7PRS',\n",
- " name='acyl-carrier-protein', compartment='c')\n",
- "omrsACP_c = Metabolite('3omrsACP_c', formula='C25H45N2O9PRS',\n",
- " name='3-Oxotetradecanoyl-acyl-carrier-protein', compartment='c')\n",
- "co2_c = Metabolite('co2_c', formula='CO2', name='CO2', compartment='c')\n",
- "malACP_c = Metabolite('malACP_c', formula='C14H22N2O10PRS',\n",
- " name='Malonyl-acyl-carrier-protein', compartment='c')\n",
- "h_c = Metabolite('h_c', formula='H', name='H', compartment='c')\n",
- "ddcaACP_c = Metabolite('ddcaACP_c', formula='C23H43N2O8PRS',\n",
- " name='Dodecanoyl-ACP-n-C120ACP', compartment='c')\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Adding metabolites to a reaction requires using a dictionary of the metabolites and their stoichiometric coefficients. A group of metabolites can be added all at once, or they can be added one at a time."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "reaction.add_metabolites({malACP_c: -1.0,\n",
- " h_c: -1.0,\n",
- " ddcaACP_c: -1.0,\n",
- " co2_c: 1.0,\n",
- " ACP_c: 1.0,\n",
- " omrsACP_c: 1.0})\n",
- "\n",
- "\n",
- "reaction.reaction # This gives a string representation of the reaction"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 3,
- "text": [
- "'malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c'"
- ]
- }
- ],
- "prompt_number": 3
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Building a Model\n",
+ "\n",
+ "This simple example demonstrates how to create a model, create a reaction, and then add the reaction to the model.\n",
+ "\n",
+ "We'll use the '3OAS140' reaction from the STM_1.0 model:\n",
+ "\n",
+ "1.0 malACP[c] + 1.0 h[c] + 1.0 ddcaACP[c] $\\rightarrow$ 1.0 co2[c] + 1.0 ACP[c] + 1.0 3omrsACP[c]\n",
+ "\n",
+ "First, create the model and reaction."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from cobra import Model, Reaction, Metabolite\n",
+ "# Best practise: SBML compliant IDs\n",
+ "cobra_model = Model('example_cobra_model')\n",
+ "\n",
+ "reaction = Reaction('3OAS140')\n",
+ "reaction.name = '3 oxoacyl acyl carrier protein synthase n C140 '\n",
+ "reaction.subsystem = 'Cell Envelope Biosynthesis'\n",
+ "reaction.lower_bound = 0. # This is the default\n",
+ "reaction.upper_bound = 1000. # This is the default\n",
+ "reaction.objective_coefficient = 0. # this is the default"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We need to create metabolites as well. If we were using an existing model, we could use get_by_id to get the apporpriate Metabolite objects instead."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "ACP_c = Metabolite('ACP_c',\n",
+ " formula='C11H21N2O7PRS',\n",
+ " name='acyl-carrier-protein',\n",
+ " compartment='c')\n",
+ "omrsACP_c = Metabolite('3omrsACP_c',\n",
+ " formula='C25H45N2O9PRS',\n",
+ " name='3-Oxotetradecanoyl-acyl-carrier-protein',\n",
+ " compartment='c')\n",
+ "co2_c = Metabolite('co2_c',\n",
+ " formula='CO2',\n",
+ " name='CO2',\n",
+ " compartment='c')\n",
+ "malACP_c = Metabolite('malACP_c',\n",
+ " formula='C14H22N2O10PRS',\n",
+ " name='Malonyl-acyl-carrier-protein',\n",
+ " compartment='c')\n",
+ "h_c = Metabolite('h_c',\n",
+ " formula='H',\n",
+ " name='H',\n",
+ " compartment='c')\n",
+ "ddcaACP_c = Metabolite('ddcaACP_c',\n",
+ " formula='C23H43N2O8PRS',\n",
+ " name='Dodecanoyl-ACP-n-C120ACP',\n",
+ " compartment='c')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Adding metabolites to a reaction requires using a dictionary of the metabolites and their stoichiometric coefficients. A group of metabolites can be added all at once, or they can be added one at a time."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "'malACP_c + h_c + ddcaACP_c --> 3omrsACP_c + ACP_c + co2_c'"
+ ]
+ },
+ "execution_count": 3,
"metadata": {},
- "source": [
- "The gene_reaction_rule is a boolean representation of the gene requirements for this reaction to be active as described in [Schellenberger et al 2011 Nature Protocols 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308). We will assign the gene reaction rule string, which will automatically create the corresponding gene objects."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "reaction.add_metabolites({malACP_c: -1.0,\n",
+ " h_c: -1.0,\n",
+ " ddcaACP_c: -1.0,\n",
+ " co2_c: 1.0,\n",
+ " ACP_c: 1.0,\n",
+ " omrsACP_c: 1.0})\n",
+ "\n",
+ "\n",
+ "reaction.reaction # This gives a string representation of the reaction"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The gene_reaction_rule is a boolean representation of the gene requirements for this reaction to be active as described in [Schellenberger et al 2011 Nature Protocols 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308). We will assign the gene reaction rule string, which will automatically create the corresponding gene objects."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "reaction.gene_reaction_rule = '( STM2378 or STM1197 )'\n",
- "reaction.genes"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "frozenset({<Gene STM1197 at 0x7feea0ae9850>, <Gene STM2378 at 0x7feea0ae9b10>})"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "frozenset({<Gene STM2378 at 0x3739b10>, <Gene STM1197 at 0x3739b50>})"
- ]
- }
- ],
- "prompt_number": 4
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "reaction.gene_reaction_rule = '( STM2378 or STM1197 )'\n",
+ "reaction.genes"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "At this point in time, the model is still empty"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "At this point in time, the model is still empty"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "0 reactions in initial model\n",
+ "0 metabolites in initial model\n",
+ "0 genes in initial model\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print('%i reactions in initial model' % len(cobra_model.reactions))\n",
- "print('%i metabolites in initial model' % len(cobra_model.metabolites))\n",
- "print('%i genes in initial model' % len(cobra_model.genes))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "0 reactions in initial model\n",
- "0 metabolites in initial model\n",
- "0 genes in initial model\n"
- ]
- }
- ],
- "prompt_number": 5
- },
+ }
+ ],
+ "source": [
+ "print('%i reactions in initial model' % len(cobra_model.reactions))\n",
+ "print('%i metabolites in initial model' % len(cobra_model.metabolites))\n",
+ "print('%i genes in initial model' % len(cobra_model.genes))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We will add the reaction to the model, which will also add all associated metabolites and genes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We will add the reaction to the model, which will also add all associated metabolites and genes"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "1 reaction in model\n",
+ "6 metabolites in model\n",
+ "2 genes in model\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra_model.add_reaction(reaction)\n",
- "\n",
- "# Now there are things in the model\n",
- "print('%i reaction in model' % len(cobra_model.reactions))\n",
- "print('%i metabolites in model' % len(cobra_model.metabolites))\n",
- "print('%i genes in model' % len(cobra_model.genes))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "1 reaction in model\n",
- "6 metabolites in model\n",
- "2 genes in model\n"
- ]
- }
- ],
- "prompt_number": 6
- },
+ }
+ ],
+ "source": [
+ "cobra_model.add_reaction(reaction)\n",
+ "\n",
+ "# Now there are things in the model\n",
+ "print('%i reaction in model' % len(cobra_model.reactions))\n",
+ "print('%i metabolites in model' % len(cobra_model.metabolites))\n",
+ "print('%i genes in model' % len(cobra_model.genes))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can iterate through the model objects to observe the contents"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can iterate through the model objects to observe the contents"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Reactions\n",
+ "---------\n",
+ "3OAS140 : malACP_c + h_c + ddcaACP_c --> 3omrsACP_c + ACP_c + co2_c\n",
+ "Metabolites\n",
+ "-----------\n",
+ "3omrsACP_c : C25H45N2O9PRS\n",
+ "ACP_c : C11H21N2O7PRS\n",
+ "co2_c : CO2\n",
+ "malACP_c : C14H22N2O10PRS\n",
+ "h_c : H\n",
+ "ddcaACP_c : C23H43N2O8PRS\n",
+ "Genes\n",
+ "-----\n",
+ "STM2378 is associated with reactions: {3OAS140}\n",
+ "STM1197 is associated with reactions: {3OAS140}\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "# Iterate through the the objects in the model\n",
- "print(\"Reactions\")\n",
- "print(\"---------\")\n",
- "for x in cobra_model.reactions:\n",
- " print(\"%s : %s\" % (repr(x), x.reaction))\n",
- "print(\"Metabolites\")\n",
- "print(\"-----------\")\n",
- "for x in cobra_model.metabolites:\n",
- " print('%s : %s' % (repr(x), x.formula))\n",
- "print(\"Genes\")\n",
- "print(\"-----\")\n",
- "for x in cobra_model.genes:\n",
- " reactions_list_str = \", \".join((repr(i) for i in x.reactions))\n",
- " print(\"%s is associated with reactions: %s\" % (repr(x), reactions_list_str))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "Reactions\n",
- "---------\n",
- "<Reaction 3OAS140 at 0x4a18b90> : malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c\n",
- "Metabolites\n",
- "-----------\n",
- "<Metabolite co2_c at 0x594ba10> : CO2\n",
- "<Metabolite malACP_c at 0x594ba90> : C14H22N2O10PRS\n",
- "<Metabolite h_c at 0x594bb10> : H\n",
- "<Metabolite 3omrsACP_c at 0x594b950> : C25H45N2O9PRS\n",
- "<Metabolite ACP_c at 0x594b990> : C11H21N2O7PRS\n",
- "<Metabolite ddcaACP_c at 0x594bb90> : C23H43N2O8PRS\n",
- "Genes\n",
- "-----\n",
- "<Gene STM2378 at 0x3739b10> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>\n",
- "<Gene STM1197 at 0x3739b50> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>\n"
- ]
- }
- ],
- "prompt_number": 7
}
],
- "metadata": {}
+ "source": [
+ "# Iterate through the the objects in the model\n",
+ "print(\"Reactions\")\n",
+ "print(\"---------\")\n",
+ "for x in cobra_model.reactions:\n",
+ " print(\"%s : %s\" % (x.id, x.reaction))\n",
+ "print(\"Metabolites\")\n",
+ "print(\"-----------\")\n",
+ "for x in cobra_model.metabolites:\n",
+ " print('%s : %s' % (x.id, x.formula))\n",
+ "print(\"Genes\")\n",
+ "print(\"-----\")\n",
+ "for x in cobra_model.genes:\n",
+ " reactions_list_str = \"{\" + \", \".join((i.id for i in x.reactions)) + \"}\"\n",
+ " print(\"%s is associated with reactions: %s\" % (x.id, reactions_list_str))"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/building_model.rst b/documentation_builder/building_model.rst
index fa1edb1..8a654d0 100644
--- a/documentation_builder/building_model.rst
+++ b/documentation_builder/building_model.rst
@@ -2,10 +2,8 @@
Building a Model
================
-This simple example (available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/building_model.ipynb>`__)
-demonstrates how to create a model, create a reaction, and then add the
-reaction to the model.
+This simple example demonstrates how to create a model, create a
+reaction, and then add the reaction to the model.
We'll use the '3OAS140' reaction from the STM\_1.0 model:
@@ -33,16 +31,30 @@ objects instead.
.. code:: python
- ACP_c = Metabolite('ACP_c', formula='C11H21N2O7PRS',
- name='acyl-carrier-protein', compartment='c')
- omrsACP_c = Metabolite('3omrsACP_c', formula='C25H45N2O9PRS',
- name='3-Oxotetradecanoyl-acyl-carrier-protein', compartment='c')
- co2_c = Metabolite('co2_c', formula='CO2', name='CO2', compartment='c')
- malACP_c = Metabolite('malACP_c', formula='C14H22N2O10PRS',
- name='Malonyl-acyl-carrier-protein', compartment='c')
- h_c = Metabolite('h_c', formula='H', name='H', compartment='c')
- ddcaACP_c = Metabolite('ddcaACP_c', formula='C23H43N2O8PRS',
- name='Dodecanoyl-ACP-n-C120ACP', compartment='c')
+ ACP_c = Metabolite('ACP_c',
+ formula='C11H21N2O7PRS',
+ name='acyl-carrier-protein',
+ compartment='c')
+ omrsACP_c = Metabolite('3omrsACP_c',
+ formula='C25H45N2O9PRS',
+ name='3-Oxotetradecanoyl-acyl-carrier-protein',
+ compartment='c')
+ co2_c = Metabolite('co2_c',
+ formula='CO2',
+ name='CO2',
+ compartment='c')
+ malACP_c = Metabolite('malACP_c',
+ formula='C14H22N2O10PRS',
+ name='Malonyl-acyl-carrier-protein',
+ compartment='c')
+ h_c = Metabolite('h_c',
+ formula='H',
+ name='H',
+ compartment='c')
+ ddcaACP_c = Metabolite('ddcaACP_c',
+ formula='C23H43N2O8PRS',
+ name='Dodecanoyl-ACP-n-C120ACP',
+ compartment='c')
Adding metabolites to a reaction requires using a dictionary of the
metabolites and their stoichiometric coefficients. A group of
@@ -63,9 +75,10 @@ time.
+
.. parsed-literal::
- 'malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c'
+ 'malACP_c + h_c + ddcaACP_c --> 3omrsACP_c + ACP_c + co2_c'
@@ -78,14 +91,15 @@ the corresponding gene objects.
.. code:: python
- reaction.gene_reaction_rule = '( STM2378 or STM1197 )'
+ reaction.gene_reaction_rule = '( STM2378 or STM1197 )'
reaction.genes
+
.. parsed-literal::
- frozenset({<Gene STM2378 at 0x3739b10>, <Gene STM1197 at 0x3739b50>})
+ frozenset({<Gene STM1197 at 0x7feea0ae9850>, <Gene STM2378 at 0x7feea0ae9b10>})
@@ -97,6 +111,7 @@ At this point in time, the model is still empty
print('%i metabolites in initial model' % len(cobra_model.metabolites))
print('%i genes in initial model' % len(cobra_model.genes))
+
.. parsed-literal::
0 reactions in initial model
@@ -116,6 +131,7 @@ associated metabolites and genes
print('%i metabolites in model' % len(cobra_model.metabolites))
print('%i genes in model' % len(cobra_model.genes))
+
.. parsed-literal::
1 reaction in model
@@ -131,32 +147,33 @@ We can iterate through the model objects to observe the contents
print("Reactions")
print("---------")
for x in cobra_model.reactions:
- print("%s : %s" % (repr(x), x.reaction))
+ print("%s : %s" % (x.id, x.reaction))
print("Metabolites")
print("-----------")
for x in cobra_model.metabolites:
- print('%s : %s' % (repr(x), x.formula))
+ print('%s : %s' % (x.id, x.formula))
print("Genes")
print("-----")
for x in cobra_model.genes:
- reactions_list_str = ", ".join((repr(i) for i in x.reactions))
- print("%s is associated with reactions: %s" % (repr(x), reactions_list_str))
+ reactions_list_str = "{" + ", ".join((i.id for i in x.reactions)) + "}"
+ print("%s is associated with reactions: %s" % (x.id, reactions_list_str))
+
.. parsed-literal::
Reactions
---------
- <Reaction 3OAS140 at 0x4a18b90> : malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c
+ 3OAS140 : malACP_c + h_c + ddcaACP_c --> 3omrsACP_c + ACP_c + co2_c
Metabolites
-----------
- <Metabolite co2_c at 0x594ba10> : CO2
- <Metabolite malACP_c at 0x594ba90> : C14H22N2O10PRS
- <Metabolite h_c at 0x594bb10> : H
- <Metabolite 3omrsACP_c at 0x594b950> : C25H45N2O9PRS
- <Metabolite ACP_c at 0x594b990> : C11H21N2O7PRS
- <Metabolite ddcaACP_c at 0x594bb90> : C23H43N2O8PRS
+ 3omrsACP_c : C25H45N2O9PRS
+ ACP_c : C11H21N2O7PRS
+ co2_c : CO2
+ malACP_c : C14H22N2O10PRS
+ h_c : H
+ ddcaACP_c : C23H43N2O8PRS
Genes
-----
- <Gene STM2378 at 0x3739b10> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>
- <Gene STM1197 at 0x3739b50> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>
+ STM2378 is associated with reactions: {3OAS140}
+ STM1197 is associated with reactions: {3OAS140}
diff --git a/documentation_builder/cobra.flux_analysis.rst b/documentation_builder/cobra.flux_analysis.rst
index b424df7..430bc07 100644
--- a/documentation_builder/cobra.flux_analysis.rst
+++ b/documentation_builder/cobra.flux_analysis.rst
@@ -28,6 +28,14 @@ cobra.flux_analysis.essentiality module
:undoc-members:
:show-inheritance:
+cobra.flux_analysis.gapfilling module
+-------------------------------------
+
+.. automodule:: cobra.flux_analysis.gapfilling
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
cobra.flux_analysis.loopless module
-----------------------------------
@@ -44,14 +52,6 @@ cobra.flux_analysis.moma module
:undoc-members:
:show-inheritance:
-cobra.flux_analysis.objective module
-------------------------------------
-
-.. automodule:: cobra.flux_analysis.objective
- :members:
- :undoc-members:
- :show-inheritance:
-
cobra.flux_analysis.parsimonious module
---------------------------------------
diff --git a/documentation_builder/cobra.io.rst b/documentation_builder/cobra.io.rst
index e03b13f..ad3615f 100644
--- a/documentation_builder/cobra.io.rst
+++ b/documentation_builder/cobra.io.rst
@@ -28,6 +28,14 @@ cobra.io.sbml module
:undoc-members:
:show-inheritance:
+cobra.io.sbml3 module
+---------------------
+
+.. automodule:: cobra.io.sbml3
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
Module contents
---------------
diff --git a/documentation_builder/cobra.mlab.rst b/documentation_builder/cobra.mlab.rst
deleted file mode 100644
index 814ee8e..0000000
--- a/documentation_builder/cobra.mlab.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-cobra.mlab package
-==================
-
-Submodules
-----------
-
-cobra.mlab.mlab module
-----------------------
-
-.. automodule:: cobra.mlab.mlab
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: cobra.mlab
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/documentation_builder/cobra.rst b/documentation_builder/cobra.rst
index 1f55d3b..e5e9693 100644
--- a/documentation_builder/cobra.rst
+++ b/documentation_builder/cobra.rst
@@ -10,8 +10,6 @@ Subpackages
cobra.flux_analysis
cobra.io
cobra.manipulation
- cobra.mlab
- cobra.solvers
cobra.topology
Module contents
diff --git a/documentation_builder/cobra.solvers.rst b/documentation_builder/cobra.solvers.rst
deleted file mode 100644
index a91750a..0000000
--- a/documentation_builder/cobra.solvers.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-cobra.solvers package
-=====================
-
-Submodules
-----------
-
-cobra.solvers.cglpk module
---------------------------
-
-.. automodule:: cobra.solvers.cglpk
- :members:
- :undoc-members:
- :show-inheritance:
-
-cobra.solvers.cplex_solver module
----------------------------------
-
-.. automodule:: cobra.solvers.cplex_solver
- :members:
- :undoc-members:
- :show-inheritance:
-
-cobra.solvers.glpk_solver module
---------------------------------
-
-.. automodule:: cobra.solvers.glpk_solver
- :members:
- :undoc-members:
- :show-inheritance:
-
-cobra.solvers.gurobi_solver module
-----------------------------------
-
-.. automodule:: cobra.solvers.gurobi_solver
- :members:
- :undoc-members:
- :show-inheritance:
-
-cobra.solvers.parameters module
--------------------------------
-
-.. automodule:: cobra.solvers.parameters
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: cobra.solvers
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/documentation_builder/conf.py b/documentation_builder/conf.py
index 5e908eb..cb7304f 100644
--- a/documentation_builder/conf.py
+++ b/documentation_builder/conf.py
@@ -35,10 +35,9 @@ class Mock(object):
else:
return Mock()
-MOCK_MODULES = ['numpy',
- 'scipy', 'scipy.sparse', 'scipy.io', 'scipy.stats',
- 'glpk', 'gurobipy', 'gurobipy.GRB', 'cplex',
- 'mlabwrap', 'pp', 'libsbml']
+MOCK_MODULES = ['numpy', 'scipy', 'scipy.sparse', 'scipy.io', 'scipy.stats',
+ 'glpk', 'gurobipy', 'gurobipy.GRB', 'cplex', 'pp', 'libsbml',
+ 'cplex.exceptions']
for mod_name in MOCK_MODULES:
sys.modules[mod_name] = Mock()
@@ -50,7 +49,8 @@ for mod_name in MOCK_MODULES:
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx',
- 'sphinx.ext.mathjax', 'sphinx.ext.viewcode']
+ 'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
+ 'sphinx.ext.napoleon', 'sphinx.ext.mathjax']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -66,7 +66,7 @@ master_doc = 'index'
# General information about the project.
project = u'cobra'
-copyright = u'2014, Daniel Robert Hyduke and Ali Ebrahim'
+copyright = u'2015, Daniel Robert Hyduke and Ali Ebrahim'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -119,7 +119,7 @@ mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'default'
+#html_theme = 'alabaster'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
@@ -148,7 +148,7 @@ html_theme = 'default'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+#html_static_path = ['_static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
diff --git a/documentation_builder/deletions.ipynb b/documentation_builder/deletions.ipynb
index 5f01bb1..b55bfb3 100644
--- a/documentation_builder/deletions.ipynb
+++ b/documentation_builder/deletions.ipynb
@@ -1,401 +1,852 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:3e35e7bfbc1e247a87ee168c2754042ee867b89916ce0bf24b85e069c1568831"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Simulating Deletions"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/deletions.ipynb)."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from time import time\n",
- "\n",
- "\n",
- "from cobra.test import create_test_model, salmonella_pickle, ecoli_pickle\n",
- "from cobra.flux_analysis import single_deletion\n",
- "from cobra.flux_analysis import double_deletion\n",
- "\n",
- "\n",
- "cobra_model = create_test_model(salmonella_pickle)\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Single Deletions"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Perform all single gene deletions on a model"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start = time() # start timer()\n",
- "growth_rates, statuses = single_deletion(cobra_model)\n",
- "print(\"All single gene deletions completed in %.2f sec\" % (time() - start))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "All single gene deletions completed in 4.01 sec\n"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "These can also be done for only a subset of genes"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "single_deletion(cobra_model, element_list=cobra_model.genes[:100]);\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Single deletions can also be run on reactions"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start = time() # start timer()\n",
- "growth_rates, statuses = single_deletion(cobra_model, element_type=\"reaction\")\n",
- "print(\"All single reaction deletions completed in %.2f sec\" % (time() - start))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "All single reaction deletions completed in 7.41 sec\n"
- ]
- }
- ],
- "prompt_number": 4
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Double Deletions"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Double deletions run in a similar way"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start = time() # start timer()\n",
- "double_deletion(cobra_model, element_list_1=cobra_model.genes[:100])\n",
- "print(\"Double gene deletions for 100 genes completed in %.2f sec\" % (time() - start))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "Double gene deletions for 100 genes completed in 4.94 sec\n"
- ]
- }
- ],
- "prompt_number": 5
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "By default, the double deletion function will automatically use multiprocessing, splitting the task over up to 4 cores if they are available. The number of cores can be manually sepcified as well. Setting use of a single core will disable use of the multiprocessing library, which often aids debuggging."
- ]
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Simulating Deletions"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "import pandas\n",
+ "from time import time\n",
+ "\n",
+ "import cobra.test\n",
+ "\n",
+ "cobra_model = cobra.test.create_test_model(\"textbook\")\n",
+ "ecoli_model = cobra.test.create_test_model(\"ecoli\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Single Deletions"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Perform all single gene deletions on a model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "growth_rates, statuses = cobra.flux_analysis.single_gene_deletion(cobra_model)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "These can also be done for only a subset of genes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start = time() # start timer()\n",
- "double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],\n",
- " number_of_processes=2)\n",
- "t1 = time() - start\n",
- "print(\"Double gene deletions for 100 genes completed in %.2f sec with 2 cores\" % t1)\n",
- "\n",
- "start = time() # start timer()\n",
- "double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],\n",
- " number_of_processes=1)\n",
- "t2 = time() - start\n",
- "print(\"Double gene deletions for 100 genes completed in %.2f sec with 1 core\" % t2)\n",
- "\n",
- "print(\"Speedup of %.2fx\" % (t2/t1))"
- ],
- "language": "python",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>growth_rates</th>\n",
+ " <th>status</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>b0116</th>\n",
+ " <td>0.782351</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0118</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0351</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0356</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0474</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0726</th>\n",
+ " <td>0.858307</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0727</th>\n",
+ " <td>0.858307</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b1241</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b1276</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b1478</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b1849</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b2296</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b2587</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3115</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3734</th>\n",
+ " <td>0.374230</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3735</th>\n",
+ " <td>0.374230</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3736</th>\n",
+ " <td>0.374230</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3737</th>\n",
+ " <td>0.374230</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3738</th>\n",
+ " <td>0.374230</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>s0001</th>\n",
+ " <td>0.211141</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " growth_rates status\n",
+ "b0116 0.782351 optimal\n",
+ "b0118 0.873922 optimal\n",
+ "b0351 0.873922 optimal\n",
+ "b0356 0.873922 optimal\n",
+ "b0474 0.873922 optimal\n",
+ "b0726 0.858307 optimal\n",
+ "b0727 0.858307 optimal\n",
+ "b1241 0.873922 optimal\n",
+ "b1276 0.873922 optimal\n",
+ "b1478 0.873922 optimal\n",
+ "b1849 0.873922 optimal\n",
+ "b2296 0.873922 optimal\n",
+ "b2587 0.873922 optimal\n",
+ "b3115 0.873922 optimal\n",
+ "b3734 0.374230 optimal\n",
+ "b3735 0.374230 optimal\n",
+ "b3736 0.374230 optimal\n",
+ "b3737 0.374230 optimal\n",
+ "b3738 0.374230 optimal\n",
+ "s0001 0.211141 optimal"
+ ]
+ },
+ "execution_count": 3,
"metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "Double gene deletions for 100 genes completed in 4.02 sec with 2 cores\n",
- "Double gene deletions for 100 genes completed in 6.77 sec with 1 core"
- ]
- },
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "\n",
- "Speedup of 1.69x\n"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "growth_rates, statuses = cobra.flux_analysis.single_gene_deletion(cobra_model, cobra_model.genes[:20])\n",
+ "pandas.DataFrame.from_dict({\"growth_rates\": growth_rates, \"status\": statuses})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "This can also be done for reactions"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>growth_rates</th>\n",
+ " <th>status</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>ACALD</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACALDt</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACKr</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTa</th>\n",
+ " <td>-3.963237e-27</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTb</th>\n",
+ " <td>6.162976e-33</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACt2r</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ADK1</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGDH</th>\n",
+ " <td>8.583074e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGt2r</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ALCD2x</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPM</th>\n",
+ " <td>9.166475e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPS4r</th>\n",
+ " <td>3.742299e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Biomass_Ecoli_core</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CO2t</th>\n",
+ " <td>4.616696e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CS</th>\n",
+ " <td>-5.916457e-30</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CYTBD</th>\n",
+ " <td>2.116629e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>D_LACt2</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ENO</th>\n",
+ " <td>-3.266892e-18</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ETOHt2r</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>EX_ac_e</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>optimal</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " growth_rates status\n",
+ "ACALD 8.739215e-01 optimal\n",
+ "ACALDt 8.739215e-01 optimal\n",
+ "ACKr 8.739215e-01 optimal\n",
+ "ACONTa -3.963237e-27 optimal\n",
+ "ACONTb 6.162976e-33 optimal\n",
+ "ACt2r 8.739215e-01 optimal\n",
+ "ADK1 8.739215e-01 optimal\n",
+ "AKGDH 8.583074e-01 optimal\n",
+ "AKGt2r 8.739215e-01 optimal\n",
+ "ALCD2x 8.739215e-01 optimal\n",
+ "ATPM 9.166475e-01 optimal\n",
+ "ATPS4r 3.742299e-01 optimal\n",
+ "Biomass_Ecoli_core 0.000000e+00 optimal\n",
+ "CO2t 4.616696e-01 optimal\n",
+ "CS -5.916457e-30 optimal\n",
+ "CYTBD 2.116629e-01 optimal\n",
+ "D_LACt2 8.739215e-01 optimal\n",
+ "ENO -3.266892e-18 optimal\n",
+ "ETOHt2r 8.739215e-01 optimal\n",
+ "EX_ac_e 8.739215e-01 optimal"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "source": [
- "Double deletions can also be run for reactions"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "growth_rates, statuses = cobra.flux_analysis.single_reaction_deletion(cobra_model, cobra_model.reactions[:20])\n",
+ "pandas.DataFrame.from_dict({\"growth_rates\": growth_rates, \"status\": statuses})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Double Deletions\n",
+ "\n",
+ "Double deletions run in a similar way. Passing in return_frame=True will cause them to format the results as a pandas Dataframe"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start = time()\n",
- "double_deletion(cobra_model, element_list_1=cobra_model.reactions[:100],\n",
- " element_type=\"reaction\")\n",
- "t = time() - start\n",
- "print(\"Double reaction deletions for 100 reactions completed in %.2f sec\" % t)"
- ],
- "language": "python",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>b0724</th>\n",
+ " <th>b0723</th>\n",
+ " <th>b0721</th>\n",
+ " <th>b0729</th>\n",
+ " <th>b0728</th>\n",
+ " <th>b2464</th>\n",
+ " <th>b0008</th>\n",
+ " <th>b2935</th>\n",
+ " <th>b2465</th>\n",
+ " <th>b3919</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>b0724</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0723</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0721</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0729</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0728</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b2464</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.864759</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b0008</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.864759</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b2935</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b2465</th>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.814298</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>b3919</th>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " <td>0.704037</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " b0724 b0723 b0721 b0729 b0728 b2464 b0008 \\\n",
+ "b0724 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 \n",
+ "b0723 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 \n",
+ "b0721 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 0.814298 \n",
+ "b0729 0.814298 0.814298 0.814298 0.858307 0.858307 0.858307 0.858307 \n",
+ "b0728 0.814298 0.814298 0.814298 0.858307 0.858307 0.858307 0.858307 \n",
+ "b2464 0.814298 0.814298 0.814298 0.858307 0.858307 0.873922 0.864759 \n",
+ "b0008 0.814298 0.814298 0.814298 0.858307 0.858307 0.864759 0.873922 \n",
+ "b2935 0.814298 0.814298 0.814298 0.858307 0.858307 0.873922 0.873922 \n",
+ "b2465 0.814298 0.814298 0.814298 0.858307 0.858307 0.873922 0.873922 \n",
+ "b3919 0.704037 0.704037 0.704037 0.704037 0.704037 0.704037 0.704037 \n",
+ "\n",
+ " b2935 b2465 b3919 \n",
+ "b0724 0.814298 0.814298 0.704037 \n",
+ "b0723 0.814298 0.814298 0.704037 \n",
+ "b0721 0.814298 0.814298 0.704037 \n",
+ "b0729 0.858307 0.858307 0.704037 \n",
+ "b0728 0.858307 0.858307 0.704037 \n",
+ "b2464 0.873922 0.873922 0.704037 \n",
+ "b0008 0.873922 0.873922 0.704037 \n",
+ "b2935 0.873922 0.000000 0.704037 \n",
+ "b2465 0.000000 0.873922 0.704037 \n",
+ "b3919 0.704037 0.704037 0.704037 "
+ ]
+ },
+ "execution_count": 5,
"metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "Double reaction deletions for 100 reactions completed in 0.93 sec\n"
- ]
- }
- ],
- "prompt_number": 7
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.flux_analysis.double_gene_deletion(cobra_model, cobra_model.genes[-10:], return_frame=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "By default, the double deletion function will automatically use multiprocessing, splitting the task over up to 4 cores if they are available. The number of cores can be manually sepcified as well. Setting use of a single core will disable use of the multiprocessing library, which often aids debuggging."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "If pandas is installed, the results can be returned formatted as a pandas.DataFrame"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Double gene deletions for 100 genes completed in 1.69 sec with 2 cores\n",
+ "Double gene deletions for 100 genes completed in 2.02 sec with 1 core\n",
+ "Speedup of 1.20x\n"
]
- },
+ }
+ ],
+ "source": [
+ "start = time() # start timer()\n",
+ "cobra.flux_analysis.double_gene_deletion(ecoli_model, ecoli_model.genes[:100], number_of_processes=2)\n",
+ "t1 = time() - start\n",
+ "print(\"Double gene deletions for 100 genes completed in %.2f sec with 2 cores\" % t1)\n",
+ "\n",
+ "start = time() # start timer()\n",
+ "cobra.flux_analysis.double_gene_deletion(ecoli_model, ecoli_model.genes[:100], number_of_processes=1)\n",
+ "t2 = time() - start\n",
+ "print(\"Double gene deletions for 100 genes completed in %.2f sec with 1 core\" % t2)\n",
+ "\n",
+ "print(\"Speedup of %.2fx\" % (t2/t1))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Double deletions can also be run for reactions"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "frame = double_deletion(cobra_model, element_list_1=cobra_model.reactions[300:308],\n",
- " element_type=\"reaction\", return_frame=True)\n",
- "frame[frame < 1e-9] = 0. # round small values to 0\n",
- "frame"
- ],
- "language": "python",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>ACALD</th>\n",
+ " <th>ACALDt</th>\n",
+ " <th>ACKr</th>\n",
+ " <th>ACONTa</th>\n",
+ " <th>ACONTb</th>\n",
+ " <th>ACt2r</th>\n",
+ " <th>ADK1</th>\n",
+ " <th>AKGDH</th>\n",
+ " <th>AKGt2r</th>\n",
+ " <th>ALCD2x</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>ACALD</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACALDt</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACKr</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTa</th>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTb</th>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>0.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACt2r</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ADK1</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGDH</th>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.858307</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGt2r</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ALCD2x</th>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.858307</td>\n",
+ " <td>0.873922</td>\n",
+ " <td>0.873922</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " ACALD ACALDt ACKr ACONTa ACONTb ACt2r ADK1 \\\n",
+ "ACALD 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "ACALDt 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "ACKr 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "ACONTa 0.000000 0.000000 0.000000 0 0 0.000000 0.000000 \n",
+ "ACONTb 0.000000 0.000000 0.000000 0 0 0.000000 0.000000 \n",
+ "ACt2r 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "ADK1 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "AKGDH 0.858307 0.858307 0.858307 0 0 0.858307 0.858307 \n",
+ "AKGt2r 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "ALCD2x 0.873922 0.873922 0.873922 0 0 0.873922 0.873922 \n",
+ "\n",
+ " AKGDH AKGt2r ALCD2x \n",
+ "ACALD 0.858307 0.873922 0.873922 \n",
+ "ACALDt 0.858307 0.873922 0.873922 \n",
+ "ACKr 0.858307 0.873922 0.873922 \n",
+ "ACONTa 0.000000 0.000000 0.000000 \n",
+ "ACONTb 0.000000 0.000000 0.000000 \n",
+ "ACt2r 0.858307 0.873922 0.873922 \n",
+ "ADK1 0.858307 0.873922 0.873922 \n",
+ "AKGDH 0.858307 0.858307 0.858307 \n",
+ "AKGt2r 0.858307 0.873922 0.873922 \n",
+ "ALCD2x 0.858307 0.873922 0.873922 "
+ ]
+ },
+ "execution_count": 7,
"metadata": {},
- "outputs": [
- {
- "html": [
- "<div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
- "<table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr style=\"text-align: right;\">\n",
- " <th></th>\n",
- " <th>ARBtex</th>\n",
- " <th>ARGAGMt7pp</th>\n",
- " <th>ARGDC</th>\n",
- " <th>ARGDCpp</th>\n",
- " <th>ARGORNt7pp</th>\n",
- " <th>ARGSL</th>\n",
- " <th>ARGSS</th>\n",
- " <th>ARGTRS</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr>\n",
- " <th>ARBtex</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGAGMt7pp</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGDC</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGDCpp</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGORNt7pp</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGSL</th>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.000000</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGSS</th>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0.000000</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.000000</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>ARGTRS</th>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0.380008</td>\n",
- " <td> 0</td>\n",
- " <td> 0</td>\n",
- " <td> 0.380008</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
- ],
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 8,
- "text": [
- " ARBtex ARGAGMt7pp ARGDC ARGDCpp ARGORNt7pp ARGSL \\\n",
- "ARBtex 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "ARGAGMt7pp 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "ARGDC 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "ARGDCpp 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "ARGORNt7pp 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "ARGSL 0.000000 0.000000 0.000000 0.000000 0.000000 0 \n",
- "ARGSS 0.000000 0.000000 0.000000 0.000000 0.000000 0 \n",
- "ARGTRS 0.380008 0.380008 0.380008 0.380008 0.380008 0 \n",
- "\n",
- " ARGSS ARGTRS \n",
- "ARBtex 0 0.380008 \n",
- "ARGAGMt7pp 0 0.380008 \n",
- "ARGDC 0 0.380008 \n",
- "ARGDCpp 0 0.380008 \n",
- "ARGORNt7pp 0 0.380008 \n",
- "ARGSL 0 0.000000 \n",
- "ARGSS 0 0.000000 \n",
- "ARGTRS 0 0.380008 "
- ]
- }
- ],
- "prompt_number": 8
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "cobra.flux_analysis.double_reaction_deletion(cobra_model, cobra_model.reactions[:10], return_frame=True)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
}
- ]
-}
\ No newline at end of file
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/deletions.rst b/documentation_builder/deletions.rst
index ff9fc57..5c39e20 100644
--- a/documentation_builder/deletions.rst
+++ b/documentation_builder/deletions.rst
@@ -2,20 +2,15 @@
Simulating Deletions
====================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/deletions.ipynb>`__.
-
.. code:: python
+ import pandas
from time import time
+ import cobra.test
- from cobra.test import create_test_model, salmonella_pickle, ecoli_pickle
- from cobra.flux_analysis import single_deletion
- from cobra.flux_analysis import double_deletion
-
-
- cobra_model = create_test_model(salmonella_pickle)
+ cobra_model = cobra.test.create_test_model("textbook")
+ ecoli_model = cobra.test.create_test_model("ecoli")
Single Deletions
----------------
@@ -24,48 +19,431 @@ Perform all single gene deletions on a model
.. code:: python
- start = time() # start timer()
- growth_rates, statuses = single_deletion(cobra_model)
- print("All single gene deletions completed in %.2f sec" % (time() - start))
+ growth_rates, statuses = cobra.flux_analysis.single_gene_deletion(cobra_model)
-.. parsed-literal::
+These can also be done for only a subset of genes
- All single gene deletions completed in 4.01 sec
+.. code:: python
+ growth_rates, statuses = cobra.flux_analysis.single_gene_deletion(cobra_model, cobra_model.genes[:20])
+ pandas.DataFrame.from_dict({"growth_rates": growth_rates, "status": statuses})
-These can also be done for only a subset of genes
-.. code:: python
- single_deletion(cobra_model, element_list=cobra_model.genes[:100]);
-Single deletions can also be run on reactions
+.. raw:: html
+
+ <div>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th></th>
+ <th>growth_rates</th>
+ <th>status</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th>b0116</th>
+ <td>0.782351</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0118</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0351</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0356</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0474</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0726</th>
+ <td>0.858307</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b0727</th>
+ <td>0.858307</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b1241</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b1276</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b1478</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b1849</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b2296</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b2587</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3115</th>
+ <td>0.873922</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3734</th>
+ <td>0.374230</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3735</th>
+ <td>0.374230</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3736</th>
+ <td>0.374230</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3737</th>
+ <td>0.374230</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>b3738</th>
+ <td>0.374230</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>s0001</th>
+ <td>0.211141</td>
+ <td>optimal</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+
+
+This can also be done for reactions
.. code:: python
- start = time() # start timer()
- growth_rates, statuses = single_deletion(cobra_model, element_type="reaction")
- print("All single reaction deletions completed in %.2f sec" % (time() - start))
+ growth_rates, statuses = cobra.flux_analysis.single_reaction_deletion(cobra_model, cobra_model.reactions[:20])
+ pandas.DataFrame.from_dict({"growth_rates": growth_rates, "status": statuses})
-.. parsed-literal::
- All single reaction deletions completed in 7.41 sec
+
+
+.. raw:: html
+
+ <div>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th></th>
+ <th>growth_rates</th>
+ <th>status</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th>ACALD</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ACALDt</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ACKr</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ACONTa</th>
+ <td>-3.963237e-27</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ACONTb</th>
+ <td>6.162976e-33</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ACt2r</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ADK1</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>AKGDH</th>
+ <td>8.583074e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>AKGt2r</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ALCD2x</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ATPM</th>
+ <td>9.166475e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ATPS4r</th>
+ <td>3.742299e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>Biomass_Ecoli_core</th>
+ <td>0.000000e+00</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>CO2t</th>
+ <td>4.616696e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>CS</th>
+ <td>-5.916457e-30</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>CYTBD</th>
+ <td>2.116629e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>D_LACt2</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ENO</th>
+ <td>-3.266892e-18</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>ETOHt2r</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ <tr>
+ <th>EX_ac_e</th>
+ <td>8.739215e-01</td>
+ <td>optimal</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
Double Deletions
----------------
-Double deletions run in a similar way
+Double deletions run in a similar way. Passing in return\_frame=True
+will cause them to format the results as a pandas Dataframe
.. code:: python
- start = time() # start timer()
- double_deletion(cobra_model, element_list_1=cobra_model.genes[:100])
- print("Double gene deletions for 100 genes completed in %.2f sec" % (time() - start))
+ cobra.flux_analysis.double_gene_deletion(cobra_model, cobra_model.genes[-10:], return_frame=True)
-.. parsed-literal::
- Double gene deletions for 100 genes completed in 4.94 sec
+
+
+.. raw:: html
+
+ <div>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th></th>
+ <th>b0724</th>
+ <th>b0723</th>
+ <th>b0721</th>
+ <th>b0729</th>
+ <th>b0728</th>
+ <th>b2464</th>
+ <th>b0008</th>
+ <th>b2935</th>
+ <th>b2465</th>
+ <th>b3919</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th>b0724</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b0723</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b0721</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b0729</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b0728</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b2464</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.864759</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b0008</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.864759</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b2935</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.000000</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b2465</th>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.814298</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.000000</td>
+ <td>0.873922</td>
+ <td>0.704037</td>
+ </tr>
+ <tr>
+ <th>b3919</th>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ <td>0.704037</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
By default, the double deletion function will automatically use
@@ -77,158 +455,183 @@ library, which often aids debuggging.
.. code:: python
start = time() # start timer()
- double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],
- number_of_processes=2)
+ cobra.flux_analysis.double_gene_deletion(ecoli_model, ecoli_model.genes[:100], number_of_processes=2)
t1 = time() - start
print("Double gene deletions for 100 genes completed in %.2f sec with 2 cores" % t1)
start = time() # start timer()
- double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],
- number_of_processes=1)
+ cobra.flux_analysis.double_gene_deletion(ecoli_model, ecoli_model.genes[:100], number_of_processes=1)
t2 = time() - start
print("Double gene deletions for 100 genes completed in %.2f sec with 1 core" % t2)
print("Speedup of %.2fx" % (t2/t1))
+
.. parsed-literal::
- Double gene deletions for 100 genes completed in 4.02 sec with 2 cores
- Double gene deletions for 100 genes completed in 6.77 sec with 1 core
- Speedup of 1.69x
+ Double gene deletions for 100 genes completed in 1.69 sec with 2 cores
+ Double gene deletions for 100 genes completed in 2.02 sec with 1 core
+ Speedup of 1.20x
Double deletions can also be run for reactions
.. code:: python
- start = time()
- double_deletion(cobra_model, element_list_1=cobra_model.reactions[:100],
- element_type="reaction")
- t = time() - start
- print("Double reaction deletions for 100 reactions completed in %.2f sec" % t)
-
-.. parsed-literal::
-
- Double reaction deletions for 100 reactions completed in 0.93 sec
-
-
-If pandas is installed, the results can be returned formatted as a
-pandas.DataFrame
+ cobra.flux_analysis.double_reaction_deletion(cobra_model, cobra_model.reactions[:10], return_frame=True)
-.. code:: python
-
- frame = double_deletion(cobra_model, element_list_1=cobra_model.reactions[300:308],
- element_type="reaction", return_frame=True)
- frame[frame < 1e-9] = 0. # round small values to 0
- frame
.. raw:: html
- <div style="max-height:1000px;max-width:1500px;overflow:auto;">
+ <div>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
- <th>ARBtex</th>
- <th>ARGAGMt7pp</th>
- <th>ARGDC</th>
- <th>ARGDCpp</th>
- <th>ARGORNt7pp</th>
- <th>ARGSL</th>
- <th>ARGSS</th>
- <th>ARGTRS</th>
+ <th>ACALD</th>
+ <th>ACALDt</th>
+ <th>ACKr</th>
+ <th>ACONTa</th>
+ <th>ACONTb</th>
+ <th>ACt2r</th>
+ <th>ADK1</th>
+ <th>AKGDH</th>
+ <th>AKGt2r</th>
+ <th>ALCD2x</th>
</tr>
</thead>
<tbody>
<tr>
- <th>ARBtex</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
- </tr>
- <tr>
- <th>ARGAGMt7pp</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
- </tr>
- <tr>
- <th>ARGDC</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
- </tr>
- <tr>
- <th>ARGDCpp</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
- </tr>
- <tr>
- <th>ARGORNt7pp</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
- </tr>
- <tr>
- <th>ARGSL</th>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.000000</td>
- </tr>
- <tr>
- <th>ARGSS</th>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0.000000</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.000000</td>
- </tr>
- <tr>
- <th>ARGTRS</th>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0.380008</td>
- <td> 0</td>
- <td> 0</td>
- <td> 0.380008</td>
+ <th>ACALD</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>ACALDt</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>ACKr</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>ACONTa</th>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ </tr>
+ <tr>
+ <th>ACONTb</th>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ <td>0.000000</td>
+ </tr>
+ <tr>
+ <th>ACt2r</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>ADK1</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>AKGDH</th>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ <td>0.858307</td>
+ </tr>
+ <tr>
+ <th>AKGt2r</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ </tr>
+ <tr>
+ <th>ALCD2x</th>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0</td>
+ <td>0</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
+ <td>0.858307</td>
+ <td>0.873922</td>
+ <td>0.873922</td>
</tr>
</tbody>
</table>
diff --git a/documentation_builder/faq.ipynb b/documentation_builder/faq.ipynb
index 468d075..c7d001c 100644
--- a/documentation_builder/faq.ipynb
+++ b/documentation_builder/faq.ipynb
@@ -1,330 +1,338 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:cde41ad75140ccb9197f8b812a0c01b585dd7fc2b363fb9c45596f02cafbc482"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "FAQ"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This document will address frequently asked questions not addressed in other pages of the documentation."
- ]
- },
- {
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I install cobrapy?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Please see the [INSTALL.md](https://github.com/opencobra/cobrapy/blob/master/INSTALL.md) file."
- ]
- },
- {
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I cite cobrapy?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Please cite the 2013 publication: [10.1186/1752-0509-7-74](http://dx.doi.org/doi:10.1186/1752-0509-7-74)"
- ]
- },
- {
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I rename reactions or metabolites?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "TL;DR Use Model.repair afterwards\n",
- "\n",
- "When renaming metabolites or reactions, there are issues because cobra indexes based off of ID's, which can cause errors. For example:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from __future__ import print_function\n",
- "import cobra.test\n",
- "model = cobra.test.create_test_model()\n",
- "\n",
- "for metabolite in model.metabolites:\n",
- " metabolite.id = \"test_\" + metabolite.id\n",
- "\n",
- "try:\n",
- " model.metabolites.get_by_id(model.metabolites[0].id)\n",
- "except KeyError as e:\n",
- " print(repr(e))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "KeyError('test_dcaACP_c',)\n"
- ]
- }
- ],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The Model.repair function will rebuild the necessary indexes"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.repair()\n",
- "model.metabolites.get_by_id(model.metabolites[0].id)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 2,
- "text": [
- "<Metabolite test_dcaACP_c at 0x688b450>"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I delete a gene?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "That depends on what precisely you mean by delete a gene.\n",
- "\n",
- "If you want to simulate the model with a gene knockout, use the cobra.maniupulation.delete_model_genes function. The effects of this function are reversed by cobra.manipulation.undelete_model_genes."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model = cobra.test.create_test_model()\n",
- "PGI = model.reactions.get_by_id(\"PGI\")\n",
- "print(\"bounds before knockout:\", (PGI.lower_bound, PGI.upper_bound))\n",
- "cobra.manipulation.delete_model_genes(model, [\"STM4221\"])\n",
- "print(\"bounds after knockouts\", (PGI.lower_bound, PGI.upper_bound))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "bounds before knockout: (-1000.0, 1000.0)\n",
- "bounds after knockouts (0.0, 0.0)\n"
- ]
- }
- ],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "If you want to actually remove all traces of a gene from a model, this is more difficult because this will require changing all the gene_reaction_rule strings for reactions involving the gene."
- ]
- },
- {
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I change the reversibility of a Reaction?"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Reaction.reversibility is a property in cobra which is computed when it is requested from the lower and upper bounds."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model = cobra.test.create_test_model()\n",
- "model.reactions.get_by_id(\"PGI\").reversibility"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "True"
- ]
- }
- ],
- "prompt_number": 4
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Trying to set it directly will result in an error: "
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "try:\n",
- " model.reactions.get_by_id(\"PGI\").reversibility = False\n",
- "except Exception as e:\n",
- " print(repr(e))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "AttributeError(\"can't set attribute\",)\n"
- ]
- }
- ],
- "prompt_number": 5
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# FAQ"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "This document will address frequently asked questions not addressed in other pages of the documentation."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I install cobrapy?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Please see the [INSTALL.md](https://github.com/opencobra/cobrapy/blob/master/INSTALL.md) file."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I cite cobrapy?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Please cite the 2013 publication: [10.1186/1752-0509-7-74](http://dx.doi.org/doi:10.1186/1752-0509-7-74)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I rename reactions or metabolites?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "TL;DR Use Model.repair afterwards\n",
+ "\n",
+ "When renaming metabolites or reactions, there are issues because cobra indexes based off of ID's, which can cause errors. For example:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The way to change the reversibility is to change the bounds to make the reaction irreversible."
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "KeyError('test_dcaACP_c',)\n"
]
- },
+ }
+ ],
+ "source": [
+ "from __future__ import print_function\n",
+ "import cobra.test\n",
+ "model = cobra.test.create_test_model()\n",
+ "\n",
+ "for metabolite in model.metabolites:\n",
+ " metabolite.id = \"test_\" + metabolite.id\n",
+ "\n",
+ "try:\n",
+ " model.metabolites.get_by_id(model.metabolites[0].id)\n",
+ "except KeyError as e:\n",
+ " print(repr(e))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The Model.repair function will rebuild the necessary indexes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.reactions.get_by_id(\"PGI\").lower_bound = 10\n",
- "model.reactions.get_by_id(\"PGI\").reversibility"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Metabolite test_dcaACP_c at 0x688b450>"
+ ]
+ },
+ "execution_count": 2,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "False"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.repair()\n",
+ "model.metabolites.get_by_id(model.metabolites[0].id)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I delete a gene?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "That depends on what precisely you mean by delete a gene.\n",
+ "\n",
+ "If you want to simulate the model with a gene knockout, use the cobra.maniupulation.delete_model_genes function. The effects of this function are reversed by cobra.manipulation.undelete_model_genes."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I generate an LP file from a COBRA model?"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "bounds before knockout: (-1000.0, 1000.0)\n",
+ "bounds after knockouts (0.0, 0.0)\n"
]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "While the cobrapy does not include python code to support this feature directly, many of the bundled solvers have this capability. Create the problem with one of these solvers, and use its appropriate function.\n",
- "\n",
- "Please note that unlike the LP file format, the MPS file format does not specify objective direction and is always a minimzation. Some (but not all) solvers will rewrite the maximization as a minimzation."
- ]
- },
+ }
+ ],
+ "source": [
+ "model = cobra.test.create_test_model()\n",
+ "PGI = model.reactions.get_by_id(\"PGI\")\n",
+ "print(\"bounds before knockout:\", (PGI.lower_bound, PGI.upper_bound))\n",
+ "cobra.manipulation.delete_model_genes(model, [\"STM4221\"])\n",
+ "print(\"bounds after knockouts\", (PGI.lower_bound, PGI.upper_bound))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "If you want to actually remove all traces of a gene from a model, this is more difficult because this will require changing all the gene_reaction_rule strings for reactions involving the gene."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I change the reversibility of a Reaction?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Reaction.reversibility is a property in cobra which is computed when it is requested from the lower and upper bounds."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model = cobra.test.create_test_model()\n",
- "# glpk through cglpk\n",
- "glp = cobra.solvers.cglpk.create_problem(model)\n",
- "glp.write(\"test.lp\")\n",
- "glp.write(\"test.mps\") # will not rewrite objective\n",
- "# gurobi\n",
- "gurobi_problem = cobra.solvers.gurobi_solver.create_problem(model)\n",
- "gurobi_problem.write(\"test.lp\")\n",
- "gurobi_problem.write(\"test.mps\") # rewrites objective\n",
- "# cplex\n",
- "cplex_problem = cobra.solvers.cplex_solver.create_problem(model)\n",
- "cplex_problem.write(\"test.lp\")\n",
- "cplex_problem.write(\"test.mps\") # rewrites objective"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "outputs": [],
- "prompt_number": 7
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model = cobra.test.create_test_model()\n",
+ "model.reactions.get_by_id(\"PGI\").reversibility"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Trying to set it directly will result in an error: "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "heading",
- "level": 3,
- "metadata": {},
- "source": [
- "How do I visualize my flux solutions?"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "AttributeError(\"can't set attribute\",)\n"
]
- },
+ }
+ ],
+ "source": [
+ "try:\n",
+ " model.reactions.get_by_id(\"PGI\").reversibility = False\n",
+ "except Exception as e:\n",
+ " print(repr(e))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The way to change the reversibility is to change the bounds to make the reaction irreversible."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "False"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "source": [
- "cobrapy works well with the [escher](https://escher.github.io/) package, which is well suited to this purpose. Consult the [escher documentation](https://escher.readthedocs.org/en/latest/) for examples."
- ]
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "model.reactions.get_by_id(\"PGI\").lower_bound = 10\n",
+ "model.reactions.get_by_id(\"PGI\").reversibility"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I generate an LP file from a COBRA model?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "While the cobrapy does not include python code to support this feature directly, many of the bundled solvers have this capability. Create the problem with one of these solvers, and use its appropriate function.\n",
+ "\n",
+ "Please note that unlike the LP file format, the MPS file format does not specify objective direction and is always a minimzation. Some (but not all) solvers will rewrite the maximization as a minimzation."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "model = cobra.test.create_test_model()\n",
+ "# glpk through cglpk\n",
+ "glp = cobra.solvers.cglpk.create_problem(model)\n",
+ "glp.write(\"test.lp\")\n",
+ "glp.write(\"test.mps\") # will not rewrite objective\n",
+ "# gurobi\n",
+ "gurobi_problem = cobra.solvers.gurobi_solver.create_problem(model)\n",
+ "gurobi_problem.write(\"test.lp\")\n",
+ "gurobi_problem.write(\"test.mps\") # rewrites objective\n",
+ "# cplex\n",
+ "cplex_problem = cobra.solvers.cplex_solver.create_problem(model)\n",
+ "cplex_problem.write(\"test.lp\")\n",
+ "cplex_problem.write(\"test.mps\") # rewrites objective"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### How do I visualize my flux solutions?"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "cobrapy works well with the [escher](https://escher.github.io/) package, which is well suited to this purpose. Consult the [escher documentation](https://escher.readthedocs.org/en/latest/) for examples."
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/faq.rst b/documentation_builder/faq.rst
index 1dafe99..a333331 100644
--- a/documentation_builder/faq.rst
+++ b/documentation_builder/faq.rst
@@ -40,6 +40,7 @@ indexes based off of ID's, which can cause errors. For example:
except KeyError as e:
print(repr(e))
+
.. parsed-literal::
KeyError('test_dcaACP_c',)
@@ -54,6 +55,7 @@ The Model.repair function will rebuild the necessary indexes
+
.. parsed-literal::
<Metabolite test_dcaACP_c at 0x688b450>
@@ -77,6 +79,7 @@ function are reversed by cobra.manipulation.undelete\_model\_genes.
cobra.manipulation.delete_model_genes(model, ["STM4221"])
print("bounds after knockouts", (PGI.lower_bound, PGI.upper_bound))
+
.. parsed-literal::
bounds before knockout: (-1000.0, 1000.0)
@@ -100,6 +103,7 @@ is requested from the lower and upper bounds.
+
.. parsed-literal::
True
@@ -115,6 +119,7 @@ Trying to set it directly will result in an error:
except Exception as e:
print(repr(e))
+
.. parsed-literal::
AttributeError("can't set attribute",)
@@ -130,6 +135,7 @@ reaction irreversible.
+
.. parsed-literal::
False
@@ -162,6 +168,7 @@ all) solvers will rewrite the maximization as a minimzation.
cplex_problem = cobra.solvers.cplex_solver.create_problem(model)
cplex_problem.write("test.lp")
cplex_problem.write("test.mps") # rewrites objective
+
How do I visualize my flux solutions?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/documentation_builder/gapfilling.ipynb b/documentation_builder/gapfilling.ipynb
new file mode 100644
index 0000000..3394995
--- /dev/null
+++ b/documentation_builder/gapfilling.ipynb
@@ -0,0 +1,185 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Gapfillling\n",
+ "\n",
+ "GrowMatch and SMILEY are gap-filling algorithms, which try to to make the minimal number of changes to a model and allow it to simulate growth. For more information, see [Kumar et al.](http://dx.doi.org/10.1371/journal.pcbi.1000308). Please note that these algorithms are Mixed-Integer Linear Programs, which need solvers such as gurobi or cplex to function correctly."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "import cobra.test\n",
+ "\n",
+ "model = cobra.test.create_test_model(\"salmonella\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In this model D-Fructose-6-phosphate is an essential metabolite. We will remove all the reactions using it, and at them to a separate model."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "# remove some reactions and add them to the universal reactions\n",
+ "Universal = cobra.Model(\"Universal_Reactions\")\n",
+ "for i in [i.id for i in model.metabolites.f6p_c.reactions]:\n",
+ " reaction = model.reactions.get_by_id(i)\n",
+ " Universal.add_reaction(reaction.copy())\n",
+ " reaction.remove_from_model()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now, because of these gaps, the model won't grow."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "3.067723590211908e-08"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.optimize().f"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We will use GrowMatch to add back the minimal number of reactions from this set of \"universal\" reactions (in this case just the ones we removed) to allow it to grow."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[[<Reaction GF6PTA at 0x7fcecddbc390>,\n",
+ " <Reaction MAN6PI_reverse at 0x7fcecddbc450>,\n",
+ " <Reaction F6PA_reverse at 0x7fcecddbc490>,\n",
+ " <Reaction PGI_reverse at 0x7fcecddbc510>,\n",
+ " <Reaction TKT2_reverse at 0x7fcecddbc590>]]"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.flux_analysis.growMatch(model, Universal)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can obtain multiple possible reaction sets by having the algorithm go through multiple iterations."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "---- Run 1 ----\n",
+ "FBP\n",
+ "GF6PTA\n",
+ "MAN6PI_reverse\n",
+ "PGI_reverse\n",
+ "TKT2_reverse\n",
+ "---- Run 2 ----\n",
+ "TALA\n",
+ "F6PP\n",
+ "GF6PTA\n",
+ "MAN6PI_reverse\n",
+ "F6PA_reverse\n",
+ "---- Run 3 ----\n",
+ "F6PP\n",
+ "GF6PTA\n",
+ "MAN6PI_reverse\n",
+ "F6PA_reverse\n",
+ "TKT2_reverse\n",
+ "---- Run 4 ----\n",
+ "TALA\n",
+ "FBP\n",
+ "GF6PTA\n",
+ "MAN6PI_reverse\n",
+ "PGI_reverse\n"
+ ]
+ }
+ ],
+ "source": [
+ "result = cobra.flux_analysis.growMatch(model, Universal, iterations=4)\n",
+ "for i, entries in enumerate(result):\n",
+ " print(\"---- Run %d ----\" % (i + 1))\n",
+ " for e in entries:\n",
+ " print(e.id)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/gapfilling.rst b/documentation_builder/gapfilling.rst
new file mode 100644
index 0000000..77c0d1c
--- /dev/null
+++ b/documentation_builder/gapfilling.rst
@@ -0,0 +1,104 @@
+
+Gapfillling
+===========
+
+GrowMatch and SMILEY are gap-filling algorithms, which try to to make
+the minimal number of changes to a model and allow it to simulate
+growth. For more information, see `Kumar et
+al. <http://dx.doi.org/10.1371/journal.pcbi.1000308>`__. Please note
+that these algorithms are Mixed-Integer Linear Programs, which need
+solvers such as gurobi or cplex to function correctly.
+
+.. code:: python
+
+ import cobra.test
+
+ model = cobra.test.create_test_model("salmonella")
+
+In this model D-Fructose-6-phosphate is an essential metabolite. We will
+remove all the reactions using it, and at them to a separate model.
+
+.. code:: python
+
+ # remove some reactions and add them to the universal reactions
+ Universal = cobra.Model("Universal_Reactions")
+ for i in [i.id for i in model.metabolites.f6p_c.reactions]:
+ reaction = model.reactions.get_by_id(i)
+ Universal.add_reaction(reaction.copy())
+ reaction.remove_from_model()
+
+Now, because of these gaps, the model won't grow.
+
+.. code:: python
+
+ model.optimize().f
+
+
+
+
+.. parsed-literal::
+
+ 3.067723590211908e-08
+
+
+
+We will use GrowMatch to add back the minimal number of reactions from
+this set of "universal" reactions (in this case just the ones we
+removed) to allow it to grow.
+
+.. code:: python
+
+ cobra.flux_analysis.growMatch(model, Universal)
+
+
+
+
+.. parsed-literal::
+
+ [[<Reaction GF6PTA at 0x7fcecddbc390>,
+ <Reaction MAN6PI_reverse at 0x7fcecddbc450>,
+ <Reaction F6PA_reverse at 0x7fcecddbc490>,
+ <Reaction PGI_reverse at 0x7fcecddbc510>,
+ <Reaction TKT2_reverse at 0x7fcecddbc590>]]
+
+
+
+We can obtain multiple possible reaction sets by having the algorithm go
+through multiple iterations.
+
+.. code:: python
+
+ result = cobra.flux_analysis.growMatch(model, Universal, iterations=4)
+ for i, entries in enumerate(result):
+ print("---- Run %d ----" % (i + 1))
+ for e in entries:
+ print(e.id)
+
+
+.. parsed-literal::
+
+ ---- Run 1 ----
+ FBP
+ GF6PTA
+ MAN6PI_reverse
+ PGI_reverse
+ TKT2_reverse
+ ---- Run 2 ----
+ TALA
+ F6PP
+ GF6PTA
+ MAN6PI_reverse
+ F6PA_reverse
+ ---- Run 3 ----
+ F6PP
+ GF6PTA
+ MAN6PI_reverse
+ F6PA_reverse
+ TKT2_reverse
+ ---- Run 4 ----
+ TALA
+ FBP
+ GF6PTA
+ MAN6PI_reverse
+ PGI_reverse
+
diff --git a/documentation_builder/getting_started.ipynb b/documentation_builder/getting_started.ipynb
index 748a1e8..bfd093a 100644
--- a/documentation_builder/getting_started.ipynb
+++ b/documentation_builder/getting_started.ipynb
@@ -1,857 +1,886 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:8ba1405f8cf805ab6aa98f3a22f31f1d598c18b1ec773c0ff9f569c253402679"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Getting Started"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/getting_started.ipynb)."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "To begin with, cobrapy comes with two bundled models for _Salmonella_ and _E. coli_. To load a test model, type"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from __future__ import print_function\n",
- "import cobra.test\n",
- "model = cobra.test.create_test_model(\"salmonella\")\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The reactions, metabolites, and genes attributes of the cobrapy model are are a special type of list called a DictList, and each one is made up of Reaction, Metabolite and Gene objects respectively."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(len(model.reactions))\n",
- "print(len(model.metabolites))\n",
- "print(len(model.genes))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "2546\n",
- "1802\n",
- "1264\n"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Just like a regular list, objects in the DictList can be retrived by index. For example, to get the 30th reaction in the model (at index 29 because of [0-indexing](https://en.wikipedia.org/wiki/Z ero-based_numbering)):"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.reactions[29]"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 3,
- "text": [
- "<Reaction 2AGPA180tipp at 0x7f6d94afc210>"
- ]
- }
- ],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Addictionally, items can be retrived by their id using the get_by_id() function. For example, to get the cytosolic atp metabolite object (the id is \"atp_c\"), we can do the following:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.metabolites.get_by_id(\"atp_c\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "<Metabolite atp_c at 0x7f6d94b4c610>"
- ]
- }
- ],
- "prompt_number": 4
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "As an added bonus, users with an interactive shell such as IPython will be able to tab-complete to list elements inside a list. While this is not recommended behavior for most code because of the possibility for characters like \"-\" inside ids, this is very useful while in an interactive prompt:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.reactions.EX_glc__D_e.lower_bound"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- "0.0"
- ]
- }
- ],
- "prompt_number": 5
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Reactions"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We will consider the reaction glucose 6-phosphate isomerase, which interconverts glucose 6-phosphate and fructose 6-phosphate. The reaction id for this reaction in our test model is PGI."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi = model.reactions.get_by_id(\"PGI\")\n",
- "pgi"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "<Reaction PGI at 0x7f6d93e62110>"
- ]
- }
- ],
- "prompt_number": 6
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can view the full name and reaction catalyzed as strings"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(pgi.name)\n",
- "print(pgi.reaction)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "glucose 6 phosphate isomerase\n",
- "g6p_c <=> f6p_c\n"
- ]
- }
- ],
- "prompt_number": 7
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can also view reaction upper and lower bounds. Because the pgi.lower_bound < 0, and pgi.upper_bound > 0, pgi is reversible"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)\n",
- "print(pgi.reversibility)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "-1000.0 < pgi < 1000.0\n",
- "True\n"
- ]
- }
- ],
- "prompt_number": 8
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can also ensure the reaction is mass balanced. This function will return elements which violate mass balance. If it comes back empty, then the reaction is mass balanced."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.check_mass_balance()"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 9,
- "text": [
- "[]"
- ]
- }
- ],
- "prompt_number": 9
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "In order to add a metabolite, we pass in a dict with the metabolite object and its coefficient"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.add_metabolites({model.metabolites.get_by_id(\"h_c\"): -1})\n",
- "pgi.reaction"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 10,
- "text": [
- "'g6p_c + h_c <=> f6p_c'"
- ]
- }
- ],
- "prompt_number": 10
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The reaction is no longer mass balanced"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.check_mass_balance()"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 11,
- "text": [
- "['PGI', {'C': 0.0, 'H': -1.0, 'O': 0.0, 'P': 0.0}]"
- ]
- }
- ],
- "prompt_number": 11
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can remove the metabolite, and the reaction will be balanced once again."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.pop(model.metabolites.get_by_id(\"h_c\"))\n",
- "print(pgi.reaction)\n",
- "print(pgi.check_mass_balance())"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "g6p_c <=> f6p_c\n",
- "[]\n"
- ]
- }
- ],
- "prompt_number": 12
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "It is also possible to build the reaction from a string. However, care must be taken when doing this to ensure reaction id's match those in the model. The direction of the arrow is also used to update the upper and lower bounds."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.reaction = \"g6p_c --> f6p_c + h_c + green_eggs + ham\""
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "unknown metabolite 'green_eggs' created\n",
- "unknown metabolite 'ham' created\n"
- ]
- }
- ],
- "prompt_number": 13
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.reaction"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 14,
- "text": [
- "'g6p_c --> ham + green_eggs + f6p_c + h_c'"
- ]
- }
- ],
- "prompt_number": 14
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.reaction = \"g6p_c <=> f6p_c\"\n",
- "pgi.reaction"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 15,
- "text": [
- "'g6p_c <=> f6p_c'"
- ]
- }
- ],
- "prompt_number": 15
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Metabolites"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We will consider cytosolic atp as our metabolite, which has the id atp_c in our test model."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "atp = model.metabolites.get_by_id(\"atp_c\")\n",
- "atp"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 16,
- "text": [
- "<Metabolite atp_c at 0x7f6d94b4c610>"
- ]
- }
- ],
- "prompt_number": 16
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can print out the metabolite name and compartment (cytosol in this case)."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(atp.name)\n",
- "print(atp.compartment)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "ATP\n",
- "c\n"
- ]
- }
- ],
- "prompt_number": 17
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can see that ATP is a charged molecule in our model."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "atp.charge"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 18,
- "text": [
- "-4"
- ]
- }
- ],
- "prompt_number": 18
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We can see the chemical formula for the metabolite as well."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(atp.formula)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "C10H12N5O13P3\n"
- ]
- }
- ],
- "prompt_number": 19
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The reactions attribute gives a frozenset of all reactions using the given metabolite. We can use this to count the number of reactions which use atp."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "len(atp.reactions)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 20,
- "text": [
- "348"
- ]
- }
- ],
- "prompt_number": 20
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A metabolite like glucose 6-phosphate will participate in fewer reactions."
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Getting Started\n",
+ "\n",
+ "To begin with, cobrapy comes with bundled models for _Salmonella_ and _E. coli_, as well as a \"textbook\" model of _E. coli_ core metabolism. To load a test model, type"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from __future__ import print_function\n",
+ "import cobra.test\n",
+ "\n",
+ "model = cobra.test.create_test_model(\"textbook\") # \"ecoli\" and \"salmonella\" are also valid arguments"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The reactions, metabolites, and genes attributes of the cobrapy model are a special type of list called a DictList, and each one is made up of Reaction, Metabolite and Gene objects respectively."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "95\n",
+ "72\n",
+ "137\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.metabolites.get_by_id(\"g6p_c\").reactions"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 21,
- "text": [
- "frozenset({<Reaction AB6PGH at 0x7f6d93b3d990>,\n",
- " <Reaction TRE6PH at 0x7f6d93d32050>,\n",
- " <Reaction TRE6PS at 0x7f6d93d32310>,\n",
- " <Reaction PGI at 0x7f6d93e62110>,\n",
- " <Reaction PGMT at 0x7f6d93e62690>,\n",
- " <Reaction HEX1 at 0x7f6d940be9d0>,\n",
- " <Reaction GLCptspp at 0x7f6d9412a650>,\n",
- " <Reaction G6PDH2r at 0x7f6d94155790>,\n",
- " <Reaction G6PP at 0x7f6d94155990>,\n",
- " <Reaction G6Pt6_2pp at 0x7f6d94155a50>})"
- ]
- }
- ],
- "prompt_number": 21
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Genes"
+ }
+ ],
+ "source": [
+ "print(len(model.reactions))\n",
+ "print(len(model.metabolites))\n",
+ "print(len(model.genes))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Just like a regular list, objects in the DictList can be retrived by index. For example, to get the 30th reaction in the model (at index 29 because of [0-indexing](https://en.wikipedia.org/wiki/Z ero-based_numbering)):"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Reaction EX_glu__L_e at 0x7fbbe05e5590>"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.reactions[29]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Addictionally, items can be retrived by their id using the get_by_id() function. For example, to get the cytosolic atp metabolite object (the id is \"atp_c\"), we can do the following:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Metabolite atp_c at 0x7fbbe0617350>"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.metabolites.get_by_id(\"atp_c\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "As an added bonus, users with an interactive shell such as IPython will be able to tab-complete to list elements inside a list. While this is not recommended behavior for most code because of the possibility for characters like \"-\" inside ids, this is very useful while in an interactive prompt:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "-10.0"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.reactions.EX_glc__D_e.lower_bound"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Reactions"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We will consider the reaction glucose 6-phosphate isomerase, which interconverts glucose 6-phosphate and fructose 6-phosphate. The reaction id for this reaction in our test model is PGI."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Reaction PGI at 0x7fbbe0611790>"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi = model.reactions.get_by_id(\"PGI\")\n",
+ "pgi"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can view the full name and reaction catalyzed as strings"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "glucose-6-phosphate isomerase\n",
+ "g6p_c <=> f6p_c\n"
]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The gene_reaction_rule is a boolean representation of the gene requirements for this reaction to be active as described in [Schellenberger et al 2011 Nature Protocols 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308).\n",
- "\n",
- "The GPR is stored as the gene_reaction_rule for a Reaction object as a string."
+ }
+ ],
+ "source": [
+ "print(pgi.name)\n",
+ "print(pgi.reaction)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can also view reaction upper and lower bounds. Because the pgi.lower_bound < 0, and pgi.upper_bound > 0, pgi is reversible"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "-1000.0 < pgi < 1000.0\n",
+ "True\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "gpr = pgi.gene_reaction_rule\n",
- "gpr"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 22,
- "text": [
- "'STM4221'"
- ]
- }
- ],
- "prompt_number": 22
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Corresponding gene objects also exist. These objects are tracked by the reactions itself, as well as by the model"
+ }
+ ],
+ "source": [
+ "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)\n",
+ "print(pgi.reversibility)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can also ensure the reaction is mass balanced. This function will return elements which violate mass balance. If it comes back empty, then the reaction is mass balanced."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{}"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.check_mass_balance()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In order to add a metabolite, we pass in a dict with the metabolite object and its coefficient"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'g6p_c + h_c <=> f6p_c'"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.add_metabolites({model.metabolites.get_by_id(\"h_c\"): -1})\n",
+ "pgi.reaction"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The reaction is no longer mass balanced"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'H': -1.0}"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.check_mass_balance()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can remove the metabolite, and the reaction will be balanced once again."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "g6p_c <=> f6p_c\n",
+ "{}\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.genes"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 23,
- "text": [
- "frozenset({<Gene STM4221 at 0x7f6d93e62190>})"
- ]
- }
- ],
- "prompt_number": 23
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi_gene = model.genes.get_by_id(\"STM4221\")\n",
- "pgi_gene"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 24,
- "text": [
- "<Gene STM4221 at 0x7f6d93e62190>"
- ]
- }
- ],
- "prompt_number": 24
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Each gene keeps track of the reactions it catalyzes"
+ }
+ ],
+ "source": [
+ "pgi.pop(model.metabolites.get_by_id(\"h_c\"))\n",
+ "print(pgi.reaction)\n",
+ "print(pgi.check_mass_balance())"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "It is also possible to build the reaction from a string. However, care must be taken when doing this to ensure reaction id's match those in the model. The direction of the arrow is also used to update the upper and lower bounds."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "unknown metabolite 'green_eggs' created\n",
+ "unknown metabolite 'ham' created\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi_gene.reactions"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 25,
- "text": [
- "frozenset({<Reaction PGI at 0x7f6d93e62110>})"
- ]
- }
- ],
- "prompt_number": 25
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Altering the gene_reaction_rule will create new gene objects if necessary and update all relationships."
+ }
+ ],
+ "source": [
+ "pgi.reaction = \"g6p_c --> f6p_c + h_c + green_eggs + ham\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'g6p_c --> green_eggs + ham + h_c + f6p_c'"
+ ]
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.reaction"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'g6p_c <=> f6p_c'"
+ ]
+ },
+ "execution_count": 15,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.reaction = \"g6p_c <=> f6p_c\"\n",
+ "pgi.reaction"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Metabolites"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We will consider cytosolic atp as our metabolite, which has the id atp_c in our test model."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Metabolite atp_c at 0x7fbbe0617350>"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "atp = model.metabolites.get_by_id(\"atp_c\")\n",
+ "atp"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can print out the metabolite name and compartment (cytosol in this case)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "ATP\n",
+ "c\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi.gene_reaction_rule = \"(spam or eggs)\"\n",
- "pgi.genes"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 26,
- "text": [
- "frozenset({<Gene eggs at 0x7f6d93ad5ad0>, <Gene spam at 0x7f6d93ad5b10>})"
- ]
- }
- ],
- "prompt_number": 26
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "pgi_gene.reactions"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 27,
- "text": [
- "frozenset()"
- ]
- }
- ],
- "prompt_number": 27
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Newly created genes are also added to the model"
+ }
+ ],
+ "source": [
+ "print(atp.name)\n",
+ "print(atp.compartment)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can see that ATP is a charged molecule in our model."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "-4"
+ ]
+ },
+ "execution_count": 18,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "atp.charge"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can see the chemical formula for the metabolite as well."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "C10H12N5O13P3\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.genes.get_by_id(\"spam\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 28,
- "text": [
- "<Gene spam at 0x7f6d93ad5b10>"
- ]
- }
- ],
- "prompt_number": 28
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The delete_model_genes function will evaluate the gpr and set the upper and lower bounds to 0 if the reaction is knocked out. This function can preserve existing deletions or reset them using the cumulative_deletions flag."
+ }
+ ],
+ "source": [
+ "print(atp.formula)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The reactions attribute gives a frozenset of all reactions using the given metabolite. We can use this to count the number of reactions which use atp."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "13"
+ ]
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "len(atp.reactions)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "A metabolite like glucose 6-phosphate will participate in fewer reactions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "frozenset({<Reaction G6PDH2r at 0x7fbbe05fd050>,\n",
+ " <Reaction GLCpts at 0x7fbbe05fd150>,\n",
+ " <Reaction PGI at 0x7fbbe0611790>,\n",
+ " <Reaction Biomass_Ecoli_core at 0x7fbbe0650ed0>})"
+ ]
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.metabolites.get_by_id(\"g6p_c\").reactions"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Genes"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The gene_reaction_rule is a boolean representation of the gene requirements for this reaction to be active as described in [Schellenberger et al 2011 Nature Protocols 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308).\n",
+ "\n",
+ "The GPR is stored as the gene_reaction_rule for a Reaction object as a string."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'b4025'"
+ ]
+ },
+ "execution_count": 22,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "gpr = pgi.gene_reaction_rule\n",
+ "gpr"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Corresponding gene objects also exist. These objects are tracked by the reactions itself, as well as by the model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "frozenset({<Gene b4025 at 0x7fbbe063dc90>})"
+ ]
+ },
+ "execution_count": 23,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.genes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Gene b4025 at 0x7fbbe063dc90>"
+ ]
+ },
+ "execution_count": 24,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi_gene = model.genes.get_by_id(\"b4025\")\n",
+ "pgi_gene"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Each gene keeps track of the reactions it catalyzes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "frozenset({<Reaction PGI at 0x7fbbe0611790>})"
+ ]
+ },
+ "execution_count": 25,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi_gene.reactions"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Altering the gene_reaction_rule will create new gene objects if necessary and update all relationships."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "frozenset({<Gene eggs at 0x7fbbe0611b50>, <Gene spam at 0x7fbbe0611e90>})"
+ ]
+ },
+ "execution_count": 26,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi.gene_reaction_rule = \"(spam or eggs)\"\n",
+ "pgi.genes"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "frozenset()"
+ ]
+ },
+ "execution_count": 27,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pgi_gene.reactions"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Newly created genes are also added to the model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Gene spam at 0x7fbbe0611e90>"
+ ]
+ },
+ "execution_count": 28,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.genes.get_by_id(\"spam\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The delete_model_genes function will evaluate the gpr and set the upper and lower bounds to 0 if the reaction is knocked out. This function can preserve existing deletions or reset them using the cumulative_deletions flag."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "-1000 < pgi < 1000\n",
+ "0.0 < pgi < 0.0\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.manipulation.delete_model_genes(model, [\"spam\"], cumulative_deletions=True)\n",
- "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)\n",
- "cobra.manipulation.delete_model_genes(model, [\"eggs\"], cumulative_deletions=True)\n",
- "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "-1000 < pgi < 1000\n",
- "0.0 < pgi < 0.0\n"
- ]
- }
- ],
- "prompt_number": 29
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The undelete_model_genes can be used to reset a gene deletion"
+ }
+ ],
+ "source": [
+ "cobra.manipulation.delete_model_genes(model, [\"spam\"], cumulative_deletions=True)\n",
+ "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)\n",
+ "cobra.manipulation.delete_model_genes(model, [\"eggs\"], cumulative_deletions=True)\n",
+ "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The undelete_model_genes can be used to reset a gene deletion"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "-1000 < pgi < 1000\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.manipulation.undelete_model_genes(model)\n",
- "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "-1000 < pgi < 1000\n"
- ]
- }
- ],
- "prompt_number": 30
}
],
- "metadata": {}
+ "source": [
+ "cobra.manipulation.undelete_model_genes(model)\n",
+ "print(pgi.lower_bound, \"< pgi <\", pgi.upper_bound)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
}
- ]
-}
\ No newline at end of file
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/getting_started.rst b/documentation_builder/getting_started.rst
index 216afb2..7658ece 100644
--- a/documentation_builder/getting_started.rst
+++ b/documentation_builder/getting_started.rst
@@ -2,21 +2,20 @@
Getting Started
===============
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/getting_started.ipynb>`__.
-
-To begin with, cobrapy comes with two bundled models for *Salmonella*
-and *E. coli*. To load a test model, type
+To begin with, cobrapy comes with bundled models for *Salmonella* and
+*E. coli*, as well as a "textbook" model of *E. coli* core metabolism.
+To load a test model, type
.. code:: python
from __future__ import print_function
import cobra.test
- model = cobra.test.create_test_model("salmonella")
+
+ model = cobra.test.create_test_model("textbook") # "ecoli" and "salmonella" are also valid arguments
The reactions, metabolites, and genes attributes of the cobrapy model
-are are a special type of list called a DictList, and each one is made
-up of Reaction, Metabolite and Gene objects respectively.
+are a special type of list called a DictList, and each one is made up of
+Reaction, Metabolite and Gene objects respectively.
.. code:: python
@@ -24,11 +23,12 @@ up of Reaction, Metabolite and Gene objects respectively.
print(len(model.metabolites))
print(len(model.genes))
+
.. parsed-literal::
- 2546
- 1802
- 1264
+ 95
+ 72
+ 137
Just like a regular list, objects in the DictList can be retrived by
@@ -42,9 +42,10 @@ because of
+
.. parsed-literal::
- <Reaction 2AGPA180tipp at 0x7f227ada62d0>
+ <Reaction EX_glu__L_e at 0x7fbbe05e5590>
@@ -58,9 +59,10 @@ id is "atp\_c"), we can do the following:
+
.. parsed-literal::
- <Metabolite atp_c at 0x7f227adf56d0>
+ <Metabolite atp_c at 0x7fbbe0617350>
@@ -76,9 +78,10 @@ interactive prompt:
+
.. parsed-literal::
- 0.0
+ -10.0
@@ -96,9 +99,10 @@ id for this reaction in our test model is PGI.
+
.. parsed-literal::
- <Reaction PGI at 0x7f227a10b1d0>
+ <Reaction PGI at 0x7fbbe0611790>
@@ -109,9 +113,10 @@ We can view the full name and reaction catalyzed as strings
print(pgi.name)
print(pgi.reaction)
+
.. parsed-literal::
- glucose 6 phosphate isomerase
+ glucose-6-phosphate isomerase
g6p_c <=> f6p_c
@@ -123,6 +128,7 @@ pgi.lower\_bound < 0, and pgi.upper\_bound > 0, pgi is reversible
print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
print(pgi.reversibility)
+
.. parsed-literal::
-1000.0 < pgi < 1000.0
@@ -139,9 +145,10 @@ the reaction is mass balanced.
+
.. parsed-literal::
- []
+ {}
@@ -155,6 +162,7 @@ object and its coefficient
+
.. parsed-literal::
'g6p_c + h_c <=> f6p_c'
@@ -169,9 +177,10 @@ The reaction is no longer mass balanced
+
.. parsed-literal::
- ['PGI', {'C': 0.0, 'H': -1.0, 'O': 0.0, 'P': 0.0}]
+ {'H': -1.0}
@@ -184,10 +193,11 @@ again.
print(pgi.reaction)
print(pgi.check_mass_balance())
+
.. parsed-literal::
g6p_c <=> f6p_c
- []
+ {}
It is also possible to build the reaction from a string. However, care
@@ -199,6 +209,7 @@ lower bounds.
pgi.reaction = "g6p_c --> f6p_c + h_c + green_eggs + ham"
+
.. parsed-literal::
unknown metabolite 'green_eggs' created
@@ -211,9 +222,24 @@ lower bounds.
+
.. parsed-literal::
- 'g6p_c --> f6p_c + green_eggs + ham + h_c'
+ 'g6p_c --> green_eggs + ham + h_c + f6p_c'
+
+
+
+.. code:: python
+
+ pgi.reaction = "g6p_c <=> f6p_c"
+ pgi.reaction
+
+
+
+
+.. parsed-literal::
+
+ 'g6p_c <=> f6p_c'
@@ -230,9 +256,10 @@ atp\_c in our test model.
+
.. parsed-literal::
- <Metabolite atp_c at 0x7f227adf56d0>
+ <Metabolite atp_c at 0x7fbbe0617350>
@@ -244,6 +271,7 @@ case).
print(atp.name)
print(atp.compartment)
+
.. parsed-literal::
ATP
@@ -258,6 +286,7 @@ We can see that ATP is a charged molecule in our model.
+
.. parsed-literal::
-4
@@ -270,6 +299,7 @@ We can see the chemical formula for the metabolite as well.
print(atp.formula)
+
.. parsed-literal::
C10H12N5O13P3
@@ -285,9 +315,10 @@ use atp.
+
.. parsed-literal::
- 348
+ 13
@@ -300,18 +331,13 @@ reactions.
+
.. parsed-literal::
- frozenset({<Reaction AB6PGH at 0x7f2279de6a50>,
- <Reaction TRE6PH at 0x7f2279fdb110>,
- <Reaction TRE6PS at 0x7f2279fdb3d0>,
- <Reaction PGI at 0x7f227a10b1d0>,
- <Reaction PGMT at 0x7f227a10b750>,
- <Reaction HEX1 at 0x7f227a368a90>,
- <Reaction GLCptspp at 0x7f227a3d2710>,
- <Reaction G6PDH2r at 0x7f227a3fd850>,
- <Reaction G6PP at 0x7f227a3fda50>,
- <Reaction G6Pt6_2pp at 0x7f227a3fdb10>})
+ frozenset({<Reaction G6PDH2r at 0x7fbbe05fd050>,
+ <Reaction GLCpts at 0x7fbbe05fd150>,
+ <Reaction PGI at 0x7fbbe0611790>,
+ <Reaction Biomass_Ecoli_core at 0x7fbbe0650ed0>})
@@ -333,9 +359,10 @@ string.
+
.. parsed-literal::
- 'STM4221'
+ 'b4025'
@@ -348,22 +375,24 @@ reactions itself, as well as by the model
+
.. parsed-literal::
- frozenset({<Gene STM4221 at 0x7f227a10b250>})
+ frozenset({<Gene b4025 at 0x7fbbe063dc90>})
.. code:: python
- pgi_gene = model.genes.get_by_id("STM4221")
+ pgi_gene = model.genes.get_by_id("b4025")
pgi_gene
+
.. parsed-literal::
- <Gene STM4221 at 0x7f227a10b250>
+ <Gene b4025 at 0x7fbbe063dc90>
@@ -375,9 +404,10 @@ Each gene keeps track of the reactions it catalyzes
+
.. parsed-literal::
- frozenset({<Reaction PGI at 0x7f227a10b1d0>})
+ frozenset({<Reaction PGI at 0x7fbbe0611790>})
@@ -391,9 +421,10 @@ necessary and update all relationships.
+
.. parsed-literal::
- frozenset({<Gene eggs at 0x7f2279d7ec90>, <Gene spam at 0x7f2279d7edd0>})
+ frozenset({<Gene eggs at 0x7fbbe0611b50>, <Gene spam at 0x7fbbe0611e90>})
@@ -403,6 +434,7 @@ necessary and update all relationships.
+
.. parsed-literal::
frozenset()
@@ -417,9 +449,10 @@ Newly created genes are also added to the model
+
.. parsed-literal::
- <Gene spam at 0x7f2279d7edd0>
+ <Gene spam at 0x7fbbe0611e90>
@@ -435,9 +468,10 @@ cumulative\_deletions flag.
cobra.manipulation.delete_model_genes(model, ["eggs"], cumulative_deletions=True)
print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
+
.. parsed-literal::
- 0 < pgi < 1000
+ -1000 < pgi < 1000
0.0 < pgi < 0.0
@@ -448,7 +482,8 @@ The undelete\_model\_genes can be used to reset a gene deletion
cobra.manipulation.undelete_model_genes(model)
print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
+
.. parsed-literal::
- 0 < pgi < 1000
+ -1000 < pgi < 1000
diff --git a/documentation_builder/index.rst b/documentation_builder/index.rst
index 2038d71..ced5671 100644
--- a/documentation_builder/index.rst
+++ b/documentation_builder/index.rst
@@ -3,6 +3,10 @@ Documentation for COBRApy
For installation instructions, please see `INSTALL.md
<https://github.com/opencobra/cobrapy/blob/master/INSTALL.md>`_.
+Many of the examples below are viewable as IPython notebooks, which can
+be viewed at `nbviewer
+<http://nbviewer.ipython.org/github/opencobra/cobrapy/tree/master/documentation_builder/>`_.
+
.. toctree::
:numbered:
:maxdepth: 2
@@ -16,6 +20,9 @@ For installation instructions, please see `INSTALL.md
milp
qp
loopless
+ gapfilling
+ solvers
+ pymatbridge
faq
cobra
diff --git a/documentation_builder/io.ipynb b/documentation_builder/io.ipynb
index 2f72a57..7e9508f 100644
--- a/documentation_builder/io.ipynb
+++ b/documentation_builder/io.ipynb
@@ -1,310 +1,316 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:7291cbe8367fe9d4f6ab1d7e394dbff9483b4b934edc182d648a499b003690ab"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Reading and Writing Models"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/io.ipynb).\n",
- "\n",
- "Functions for reading and writing models to various formats are included with cobrapy. The package also ships with models of *E. coli* and *Salmonella* in various formats for testing purposes. In this example, we will use these functions to read models from these test files in various formats."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "import cobra.test\n",
- "\n",
- "print(\"E. coli test files: \")\n",
- "print(\", \".join([i for i in dir(cobra.test) if i.startswith(\"ecoli\")]))\n",
- "print(\"\")\n",
- "print(\"Salmonella test files: \")\n",
- "print(\", \".join([i for i in dir(cobra.test) if i.startswith(\"salmonella\")]))\n",
- "\n",
- "salmonella_model = cobra.test.create_test_model(\"salmonella\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "E. coli test files: \n",
- "ecoli_json, ecoli_mat, ecoli_pickle, ecoli_sbml\n",
- "\n",
- "Salmonella test files: \n",
- "salmonella_fbc_sbml, salmonella_pickle, salmonella_sbml\n"
- ]
- }
- ],
- "prompt_number": 1
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "JSON"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "cobrapy has a [JSON](https://en.wikipedia.org/wiki/JSON) (JavaScript Object Notation) representation. This is the ideal format for storing a cobra model on a computer, or for interoperability with [escher](https://escher.github.io). Additional fields, however, will not be saved."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.load_json_model(cobra.test.ecoli_json)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 2,
- "text": [
- "<Model iJO1366 at 0x7f8d2fa20150>"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.write_sbml_model(salmonella_model, \"test.json\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 3
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "SBML"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The [Systems Biology Markup Language](http://sbml.org) is an XML-based standard format for distributing models. Cobrapy can use [libsbml](http://sbml.org/Software/libSBML), which must be installed separately (see installation instructions) to read and write SBML files.\n",
- "\n",
- "Initially, the COBRA format for SBML files used the \"notes\" field in SBML files. More recently, however, the [FBC extension](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29) to SBML has come into existence, which defines its own fields.\n",
- "\n",
- "Cobrapy can handle both formats (assuming libsbml has been installed correctly). When reading in a model, it will automatically detect whether fbc was used or not. When writing a model, the use_fbc_package can be used."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.read_sbml_model(cobra.test.salmonella_sbml)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "<Model Salmonella_consensus_build_1 at 0x7f8d480ad710>"
- ]
- }
- ],
- "prompt_number": 4
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.read_sbml_model(cobra.test.salmonella_fbc_sbml)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- "<Model Salmonella_consensus_build_1 at 0x7f8d480ad5d0>"
- ]
- }
- ],
- "prompt_number": 5
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.write_sbml_model(salmonella_model, \"test.xml\",\n",
- " use_fbc_package=False)\n",
- "cobra.io.write_sbml_model(salmonella_model, \"test_fbc.xml\",\n",
- " use_fbc_package=True)\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 6
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "MATLAB"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Often, models may be imported and exported soley for the purposes of working with the same models in cobrapy and the [MATLAB cobra toolbox](http://opencobra.github.io/cobratoolbox/). MATLAB has its own \".mat\" format for storing variables. Reading and writing to these mat files from python requires scipy, and is generally much faster than using libsbml.\n",
- "\n",
- "A mat file can contain multiple MATLAB variables. Therefore, the variable name of the model in the MATLAB file can be passed into the reading function:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.load_matlab_model(cobra.test.ecoli_mat, variable_name=\"iJO1366\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 7,
- "text": [
- "<Model iJO1366 at 0x7f8d48090b50>"
- ]
- }
- ],
- "prompt_number": 7
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Reading and Writing Models\n",
+ "\n",
+ "Cobrapy supports reading and writing models in SBML (with and without FBC), JSON, MAT, and pickle formats. Generally, SBML with FBC is the preferred format for general use.\n",
+ "\n",
+ "The package also ships with test models in various formats for testing purposes."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "If the mat file contains only a single model, cobra can figure out which variable to read from, and the variable_name paramter is unnecessary."
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "mini test files: \n",
+ "mini.mat, mini_cobra.xml, mini.json, mini_fbc2.xml, mini_fbc1.xml, mini.pickle\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.load_matlab_model(cobra.test.ecoli_mat)"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 8,
- "text": [
- "<Model iJO1366 at 0x7f8d2d85af10>"
- ]
- }
- ],
- "prompt_number": 8
- },
+ }
+ ],
+ "source": [
+ "import cobra.test\n",
+ "import os\n",
+ "\n",
+ "print(\"mini test files: \")\n",
+ "print(\", \".join([i for i in os.listdir(cobra.test.data_directory) if i.startswith(\"mini\")]))\n",
+ "\n",
+ "textbook_model = cobra.test.create_test_model(\"textbook\")\n",
+ "ecoli_model = cobra.test.create_test_model(\"ecoli\")\n",
+ "salmonella_model = cobra.test.create_test_model(\"salmonella\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## SBML"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The [Systems Biology Markup Language](http://sbml.org) is an XML-based standard format for distributing models which has support for COBRA models through the [FBC extension](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29) version 2.\n",
+ "\n",
+ "Cobrapy has native support for reading and writing SBML with FBCv2. Please note that all id's in the model must conform to the SBML SID requirements in order to generate a valid SBML file."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "<Model mini_textbook at 0x7f82fc4aec90>"
+ ]
+ },
+ "execution_count": 2,
"metadata": {},
- "source": [
- "Saving models to mat files is also relatively straightforward"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.io.read_sbml_model(os.path.join(cobra.test.data_directory, \"mini_fbc2.xml\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "cobra.io.write_sbml_model(textbook_model, \"test_fbc2.xml\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "There are other dialects of SBML prior to FBC 2 which have previously been use to encode COBRA models. The primary ones is the \"COBRA\" dialect which used the \"notes\" fields in SBML files.\n",
+ "\n",
+ "Cobrapy can use [libsbml](http://sbml.org/Software/libSBML), which must be installed separately (see installation instructions) to read and write these files. When reading in a model, it will automatically detect whether fbc was used or not. When writing a model, the use_fbc_package flag can be used can be used."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cobra.io.save_matlab_model(ecoli_model, \"test_ecoli_model.mat\")"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Model mini_textbook at 0x7f82cc744c10>"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "outputs": [
- {
- "ename": "NameError",
- "evalue": "name 'ecoli_model' is not defined",
- "output_type": "pyerr",
- "traceback": [
- "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)",
- "\u001b[1;32m<ipython-input-9-899c9ca38882>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mcobra\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mio\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msave_matlab_model\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mecoli_model\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\"test_ecoli_model.mat\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[1;31mNameError\u001b[0m: name 'ecoli_model' is not defined"
- ]
- }
- ],
- "prompt_number": 9
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.io.read_sbml_model(os.path.join(cobra.test.data_directory, \"mini_cobra.xml\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "cobra.io.write_sbml_model(textbook_model, \"test_cobra.xml\", use_fbc_package=False)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## JSON\n",
+ "\n",
+ "cobrapy models have a [JSON](https://en.wikipedia.org/wiki/JSON) (JavaScript Object Notation) representation. This format was crated for interoperability with [escher](https://escher.github.io). Additional fields, however, will not be saved."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "heading",
- "level": 2,
+ "data": {
+ "text/plain": [
+ "<Model mini_textbook at 0x7f82fc4d4f50>"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "source": [
- "Pickle"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.io.load_json_model(os.path.join(cobra.test.data_directory, \"mini.json\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "cobra.io.write_sbml_model(textbook_model, \"test.json\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## MATLAB"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Often, models may be imported and exported soley for the purposes of working with the same models in cobrapy and the [MATLAB cobra toolbox](http://opencobra.github.io/cobratoolbox/). MATLAB has its own \".mat\" format for storing variables. Reading and writing to these mat files from python requires scipy.\n",
+ "\n",
+ "A mat file can contain multiple MATLAB variables. Therefore, the variable name of the model in the MATLAB file can be passed into the reading function:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "<Model mini_textbook at 0x7f82cc97b110>"
+ ]
+ },
+ "execution_count": 8,
"metadata": {},
- "source": [
- "Cobra models can be serialized using the python serialization format, [pickle](https://docs.python.org/2/library/pickle.html). While this will save any extra fields which may have been created, it does not work with any other tools and can break between cobrapy major versions. JSON is generally the preferred format."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cobra.io.load_matlab_model(os.path.join(cobra.test.data_directory, \"mini.mat\"),\n",
+ " variable_name=\"mini_textbook\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "If the mat file contains only a single model, cobra can figure out which variable to read from, and the variable_name paramter is unnecessary."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from cPickle import load, dump\n",
- "\n",
- "# read in the test models\n",
- "with open(cobra.test.ecoli_pickle, \"rb\") as infile:\n",
- " ecoli_model = load(infile)\n",
- "with open(cobra.test.salmonella_pickle, \"rb\") as infile:\n",
- " salmonella_model = load(infile)\n",
- "\n",
- "# output to a file\n",
- "with open(\"test_output.pickle\", \"wb\") as outfile:\n",
- " dump(salmonella_model, outfile)\n"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Model mini_textbook at 0x7f82fc4d4450>"
+ ]
+ },
+ "execution_count": 9,
"metadata": {},
- "outputs": []
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "cobra.io.load_matlab_model(os.path.join(cobra.test.data_directory, \"mini.mat\"))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Saving models to mat files is also relatively straightforward"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "cobra.io.save_matlab_model(textbook_model, \"test.mat\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Pickle"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Cobra models can be serialized using the python serialization format, [pickle](https://docs.python.org/2/library/pickle.html). While this will save any extra fields which may have been created, it does not work with any other tools and can break between cobrapy major versions. JSON, SBML, and MAT are generally the preferred format."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from pickle import load, dump\n",
+ "\n",
+ "# read in the test models\n",
+ "with open(os.path.join(cobra.test.data_directory, \"mini.pickle\"), \"rb\") as infile:\n",
+ " mini_model = load(infile)\n",
+ "\n",
+ "# output to a file\n",
+ "with open(\"test.pickle\", \"wb\") as outfile:\n",
+ " dump(textbook_model, outfile)"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/io.rst b/documentation_builder/io.rst
index bcd8112..e2fb878 100644
--- a/documentation_builder/io.rst
+++ b/documentation_builder/io.rst
@@ -2,108 +2,113 @@
Reading and Writing Models
==========================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/io.ipynb>`__.
+Cobrapy supports reading and writing models in SBML (with and without
+FBC), JSON, MAT, and pickle formats. Generally, SBML with FBC is the
+preferred format for general use.
-Functions for reading and writing models to various formats are included
-with cobrapy. The package also ships with models of *E. coli* and
-*Salmonella* in various formats for testing purposes. In this example,
-we will use these functions to read models from these test files in
-various formats.
+The package also ships with test models in various formats for testing
+purposes.
.. code:: python
import cobra.test
+ import os
- print("E. coli test files: ")
- print(", ".join([i for i in dir(cobra.test) if i.startswith("ecoli")]))
- print("")
- print("Salmonella test files: ")
- print(", ".join([i for i in dir(cobra.test) if i.startswith("salmonella")]))
+ print("mini test files: ")
+ print(", ".join([i for i in os.listdir(cobra.test.data_directory) if i.startswith("mini")]))
+ textbook_model = cobra.test.create_test_model("textbook")
+ ecoli_model = cobra.test.create_test_model("ecoli")
salmonella_model = cobra.test.create_test_model("salmonella")
+
.. parsed-literal::
- E. coli test files:
- ecoli_json, ecoli_mat, ecoli_pickle, ecoli_sbml
-
- Salmonella test files:
- salmonella_fbc_sbml, salmonella_pickle, salmonella_sbml
+ mini test files:
+ mini.mat, mini_cobra.xml, mini.json, mini_fbc2.xml, mini_fbc1.xml, mini.pickle
-JSON
+SBML
----
-cobrapy has a `JSON <https://en.wikipedia.org/wiki/JSON>`__ (JavaScript
-Object Notation) representation. This is the ideal format for storing a
-cobra model on a computer, or for interoperability with
-`escher <https://escher.github.io>`__. Additional fields, however, will
-not be saved.
+The `Systems Biology Markup Language <http://sbml.org>`__ is an
+XML-based standard format for distributing models which has support for
+COBRA models through the `FBC
+extension <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29>`__
+version 2.
+
+Cobrapy has native support for reading and writing SBML with FBCv2.
+Please note that all id's in the model must conform to the SBML SID
+requirements in order to generate a valid SBML file.
.. code:: python
- cobra.io.load_json_model(cobra.test.ecoli_json)
+ cobra.io.read_sbml_model(os.path.join(cobra.test.data_directory, "mini_fbc2.xml"))
+
.. parsed-literal::
- <Model iJO1366 at 0x7f8d2fa20150>
+ <Model mini_textbook at 0x7f82fc4aec90>
.. code:: python
- cobra.io.write_sbml_model(salmonella_model, "test.json")
-SBML
-----
-
-The `Systems Biology Markup Language <http://sbml.org>`__ is an
-XML-based standard format for distributing models. Cobrapy can use
-`libsbml <http://sbml.org/Software/libSBML>`__, which must be installed
-separately (see installation instructions) to read and write SBML files.
+ cobra.io.write_sbml_model(textbook_model, "test_fbc2.xml")
-Initially, the COBRA format for SBML files used the "notes" field in
-SBML files. More recently, however, the `FBC
-extension <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29>`__
-to SBML has come into existence, which defines its own fields.
+There are other dialects of SBML prior to FBC 2 which have previously
+been use to encode COBRA models. The primary ones is the "COBRA" dialect
+which used the "notes" fields in SBML files.
-Cobrapy can handle both formats (assuming libsbml has been installed
-correctly). When reading in a model, it will automatically detect
+Cobrapy can use `libsbml <http://sbml.org/Software/libSBML>`__, which
+must be installed separately (see installation instructions) to read and
+write these files. When reading in a model, it will automatically detect
whether fbc was used or not. When writing a model, the use\_fbc\_package
-can be used.
+flag can be used can be used.
.. code:: python
- cobra.io.read_sbml_model(cobra.test.salmonella_sbml)
+ cobra.io.read_sbml_model(os.path.join(cobra.test.data_directory, "mini_cobra.xml"))
+
.. parsed-literal::
- <Model Salmonella_consensus_build_1 at 0x7f8d480ad710>
+ <Model mini_textbook at 0x7f82cc744c10>
.. code:: python
- cobra.io.read_sbml_model(cobra.test.salmonella_fbc_sbml)
+ cobra.io.write_sbml_model(textbook_model, "test_cobra.xml", use_fbc_package=False)
+
+JSON
+----
+
+cobrapy models have a `JSON <https://en.wikipedia.org/wiki/JSON>`__
+(JavaScript Object Notation) representation. This format was crated for
+interoperability with `escher <https://escher.github.io>`__. Additional
+fields, however, will not be saved.
+
+.. code:: python
+
+ cobra.io.load_json_model(os.path.join(cobra.test.data_directory, "mini.json"))
+
.. parsed-literal::
- <Model Salmonella_consensus_build_1 at 0x7f8d480ad5d0>
+ <Model mini_textbook at 0x7f82fc4d4f50>
.. code:: python
- cobra.io.write_sbml_model(salmonella_model, "test.xml",
- use_fbc_package=False)
- cobra.io.write_sbml_model(salmonella_model, "test_fbc.xml",
- use_fbc_package=True)
+ cobra.io.write_sbml_model(textbook_model, "test.json")
MATLAB
------
@@ -112,8 +117,7 @@ Often, models may be imported and exported soley for the purposes of
working with the same models in cobrapy and the `MATLAB cobra
toolbox <http://opencobra.github.io/cobratoolbox/>`__. MATLAB has its
own ".mat" format for storing variables. Reading and writing to these
-mat files from python requires scipy, and is generally much faster than
-using libsbml.
+mat files from python requires scipy.
A mat file can contain multiple MATLAB variables. Therefore, the
variable name of the model in the MATLAB file can be passed into the
@@ -121,13 +125,15 @@ reading function:
.. code:: python
- cobra.io.load_matlab_model(cobra.test.ecoli_mat, variable_name="iJO1366")
+ cobra.io.load_matlab_model(os.path.join(cobra.test.data_directory, "mini.mat"),
+ variable_name="mini_textbook")
+
.. parsed-literal::
- <Model iJO1366 at 0x7f8d48090b50>
+ <Model mini_textbook at 0x7f82cc97b110>
@@ -136,13 +142,14 @@ variable to read from, and the variable\_name paramter is unnecessary.
.. code:: python
- cobra.io.load_matlab_model(cobra.test.ecoli_mat)
+ cobra.io.load_matlab_model(os.path.join(cobra.test.data_directory, "mini.mat"))
+
.. parsed-literal::
- <Model iJO1366 at 0x7f8d2d85af10>
+ <Model mini_textbook at 0x7f82fc4d4450>
@@ -150,20 +157,7 @@ Saving models to mat files is also relatively straightforward
.. code:: python
- cobra.io.save_matlab_model(ecoli_model, "test_ecoli_model.mat")
-
-::
-
-
- ---------------------------------------------------------------------------
- NameError Traceback (most recent call last)
-
- <ipython-input-9-899c9ca38882> in <module>()
- ----> 1 cobra.io.save_matlab_model(ecoli_model, "test_ecoli_model.mat")
-
-
- NameError: name 'ecoli_model' is not defined
-
+ cobra.io.save_matlab_model(textbook_model, "test.mat")
Pickle
------
@@ -171,19 +165,17 @@ Pickle
Cobra models can be serialized using the python serialization format,
`pickle <https://docs.python.org/2/library/pickle.html>`__. While this
will save any extra fields which may have been created, it does not work
-with any other tools and can break between cobrapy major versions. JSON
-is generally the preferred format.
+with any other tools and can break between cobrapy major versions. JSON,
+SBML, and MAT are generally the preferred format.
.. code:: python
- from cPickle import load, dump
+ from pickle import load, dump
# read in the test models
- with open(cobra.test.ecoli_pickle, "rb") as infile:
- ecoli_model = load(infile)
- with open(cobra.test.salmonella_pickle, "rb") as infile:
- salmonella_model = load(infile)
+ with open(os.path.join(cobra.test.data_directory, "mini.pickle"), "rb") as infile:
+ mini_model = load(infile)
# output to a file
- with open("test_output.pickle", "wb") as outfile:
- dump(salmonella_model, outfile)
+ with open("test.pickle", "wb") as outfile:
+ dump(textbook_model, outfile)
diff --git a/documentation_builder/loopless.ipynb b/documentation_builder/loopless.ipynb
index d536413..7015d42 100644
--- a/documentation_builder/loopless.ipynb
+++ b/documentation_builder/loopless.ipynb
@@ -1,268 +1,283 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:9166596ba510dcfab5d2ea0acf45d2627a466ed67974cf738510c3aef3d47f92"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Loopless FBA"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/loopless.ipynb).\n",
- "\n",
- "The goal of this procedure is identification of a thermodynamically consistent flux state without loops, as implied by the name.\n",
- "\n",
- "Usually, the model has the following constraints.\n",
- "$$ S \\cdot v = 0 $$\n",
- "$$ lb \\le v \\le ub $$\n",
- "\n",
- "However, this will allow for thermodynamically infeasible loops (referred to as type 3 loops) to occur, where flux flows around a cycle without any net change of metabolites. For most cases, this is not a major issue, as solutions with these loops can usually be converted to equivalent solutions without them. However, if a flux state is desired which does not exhibit any of these loops, loopless FBA can be used. The formulation used here is modified from [Schellenberger et al.](ht [...]
- "\n",
- "We can make the model irreversible, so that all reactions will satisfy\n",
- "$$ 0 \\le lb \\le v \\le ub \\le \\max(ub) $$\n",
- "\n",
- "We will add in boolean indicators as well, such that\n",
- "$$ \\max(ub) i \\ge v $$\n",
- "$$ i \\in {0, 1} $$\n",
- "\n",
- "We also want to ensure that an entry in the row space of S also exists with negative values wherever v is nonzero. In this expression, $1-i$ acts as a not to indicate inactivity of a reaction.\n",
- "\n",
- "$$ S^\\mathsf T x - (1 - i) (\\max(ub) + 1) \\le -1 $$\n",
- "\n",
- "We will construct an LP integrating both constraints.\n",
- "\n",
- "$$ \\left(\n",
- "\\begin{matrix}\n",
- "S & 0 & 0\\\\\n",
- "-I & \\max(ub)I & 0 \\\\\n",
- "0 & (\\max(ub) + 1)I & S^\\mathsf T\n",
- "\\end{matrix}\n",
- "\\right)\n",
- "\\cdot\n",
- "\\left(\n",
- "\\begin{matrix}\n",
- "v \\\\\n",
- "i \\\\\n",
- "x\n",
- "\\end{matrix}\n",
- "\\right)\n",
- "\\begin{matrix}\n",
- "&=& 0 \\\\\n",
- "&\\ge& 0 \\\\\n",
- "&\\le& \\max(ub)\n",
- "\\end{matrix}$$\n",
- "\n",
- "Note that these extra constraints are not applied to boundary reactions which bring metabolites in and out of the system."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "import cobra.test\n",
- "from cobra import Reaction, Metabolite, Model\n",
- "from cobra.flux_analysis.loopless import construct_loopless_model\n",
- "from cobra.solvers import get_solver_name\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We will demonstrate with a toy model which has a simple loop cycling A -> B -> C -> A, with A allowed to enter the system and C allowed to leave. A graphical view of the system is drawn below:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "figure(figsize=(10.5, 4.5), frameon=False)\n",
- "gca().axis(\"off\")\n",
- "xlim(0.5, 3.5)\n",
- "ylim(0.7, 2.2)\n",
- "arrow_params = {\"head_length\": 0.08, \"head_width\": 0.1, \"ec\": \"k\", \"fc\": \"k\"}\n",
- "text_params = {\"fontsize\": 25, \"horizontalalignment\": \"center\", \"verticalalignment\": \"center\"}\n",
- "arrow(0.5, 1, 0.85, 0, **arrow_params) # EX_A\n",
- "arrow(1.5, 1, 0.425, 0.736, **arrow_params) # v1\n",
- "arrow(2.04, 1.82, 0.42, -0.72, **arrow_params) # v2\n",
- "arrow(2.4, 1, -0.75, 0, **arrow_params) # v3\n",
- "arrow(2.6, 1, 0.75, 0, **arrow_params)\n",
- "# reaction labels\n",
- "text(0.9, 1.15, \"EX_A\", **text_params)\n",
- "text(1.6, 1.5, r\"v$_1$\", **text_params)\n",
- "text(2.4, 1.5, r\"v$_2$\", **text_params)\n",
- "text(2, 0.85, r\"v$_3$\", **text_params)\n",
- "text(2.9, 1.15, \"DM_C\", **text_params)\n",
- "# metabolite labels\n",
- "scatter(1.5, 1, s=250, color='#c994c7')\n",
- "text(1.5, 0.9, \"A\", **text_params)\n",
- "scatter(2, 1.84, s=250, color='#c994c7')\n",
- "text(2, 1.95, \"B\", **text_params)\n",
- "scatter(2.5, 1, s=250, color='#c994c7')\n",
- "text(2.5, 0.9, \"C\", **text_params);"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAnIAAAEcCAYAAABDOFkiAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzt3Xe4JFWd//H3dzIMDEiOgigGFhdEJIkBwbACZgWRjP4M\nBEVXxDWCmJY1O7oGQBEDqKigiAl0DczOggkRFRRUBETJDDDx+/ujTjOXy823u6ur+/16nvvUrb7V\nXd+BDp8+p845kZlIkiSpeWbUXYAkSZKmxiAnSZLUUAY5SZKkhjLISZIkNZRBTpIkqaEMcpIkSQ1l\nkJMkSWoog5wkSVJDGeQkSZIayiAnSZLUUAY5SZKkhjLISZIkNZRBTpIkqaEMcpIkSQ1lkJMkSWoo\ng5wkSVJDGeQkSZIayiAnSZLUUAY5SZKkhjLISZIkNZRBTpIkqaEMcpIkSQ1lkJMkSWoog5wkSVJD\nGeQkSZIay [...]
- "text": [
- "<matplotlib.figure.Figure at 0x2d53490>"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "test_model = Model()\n",
- "test_model.add_metabolites(Metabolite(\"A\"))\n",
- "test_model.add_metabolites(Metabolite(\"B\"))\n",
- "test_model.add_metabolites(Metabolite(\"C\"))\n",
- "EX_A = Reaction(\"EX_A\")\n",
- "EX_A.add_metabolites({test_model.metabolites.A: 1})\n",
- "DM_C = Reaction(\"DM_C\")\n",
- "DM_C.add_metabolites({test_model.metabolites.C: -1})\n",
- "v1 = Reaction(\"v1\")\n",
- "v1.add_metabolites({test_model.metabolites.A: -1, test_model.metabolites.B: 1})\n",
- "v2 = Reaction(\"v2\")\n",
- "v2.add_metabolites({test_model.metabolites.B: -1, test_model.metabolites.C: 1})\n",
- "v3 = Reaction(\"v3\")\n",
- "v3.add_metabolites({test_model.metabolites.C: -1, test_model.metabolites.A: 1})\n",
- "DM_C.objective_coefficient = 1\n",
- "test_model.add_reactions([EX_A, DM_C, v1, v2, v3])\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "While this model contains a loop, a flux state exists which has no flux through reaction v3, and is identified by loopless FBA."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "construct_loopless_model(test_model).optimize()"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "<Solution 1000.00 at 0x62cd250>"
- ]
- }
- ],
- "prompt_number": 4
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Loopless FBA\n",
+ "\n",
+ "The goal of this procedure is identification of a thermodynamically consistent flux state without loops, as implied by the name.\n",
+ "\n",
+ "Usually, the model has the following constraints.\n",
+ "$$ S \\cdot v = 0 $$\n",
+ "$$ lb \\le v \\le ub $$\n",
+ "\n",
+ "However, this will allow for thermodynamically infeasible loops (referred to as type 3 loops) to occur, where flux flows around a cycle without any net change of metabolites. For most cases, this is not a major issue, as solutions with these loops can usually be converted to equivalent solutions without them. However, if a flux state is desired which does not exhibit any of these loops, loopless FBA can be used. The formulation used here is modified from [Schellenberger et al.](http [...]
+ "\n",
+ "We can make the model irreversible, so that all reactions will satisfy\n",
+ "$$ 0 \\le lb \\le v \\le ub \\le \\max(ub) $$\n",
+ "\n",
+ "We will add in boolean indicators as well, such that\n",
+ "$$ \\max(ub) i \\ge v $$\n",
+ "$$ i \\in {0, 1} $$\n",
+ "\n",
+ "We also want to ensure that an entry in the row space of S also exists with negative values wherever v is nonzero. In this expression, $1-i$ acts as a not to indicate inactivity of a reaction.\n",
+ "\n",
+ "$$ S^\\mathsf T x - (1 - i) (\\max(ub) + 1) \\le -1 $$\n",
+ "\n",
+ "We will construct an LP integrating both constraints.\n",
+ "\n",
+ "$$ \\left(\n",
+ "\\begin{matrix}\n",
+ "S & 0 & 0\\\\\n",
+ "-I & \\max(ub)I & 0 \\\\\n",
+ "0 & (\\max(ub) + 1)I & S^\\mathsf T\n",
+ "\\end{matrix}\n",
+ "\\right)\n",
+ "\\cdot\n",
+ "\\left(\n",
+ "\\begin{matrix}\n",
+ "v \\\\\n",
+ "i \\\\\n",
+ "x\n",
+ "\\end{matrix}\n",
+ "\\right)\n",
+ "\\begin{matrix}\n",
+ "&=& 0 \\\\\n",
+ "&\\ge& 0 \\\\\n",
+ "&\\le& \\max(ub)\n",
+ "\\end{matrix}$$\n",
+ "\n",
+ "Note that these extra constraints are not applied to boundary reactions which bring metabolites in and out of the system."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from matplotlib.pylab import *\n",
+ "%matplotlib inline\n",
+ "\n",
+ "import cobra.test\n",
+ "from cobra import Reaction, Metabolite, Model\n",
+ "from cobra.flux_analysis.loopless import construct_loopless_model\n",
+ "from cobra.solvers import get_solver_name"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We will demonstrate with a toy model which has a simple loop cycling A -> B -> C -> A, with A allowed to enter the system and C allowed to leave. A graphical view of the system is drawn below:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAnIAAAEcCAYAAABDOFkiAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzt3Xe4JFWd//H3dzJpQJAMC6K4iLCoKEmMgLoSBBVBJaNr\nIKzgT8UsioHFrKMrCijiKmYxYQDMzM6CCREVBFQERIkyAxO/vz/qNHO53Hy7u7q636/nuU/d6lvd\n9R3o8Olz6pwTmYkkSZKaZ0bdBUiSJGlqDHKSJEkNZZCTJElqKIOcJElSQxnkJEmSGsogJ0mS1FAG\nOUmSpIYyyEmSJDWUQU6SJKmhDHKSJEkNZZCTJElqKIOcJElSQxnkJEmSGsogJ0mS1FAGOUmSpIYy\nyEmSJDWUQU6SJKmhDHKSJEkNZZCTJElqKIOcJElSQxnkJEmSGsogJ0mS1FAGOUmSpIYyyEmSJDWU\nQU6S [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7f003ad8eb50>"
+ ]
+ },
"metadata": {},
- "source": [
- "However, if flux is forced through v3, then there is no longer a feasible loopless solution."
- ]
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "figure(figsize=(10.5, 4.5), frameon=False)\n",
+ "gca().axis(\"off\")\n",
+ "xlim(0.5, 3.5)\n",
+ "ylim(0.7, 2.2)\n",
+ "arrow_params = {\"head_length\": 0.08, \"head_width\": 0.1, \"ec\": \"k\", \"fc\": \"k\"}\n",
+ "text_params = {\"fontsize\": 25, \"horizontalalignment\": \"center\", \"verticalalignment\": \"center\"}\n",
+ "arrow(0.5, 1, 0.85, 0, **arrow_params) # EX_A\n",
+ "arrow(1.5, 1, 0.425, 0.736, **arrow_params) # v1\n",
+ "arrow(2.04, 1.82, 0.42, -0.72, **arrow_params) # v2\n",
+ "arrow(2.4, 1, -0.75, 0, **arrow_params) # v3\n",
+ "arrow(2.6, 1, 0.75, 0, **arrow_params)\n",
+ "# reaction labels\n",
+ "text(0.9, 1.15, \"EX_A\", **text_params)\n",
+ "text(1.6, 1.5, r\"v$_1$\", **text_params)\n",
+ "text(2.4, 1.5, r\"v$_2$\", **text_params)\n",
+ "text(2, 0.85, r\"v$_3$\", **text_params)\n",
+ "text(2.9, 1.15, \"DM_C\", **text_params)\n",
+ "# metabolite labels\n",
+ "scatter(1.5, 1, s=250, color='#c994c7')\n",
+ "text(1.5, 0.9, \"A\", **text_params)\n",
+ "scatter(2, 1.84, s=250, color='#c994c7')\n",
+ "text(2, 1.95, \"B\", **text_params)\n",
+ "scatter(2.5, 1, s=250, color='#c994c7')\n",
+ "text(2.5, 0.9, \"C\", **text_params);"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "test_model = Model()\n",
+ "test_model.add_metabolites(Metabolite(\"A\"))\n",
+ "test_model.add_metabolites(Metabolite(\"B\"))\n",
+ "test_model.add_metabolites(Metabolite(\"C\"))\n",
+ "EX_A = Reaction(\"EX_A\")\n",
+ "EX_A.add_metabolites({test_model.metabolites.A: 1})\n",
+ "DM_C = Reaction(\"DM_C\")\n",
+ "DM_C.add_metabolites({test_model.metabolites.C: -1})\n",
+ "v1 = Reaction(\"v1\")\n",
+ "v1.add_metabolites({test_model.metabolites.A: -1, test_model.metabolites.B: 1})\n",
+ "v2 = Reaction(\"v2\")\n",
+ "v2.add_metabolites({test_model.metabolites.B: -1, test_model.metabolites.C: 1})\n",
+ "v3 = Reaction(\"v3\")\n",
+ "v3.add_metabolites({test_model.metabolites.C: -1, test_model.metabolites.A: 1})\n",
+ "DM_C.objective_coefficient = 1\n",
+ "test_model.add_reactions([EX_A, DM_C, v1, v2, v3])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "While this model contains a loop, a flux state exists which has no flux through reaction v3, and is identified by loopless FBA."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "v3.lower_bound = 1\n",
- "construct_loopless_model(test_model).optimize()"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Solution 1000.00 at 0x7f003ad82850>"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- "<Solution 'infeasible' at 0x62cd5d0>"
- ]
- }
- ],
- "prompt_number": 5
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "construct_loopless_model(test_model).optimize()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "However, if flux is forced through v3, then there is no longer a feasible loopless solution."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "<Solution 'infeasible' at 0x7f003ad82f10>"
+ ]
+ },
+ "execution_count": 5,
"metadata": {},
- "source": [
- "Loopless FBA is also possible on genome scale models, but it requires a capable MILP solver."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "v3.lower_bound = 1\n",
+ "construct_loopless_model(test_model).optimize()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Loopless FBA is also possible on genome scale models, but it requires a capable MILP solver."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "salmonella = cobra.test.create_test_model()\n",
- "construct_loopless_model(salmonella).optimize(solver=get_solver_name(mip=True))"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Solution 0.38 at 0x7f003a496190>"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "<Solution 0.38 at 0x9e67650>"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "salmonella = cobra.test.create_test_model(\"salmonella\")\n",
+ "construct_loopless_model(salmonella).optimize(solver=get_solver_name(mip=True))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "ecoli = cobra.test.create_test_model(\"ecoli\")\n",
- "construct_loopless_model(ecoli).optimize(solver=get_solver_name(mip=True))"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Solution 0.98 at 0x7f003ae06b50>"
+ ]
+ },
+ "execution_count": 7,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 7,
- "text": [
- "<Solution 0.98 at 0x8e463d0>"
- ]
- }
- ],
- "prompt_number": 7
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "ecoli = cobra.test.create_test_model(\"ecoli\")\n",
+ "construct_loopless_model(ecoli).optimize(solver=get_solver_name(mip=True))"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/loopless.rst b/documentation_builder/loopless.rst
index 88ddb99..38f5dcc 100644
--- a/documentation_builder/loopless.rst
+++ b/documentation_builder/loopless.rst
@@ -2,9 +2,6 @@
Loopless FBA
============
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/loopless.ipynb>`__.
-
The goal of this procedure is identification of a thermodynamically
consistent flux state without loops, as implied by the name.
@@ -69,6 +66,9 @@ which bring metabolites in and out of the system.
.. code:: python
+ from matplotlib.pylab import *
+ %matplotlib inline
+
import cobra.test
from cobra import Reaction, Metabolite, Model
from cobra.flux_analysis.loopless import construct_loopless_model
@@ -106,7 +106,8 @@ leave. A graphical view of the system is drawn below:
text(2.5, 0.9, "C", **text_params);
-.. image:: loopless_files/loopless_4_0.png
+
+.. image:: loopless_files/loopless_3_0.png
.. code:: python
@@ -137,9 +138,10 @@ through reaction v3, and is identified by loopless FBA.
+
.. parsed-literal::
- <Solution 1000.00 at 0x62cd250>
+ <Solution 1000.00 at 0x7f003ad82850>
@@ -153,9 +155,10 @@ feasible loopless solution.
+
.. parsed-literal::
- <Solution 'infeasible' at 0x62cd5d0>
+ <Solution 'infeasible' at 0x7f003ad82f10>
@@ -164,14 +167,15 @@ capable MILP solver.
.. code:: python
- salmonella = cobra.test.create_test_model()
+ salmonella = cobra.test.create_test_model("salmonella")
construct_loopless_model(salmonella).optimize(solver=get_solver_name(mip=True))
+
.. parsed-literal::
- <Solution 0.38 at 0x9e67650>
+ <Solution 0.38 at 0x7f003a496190>
@@ -182,8 +186,9 @@ capable MILP solver.
+
.. parsed-literal::
- <Solution 0.98 at 0x8e463d0>
+ <Solution 0.98 at 0x7f003ae06b50>
diff --git a/documentation_builder/loopless_files/loopless_3_0.png b/documentation_builder/loopless_files/loopless_3_0.png
new file mode 100644
index 0000000..6b1bc6c
Binary files /dev/null and b/documentation_builder/loopless_files/loopless_3_0.png differ
diff --git a/documentation_builder/loopless_files/loopless_4_0.png b/documentation_builder/loopless_files/loopless_4_0.png
deleted file mode 100644
index f2fb04b..0000000
Binary files a/documentation_builder/loopless_files/loopless_4_0.png and /dev/null differ
diff --git a/documentation_builder/milp.ipynb b/documentation_builder/milp.ipynb
index 8d73ba8..58a489d 100644
--- a/documentation_builder/milp.ipynb
+++ b/documentation_builder/milp.ipynb
@@ -1,429 +1,418 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:15b2c40ef0fb93bc5f72342223ba2b9be518efe687bdef60766ecf17864db66d"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Mixed-Integer Linear Programming"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/milp.ipynb)."
- ]
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Ice Cream"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example was originally contributed by Joshua Lerman.\n",
- "\n",
- "An ice cream stand sells cones and popsicles. It wants to maximize its profit, but is subject to a budget.\n",
- "\n",
- "We can write this problem as a linear program:\n",
- "\n",
- "> **max** cone $\\cdot$ cone_margin + popsicle $\\cdot$ popsicle margin\n",
- "\n",
- "> *subject to*\n",
- "\n",
- "> cone $\\cdot$ cone_cost + popsicle $\\cdot$ popsicle_cost $\\le$ budget"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cone_selling_price = 7.\n",
- "cone_production_cost = 3.\n",
- "popsicle_selling_price = 2.\n",
- "popsicle_production_cost = 1.\n",
- "starting_budget = 100.\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This problem can be written as a cobra.Model"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from cobra import Model, Metabolite, Reaction\n",
- "\n",
- "cone = Reaction(\"cone\")\n",
- "popsicle = Reaction(\"popsicle\")\n",
- "\n",
- "# constrainted to a budget\n",
- "budget = Metabolite(\"budget\")\n",
- "budget._constraint_sense = \"L\"\n",
- "budget._bound = starting_budget\n",
- "cone.add_metabolites({budget: cone_production_cost})\n",
- "popsicle.add_metabolites({budget: popsicle_production_cost})\n",
- "\n",
- "# objective coefficient is the profit to be made from each unit\n",
- "cone.objective_coefficient = cone_selling_price - cone_production_cost\n",
- "popsicle.objective_coefficient = popsicle_selling_price - \\\n",
- " popsicle_production_cost\n",
- "\n",
- "m = Model(\"lerman_ice_cream_co\")\n",
- "m.add_reactions((cone, popsicle))\n",
- "\n",
- "m.optimize().x_dict"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 2,
- "text": [
- "{'cone': 33.333333333333336, 'popsicle': 0.0}"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "In reality, cones and popsicles can only be sold in integer amounts. We can use the variable kind attribute of a cobra.Reaction to enforce this."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "cone.variable_kind = \"integer\"\n",
- "popsicle.variable_kind = \"integer\"\n",
- "m.optimize().x_dict"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 3,
- "text": [
- "{'cone': 33.0, 'popsicle': 1.0}"
- ]
- }
- ],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Now the model makes both popsicles and cones."
- ]
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Restaurant Order"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "To tackle the less immediately obvious problem from the following [XKCD comic](http://xkcd.com/287/):"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from IPython.display import Image\n",
- "Image(url=r\"http://imgs.xkcd.com/comics/np_complete.png\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "html": [
- "<img src=\"http://imgs.xkcd.com/comics/np_complete.png\"/>"
- ],
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "<IPython.core.display.Image at 0x2902d90>"
- ]
- }
- ],
- "prompt_number": 4
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We want a solution satisfying the following constraints:\n",
- "\n",
- "$\\left(\\begin{matrix}2.15&2.75&3.35&3.55&4.20&5.80\\end{matrix}\\right) \\cdot \\vec v = 15.05$\n",
- "\n",
- "$\\vec v_i \\ge 0$\n",
- "\n",
- "$\\vec v_i \\in \\mathbb{Z}$\n",
- "\n",
- "This problem can be written as a COBRA model as well."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "total_cost = Metabolite(\"constraint\")\n",
- "total_cost._bound = 15.05\n",
- "\n",
- "costs = {\"mixed_fruit\": 2.15, \"french_fries\": 2.75, \"side_salad\": 3.35,\n",
- " \"hot_wings\": 3.55, \"mozarella_sticks\": 4.20, \"sampler_plate\": 5.80}\n",
- "\n",
- "m = Model(\"appetizers\")\n",
- "\n",
- "for item, cost in costs.items():\n",
- " r = Reaction(item)\n",
- " r.add_metabolites({total_cost: cost})\n",
- " r.variable_kind = \"integer\"\n",
- " m.add_reaction(r)\n",
- "\n",
- "# To add to the problem, suppose we don't want to eat all mixed fruit.\n",
- "m.reactions.mixed_fruit.objective_coefficient = 1\n",
- " \n",
- "m.optimize(objective_sense=\"minimize\").x_dict"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- "{'french_fries': 0.0,\n",
- " 'hot_wings': 2.0,\n",
- " 'mixed_fruit': 1.0,\n",
- " 'mozarella_sticks': 0.0,\n",
- " 'sampler_plate': 1.0,\n",
- " 'side_salad': 0.0}"
- ]
- }
- ],
- "prompt_number": 5
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Mixed-Integer Linear Programming\n",
+ "\n",
+ "## Ice Cream\n",
+ "\n",
+ "This example was originally contributed by Joshua Lerman.\n",
+ "\n",
+ "An ice cream stand sells cones and popsicles. It wants to maximize its profit, but is subject to a budget.\n",
+ "\n",
+ "We can write this problem as a linear program:\n",
+ "\n",
+ "> **max** cone $\\cdot$ cone_margin + popsicle $\\cdot$ popsicle margin\n",
+ "\n",
+ "> *subject to*\n",
+ "\n",
+ "> cone $\\cdot$ cone_cost + popsicle $\\cdot$ popsicle_cost $\\le$ budget"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "cone_selling_price = 7.\n",
+ "cone_production_cost = 3.\n",
+ "popsicle_selling_price = 2.\n",
+ "popsicle_production_cost = 1.\n",
+ "starting_budget = 100."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "This problem can be written as a cobra.Model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "{'cone': 33.333333333333336, 'popsicle': 0.0}"
+ ]
+ },
+ "execution_count": 2,
"metadata": {},
- "source": [
- "There is another solution to this problem, which would have been obtained if we had maximized for mixed fruit instead of minimizing."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from cobra import Model, Metabolite, Reaction\n",
+ "\n",
+ "cone = Reaction(\"cone\")\n",
+ "popsicle = Reaction(\"popsicle\")\n",
+ "\n",
+ "# constrainted to a budget\n",
+ "budget = Metabolite(\"budget\")\n",
+ "budget._constraint_sense = \"L\"\n",
+ "budget._bound = starting_budget\n",
+ "cone.add_metabolites({budget: cone_production_cost})\n",
+ "popsicle.add_metabolites({budget: popsicle_production_cost})\n",
+ "\n",
+ "# objective coefficient is the profit to be made from each unit\n",
+ "cone.objective_coefficient = cone_selling_price - cone_production_cost\n",
+ "popsicle.objective_coefficient = popsicle_selling_price - \\\n",
+ " popsicle_production_cost\n",
+ "\n",
+ "m = Model(\"lerman_ice_cream_co\")\n",
+ "m.add_reactions((cone, popsicle))\n",
+ "\n",
+ "m.optimize().x_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In reality, cones and popsicles can only be sold in integer amounts. We can use the variable kind attribute of a cobra.Reaction to enforce this."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "m.optimize(objective_sense=\"maximize\").x_dict"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{'cone': 33.0, 'popsicle': 1.0}"
+ ]
+ },
+ "execution_count": 3,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "{'french_fries': 0.0,\n",
- " 'hot_wings': 0.0,\n",
- " 'mixed_fruit': 7.0,\n",
- " 'mozarella_sticks': 0.0,\n",
- " 'sampler_plate': 0.0,\n",
- " 'side_salad': 0.0}"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "cone.variable_kind = \"integer\"\n",
+ "popsicle.variable_kind = \"integer\"\n",
+ "m.optimize().x_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now the model makes both popsicles and cones."
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Restaurant Order\n",
+ "\n",
+ "To tackle the less immediately obvious problem from the following [XKCD comic](http://xkcd.com/287/):"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "heading",
- "level": 2,
+ "data": {
+ "text/html": [
+ "<img src=\"http://imgs.xkcd.com/comics/np_complete.png\"/>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Image object>"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "source": [
- "Boolean Indicators"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from IPython.display import Image\n",
+ "Image(url=r\"http://imgs.xkcd.com/comics/np_complete.png\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We want a solution satisfying the following constraints:\n",
+ "\n",
+ "$\\left(\\begin{matrix}2.15&2.75&3.35&3.55&4.20&5.80\\end{matrix}\\right) \\cdot \\vec v = 15.05$\n",
+ "\n",
+ "$\\vec v_i \\ge 0$\n",
+ "\n",
+ "$\\vec v_i \\in \\mathbb{Z}$\n",
+ "\n",
+ "This problem can be written as a COBRA model as well."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "{'french_fries': 0.0,\n",
+ " 'hot_wings': 2.0,\n",
+ " 'mixed_fruit': 1.0,\n",
+ " 'mozarella_sticks': 0.0,\n",
+ " 'sampler_plate': 1.0,\n",
+ " 'side_salad': 0.0}"
+ ]
+ },
+ "execution_count": 5,
"metadata": {},
- "source": [
- "To give a COBRA-related example, we can create boolean variables as integers, which can serve as indicators for a reaction being active in a model. For a reaction flux $v$ with lower bound -1000 and upper bound 1000, we can create a binary variable $b$ with the following constraints:\n",
- "\n",
- "$b \\in \\{0, 1\\}$\n",
- "\n",
- "$-1000 \\cdot b \\le v \\le 1000 \\cdot b$\n",
- "\n",
- "To introduce the above constraints into a cobra model, we can rewrite them as follows\n",
- "\n",
- "$v \\le b \\cdot 1000 \\Rightarrow v- 1000\\cdot b \\le 0$\n",
- "\n",
- "$-1000 \\cdot b \\le v \\Rightarrow v + 1000\\cdot b \\ge 0$"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "total_cost = Metabolite(\"constraint\")\n",
+ "total_cost._bound = 15.05\n",
+ "\n",
+ "costs = {\"mixed_fruit\": 2.15, \"french_fries\": 2.75, \"side_salad\": 3.35,\n",
+ " \"hot_wings\": 3.55, \"mozarella_sticks\": 4.20, \"sampler_plate\": 5.80}\n",
+ "\n",
+ "m = Model(\"appetizers\")\n",
+ "\n",
+ "for item, cost in costs.items():\n",
+ " r = Reaction(item)\n",
+ " r.add_metabolites({total_cost: cost})\n",
+ " r.variable_kind = \"integer\"\n",
+ " m.add_reaction(r)\n",
+ "\n",
+ "# To add to the problem, suppose we don't want to eat all mixed fruit.\n",
+ "m.reactions.mixed_fruit.objective_coefficient = 1\n",
+ " \n",
+ "m.optimize(objective_sense=\"minimize\").x_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "There is another solution to this problem, which would have been obtained if we had maximized for mixed fruit instead of minimizing."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "import cobra.test\n",
- "model = cobra.test.create_test_model(cobra.test.ecoli_pickle)\n",
- "\n",
- "# an indicator for pgi\n",
- "pgi = model.reactions.get_by_id(\"PGI\")\n",
- "# make a boolean variable\n",
- "pgi_indicator = Reaction(\"indicator_PGI\")\n",
- "pgi_indicator.lower_bound = 0\n",
- "pgi_indicator.upper_bound = 1\n",
- "pgi_indicator.variable_kind = \"integer\"\n",
- "# create constraint for v - 1000 b <= 0\n",
- "pgi_plus = Metabolite(\"PGI_plus\")\n",
- "pgi_plus._constraint_sense = \"L\"\n",
- "# create constraint for v + 1000 b >= 0\n",
- "pgi_minus = Metabolite(\"PGI_minus\")\n",
- "pgi_minus._constraint_sense = \"G\"\n",
- "\n",
- "pgi_indicator.add_metabolites({pgi_plus: -1000, pgi_minus: 1000})\n",
- "pgi.add_metabolites({pgi_plus: 1, pgi_minus: 1})\n",
- "model.add_reaction(pgi_indicator)\n",
- "\n",
- "\n",
- "# an indicator for zwf\n",
- "zwf = model.reactions.get_by_id(\"G6PDH2r\")\n",
- "zwf_indicator = Reaction(\"indicator_ZWF\")\n",
- "zwf_indicator.lower_bound = 0\n",
- "zwf_indicator.upper_bound = 1\n",
- "zwf_indicator.variable_kind = \"integer\"\n",
- "# create constraint for v - 1000 b <= 0\n",
- "zwf_plus = Metabolite(\"ZWF_plus\")\n",
- "zwf_plus._constraint_sense = \"L\"\n",
- "# create constraint for v + 1000 b >= 0\n",
- "zwf_minus = Metabolite(\"ZWF_minus\")\n",
- "zwf_minus._constraint_sense = \"G\"\n",
- "\n",
- "zwf_indicator.add_metabolites({zwf_plus: -1000, zwf_minus: 1000})\n",
- "zwf.add_metabolites({zwf_plus: 1, zwf_minus: 1})\n",
- "\n",
- "# add the indicator reactions to the model\n",
- "model.add_reaction(zwf_indicator)\n"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{'french_fries': 0.0,\n",
+ " 'hot_wings': 0.0,\n",
+ " 'mixed_fruit': 7.0,\n",
+ " 'mozarella_sticks': 0.0,\n",
+ " 'sampler_plate': 0.0,\n",
+ " 'side_salad': 0.0}"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "outputs": [],
- "prompt_number": 7
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "m.optimize(objective_sense=\"maximize\").x_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Boolean Indicators\n",
+ "\n",
+ "To give a COBRA-related example, we can create boolean variables as integers, which can serve as indicators for a reaction being active in a model. For a reaction flux $v$ with lower bound -1000 and upper bound 1000, we can create a binary variable $b$ with the following constraints:\n",
+ "\n",
+ "$b \\in \\{0, 1\\}$\n",
+ "\n",
+ "$-1000 \\cdot b \\le v \\le 1000 \\cdot b$\n",
+ "\n",
+ "To introduce the above constraints into a cobra model, we can rewrite them as follows\n",
+ "\n",
+ "$v \\le b \\cdot 1000 \\Rightarrow v- 1000\\cdot b \\le 0$\n",
+ "\n",
+ "$-1000 \\cdot b \\le v \\Rightarrow v + 1000\\cdot b \\ge 0$"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "import cobra.test\n",
+ "model = cobra.test.create_test_model(\"textbook\")\n",
+ "\n",
+ "# an indicator for pgi\n",
+ "pgi = model.reactions.get_by_id(\"PGI\")\n",
+ "# make a boolean variable\n",
+ "pgi_indicator = Reaction(\"indicator_PGI\")\n",
+ "pgi_indicator.lower_bound = 0\n",
+ "pgi_indicator.upper_bound = 1\n",
+ "pgi_indicator.variable_kind = \"integer\"\n",
+ "# create constraint for v - 1000 b <= 0\n",
+ "pgi_plus = Metabolite(\"PGI_plus\")\n",
+ "pgi_plus._constraint_sense = \"L\"\n",
+ "# create constraint for v + 1000 b >= 0\n",
+ "pgi_minus = Metabolite(\"PGI_minus\")\n",
+ "pgi_minus._constraint_sense = \"G\"\n",
+ "\n",
+ "pgi_indicator.add_metabolites({pgi_plus: -1000, pgi_minus: 1000})\n",
+ "pgi.add_metabolites({pgi_plus: 1, pgi_minus: 1})\n",
+ "model.add_reaction(pgi_indicator)\n",
+ "\n",
+ "\n",
+ "# an indicator for zwf\n",
+ "zwf = model.reactions.get_by_id(\"G6PDH2r\")\n",
+ "zwf_indicator = Reaction(\"indicator_ZWF\")\n",
+ "zwf_indicator.lower_bound = 0\n",
+ "zwf_indicator.upper_bound = 1\n",
+ "zwf_indicator.variable_kind = \"integer\"\n",
+ "# create constraint for v - 1000 b <= 0\n",
+ "zwf_plus = Metabolite(\"ZWF_plus\")\n",
+ "zwf_plus._constraint_sense = \"L\"\n",
+ "# create constraint for v + 1000 b >= 0\n",
+ "zwf_minus = Metabolite(\"ZWF_minus\")\n",
+ "zwf_minus._constraint_sense = \"G\"\n",
+ "\n",
+ "zwf_indicator.add_metabolites({zwf_plus: -1000, zwf_minus: 1000})\n",
+ "zwf.add_metabolites({zwf_plus: 1, zwf_minus: 1})\n",
+ "\n",
+ "# add the indicator reactions to the model\n",
+ "model.add_reaction(zwf_indicator)\n"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In a model with both these reactions active, the indicators will also be active"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "In a model with both these reactions active, the indicators will also be active"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "PGI indicator = 1\n",
+ "ZWF indicator = 1\n",
+ "PGI flux = 4.86\n",
+ "ZWF flux = 4.96\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "solution = model.optimize()\n",
- "print(\"PGI indicator = %d\" % solution.x_dict[\"indicator_PGI\"])\n",
- "print(\"ZWF indicator = %d\" % solution.x_dict[\"indicator_ZWF\"])\n",
- "print(\"PGI flux = %.2f\" % solution.x_dict[\"PGI\"])\n",
- "print(\"ZWF flux = %.2f\" % solution.x_dict[\"G6PDH2r\"])"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "PGI indicator = 1\n",
- "ZWF indicator = 1\n",
- "PGI flux = 5.92\n",
- "ZWF flux = 4.08\n"
- ]
- }
- ],
- "prompt_number": 8
- },
+ }
+ ],
+ "source": [
+ "solution = model.optimize()\n",
+ "print(\"PGI indicator = %d\" % solution.x_dict[\"indicator_PGI\"])\n",
+ "print(\"ZWF indicator = %d\" % solution.x_dict[\"indicator_ZWF\"])\n",
+ "print(\"PGI flux = %.2f\" % solution.x_dict[\"PGI\"])\n",
+ "print(\"ZWF flux = %.2f\" % solution.x_dict[\"G6PDH2r\"])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Because these boolean indicators are in the model, additional constraints can be applied on them. For example, we can prevent both reactions from being active at the same time by adding the following constraint:\n",
+ "\n",
+ "$b_\\text{pgi} + b_\\text{zwf} = 1$"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Because these boolean indicators are in the model, additional constraints can be applied on them. For example, we can prevent both reactions from being active at the same time by adding the following constraint:\n",
- "\n",
- "$b_\\text{pgi} + b_\\text{zwf} = 1$"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "PGI indicator = 1\n",
+ "ZWF indicator = 0\n",
+ "PGI flux = 9.82\n",
+ "ZWF flux = 0.00\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "or_constraint = Metabolite(\"or\")\n",
- "or_constraint._bound = 1\n",
- "zwf_indicator.add_metabolites({or_constraint: 1})\n",
- "pgi_indicator.add_metabolites({or_constraint: 1})\n",
- "\n",
- "solution = model.optimize()\n",
- "print(\"PGI indicator = %d\" % solution.x_dict[\"indicator_PGI\"])\n",
- "print(\"ZWF indicator = %d\" % solution.x_dict[\"indicator_ZWF\"])\n",
- "print(\"PGI flux = %.2f\" % solution.x_dict[\"PGI\"])\n",
- "print(\"ZWF flux = %.2f\" % solution.x_dict[\"G6PDH2r\"])"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "PGI indicator = 0\n",
- "ZWF indicator = 1\n",
- "PGI flux = 0.00\n",
- "ZWF flux = 3.98\n"
- ]
- }
- ],
- "prompt_number": 9
}
],
- "metadata": {}
+ "source": [
+ "or_constraint = Metabolite(\"or\")\n",
+ "or_constraint._bound = 1\n",
+ "zwf_indicator.add_metabolites({or_constraint: 1})\n",
+ "pgi_indicator.add_metabolites({or_constraint: 1})\n",
+ "\n",
+ "solution = model.optimize()\n",
+ "print(\"PGI indicator = %d\" % solution.x_dict[\"indicator_PGI\"])\n",
+ "print(\"ZWF indicator = %d\" % solution.x_dict[\"indicator_ZWF\"])\n",
+ "print(\"PGI flux = %.2f\" % solution.x_dict[\"PGI\"])\n",
+ "print(\"ZWF flux = %.2f\" % solution.x_dict[\"G6PDH2r\"])"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/milp.rst b/documentation_builder/milp.rst
index 9c6da63..7cc3595 100644
--- a/documentation_builder/milp.rst
+++ b/documentation_builder/milp.rst
@@ -2,9 +2,6 @@
Mixed-Integer Linear Programming
================================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/milp.ipynb>`__.
-
Ice Cream
---------
@@ -59,6 +56,7 @@ This problem can be written as a cobra.Model
+
.. parsed-literal::
{'cone': 33.333333333333336, 'popsicle': 0.0}
@@ -76,6 +74,7 @@ can use the variable kind attribute of a cobra.Reaction to enforce this.
+
.. parsed-literal::
{'cone': 33.0, 'popsicle': 1.0}
@@ -97,6 +96,7 @@ comic <http://xkcd.com/287/>`__:
+
.. raw:: html
<img src="http://imgs.xkcd.com/comics/np_complete.png"/>
@@ -136,6 +136,7 @@ This problem can be written as a COBRA model as well.
+
.. parsed-literal::
{'french_fries': 0.0,
@@ -156,6 +157,7 @@ obtained if we had maximized for mixed fruit instead of minimizing.
+
.. parsed-literal::
{'french_fries': 0.0,
@@ -190,7 +192,7 @@ them as follows
.. code:: python
import cobra.test
- model = cobra.test.create_test_model(cobra.test.ecoli_pickle)
+ model = cobra.test.create_test_model("textbook")
# an indicator for pgi
pgi = model.reactions.get_by_id("PGI")
@@ -230,6 +232,7 @@ them as follows
# add the indicator reactions to the model
model.add_reaction(zwf_indicator)
+
In a model with both these reactions active, the indicators will also be
active
@@ -241,12 +244,13 @@ active
print("PGI flux = %.2f" % solution.x_dict["PGI"])
print("ZWF flux = %.2f" % solution.x_dict["G6PDH2r"])
+
.. parsed-literal::
PGI indicator = 1
ZWF indicator = 1
- PGI flux = 5.92
- ZWF flux = 4.08
+ PGI flux = 4.86
+ ZWF flux = 4.96
Because these boolean indicators are in the model, additional
@@ -269,10 +273,11 @@ constraint:
print("PGI flux = %.2f" % solution.x_dict["PGI"])
print("ZWF flux = %.2f" % solution.x_dict["G6PDH2r"])
+
.. parsed-literal::
- PGI indicator = 0
- ZWF indicator = 1
- PGI flux = 0.00
- ZWF flux = 3.98
+ PGI indicator = 1
+ ZWF indicator = 0
+ PGI flux = 9.82
+ ZWF flux = 0.00
diff --git a/documentation_builder/phenotype_phase_plane.ipynb b/documentation_builder/phenotype_phase_plane.ipynb
index 885a0a9..c5eb486 100644
--- a/documentation_builder/phenotype_phase_plane.ipynb
+++ b/documentation_builder/phenotype_phase_plane.ipynb
@@ -1,199 +1,189 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:a2c88dc327a82c024dc7b203f410ef1fda65199a58de7677a827da6f351ebd06"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Phenotype Phase Plane"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/phenotype_phase_plane.ipynb)."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Load iJO1366 as a test model and import cobra"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from time import time\n",
- "\n",
- "import cobra\n",
- "from cobra.test import ecoli_pickle, create_test_model\n",
- "\n",
- "from cobra.flux_analysis.phenotype_phase_plane import \\\n",
- " calculate_phenotype_phase_plane\n",
- "\n",
- "model = create_test_model(ecoli_pickle)\n",
- "model"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 1,
- "text": [
- "<Model iJO1366 at 0x5b0abd0>"
- ]
- }
- ],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "We want to make a phenotype phase plane to evaluate uptakes of Glucose and Oxygen.\n",
- "\n",
- "With [matplotlib](http://matplotlib.org) installed, this is as simple as"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "data = calculate_phenotype_phase_plane(model, \"EX_glc_e\", \"EX_o2_e\")\n",
- "data.plot_matplotlib();"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvWmMVQd69/k7+7n7Wgu72TEGDNhgsA023pe2e+90T97u\nqDOKEs0kSif5kA/RfMh8mUgjRZEyM4r0ZvTOm7zpJE7H7aW9YjDGBoxZzGIwOwaqiqpbd9/PPh8O\np/pSXUCBocDt+5OQEHVv3cO95z7nf57l/0CXLl26dOnSpUuXLl26dOnSpUuXLl26dOnSpUuXLl26\ndOnSpUuXLl26dPmaIFzth57neVN1IF26dOny24IgCFeMreJUHkiXLl26fN3pBt0uXbp0mUK6QbdL\nly5dppBu0O3SpUuXKaQbdLt06dJlCukG3S5dunSZQrpBt0uXLl2mkG7Q7dKlS5cppBt0u3Tp0mUK\n6QbdLl26d [...]
- "text": [
- "<matplotlib.figure.Figure at 0x6863750>"
- ]
- }
- ],
- "prompt_number": 2
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Phenotype Phase Plane\n",
+ "\n",
+ "Phenotype phase planes will show distinct phases of optimal growth with different use of two different substrates. For more information, see [Edwards et al.](http://dx.doi.org/10.1002/bit.10047)\n",
+ "\n",
+ "Cobrapy supports calculating and plotting (using [matplotlib](http://matplotlib.org)) these phenotype phase planes. Here, we will make one for the \"textbook\" _E. coli_ core model."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "%matplotlib inline\n",
+ "from time import time\n",
+ "\n",
+ "\n",
+ "import cobra.test\n",
+ "from cobra.flux_analysis import calculate_phenotype_phase_plane\n",
+ "\n",
+ "model = cobra.test.create_test_model(\"textbook\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We want to make a phenotype phase plane to evaluate uptakes of Glucose and Oxygen."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvXeYHOd15vv7KnVO0z0JGAQCnAGYwQzmnKNkURQVKK1s\nS6Ys2V7JkmV7bTquvbvXe6/WsnVtK1kiRZGEmASRFJMokmIAEwiQAJEBTujpiZ1Dxf3jq+YMIWQM\nBqDY7/PMg5mq6kJ9PT2n3jrnPe8RnufRQgsttNDC7EA53BfQQgsttPBBQivottBCCy3MIlpBt4UW\nWmhhFtEKui200EILs4hW0G2hhRZamEW0gm4LLbTQwiyiFXRbaKGFFmYRraDbQgsttDCLaAXdFlpo\noYVZRCvottBCCy3MIlpBt4UWWmhhFtEKui200EILs4hW0G2hhRZamEW0gm4LLbTQwiyiFXRbaKGF\nFmYR [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7fe334311210>"
+ ]
+ },
"metadata": {},
- "source": [
- "If [brewer2mpl](https://pypi.python.org/pypi/brewer2mpl/) is installed, other color schemes can be used as well"
- ]
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "data = calculate_phenotype_phase_plane(model, \"EX_glc__D_e\", \"EX_o2_e\")\n",
+ "data.plot_matplotlib();"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "If [brewer2mpl](https://pypi.python.org/pypi/brewer2mpl/) is installed, other color schemes can be used as well"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "data.plot_matplotlib(\"Pastel1\")\n",
- "data.plot_matplotlib(\"Dark2\");"
- ],
- "language": "python",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsnXdYU4f6xz/nnAwghA2CouAA3HuPaq3XrbV111FXq7Va\nW7un3eN6a+u2w2rVWq2tVWsdddQ9cG8FFREwKIIIJIQkJ+f3x0ku1OsW0P6az/PwtHKS4zkY3nzz\nju8rKIqCBw8ePHgoHcT7fQEePHjw8E/CE3Q9ePDgoRTxBF0PHjx4KEU8QdeDBw8eShFP0PXgwYOH\nUsQTdD148OChFPEEXQ8ePHgoRTxB14MHDx5KEU/Q9eDBg4dSxBN0PXjw4KEU8QRdDx48eChFPEHX\ngwcPHkoRT9D14MGDh1LEE3Q9ePDgoRTxBF0PHjx4KEU8QdeDBw8eShFP0PXgwYOHUsQTdD148OCh\nFNHc [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7fe301c440d0>"
+ ]
+ },
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvXdYlPm5//+awjQYOkgXEKSjKGIvqCh2xe5aVrfvZjeb\n5JyTnJPv9/dLTk7JycmWbLLZddW1966IIlIUsaGIir0BgkqRDtNnvn+wDxkJKrqK7mZe17XXlSsM\nw8dnnrk/7+f+3Pf7Bhs2bNiwYcOGDRs2bNiwYcOGDRs2bNiwYcOGDRs2bNiwYcOGDRs2bNiw8Q+C\n6HE/tFgslq5aiA0bNmz8WBCJRI+MreKuXIgNGzZs/KNjC7o2bNiw0YXYgq4NGzZsdCG2oGvDhg0b\nXYgt6NqwYcNGF2ILujZs2LDRhdiCrg0bNmx0Ibaga8OGDRtdiC3o2rBhw0YXYgu6NmzYsNGF2IKu\nDRs2bHQh0 [...]
- "text": [
- "<matplotlib.figure.Figure at 0x8584090>"
- ]
- },
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvXd4FYeZt31POb2rIYQ6TaKI3jHFuOAS4rjFzrrEduom\nu2lfdt9seXfz7fvuty3ZbIqdxI7tuMYOToxtcKim9947CCGE2um9zHx/DKMcZAECg8D23Nfly1zo\nHGmYM3rmN0/5PWBgYGBgYGBgYGBgYGBgYGBgYGBgYGBgYGBgYGBgYGBgYGBgYGDwKUG42BdVVVX7\n6kAMDAwMPikIgnDB2Cr25YEYGBgYfNoxgq6BgYFBH2IEXQMDA4M+xAi6BgYGBn2IEXQNDAwM+hAj\n6BoYGBj0IUbQNTAwMOhDjKBrYGBg0IcYQdfAwMCgDzGCroGBgUEfYgRdAwMDgz5Evt4HYGDwUVEU\nhUwmg6qqm [...]
- "text": [
- "<matplotlib.figure.Figure at 0x8584590>"
- ]
- }
- ],
- "prompt_number": 3
+ "output_type": "display_data"
},
{
- "cell_type": "markdown",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsnXecFPX5x9/faduvH9zR69GbiHSwF6wxscaoscQSjYlJ\nNOUX0ajxpzGJJYm/mJjEkqgxUWMDpIrYQAHp3AEHHHBw/W77zs7M74/vrHcSOseBcd+v1730dnaH\nmb3dZz7zfJ/n8wjHcciSJUuWLB2DcrQPIEuWLFm+TGSDbpYsWbJ0INmgmyVLliwdSDboZsmSJUsH\nkg26WbJkydKBZINulixZsnQg2aCbJUuWLB1INuhmyZIlSweSDbpZsmTJ0oFkg26WLFmydCDZoJsl\nS5YsHUg26GbJkiVLB5INulmyZMnSgWSDbpYsWbJ0INmgmyVLliwdSDboZsmSJUsHkg26WbJkydKB\nZINu [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7fe301e8f650>"
+ ]
+ },
"metadata": {},
- "source": [
- "The number of points which are plotted in each dimension can also be changed"
- ]
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "data.plot_matplotlib(\"Pastel1\")\n",
+ "data.plot_matplotlib(\"Dark2\");"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The number of points which are plotted in each dimension can also be changed"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "calculate_phenotype_phase_plane(model, \"EX_glc_e\", \"EX_o2_e\",\n",
- " reaction1_npoints=20,\n",
- " reaction2_npoints=20).plot_matplotlib();"
- ],
- "language": "python",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvXeYHNWV/v+5VZ3D5KgMQoEkBBIiCBA5KCDA2BgHbGOb\ntb1417v79dfrdeC3Oa+/Xq/Xuw5gY2NsAzYgiYxBIJIAIQRC0owEitMTemLn7qq6vz9u1UzPTPcE\naYIw/T6PHlBX3epbrZlTp8857/sKKSUllFBCCSVMDbTp3kAJJZRQwgcJpaBbQgkllDCFKAXdEkoo\noYQpRCnollBCCSVMIUpBt4QSSihhClEKuiWUUEIJU4hS0C2hhBJKmEKUgm4JJZRQwhSiFHRLKKGE\nEqYQpaBbQgkllDCFKAXdEkoooYQpRCnollBCCSVMIUpBt4QSSihhClEKuiWUUEIJU4hS0C2hhBJK\nmEKU [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7fe301e44910>"
+ ]
+ },
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAADtCAYAAAAcNaZ2AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvWdwXHd65vs7nSMyQRAEGEESBAESYM6ZFIPCKIw0Gk2w\nZj3r8ZZ9Pa7dKtf1eLcctsqurfXa63u3NPas5s7aM9LIHgVqxCQxgwlgAAmAJEgQjCBAZHSO55z7\n4fA0OwMgESipnyp9EPt049+nu5/znuf/Ps8LGWSQQQYZZJBBBhlkkEEGGWSQQQYZZJBBBhlkkEEG\nGWSQQQYZZJBBBhlkkEEGGXxNIKR7UJZlebwWkkEGGWTwVYEgCCm5VTOeC8kggwwy+LojQ7oZZJBB\nBuOIDOlmkEEGGYwjMqSbQQYZZDCOyJBuBhlkkME4IkO6GWSQQQbjiAzpZpBBBhmMIzKkm0EGGWQw\njsiQbgYZZ [...]
- "text": [
- "<matplotlib.figure.Figure at 0x8555a50>"
- ]
- }
- ],
- "prompt_number": 4
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "calculate_phenotype_phase_plane(model, \"EX_glc__D_e\", \"EX_o2_e\",\n",
+ " reaction1_npoints=20,\n",
+ " reaction2_npoints=20).plot_matplotlib();"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The code can also use multiple processes to speed up calculations"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The code can also use multiple processes to speed up calculations"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "took 0.40 seconds with 1 process\n",
+ "took 0.21 seconds with 4 process\n"
]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "start_time = time()\n",
- "calculate_phenotype_phase_plane(model, \"EX_glc_e\", \"EX_o2_e\", n_processes=1)\n",
- "print(\"took %.2f seconds with 1 process\" % (time() - start_time))\n",
- "start_time = time()\n",
- "calculate_phenotype_phase_plane(model, \"EX_glc_e\", \"EX_o2_e\", n_processes=4)\n",
- "print(\"took %.2f seconds with 4 process\" % (time() - start_time))"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "took 5.97 seconds with 1 process\n"
- ]
- },
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "took 2.97 seconds with 4 process\n"
- ]
- }
- ],
- "prompt_number": 5
}
],
- "metadata": {}
+ "source": [
+ "start_time = time()\n",
+ "calculate_phenotype_phase_plane(model, \"EX_glc__D_e\", \"EX_o2_e\", n_processes=1,\n",
+ " reaction1_npoints=100, reaction2_npoints=100)\n",
+ "print(\"took %.2f seconds with 1 process\" % (time() - start_time))\n",
+ "start_time = time()\n",
+ "calculate_phenotype_phase_plane(model, \"EX_glc__D_e\", \"EX_o2_e\", n_processes=4,\n",
+ " reaction1_npoints=100, reaction2_npoints=100)\n",
+ "print(\"took %.2f seconds with 4 process\" % (time() - start_time))"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/phenotype_phase_plane.rst b/documentation_builder/phenotype_phase_plane.rst
index 731aa58..ce7af26 100644
--- a/documentation_builder/phenotype_phase_plane.rst
+++ b/documentation_builder/phenotype_phase_plane.rst
@@ -2,45 +2,36 @@
Phenotype Phase Plane
=====================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/phenotype_phase_plane.ipynb>`__.
+Phenotype phase planes will show distinct phases of optimal growth with
+different use of two different substrates. For more information, see
+`Edwards et al. <http://dx.doi.org/10.1002/bit.10047>`__
-Load iJO1366 as a test model and import cobra
+Cobrapy supports calculating and plotting (using
+`matplotlib <http://matplotlib.org>`__) these phenotype phase planes.
+Here, we will make one for the "textbook" *E. coli* core model.
.. code:: python
+ %matplotlib inline
from time import time
- import cobra
- from cobra.test import ecoli_pickle, create_test_model
- from cobra.flux_analysis.phenotype_phase_plane import \
- calculate_phenotype_phase_plane
+ import cobra.test
+ from cobra.flux_analysis import calculate_phenotype_phase_plane
- model = create_test_model(ecoli_pickle)
- model
-
-
-
-.. parsed-literal::
-
- <Model iJO1366 at 0x5b0abd0>
-
-
+ model = cobra.test.create_test_model("textbook")
We want to make a phenotype phase plane to evaluate uptakes of Glucose
and Oxygen.
-With `matplotlib <http://matplotlib.org>`__ installed, this is as simple
-as
-
.. code:: python
- data = calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e")
+ data = calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e")
data.plot_matplotlib();
-.. image:: phenotype_phase_plane_files/phenotype_phase_plane_5_0.png
+
+.. image:: phenotype_phase_plane_files/phenotype_phase_plane_3_0.png
If `brewer2mpl <https://pypi.python.org/pypi/brewer2mpl/>`__ is
@@ -52,11 +43,12 @@ installed, other color schemes can be used as well
data.plot_matplotlib("Dark2");
-.. image:: phenotype_phase_plane_files/phenotype_phase_plane_7_0.png
+
+.. image:: phenotype_phase_plane_files/phenotype_phase_plane_5_0.png
-.. image:: phenotype_phase_plane_files/phenotype_phase_plane_7_1.png
+.. image:: phenotype_phase_plane_files/phenotype_phase_plane_5_1.png
The number of points which are plotted in each dimension can also be
@@ -64,12 +56,13 @@ changed
.. code:: python
- calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e",
+ calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e",
reaction1_npoints=20,
reaction2_npoints=20).plot_matplotlib();
-.. image:: phenotype_phase_plane_files/phenotype_phase_plane_9_0.png
+
+.. image:: phenotype_phase_plane_files/phenotype_phase_plane_7_0.png
The code can also use multiple processes to speed up calculations
@@ -77,14 +70,17 @@ The code can also use multiple processes to speed up calculations
.. code:: python
start_time = time()
- calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e", n_processes=1)
+ calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e", n_processes=1,
+ reaction1_npoints=100, reaction2_npoints=100)
print("took %.2f seconds with 1 process" % (time() - start_time))
start_time = time()
- calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e", n_processes=4)
+ calculate_phenotype_phase_plane(model, "EX_glc__D_e", "EX_o2_e", n_processes=4,
+ reaction1_npoints=100, reaction2_npoints=100)
print("took %.2f seconds with 4 process" % (time() - start_time))
+
.. parsed-literal::
- took 5.97 seconds with 1 process
- took 2.97 seconds with 4 process
+ took 0.40 seconds with 1 process
+ took 0.21 seconds with 4 process
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_3_0.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_3_0.png
new file mode 100644
index 0000000..b3f96fd
Binary files /dev/null and b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_3_0.png differ
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_0.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_0.png
index aad900d..46c5994 100644
Binary files a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_0.png and b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_0.png differ
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_1.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_1.png
new file mode 100644
index 0000000..0c2c6c4
Binary files /dev/null and b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_1.png differ
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_0.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_0.png
index 27656d6..a49bce8 100644
Binary files a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_0.png and b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_0.png differ
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_1.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_1.png
deleted file mode 100644
index 59a4019..0000000
Binary files a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_1.png and /dev/null differ
diff --git a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_9_0.png b/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_9_0.png
deleted file mode 100644
index 823143c..0000000
Binary files a/documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_9_0.png and /dev/null differ
diff --git a/documentation_builder/pymatbridge.ipynb b/documentation_builder/pymatbridge.ipynb
new file mode 100644
index 0000000..16e4a63
--- /dev/null
+++ b/documentation_builder/pymatbridge.ipynb
@@ -0,0 +1,235 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "collapsed": false
+ },
+ "source": [
+ "# Using the COBRA toolbox with cobrapy\n",
+ "\n",
+ "This example demonstrates using COBRA toolbox commands in MATLAB from python through [pymatbridge](http://arokem.github.io/python-matlab-bridge/)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-39fd5b7f-475a-40d3-b831-3adf4da6edd3\n",
+ "Send 'exit' command to kill the server\n",
+ "....MATLAB started and connected!\n"
+ ]
+ }
+ ],
+ "source": [
+ "%load_ext pymatbridge"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "import cobra.test\n",
+ "m = cobra.test.create_test_model(\"textbook\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The model_to_pymatbridge function will send the model to the workspace with the given variable name."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "from cobra.io.mat import model_to_pymatbridge\n",
+ "model_to_pymatbridge(m, variable_name=\"model\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now in the MATLAB workspace, the variable name 'model' holds a COBRA toolbox struct encoding the model."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "\n",
+ "model = \n",
+ "\n",
+ " rev: [95x1 double]\n",
+ " metNames: {72x1 cell}\n",
+ " b: [72x1 double]\n",
+ " c: [95x1 double]\n",
+ " csense: [72x1 char]\n",
+ " genes: {137x1 cell}\n",
+ " metFormulas: {72x1 cell}\n",
+ " rxns: {95x1 cell}\n",
+ " grRules: {95x1 cell}\n",
+ " rxnNames: {95x1 cell}\n",
+ " description: [8x1 char]\n",
+ " S: [72x95 double]\n",
+ " ub: [95x1 double]\n",
+ " lb: [95x1 double]\n",
+ " mets: {72x1 cell}\n",
+ " subSystems: {95x1 cell}\n",
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%matlab\n",
+ "model"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "First, we have to initialize the COBRA toolbox in MATLAB."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "%%matlab --silent\n",
+ "warning('off'); % this works around a pymatbridge bug\n",
+ "addpath(genpath('~/cobratoolbox/'));\n",
+ "initCobraToolbox();"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Commands from the COBRA toolbox can now be run on the model"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "\n",
+ "ans = \n",
+ "\n",
+ " x: [95x1 double]\n",
+ " f: 0.8739\n",
+ " y: [71x1 double]\n",
+ " w: [95x1 double]\n",
+ " stat: 1\n",
+ " origStat: 5\n",
+ " solver: 'glpk'\n",
+ " time: 0.2327\n",
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%matlab\n",
+ "optimizeCbModel(model)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "FBA in the COBRA toolbox should give the same result as cobrapy"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 5 µs, sys: 0 ns, total: 5 µs\n",
+ "Wall time: 10 µs\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "0.8739215069684305"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "%time\n",
+ "m.optimize().f"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/pymatbridge.rst b/documentation_builder/pymatbridge.rst
new file mode 100644
index 0000000..8347018
--- /dev/null
+++ b/documentation_builder/pymatbridge.rst
@@ -0,0 +1,124 @@
+
+Using the COBRA toolbox with cobrapy
+====================================
+
+This example demonstrates using COBRA toolbox commands in MATLAB from
+python through
+`pymatbridge <http://arokem.github.io/python-matlab-bridge/>`__.
+
+.. code:: python
+
+ %load_ext pymatbridge
+
+
+.. parsed-literal::
+
+ Starting MATLAB on ZMQ socket ipc:///tmp/pymatbridge-39fd5b7f-475a-40d3-b831-3adf4da6edd3
+ Send 'exit' command to kill the server
+ ....MATLAB started and connected!
+
+
+.. code:: python
+
+ import cobra.test
+ m = cobra.test.create_test_model("textbook")
+
+The model\_to\_pymatbridge function will send the model to the workspace
+with the given variable name.
+
+.. code:: python
+
+ from cobra.io.mat import model_to_pymatbridge
+ model_to_pymatbridge(m, variable_name="model")
+
+Now in the MATLAB workspace, the variable name 'model' holds a COBRA
+toolbox struct encoding the model.
+
+.. code:: python
+
+ %%matlab
+ model
+
+
+
+.. parsed-literal::
+
+
+ model =
+
+ rev: [95x1 double]
+ metNames: {72x1 cell}
+ b: [72x1 double]
+ c: [95x1 double]
+ csense: [72x1 char]
+ genes: {137x1 cell}
+ metFormulas: {72x1 cell}
+ rxns: {95x1 cell}
+ grRules: {95x1 cell}
+ rxnNames: {95x1 cell}
+ description: [8x1 char]
+ S: [72x95 double]
+ ub: [95x1 double]
+ lb: [95x1 double]
+ mets: {72x1 cell}
+ subSystems: {95x1 cell}
+
+
+
+
+First, we have to initialize the COBRA toolbox in MATLAB.
+
+.. code:: python
+
+ %%matlab --silent
+ warning('off'); % this works around a pymatbridge bug
+ addpath(genpath('~/cobratoolbox/'));
+ initCobraToolbox();
+
+Commands from the COBRA toolbox can now be run on the model
+
+.. code:: python
+
+ %%matlab
+ optimizeCbModel(model)
+
+
+
+.. parsed-literal::
+
+
+ ans =
+
+ x: [95x1 double]
+ f: 0.8739
+ y: [71x1 double]
+ w: [95x1 double]
+ stat: 1
+ origStat: 5
+ solver: 'glpk'
+ time: 0.2327
+
+
+
+
+FBA in the COBRA toolbox should give the same result as cobrapy
+
+.. code:: python
+
+ %time
+ m.optimize().f
+
+
+.. parsed-literal::
+
+ CPU times: user 5 µs, sys: 0 ns, total: 5 µs
+ Wall time: 10 µs
+
+
+
+
+.. parsed-literal::
+
+ 0.8739215069684305
+
+
diff --git a/documentation_builder/pyscript.tpl b/documentation_builder/pyscript.tpl
deleted file mode 100644
index 693dcfa..0000000
--- a/documentation_builder/pyscript.tpl
+++ /dev/null
@@ -1,29 +0,0 @@
-{%- extends 'display_priority.tpl'-%}
-
-{% block input %}
-{{ cell.input }}
-{% endblock input %}
-
-{%- block pyout -%}
-{%- block data_priority scoped -%}
-{{ super() }}
-{%- endblock -%}
-{%- endblock pyout -%}
-
-{% block data_text scoped -%}
-# Output:
-{{output.text | comment_lines }}
-{% endblock data_text %}
-
-{% block stream -%}
-# Prints:
-{{output.text | trim | comment_lines }}
-{% endblock stream %}
-
-{% block markdowncell scoped %}
-{{ cell.source | wrap_text(77) | comment_lines }}
-{% endblock markdowncell %}
-
-{% block headingcell scoped %}
-{{ '#' * cell.level }}{{ cell.source | replace('\n', ' ') | comment_lines }}
-{% endblock headingcell %}
diff --git a/documentation_builder/qp.ipynb b/documentation_builder/qp.ipynb
index 2cc820c..b12cff8 100644
--- a/documentation_builder/qp.ipynb
+++ b/documentation_builder/qp.ipynb
@@ -1,307 +1,317 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:9ad0e1c925566d6d997098a469ded1521dfd74d5e877febaec8966ea59cfdb0b"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Quadratic Programming"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/qp.ipynb)."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Suppose we want to minimize the Euclidean distance of the solution to the origin while subject to linear constraints. This will require a quadratic objective function. Consider this example problem:\n",
- "\n",
- "> **min** $\\frac{1}{2}\\left(x^2 + y^2 \\right)$\n",
- "\n",
- "> *subject to*\n",
- "\n",
- "> $x + y = 2$\n",
- "\n",
- "> $x \\ge 0$\n",
- "\n",
- "> $y \\ge 0$\n",
- "\n",
- "This problem can be visualized graphically:"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "from matplotlib.pyplot import figure, xlim, ylim\n",
- "from mpl_toolkits.axes_grid.axislines import SubplotZero\n",
- "from numpy import linspace, arange, sqrt, pi, sin, cos, sign\n",
- "# axis style\n",
- "def make_plot_ax():\n",
- " fig = figure(figsize=(6, 5));\n",
- " ax = SubplotZero(fig, 111); fig.add_subplot(ax)\n",
- " for direction in [\"xzero\", \"yzero\"]:\n",
- " ax.axis[direction].set_axisline_style(\"-|>\")\n",
- " ax.axis[direction].set_visible(True)\n",
- " for direction in [\"left\", \"right\", \"bottom\", \"top\"]:\n",
- " ax.axis[direction].set_visible(False)\n",
- " xlim(-0.1, 2.1); ylim(xlim())\n",
- " ticks = [0.5 * i for i in range(1, 5)]\n",
- " labels = [str(i) if i == int(i) else \"\" for i in ticks]\n",
- " ax.set_xticks(ticks); ax.set_yticks(ticks)\n",
- " ax.set_xticklabels(labels); ax.set_yticklabels(labels)\n",
- " ax.axis[\"yzero\"].set_axis_direction(\"left\")\n",
- " return ax\n",
- " \n",
- "ax = make_plot_ax()\n",
- "ax.plot((0, 2), (2, 0), 'b')\n",
- "ax.plot([1], [1], 'bo')\n",
- "\n",
- "# circular grid\n",
- "for r in sqrt(2.) + 0.125 * arange(-11, 6):\n",
- " t = linspace(0., pi/2., 100)\n",
- " ax.plot(r * cos(t), r * sin(t), '-.', color=\"gray\")"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAWAAAAEmCAYAAABcYEo9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzsvXlUlFe29/8tpmJGZBYJijigOKBGxTjFIcYhaqIx0RhN\n2nQnJt25Paz7/u5afXu97+17f/17+67uJLeTqG0Sp2jihOJEnEARURlEBhlkRuahqCqqipqf8/uD\nxharUIbzDAXns1bWik/BPhuo2s959t7nu2WEEPCFTCZbD0w4ApR4A7sB/P4mIarFvC3IYDAYDoSM\n3wDs9RNgXQ54mACrJ6ABgDBCSBNvizIYDIaDwHMAlnkB8PvHP+sBBBNCWnlbkMFgMBwIXgNwj4Vk\nMkIIkQmyGIPBYDgATmI7wGAwGMMVFoAZDAZDJFz68bU0chXC5DsYDAZDOvSaemU7YAaDwRAJFoAZ\nDAZDJFgAZ [...]
- "text": [
- "<matplotlib.figure.Figure at 0x407ea10>"
- ]
- }
- ],
- "prompt_number": 1
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The objective can be rewritten as $\\frac{1}{2} v^T \\cdot \\mathbf Q \\cdot v$, where\n",
- "$v = \\left(\\begin{matrix} x \\\\ y\\end{matrix} \\right)$ and\n",
- "$\\mathbf Q = \\left(\\begin{matrix} 1 & 0\\\\ 0 & 1 \\end{matrix}\\right)$\n",
- "\n",
- "The matrix $\\mathbf Q$ can be passed into a cobra model as the quadratic objective."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "import scipy\n",
- "\n",
- "from cobra import Reaction, Metabolite, Model, solvers\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The quadratic objective $\\mathbf Q$ should be formatted as a scipy sparse matrix."
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "Q = scipy.sparse.eye(2).todok()\n",
- "Q"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 3,
- "text": [
- "<2x2 sparse matrix of type '<type 'numpy.float64'>'\n",
- "\twith 2 stored elements in Dictionary Of Keys format>"
- ]
- }
- ],
- "prompt_number": 3
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "In this case, the quadratic objective is simply the identity matrix"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "Q.todense()"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "matrix([[ 1., 0.],\n",
- " [ 0., 1.]])"
- ]
- }
- ],
- "prompt_number": 4
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Quadratic Programming\n",
+ "\n",
+ "Suppose we want to minimize the Euclidean distance of the solution to the origin while subject to linear constraints. This will require a quadratic objective function. Consider this example problem:\n",
+ "\n",
+ "> **min** $\\frac{1}{2}\\left(x^2 + y^2 \\right)$\n",
+ "\n",
+ "> *subject to*\n",
+ "\n",
+ "> $x + y = 2$\n",
+ "\n",
+ "> $x \\ge 0$\n",
+ "\n",
+ "> $y \\ge 0$\n",
+ "\n",
+ "This problem can be visualized graphically:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAWAAAAEmCAYAAABcYEo9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJztnXe4XFXVh98TSOg11BCaUoNUaWKhd5UWRIoCilIFRaWJ\nrPmJgIq0CAIfXekdRIqAFOlIk16kI70KEghwvj/2DtxM5vZ1yszd7/PcB3Jm7tr73pm7Zp9VfivL\n85yiyLJsI1jkdHhkevgj8Isb8/ytVQtbMJFIJNqIrFgHPN0V8PFaMM2H8PG08F+AufM8f6mwRROJ\nRKJNKNgBZ9MBM8V/vgDMkef5q4UtmEgkEm1EoQ54koWyLM/zPCtlsUQikWgDhlW9gUQikRiqJAec\nSCQSFZEccCKRSFREcsCJRCJREckBJxKJREUkB5xIJBIVkRxwIpFIVERywIlEIlERyQEnEolERUxZ\n1cKS [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7f72a06d2bd0>"
+ ]
+ },
"metadata": {},
- "source": [
- "We need to use a solver that supports quadratic programming, such as gurobi or cplex. If a solver which supports quadratic programming is installed, this function will return its name."
- ]
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%matplotlib inline\n",
+ "from matplotlib.pyplot import figure, xlim, ylim\n",
+ "from mpl_toolkits.axes_grid.axislines import SubplotZero\n",
+ "from numpy import linspace, arange, sqrt, pi, sin, cos, sign\n",
+ "# axis style\n",
+ "def make_plot_ax():\n",
+ " fig = figure(figsize=(6, 5));\n",
+ " ax = SubplotZero(fig, 111); fig.add_subplot(ax)\n",
+ " for direction in [\"xzero\", \"yzero\"]:\n",
+ " ax.axis[direction].set_axisline_style(\"-|>\")\n",
+ " ax.axis[direction].set_visible(True)\n",
+ " for direction in [\"left\", \"right\", \"bottom\", \"top\"]:\n",
+ " ax.axis[direction].set_visible(False)\n",
+ " xlim(-0.1, 2.1); ylim(xlim())\n",
+ " ticks = [0.5 * i for i in range(1, 5)]\n",
+ " labels = [str(i) if i == int(i) else \"\" for i in ticks]\n",
+ " ax.set_xticks(ticks); ax.set_yticks(ticks)\n",
+ " ax.set_xticklabels(labels); ax.set_yticklabels(labels)\n",
+ " ax.axis[\"yzero\"].set_axis_direction(\"left\")\n",
+ " return ax\n",
+ " \n",
+ "ax = make_plot_ax()\n",
+ "ax.plot((0, 2), (2, 0), 'b')\n",
+ "ax.plot([1], [1], 'bo')\n",
+ "\n",
+ "# circular grid\n",
+ "for r in sqrt(2.) + 0.125 * arange(-11, 6):\n",
+ " t = linspace(0., pi/2., 100)\n",
+ " ax.plot(r * cos(t), r * sin(t), '-.', color=\"gray\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The objective can be rewritten as $\\frac{1}{2} v^T \\cdot \\mathbf Q \\cdot v$, where\n",
+ "$v = \\left(\\begin{matrix} x \\\\ y\\end{matrix} \\right)$ and\n",
+ "$\\mathbf Q = \\left(\\begin{matrix} 1 & 0\\\\ 0 & 1 \\end{matrix}\\right)$\n",
+ "\n",
+ "The matrix $\\mathbf Q$ can be passed into a cobra model as the quadratic objective."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "import scipy\n",
+ "\n",
+ "from cobra import Reaction, Metabolite, Model, solvers"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The quadratic objective $\\mathbf Q$ should be formatted as a scipy sparse matrix."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "print(solvers.get_solver_name(qp=True))"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<2x2 sparse matrix of type '<type 'numpy.float64'>'\n",
+ "\twith 2 stored elements in Dictionary Of Keys format>"
+ ]
+ },
+ "execution_count": 3,
"metadata": {},
- "outputs": [
- {
- "output_type": "stream",
- "stream": "stdout",
- "text": [
- "gurobi\n"
- ]
- }
- ],
- "prompt_number": 5
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "Q = scipy.sparse.eye(2).todok()\n",
+ "Q"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "In this case, the quadratic objective is simply the identity matrix"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "c = Metabolite(\"c\")\n",
- "c._bound = 2\n",
- "x = Reaction(\"x\")\n",
- "y = Reaction(\"y\")\n",
- "x.add_metabolites({c: 1})\n",
- "y.add_metabolites({c: 1})\n",
- "m = Model()\n",
- "m.add_reactions([x, y])\n",
- "sol = m.optimize(quadratic_component=Q, objective_sense=\"minimize\")\n",
- "sol.x_dict"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "matrix([[ 1., 0.],\n",
+ " [ 0., 1.]])"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "{'x': 1.0, 'y': 1.0}"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "Q.todense()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We need to use a solver that supports quadratic programming, such as gurobi or cplex. If a solver which supports quadratic programming is installed, this function will return its name."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Suppose we change the problem to have a mixed linear and quadratic objective.\n",
- "\n",
- "> **min** $\\frac{1}{2}\\left(x^2 + y^2 \\right) - y$\n",
- "\n",
- "> *subject to*\n",
- "\n",
- "> $x + y = 2$\n",
- "\n",
- "> $x \\ge 0$\n",
- "\n",
- "> $y \\ge 0$\n",
- "\n",
- "Graphically, this would be"
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "gurobi\n"
]
- },
+ }
+ ],
+ "source": [
+ "print(solvers.get_solver_name(qp=True))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "ax = make_plot_ax()\n",
- "ax.plot((0, 2), (2, 0), 'b')\n",
- "ax.plot([0.5], [1.5], 'bo')\n",
- "\n",
- "yrange = linspace(1, 2, 11)\n",
- "for r in (yrange ** 2 / 2. - yrange):\n",
- " t = linspace(-sqrt(2 * r + 1) + 0.000001, sqrt(2 * r + 1) - 0.000001, 1000)\n",
- " ax.plot(abs(t), 1 + sqrt(2 * r + 1 - t ** 2) * sign(t), '-.', color=\"gray\")"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{'x': 1.0, 'y': 1.0}"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "display_data",
- "png": "iVBORw0KGgoAAAANSUhEUgAAAWAAAAEmCAYAAABcYEo9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJzt3Xl01OW9P/D3N9tkX8m+QMJigLAEVHYBBQQEJI1aVCy1\nWEFraa+3Pafneu/5tfVeb8+5p0ewglGrqBeUFJAAGgJECJsQExJZkpCFhJCNbGQmmZnMkpnv74/c\nUJKZkOT5bjOTz+ucnlNn5lmI+Ml3ns/zfB6O53lIheO4p4FJe4Ab/sAuAG+d5Xn1YskGJIQQJ8JJ\nG4D9jgGWZYCPCbD4Al0AEM3z/B3JBiWEECchcQDm/AAE/d8/NgCI4Hm+VbIBCSHEiUgagPsNxHE8\nz/OcLIMRQogTcFN6AoQQMlpRACaEEIV4jOCzYqxVyLPeQQghjmPQpVd6AiaEEIVQACaEEIVQACaE\nEIVQACaEE [...]
- "text": [
- "<matplotlib.figure.Figure at 0x64c9c50>"
- ]
- }
- ],
- "prompt_number": 7
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "c = Metabolite(\"c\")\n",
+ "c._bound = 2\n",
+ "x = Reaction(\"x\")\n",
+ "y = Reaction(\"y\")\n",
+ "x.add_metabolites({c: 1})\n",
+ "y.add_metabolites({c: 1})\n",
+ "m = Model()\n",
+ "m.add_reactions([x, y])\n",
+ "sol = m.optimize(quadratic_component=Q, objective_sense=\"minimize\")\n",
+ "sol.x_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Suppose we change the problem to have a mixed linear and quadratic objective.\n",
+ "\n",
+ "> **min** $\\frac{1}{2}\\left(x^2 + y^2 \\right) - y$\n",
+ "\n",
+ "> *subject to*\n",
+ "\n",
+ "> $x + y = 2$\n",
+ "\n",
+ "> $x \\ge 0$\n",
+ "\n",
+ "> $y \\ge 0$\n",
+ "\n",
+ "Graphically, this would be"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "image/png": "iVBORw0KGgoAAAANSUhEUgAAAWAAAAEmCAYAAABcYEo9AAAABHNCSVQICAgIfAhkiAAAAAlwSFlz\nAAALEgAACxIB0t1+/AAAIABJREFUeJztnXn85mPVx9/XbJaZQYgsYwlpEBkV8kQ8yFIo7UIJpcWS\np4Xi3B9LSQupnhZLSKhMlsryULaKoQyyhVCWQdl3s3yfP65rdM8992/7bvfyO+/X6/divvd9nevM\nb2bO77qvc87nhCzLqIoQws7wujPgjknwv8CXr8qyJ7eobEPHcZweIlQbgCdeBHO3hsVehrmLwzMA\nK2RZ9nBlmzqO4/QIFQfgMBFYMv3yQWC5LMv+VdmGjuM4PUSlAXiBjULIsiwLtWzmOI7TA4zptAOO\n4zijFQ/AjuM4HcIDsOM4TofwAOw4jtMhPAA7juN0CA/AjuM4HcIDsOM4TofwAOw4jtMhPAA7juN0\nCA/A [...]
+ "text/plain": [
+ "<matplotlib.figure.Figure at 0x7f72705b3fd0>"
+ ]
+ },
"metadata": {},
- "source": [
- "QP solvers in cobrapy will combine linear and quadratic coefficients. The linear portion will be obtained from the same objective_coefficient attribute used with LP's."
- ]
- },
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "ax = make_plot_ax()\n",
+ "ax.plot((0, 2), (2, 0), 'b')\n",
+ "ax.plot([0.5], [1.5], 'bo')\n",
+ "\n",
+ "yrange = linspace(1, 2, 11)\n",
+ "for r in (yrange ** 2 / 2. - yrange):\n",
+ " t = linspace(-sqrt(2 * r + 1) + 0.000001, sqrt(2 * r + 1) - 0.000001, 1000)\n",
+ " ax.plot(abs(t), 1 + sqrt(2 * r + 1 - t ** 2) * sign(t), '-.', color=\"gray\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "QP solvers in cobrapy will combine linear and quadratic coefficients. The linear portion will be obtained from the same objective_coefficient attribute used with LP's."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "y.objective_coefficient = -1\n",
- "sol = m.optimize(quadratic_component=Q, objective_sense=\"minimize\")\n",
- "sol.x_dict"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{'x': 0.5, 'y': 1.5}"
+ ]
+ },
+ "execution_count": 8,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 8,
- "text": [
- "{'x': 0.5, 'y': 1.5}"
- ]
- }
- ],
- "prompt_number": 8
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "y.objective_coefficient = -1\n",
+ "sol = m.optimize(quadratic_component=Q, objective_sense=\"minimize\")\n",
+ "sol.x_dict"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/qp.rst b/documentation_builder/qp.rst
index 24cb932..e02f3e8 100644
--- a/documentation_builder/qp.rst
+++ b/documentation_builder/qp.rst
@@ -2,9 +2,6 @@
Quadratic Programming
=====================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/qp.ipynb>`__.
-
Suppose we want to minimize the Euclidean distance of the solution to
the origin while subject to linear constraints. This will require a
quadratic objective function. Consider this example problem:
@@ -23,6 +20,7 @@ This problem can be visualized graphically:
.. code:: python
+ %matplotlib inline
from matplotlib.pyplot import figure, xlim, ylim
from mpl_toolkits.axes_grid.axislines import SubplotZero
from numpy import linspace, arange, sqrt, pi, sin, cos, sign
@@ -53,7 +51,8 @@ This problem can be visualized graphically:
ax.plot(r * cos(t), r * sin(t), '-.', color="gray")
-.. image:: qp_files/qp_3_0.png
+
+.. image:: qp_files/qp_1_0.png
The objective can be rewritten as
@@ -80,6 +79,7 @@ sparse matrix.
+
.. parsed-literal::
<2x2 sparse matrix of type '<type 'numpy.float64'>'
@@ -95,6 +95,7 @@ In this case, the quadratic objective is simply the identity matrix
+
.. parsed-literal::
matrix([[ 1., 0.],
@@ -110,6 +111,7 @@ installed, this function will return its name.
print(solvers.get_solver_name(qp=True))
+
.. parsed-literal::
gurobi
@@ -130,6 +132,7 @@ installed, this function will return its name.
+
.. parsed-literal::
{'x': 1.0, 'y': 1.0}
@@ -163,7 +166,8 @@ Graphically, this would be
ax.plot(abs(t), 1 + sqrt(2 * r + 1 - t ** 2) * sign(t), '-.', color="gray")
-.. image:: qp_files/qp_14_0.png
+
+.. image:: qp_files/qp_12_0.png
QP solvers in cobrapy will combine linear and quadratic coefficients.
@@ -178,6 +182,7 @@ attribute used with LP's.
+
.. parsed-literal::
{'x': 0.5, 'y': 1.5}
diff --git a/documentation_builder/qp_files/qp_12_0.png b/documentation_builder/qp_files/qp_12_0.png
new file mode 100644
index 0000000..f04d583
Binary files /dev/null and b/documentation_builder/qp_files/qp_12_0.png differ
diff --git a/documentation_builder/qp_files/qp_14_0.png b/documentation_builder/qp_files/qp_14_0.png
deleted file mode 100644
index 37dfbe3..0000000
Binary files a/documentation_builder/qp_files/qp_14_0.png and /dev/null differ
diff --git a/documentation_builder/qp_files/qp_1_0.png b/documentation_builder/qp_files/qp_1_0.png
new file mode 100644
index 0000000..d4ef2a1
Binary files /dev/null and b/documentation_builder/qp_files/qp_1_0.png differ
diff --git a/documentation_builder/qp_files/qp_3_0.png b/documentation_builder/qp_files/qp_3_0.png
deleted file mode 100644
index 5644f61..0000000
Binary files a/documentation_builder/qp_files/qp_3_0.png and /dev/null differ
diff --git a/documentation_builder/simulating.ipynb b/documentation_builder/simulating.ipynb
index c01f7c1..d83a1c1 100644
--- a/documentation_builder/simulating.ipynb
+++ b/documentation_builder/simulating.ipynb
@@ -1,251 +1,592 @@
{
- "metadata": {
- "name": "",
- "signature": "sha256:2c978fa134850ce153ec772810bd6094669dfc51c0a9e418b2793c02738eec19"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
+ "cells": [
{
- "cells": [
- {
- "cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Simulating with FBA"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "This example is available as an IPython [notebook](http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/simulating.ipynb).\n",
- "\n",
- "Simulations using flux balance analysis can be solved using Model.optimize(). This will maximize or minimize (maximizing is the default) flux through the objective reactions.\n"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "import cobra.test\n",
- "model = cobra.test.create_test_model()\n"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [],
- "prompt_number": 1
- },
- {
- "cell_type": "heading",
- "level": 2,
- "metadata": {},
- "source": [
- "Running FBA"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.optimize()"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 2,
- "text": [
- "<Solution 0.38 at 0x660d990>"
- ]
- }
- ],
- "prompt_number": 2
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The Model.optimize() function will return a Solution object, which will also be stored at model.solution. A solution object has several attributes:\n",
- "\n",
- " - f: the objective value\n",
- " - status: the status from the linear programming solver\n",
- " - x_dict: a dictionary of {reaction_id: flux_value} (also called \"primal\")\n",
- " - x: a list for x_dict\n",
- " - y_dict: a dictionary of {metabolite_id: dual_value}.\n",
- " - y: a list for y_dict"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "For example, after the last call to model.optimize(), the status should be 'optimal' if the solver returned no errors, and f should be the objective value"
- ]
- },
- {
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.solution.status"
- ],
- "language": "python",
- "metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 3,
- "text": [
- "'optimal'"
- ]
- }
- ],
- "prompt_number": 3
- },
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Simulating with FBA\n",
+ "\n",
+ "Simulations using flux balance analysis can be solved using Model.optimize(). This will maximize or minimize (maximizing is the default) flux through the objective reactions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "import pandas\n",
+ "pandas.options.display.max_rows = 100\n",
+ "\n",
+ "import cobra.test\n",
+ "model = cobra.test.create_test_model(\"textbook\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Running FBA"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.solution.f"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Solution 0.87 at 0x7fb3f849ca10>"
+ ]
+ },
+ "execution_count": 2,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 4,
- "text": [
- "0.38000797227551136"
- ]
- }
- ],
- "prompt_number": 4
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.optimize()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The Model.optimize() function will return a Solution object, which will also be stored at model.solution. A solution object has several attributes:\n",
+ "\n",
+ " - f: the objective value\n",
+ " - status: the status from the linear programming solver\n",
+ " - x_dict: a dictionary of {reaction_id: flux_value} (also called \"primal\")\n",
+ " - x: a list for x_dict\n",
+ " - y_dict: a dictionary of {metabolite_id: dual_value}.\n",
+ " - y: a list for y_dict"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "For example, after the last call to model.optimize(), the status should be 'optimal' if the solver returned no errors, and f should be the objective value"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "heading",
- "level": 2,
+ "data": {
+ "text/plain": [
+ "'optimal'"
+ ]
+ },
+ "execution_count": 3,
"metadata": {},
- "source": [
- "Changing the Objectives"
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.solution.status"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "0.8739215069684305"
+ ]
+ },
+ "execution_count": 4,
"metadata": {},
- "source": [
- "The objective function is determined from the objective_coefficient attribute of the objective reaction(s). Currently in the model, there is only one objective reaction, with an objective coefficient of 1."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.solution.f"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Changing the Objectives\n",
+ "\n",
+ "The objective function is determined from the objective_coefficient attribute of the objective reaction(s). Currently in the model, there is only one objective reaction, with an objective coefficient of 1."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "{reaction: reaction.objective_coefficient for reaction in model.reactions\n",
- " if reaction.objective_coefficient > 0}"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{<Reaction Biomass_Ecoli_core at 0x7fb3c899be90>: 1.0}"
+ ]
+ },
+ "execution_count": 5,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 5,
- "text": [
- "{<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}"
- ]
- }
- ],
- "prompt_number": 5
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.objective"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The objective function can be changed by assigning Model.objective, which can be a reaction object (or just it's name), or a dict of {Reaction: objective_coefficient}."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/plain": [
+ "{<Reaction ATPM at 0x7fb3c899bbd0>: 1}"
+ ]
+ },
+ "execution_count": 6,
"metadata": {},
- "source": [
- "The objective function can be changed by using the function Model.change_objective, which will take either a reaction object or just its name."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# change the objective to ATPM\n",
+ "# the upper bound should be 1000 so we get the actual optimal value\n",
+ "model.reactions.get_by_id(\"ATPM\").upper_bound = 1000.\n",
+ "model.objective = \"ATPM\"\n",
+ "model.objective"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "# change the objective to ATPM\n",
- "# the upper bound should be 1000 so we get the actual optimal value\n",
- "model.reactions.get_by_id(\"ATPM\").upper_bound = 1000.\n",
- "model.change_objective(\"ATPM\")\n",
- "{reaction: reaction.objective_coefficient for reaction in model.reactions\n",
- " if reaction.objective_coefficient > 0}"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "<Solution 175.00 at 0x7fb3c895de50>"
+ ]
+ },
+ "execution_count": 7,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 6,
- "text": [
- "{<Reaction ATPM at 0x52cb190>: 1.0}"
- ]
- }
- ],
- "prompt_number": 6
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.optimize()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "The objective function can also be changed by setting Reaction.objective_coefficient directly."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.optimize()"
- ],
- "language": "python",
+ "data": {
+ "text/plain": [
+ "{<Reaction Biomass_Ecoli_core at 0x7fb3c899be90>: 1.0}"
+ ]
+ },
+ "execution_count": 9,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 7,
- "text": [
- "<Solution 119.67 at 0x4c93110>"
- ]
- }
- ],
- "prompt_number": 7
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.reactions.get_by_id(\"ATPM\").objective_coefficient = 0.\n",
+ "model.reactions.get_by_id(\"Biomass_Ecoli_core\").objective_coefficient = 1.\n",
+ "model.objective"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Running FVA\n",
+ "\n",
+ "FBA will not give always give unique solution, because multiple flux states can achieve the same optimum. FVA (or flux variability analysis) finds the ranges of each metabolic flux at the optimum."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 35,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "markdown",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>maximum</th>\n",
+ " <th>minimum</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>ACALD</th>\n",
+ " <td>9.466331e-29</td>\n",
+ " <td>3.720797e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACALDt</th>\n",
+ " <td>-6.310887e-29</td>\n",
+ " <td>3.720797e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACKr</th>\n",
+ " <td>-2.524355e-28</td>\n",
+ " <td>3.933509e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTa</th>\n",
+ " <td>6.007250e+00</td>\n",
+ " <td>6.007250e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTb</th>\n",
+ " <td>6.007250e+00</td>\n",
+ " <td>6.007250e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACt2r</th>\n",
+ " <td>6.121561e-28</td>\n",
+ " <td>3.933509e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ADK1</th>\n",
+ " <td>-4.042971e-14</td>\n",
+ " <td>0.000000e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGDH</th>\n",
+ " <td>5.064376e+00</td>\n",
+ " <td>5.064376e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGt2r</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>7.079399e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ALCD2x</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>5.729185e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPM</th>\n",
+ " <td>8.390000e+00</td>\n",
+ " <td>8.390000e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPS4r</th>\n",
+ " <td>4.551401e+01</td>\n",
+ " <td>4.551401e+01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Biomass_Ecoli_core</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>8.739215e-01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CO2t</th>\n",
+ " <td>-2.280983e+01</td>\n",
+ " <td>-2.280983e+01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CS</th>\n",
+ " <td>6.007250e+00</td>\n",
+ " <td>6.007250e+00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CYTBD</th>\n",
+ " <td>4.359899e+01</td>\n",
+ " <td>4.359899e+01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>D_LACt2</th>\n",
+ " <td>3.660315e-28</td>\n",
+ " <td>4.140787e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ENO</th>\n",
+ " <td>1.471614e+01</td>\n",
+ " <td>1.471614e+01</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ETOHt2r</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>5.729185e-15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>EX_ac_e</th>\n",
+ " <td>-3.933509e-15</td>\n",
+ " <td>0.000000e+00</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " maximum minimum\n",
+ "ACALD 9.466331e-29 3.720797e-15\n",
+ "ACALDt -6.310887e-29 3.720797e-15\n",
+ "ACKr -2.524355e-28 3.933509e-15\n",
+ "ACONTa 6.007250e+00 6.007250e+00\n",
+ "ACONTb 6.007250e+00 6.007250e+00\n",
+ "ACt2r 6.121561e-28 3.933509e-15\n",
+ "ADK1 -4.042971e-14 0.000000e+00\n",
+ "AKGDH 5.064376e+00 5.064376e+00\n",
+ "AKGt2r 0.000000e+00 7.079399e-15\n",
+ "ALCD2x 0.000000e+00 5.729185e-15\n",
+ "ATPM 8.390000e+00 8.390000e+00\n",
+ "ATPS4r 4.551401e+01 4.551401e+01\n",
+ "Biomass_Ecoli_core 8.739215e-01 8.739215e-01\n",
+ "CO2t -2.280983e+01 -2.280983e+01\n",
+ "CS 6.007250e+00 6.007250e+00\n",
+ "CYTBD 4.359899e+01 4.359899e+01\n",
+ "D_LACt2 3.660315e-28 4.140787e-15\n",
+ "ENO 1.471614e+01 1.471614e+01\n",
+ "ETOHt2r 0.000000e+00 5.729185e-15\n",
+ "EX_ac_e -3.933509e-15 0.000000e+00"
+ ]
+ },
+ "execution_count": 35,
"metadata": {},
- "source": [
- "The objective function can also be changed by setting Reaction.objective_coefficient directly."
- ]
- },
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "fva_result = cobra.flux_analysis.flux_variability_analysis(model, model.reactions[:20])\n",
+ "pandas.DataFrame.from_dict(fva_result).T"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Setting parameter fraction_of_optimium=0.90 would give the flux ranges for reactions at 90% optimality."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
{
- "cell_type": "code",
- "collapsed": false,
- "input": [
- "model.reactions.get_by_id(\"ATPM\").objective_coefficient = 0.\n",
- "model.reactions.get_by_id(\"biomass_iRR1083_metals\").objective_coefficient = 1.\n",
- "{reaction: reaction.objective_coefficient for reaction in model.reactions\n",
- " if reaction.objective_coefficient > 0}"
- ],
- "language": "python",
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>maximum</th>\n",
+ " <th>minimum</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>ACALD</th>\n",
+ " <td>9.466331e-29</td>\n",
+ " <td>-2.542370</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACALDt</th>\n",
+ " <td>-6.310887e-29</td>\n",
+ " <td>-2.542370</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACKr</th>\n",
+ " <td>-3.029226e-28</td>\n",
+ " <td>-3.813556</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTa</th>\n",
+ " <td>8.894520e+00</td>\n",
+ " <td>0.848587</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACONTb</th>\n",
+ " <td>8.894520e+00</td>\n",
+ " <td>0.848587</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ACt2r</th>\n",
+ " <td>3.407879e-28</td>\n",
+ " <td>-3.813556</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ADK1</th>\n",
+ " <td>1.716100e+01</td>\n",
+ " <td>0.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGDH</th>\n",
+ " <td>8.045934e+00</td>\n",
+ " <td>0.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>AKGt2r</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>-1.430083</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ALCD2x</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>-2.214323</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPM</th>\n",
+ " <td>8.390000e+00</td>\n",
+ " <td>8.390000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ATPS4r</th>\n",
+ " <td>5.938106e+01</td>\n",
+ " <td>34.825618</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Biomass_Ecoli_core</th>\n",
+ " <td>8.739215e-01</td>\n",
+ " <td>0.786529</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CO2t</th>\n",
+ " <td>-1.520653e+01</td>\n",
+ " <td>-26.528850</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CS</th>\n",
+ " <td>8.894520e+00</td>\n",
+ " <td>0.848587</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>CYTBD</th>\n",
+ " <td>5.123909e+01</td>\n",
+ " <td>35.984865</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>D_LACt2</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>-2.145125</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ENO</th>\n",
+ " <td>1.673252e+01</td>\n",
+ " <td>8.686588</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ETOHt2r</th>\n",
+ " <td>0.000000e+00</td>\n",
+ " <td>-2.214323</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>EX_ac_e</th>\n",
+ " <td>3.813556e+00</td>\n",
+ " <td>0.000000</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " maximum minimum\n",
+ "ACALD 9.466331e-29 -2.542370\n",
+ "ACALDt -6.310887e-29 -2.542370\n",
+ "ACKr -3.029226e-28 -3.813556\n",
+ "ACONTa 8.894520e+00 0.848587\n",
+ "ACONTb 8.894520e+00 0.848587\n",
+ "ACt2r 3.407879e-28 -3.813556\n",
+ "ADK1 1.716100e+01 0.000000\n",
+ "AKGDH 8.045934e+00 0.000000\n",
+ "AKGt2r 0.000000e+00 -1.430083\n",
+ "ALCD2x 0.000000e+00 -2.214323\n",
+ "ATPM 8.390000e+00 8.390000\n",
+ "ATPS4r 5.938106e+01 34.825618\n",
+ "Biomass_Ecoli_core 8.739215e-01 0.786529\n",
+ "CO2t -1.520653e+01 -26.528850\n",
+ "CS 8.894520e+00 0.848587\n",
+ "CYTBD 5.123909e+01 35.984865\n",
+ "D_LACt2 0.000000e+00 -2.145125\n",
+ "ENO 1.673252e+01 8.686588\n",
+ "ETOHt2r 0.000000e+00 -2.214323\n",
+ "EX_ac_e 3.813556e+00 0.000000"
+ ]
+ },
+ "execution_count": 36,
"metadata": {},
- "outputs": [
- {
- "metadata": {},
- "output_type": "pyout",
- "prompt_number": 8,
- "text": [
- "{<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}"
- ]
- }
- ],
- "prompt_number": 8
+ "output_type": "execute_result"
}
],
- "metadata": {}
+ "source": [
+ "fva_result = cobra.flux_analysis.flux_variability_analysis(model, model.reactions[:20], fraction_of_optimum=0.9)\n",
+ "pandas.DataFrame.from_dict(fva_result).T"
+ ]
}
- ]
-}
\ No newline at end of file
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/simulating.rst b/documentation_builder/simulating.rst
index 8ba70f4..6dd67bc 100644
--- a/documentation_builder/simulating.rst
+++ b/documentation_builder/simulating.rst
@@ -2,17 +2,17 @@
Simulating with FBA
===================
-This example is available as an IPython
-`notebook <http://nbviewer.ipython.org/github/opencobra/cobrapy/blob/master/documentation_builder/simulating.ipynb>`__.
-
Simulations using flux balance analysis can be solved using
Model.optimize(). This will maximize or minimize (maximizing is the
default) flux through the objective reactions.
.. code:: python
+ import pandas
+ pandas.options.display.max_rows = 100
+
import cobra.test
- model = cobra.test.create_test_model()
+ model = cobra.test.create_test_model("textbook")
Running FBA
-----------
@@ -23,9 +23,10 @@ Running FBA
+
.. parsed-literal::
- <Solution 0.38 at 0x660d990>
+ <Solution 0.87 at 0x7fb3f849ca10>
@@ -51,6 +52,7 @@ objective value
+
.. parsed-literal::
'optimal'
@@ -63,9 +65,10 @@ objective value
+
.. parsed-literal::
- 0.38000797227551136
+ 0.8739215069684305
@@ -78,35 +81,35 @@ only one objective reaction, with an objective coefficient of 1.
.. code:: python
- {reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
+ model.objective
+
.. parsed-literal::
- {<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}
+ {<Reaction Biomass_Ecoli_core at 0x7fb3c899be90>: 1.0}
-The objective function can be changed by using the function
-Model.change\_objective, which will take either a reaction object or
-just its name.
+The objective function can be changed by assigning Model.objective,
+which can be a reaction object (or just it's name), or a dict of
+{Reaction: objective\_coefficient}.
.. code:: python
# change the objective to ATPM
# the upper bound should be 1000 so we get the actual optimal value
model.reactions.get_by_id("ATPM").upper_bound = 1000.
- model.change_objective("ATPM")
- {reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
+ model.objective = "ATPM"
+ model.objective
+
.. parsed-literal::
- {<Reaction ATPM at 0x52cb190>: 1.0}
+ {<Reaction ATPM at 0x7fb3c899bbd0>: 1}
@@ -116,9 +119,10 @@ just its name.
+
.. parsed-literal::
- <Solution 119.67 at 0x4c93110>
+ <Solution 175.00 at 0x7fb3c895de50>
@@ -128,14 +132,276 @@ Reaction.objective\_coefficient directly.
.. code:: python
model.reactions.get_by_id("ATPM").objective_coefficient = 0.
- model.reactions.get_by_id("biomass_iRR1083_metals").objective_coefficient = 1.
- {reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
+ model.reactions.get_by_id("Biomass_Ecoli_core").objective_coefficient = 1.
+ model.objective
+
.. parsed-literal::
- {<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}
+ {<Reaction Biomass_Ecoli_core at 0x7fb3c899be90>: 1.0}
+
+
+
+Running FVA
+-----------
+
+FBA will not give always give unique solution, because multiple flux
+states can achieve the same optimum. FVA (or flux variability analysis)
+finds the ranges of each metabolic flux at the optimum.
+
+.. code:: python
+
+ fva_result = cobra.flux_analysis.flux_variability_analysis(model, model.reactions[:20])
+ pandas.DataFrame.from_dict(fva_result).T
+
+
+
+
+.. raw:: html
+
+ <div>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th></th>
+ <th>maximum</th>
+ <th>minimum</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th>ACALD</th>
+ <td>9.466331e-29</td>
+ <td>3.720797e-15</td>
+ </tr>
+ <tr>
+ <th>ACALDt</th>
+ <td>-6.310887e-29</td>
+ <td>3.720797e-15</td>
+ </tr>
+ <tr>
+ <th>ACKr</th>
+ <td>-2.524355e-28</td>
+ <td>3.933509e-15</td>
+ </tr>
+ <tr>
+ <th>ACONTa</th>
+ <td>6.007250e+00</td>
+ <td>6.007250e+00</td>
+ </tr>
+ <tr>
+ <th>ACONTb</th>
+ <td>6.007250e+00</td>
+ <td>6.007250e+00</td>
+ </tr>
+ <tr>
+ <th>ACt2r</th>
+ <td>6.121561e-28</td>
+ <td>3.933509e-15</td>
+ </tr>
+ <tr>
+ <th>ADK1</th>
+ <td>-4.042971e-14</td>
+ <td>0.000000e+00</td>
+ </tr>
+ <tr>
+ <th>AKGDH</th>
+ <td>5.064376e+00</td>
+ <td>5.064376e+00</td>
+ </tr>
+ <tr>
+ <th>AKGt2r</th>
+ <td>0.000000e+00</td>
+ <td>7.079399e-15</td>
+ </tr>
+ <tr>
+ <th>ALCD2x</th>
+ <td>0.000000e+00</td>
+ <td>5.729185e-15</td>
+ </tr>
+ <tr>
+ <th>ATPM</th>
+ <td>8.390000e+00</td>
+ <td>8.390000e+00</td>
+ </tr>
+ <tr>
+ <th>ATPS4r</th>
+ <td>4.551401e+01</td>
+ <td>4.551401e+01</td>
+ </tr>
+ <tr>
+ <th>Biomass_Ecoli_core</th>
+ <td>8.739215e-01</td>
+ <td>8.739215e-01</td>
+ </tr>
+ <tr>
+ <th>CO2t</th>
+ <td>-2.280983e+01</td>
+ <td>-2.280983e+01</td>
+ </tr>
+ <tr>
+ <th>CS</th>
+ <td>6.007250e+00</td>
+ <td>6.007250e+00</td>
+ </tr>
+ <tr>
+ <th>CYTBD</th>
+ <td>4.359899e+01</td>
+ <td>4.359899e+01</td>
+ </tr>
+ <tr>
+ <th>D_LACt2</th>
+ <td>3.660315e-28</td>
+ <td>4.140787e-15</td>
+ </tr>
+ <tr>
+ <th>ENO</th>
+ <td>1.471614e+01</td>
+ <td>1.471614e+01</td>
+ </tr>
+ <tr>
+ <th>ETOHt2r</th>
+ <td>0.000000e+00</td>
+ <td>5.729185e-15</td>
+ </tr>
+ <tr>
+ <th>EX_ac_e</th>
+ <td>-3.933509e-15</td>
+ <td>0.000000e+00</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+
+
+Setting parameter fraction\_of\_optimium=0.90 would give the flux ranges
+for reactions at 90% optimality.
+
+.. code:: python
+
+ fva_result = cobra.flux_analysis.flux_variability_analysis(model, model.reactions[:20], fraction_of_optimum=0.9)
+ pandas.DataFrame.from_dict(fva_result).T
+
+
+
+
+.. raw:: html
+
+ <div>
+ <table border="1" class="dataframe">
+ <thead>
+ <tr style="text-align: right;">
+ <th></th>
+ <th>maximum</th>
+ <th>minimum</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <th>ACALD</th>
+ <td>9.466331e-29</td>
+ <td>-2.542370</td>
+ </tr>
+ <tr>
+ <th>ACALDt</th>
+ <td>-6.310887e-29</td>
+ <td>-2.542370</td>
+ </tr>
+ <tr>
+ <th>ACKr</th>
+ <td>-3.029226e-28</td>
+ <td>-3.813556</td>
+ </tr>
+ <tr>
+ <th>ACONTa</th>
+ <td>8.894520e+00</td>
+ <td>0.848587</td>
+ </tr>
+ <tr>
+ <th>ACONTb</th>
+ <td>8.894520e+00</td>
+ <td>0.848587</td>
+ </tr>
+ <tr>
+ <th>ACt2r</th>
+ <td>3.407879e-28</td>
+ <td>-3.813556</td>
+ </tr>
+ <tr>
+ <th>ADK1</th>
+ <td>1.716100e+01</td>
+ <td>0.000000</td>
+ </tr>
+ <tr>
+ <th>AKGDH</th>
+ <td>8.045934e+00</td>
+ <td>0.000000</td>
+ </tr>
+ <tr>
+ <th>AKGt2r</th>
+ <td>0.000000e+00</td>
+ <td>-1.430083</td>
+ </tr>
+ <tr>
+ <th>ALCD2x</th>
+ <td>0.000000e+00</td>
+ <td>-2.214323</td>
+ </tr>
+ <tr>
+ <th>ATPM</th>
+ <td>8.390000e+00</td>
+ <td>8.390000</td>
+ </tr>
+ <tr>
+ <th>ATPS4r</th>
+ <td>5.938106e+01</td>
+ <td>34.825618</td>
+ </tr>
+ <tr>
+ <th>Biomass_Ecoli_core</th>
+ <td>8.739215e-01</td>
+ <td>0.786529</td>
+ </tr>
+ <tr>
+ <th>CO2t</th>
+ <td>-1.520653e+01</td>
+ <td>-26.528850</td>
+ </tr>
+ <tr>
+ <th>CS</th>
+ <td>8.894520e+00</td>
+ <td>0.848587</td>
+ </tr>
+ <tr>
+ <th>CYTBD</th>
+ <td>5.123909e+01</td>
+ <td>35.984865</td>
+ </tr>
+ <tr>
+ <th>D_LACt2</th>
+ <td>0.000000e+00</td>
+ <td>-2.145125</td>
+ </tr>
+ <tr>
+ <th>ENO</th>
+ <td>1.673252e+01</td>
+ <td>8.686588</td>
+ </tr>
+ <tr>
+ <th>ETOHt2r</th>
+ <td>0.000000e+00</td>
+ <td>-2.214323</td>
+ </tr>
+ <tr>
+ <th>EX_ac_e</th>
+ <td>3.813556e+00</td>
+ <td>0.000000</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
diff --git a/documentation_builder/solvers.ipynb b/documentation_builder/solvers.ipynb
new file mode 100644
index 0000000..86c355f
--- /dev/null
+++ b/documentation_builder/solvers.ipynb
@@ -0,0 +1,723 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "#Solver Interface\n",
+ "\n",
+ "Each cobrapy solver must expose the following API. The solvers all will have their own distinct LP object types, but each can be manipulated by these functions. This API can be used directly when implementing algorithms efficiently on linear programs because it has 2 primary benefits:\n",
+ "\n",
+ "1. Avoid the overhead of creating and destroying LP's for each operation\n",
+ "\n",
+ "2. Many solver objects preserve the basis between subsequent LP's, making each subsequent LP solve faster\n",
+ "\n",
+ "We will walk though the API with the cglpk solver, which links the cobrapy solver API with [GLPK](http://www.gnu.org/software/glpk/)'s C API."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [],
+ "source": [
+ "import cobra.test\n",
+ "\n",
+ "model = cobra.test.create_test_model(\"textbook\")\n",
+ "solver = cobra.solvers.cglpk"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Attributes and functions\n",
+ "\n",
+ "Each solver has some attributes:\n",
+ "\n",
+ "### solver_name\n",
+ "\n",
+ "The name of the solver. This is the name which will be used to select the solver in cobrapy functions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'cglpk'"
+ ]
+ },
+ "execution_count": 2,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.solver_name"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Solution 0.87 at 0x7f9148bb2250>"
+ ]
+ },
+ "execution_count": 3,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.optimize(solver=\"cglpk\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### \\_SUPPORTS_MILP\n",
+ "\n",
+ "The presence of this attribute tells cobrapy that the solver supports mixed-integer linear programming"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver._SUPPORTS_MILP"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### solve\n",
+ "\n",
+ "Model.optimize is a wrapper for each solver's solve function. It takes in a cobra model and returns a solution"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Solution 0.87 at 0x7f917d50ed50>"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.solve(model)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### create_problem\n",
+ "\n",
+ "This creates the LP object for the solver."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<cobra.solvers.cglpk.GLP at 0x46e8aa0>"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "lp = solver.create_problem(model, objective_sense=\"maximize\")\n",
+ "lp"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### solve_problem\n",
+ "\n",
+ "Solve the LP object and return the solution status"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'optimal'"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.solve_problem(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### format_solution\n",
+ "\n",
+ "Extract a cobra.Solution object from a solved LP object"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<Solution 0.87 at 0x7f917d50e9d0>"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.format_solution(lp, model)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### get_objective_value\n",
+ "\n",
+ "Extract the objective value from a solved LP object"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.8739215069684305"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.get_objective_value(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### get_status\n",
+ "\n",
+ "Get the solution status of a solved LP object"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'optimal'"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.get_status(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### change_variable_objective\n",
+ "\n",
+ "change the objective coefficient a reaction at a particular index. This does not change any of the other objectives which have already been set. This example will double and then revert the biomass coefficient."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "12"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.reactions.index(\"Biomass_Ecoli_core\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "1.747843013936861"
+ ]
+ },
+ "execution_count": 12,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_variable_objective(lp, 12, 2)\n",
+ "solver.solve_problem(lp)\n",
+ "solver.get_objective_value(lp)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.8739215069684305"
+ ]
+ },
+ "execution_count": 13,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_variable_objective(lp, 12, 1)\n",
+ "solver.solve_problem(lp)\n",
+ "solver.get_objective_value(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### change variable_bounds\n",
+ "\n",
+ "change the lower and upper bounds of a reaction at a particular index. This example will set the lower bound of the biomass to an infeasible value, then revert it."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'infeasible'"
+ ]
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_variable_bounds(lp, 12, 1000, 1000)\n",
+ "solver.solve_problem(lp)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'optimal'"
+ ]
+ },
+ "execution_count": 15,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_variable_bounds(lp, 12, 0, 1000)\n",
+ "solver.solve_problem(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### change_coefficient\n",
+ "\n",
+ "Change a coefficient in the stoichiometric matrix. In this example, we will set the entry for ADP in the ATMP reaction to in infeasible value, then reset it."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "16"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.metabolites.index(\"atp_c\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "10"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "model.reactions.index(\"ATPM\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'infeasible'"
+ ]
+ },
+ "execution_count": 18,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_coefficient(lp, 16, 10, -10)\n",
+ "solver.solve_problem(lp)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'optimal'"
+ ]
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.change_coefficient(lp, 16, 10, -1)\n",
+ "solver.solve_problem(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### set_parameter\n",
+ "\n",
+ "Set a solver parameter. Each solver will have its own particular set of unique paramters. However, some have unified names. For example, all solvers should accept \"tolerance_feasibility.\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [],
+ "source": [
+ "solver.set_parameter(lp, \"tolerance_feasibility\", 1e-9)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.0"
+ ]
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.set_parameter(lp, \"objective_sense\", \"minimize\")\n",
+ "solver.solve_problem(lp)\n",
+ "solver.get_objective_value(lp)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "0.8739215069684304"
+ ]
+ },
+ "execution_count": 22,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "solver.set_parameter(lp, \"objective_sense\", \"maximize\")\n",
+ "solver.solve_problem(lp)\n",
+ "solver.get_objective_value(lp)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Example with FVA\n",
+ "\n",
+ "Consider flux variability analysis (FVA), which requires maximizing and minimizing every reaction with the original biomass value fixed at its optimal value. If we used the cobra Model API in a naive implementation, we would do the following:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 23,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 144 ms, sys: 667 µs, total: 145 ms\n",
+ "Wall time: 141 ms\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%time\n",
+ "# work on a copy of the model so the original is not changed\n",
+ "fva_model = model.copy()\n",
+ "\n",
+ "# set the lower bound on the objective to be the optimal value\n",
+ "f = fva_model.optimize().f\n",
+ "for objective_reaction, coefficient in fva_model.objective.items():\n",
+ " objective_reaction.lower_bound = coefficient * f\n",
+ "\n",
+ "# now maximize and minimze every reaction to find its bounds\n",
+ "fva_result = {}\n",
+ "for r in fva_model.reactions:\n",
+ " fva_model.change_objective(r)\n",
+ " fva_result[r.id] = {}\n",
+ " fva_result[r.id][\"maximum\"] = fva_model.optimize(objective_sense=\"maximize\").f\n",
+ " fva_result[r.id][\"minimum\"] = fva_model.optimize(objective_sense=\"minimize\").f"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Instead, we could use the solver API to do this more efficiently. This is roughly how cobrapy implementes FVA. It keeps uses the same LP object and repeatedly maximizes and minimizes it. This allows the solver to preserve the basis, and is much faster. The speed increase is even more noticeable the larger the model gets."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {
+ "collapsed": false
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 9.85 ms, sys: 251 µs, total: 10.1 ms\n",
+ "Wall time: 9.94 ms\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%time\n",
+ "# create the LP object\n",
+ "lp = solver.create_problem(model)\n",
+ "\n",
+ "# set the lower bound on the objective to be the optimal value\n",
+ "solver.solve_problem(lp)\n",
+ "f = solver.get_objective_value(lp)\n",
+ "for objective_reaction, coefficient in model.objective.items():\n",
+ " objective_index = model.reactions.index(objective_reaction)\n",
+ " # old objective is no longer the objective\n",
+ " solver.change_variable_objective(lp, objective_index, 0.)\n",
+ " solver.change_variable_bounds(lp, objective_index, f * coefficient, objective_reaction.upper_bound)\n",
+ "\n",
+ "# now maximize and minimze every reaction to find its bounds\n",
+ "fva_result = {}\n",
+ "for index, r in enumerate(model.reactions):\n",
+ " solver.change_variable_objective(lp, index, 1.)\n",
+ " fva_result[r.id] = {}\n",
+ " solver.solve_problem(lp, objective_sense=\"maximize\")\n",
+ " fva_result[r.id][\"maximum\"] = solver.get_objective_value(lp)\n",
+ " solver.solve_problem(lp, objective_sense=\"minimize\")\n",
+ " fva_result[r.id][\"minimum\"] = solver.get_objective_value(lp)\n",
+ " solver.change_variable_objective(lp, index, 0.)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 2",
+ "language": "python",
+ "name": "python2"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/documentation_builder/solvers.rst b/documentation_builder/solvers.rst
new file mode 100644
index 0000000..fc714dc
--- /dev/null
+++ b/documentation_builder/solvers.rst
@@ -0,0 +1,451 @@
+
+Solver Interface
+================
+
+Each cobrapy solver must expose the following API. The solvers all will
+have their own distinct LP object types, but each can be manipulated by
+these functions. This API can be used directly when implementing
+algorithms efficiently on linear programs because it has 2 primary
+benefits:
+
+1. Avoid the overhead of creating and destroying LP's for each operation
+
+2. Many solver objects preserve the basis between subsequent LP's,
+ making each subsequent LP solve faster
+
+We will walk though the API with the cglpk solver, which links the
+cobrapy solver API with `GLPK <http://www.gnu.org/software/glpk/>`__'s C
+API.
+
+.. code:: python
+
+ import cobra.test
+
+ model = cobra.test.create_test_model("textbook")
+ solver = cobra.solvers.cglpk
+
+Attributes and functions
+------------------------
+
+Each solver has some attributes:
+
+solver\_name
+~~~~~~~~~~~~
+
+The name of the solver. This is the name which will be used to select
+the solver in cobrapy functions.
+
+.. code:: python
+
+ solver.solver_name
+
+
+
+
+.. parsed-literal::
+
+ 'cglpk'
+
+
+
+.. code:: python
+
+ model.optimize(solver="cglpk")
+
+
+
+
+.. parsed-literal::
+
+ <Solution 0.87 at 0x7f9148bb2250>
+
+
+
+\_SUPPORTS\_MILP
+~~~~~~~~~~~~~~~~
+
+The presence of this attribute tells cobrapy that the solver supports
+mixed-integer linear programming
+
+.. code:: python
+
+ solver._SUPPORTS_MILP
+
+
+
+
+.. parsed-literal::
+
+ True
+
+
+
+solve
+~~~~~
+
+Model.optimize is a wrapper for each solver's solve function. It takes
+in a cobra model and returns a solution
+
+.. code:: python
+
+ solver.solve(model)
+
+
+
+
+.. parsed-literal::
+
+ <Solution 0.87 at 0x7f917d50ed50>
+
+
+
+create\_problem
+~~~~~~~~~~~~~~~
+
+This creates the LP object for the solver.
+
+.. code:: python
+
+ lp = solver.create_problem(model, objective_sense="maximize")
+ lp
+
+
+
+
+.. parsed-literal::
+
+ <cobra.solvers.cglpk.GLP at 0x46e8aa0>
+
+
+
+solve\_problem
+~~~~~~~~~~~~~~
+
+Solve the LP object and return the solution status
+
+.. code:: python
+
+ solver.solve_problem(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'optimal'
+
+
+
+format\_solution
+~~~~~~~~~~~~~~~~
+
+Extract a cobra.Solution object from a solved LP object
+
+.. code:: python
+
+ solver.format_solution(lp, model)
+
+
+
+
+.. parsed-literal::
+
+ <Solution 0.87 at 0x7f917d50e9d0>
+
+
+
+get\_objective\_value
+~~~~~~~~~~~~~~~~~~~~~
+
+Extract the objective value from a solved LP object
+
+.. code:: python
+
+ solver.get_objective_value(lp)
+
+
+
+
+.. parsed-literal::
+
+ 0.8739215069684305
+
+
+
+get\_status
+~~~~~~~~~~~
+
+Get the solution status of a solved LP object
+
+.. code:: python
+
+ solver.get_status(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'optimal'
+
+
+
+change\_variable\_objective
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+change the objective coefficient a reaction at a particular index. This
+does not change any of the other objectives which have already been set.
+This example will double and then revert the biomass coefficient.
+
+.. code:: python
+
+ model.reactions.index("Biomass_Ecoli_core")
+
+
+
+
+.. parsed-literal::
+
+ 12
+
+
+
+.. code:: python
+
+ solver.change_variable_objective(lp, 12, 2)
+ solver.solve_problem(lp)
+ solver.get_objective_value(lp)
+
+
+
+
+.. parsed-literal::
+
+ 1.747843013936861
+
+
+
+.. code:: python
+
+ solver.change_variable_objective(lp, 12, 1)
+ solver.solve_problem(lp)
+ solver.get_objective_value(lp)
+
+
+
+
+.. parsed-literal::
+
+ 0.8739215069684305
+
+
+
+change variable\_bounds
+~~~~~~~~~~~~~~~~~~~~~~~
+
+change the lower and upper bounds of a reaction at a particular index.
+This example will set the lower bound of the biomass to an infeasible
+value, then revert it.
+
+.. code:: python
+
+ solver.change_variable_bounds(lp, 12, 1000, 1000)
+ solver.solve_problem(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'infeasible'
+
+
+
+.. code:: python
+
+ solver.change_variable_bounds(lp, 12, 0, 1000)
+ solver.solve_problem(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'optimal'
+
+
+
+change\_coefficient
+~~~~~~~~~~~~~~~~~~~
+
+Change a coefficient in the stoichiometric matrix. In this example, we
+will set the entry for ADP in the ATMP reaction to in infeasible value,
+then reset it.
+
+.. code:: python
+
+ model.metabolites.index("atp_c")
+
+
+
+
+.. parsed-literal::
+
+ 16
+
+
+
+.. code:: python
+
+ model.reactions.index("ATPM")
+
+
+
+
+.. parsed-literal::
+
+ 10
+
+
+
+.. code:: python
+
+ solver.change_coefficient(lp, 16, 10, -10)
+ solver.solve_problem(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'infeasible'
+
+
+
+.. code:: python
+
+ solver.change_coefficient(lp, 16, 10, -1)
+ solver.solve_problem(lp)
+
+
+
+
+.. parsed-literal::
+
+ 'optimal'
+
+
+
+set\_parameter
+~~~~~~~~~~~~~~
+
+Set a solver parameter. Each solver will have its own particular set of
+unique paramters. However, some have unified names. For example, all
+solvers should accept "tolerance\_feasibility."
+
+.. code:: python
+
+ solver.set_parameter(lp, "tolerance_feasibility", 1e-9)
+
+.. code:: python
+
+ solver.set_parameter(lp, "objective_sense", "minimize")
+ solver.solve_problem(lp)
+ solver.get_objective_value(lp)
+
+
+
+
+.. parsed-literal::
+
+ 0.0
+
+
+
+.. code:: python
+
+ solver.set_parameter(lp, "objective_sense", "maximize")
+ solver.solve_problem(lp)
+ solver.get_objective_value(lp)
+
+
+
+
+.. parsed-literal::
+
+ 0.8739215069684304
+
+
+
+Example with FVA
+----------------
+
+Consider flux variability analysis (FVA), which requires maximizing and
+minimizing every reaction with the original biomass value fixed at its
+optimal value. If we used the cobra Model API in a naive implementation,
+we would do the following:
+
+.. code:: python
+
+ %%time
+ # work on a copy of the model so the original is not changed
+ fva_model = model.copy()
+
+ # set the lower bound on the objective to be the optimal value
+ f = fva_model.optimize().f
+ for objective_reaction, coefficient in fva_model.objective.items():
+ objective_reaction.lower_bound = coefficient * f
+
+ # now maximize and minimze every reaction to find its bounds
+ fva_result = {}
+ for r in fva_model.reactions:
+ fva_model.change_objective(r)
+ fva_result[r.id] = {}
+ fva_result[r.id]["maximum"] = fva_model.optimize(objective_sense="maximize").f
+ fva_result[r.id]["minimum"] = fva_model.optimize(objective_sense="minimize").f
+
+
+.. parsed-literal::
+
+ CPU times: user 144 ms, sys: 667 µs, total: 145 ms
+ Wall time: 141 ms
+
+
+Instead, we could use the solver API to do this more efficiently. This
+is roughly how cobrapy implementes FVA. It keeps uses the same LP object
+and repeatedly maximizes and minimizes it. This allows the solver to
+preserve the basis, and is much faster. The speed increase is even more
+noticeable the larger the model gets.
+
+.. code:: python
+
+ %%time
+ # create the LP object
+ lp = solver.create_problem(model)
+
+ # set the lower bound on the objective to be the optimal value
+ solver.solve_problem(lp)
+ f = solver.get_objective_value(lp)
+ for objective_reaction, coefficient in model.objective.items():
+ objective_index = model.reactions.index(objective_reaction)
+ # old objective is no longer the objective
+ solver.change_variable_objective(lp, objective_index, 0.)
+ solver.change_variable_bounds(lp, objective_index, f * coefficient, objective_reaction.upper_bound)
+
+ # now maximize and minimze every reaction to find its bounds
+ fva_result = {}
+ for index, r in enumerate(model.reactions):
+ solver.change_variable_objective(lp, index, 1.)
+ fva_result[r.id] = {}
+ solver.solve_problem(lp, objective_sense="maximize")
+ fva_result[r.id]["maximum"] = solver.get_objective_value(lp)
+ solver.solve_problem(lp, objective_sense="minimize")
+ fva_result[r.id]["minimum"] = solver.get_objective_value(lp)
+ solver.change_variable_objective(lp, index, 0.)
+
+
+.. parsed-literal::
+
+ CPU times: user 9.85 ms, sys: 251 µs, total: 10.1 ms
+ Wall time: 9.94 ms
+
diff --git a/examples/building_model.py b/examples/building_model.py
deleted file mode 100644
index ab6dade..0000000
--- a/examples/building_model.py
+++ /dev/null
@@ -1,126 +0,0 @@
-
-## Building a Model
-
-# This simple example (available as an IPython [notebook](http://nbviewer.ipyth
-# on.org/github/opencobra/cobrapy/blob/master/documentation_builder/building_mo
-# del.ipynb)) demonstrates how to create a model, create a reaction, and then
-# add the reaction to the model.
-#
-# We'll use the '3OAS140' reaction from the STM_1.0 model:
-#
-# 1.0 malACP[c] + 1.0 h[c] + 1.0 ddcaACP[c] $\rightarrow$ 1.0 co2[c] + 1.0
-# ACP[c] + 1.0 3omrsACP[c]
-
-# First, create the model and reaction.
-
-from cobra import Model, Reaction, Metabolite
-# Best practise: SBML compliant IDs
-cobra_model = Model('example_cobra_model')
-
-reaction = Reaction('3OAS140')
-reaction.name = '3 oxoacyl acyl carrier protein synthase n C140 '
-reaction.subsystem = 'Cell Envelope Biosynthesis'
-reaction.lower_bound = 0. # This is the default
-reaction.upper_bound = 1000. # This is the default
-reaction.objective_coefficient = 0. # this is the default
-
-
-# We need to create metabolites as well. If we were using an existing model, we
-# could use get_by_id to get the apporpriate Metabolite objects instead.
-
-ACP_c = Metabolite('ACP_c', formula='C11H21N2O7PRS',
- name='acyl-carrier-protein', compartment='c')
-omrsACP_c = Metabolite('3omrsACP_c', formula='C25H45N2O9PRS',
- name='3-Oxotetradecanoyl-acyl-carrier-protein', compartment='c')
-co2_c = Metabolite('co2_c', formula='CO2', name='CO2', compartment='c')
-malACP_c = Metabolite('malACP_c', formula='C14H22N2O10PRS',
- name='Malonyl-acyl-carrier-protein', compartment='c')
-h_c = Metabolite('h_c', formula='H', name='H', compartment='c')
-ddcaACP_c = Metabolite('ddcaACP_c', formula='C23H43N2O8PRS',
- name='Dodecanoyl-ACP-n-C120ACP', compartment='c')
-
-
-# Adding metabolites to a reaction requires using a dictionary of the
-# metabolites and their stoichiometric coefficients. A group of metabolites can
-# be added all at once, or they can be added one at a time.
-
-reaction.add_metabolites({malACP_c: -1.0,
- h_c: -1.0,
- ddcaACP_c: -1.0,
- co2_c: 1.0,
- ACP_c: 1.0,
- omrsACP_c: 1.0})
-
-
-reaction.reaction # This gives a string representation of the reaction
-# Output:
-# 'malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c'
-
-# The gene_reaction_rule is a boolean representation of the gene requirements
-# for this reaction to be active as described in [Schellenberger et al 2011
-# Nature Protocols
-# 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308). We will assign
-# the gene reaction rule string, which will automatically create the
-# corresponding gene objects.
-
-reaction.gene_reaction_rule = '( STM2378 or STM1197 )'
-reaction.genes
-# Output:
-# frozenset({<Gene STM2378 at 0x3739b10>, <Gene STM1197 at 0x3739b50>})
-
-# At this point in time, the model is still empty
-
-print('%i reactions in initial model' % len(cobra_model.reactions))
-print('%i metabolites in initial model' % len(cobra_model.metabolites))
-print('%i genes in initial model' % len(cobra_model.genes))
-# Prints:
-# 0 reactions in initial model
-# 0 metabolites in initial model
-# 0 genes in initial model
-
-# We will add the reaction to the model, which will also add all associated
-# metabolites and genes
-
-cobra_model.add_reaction(reaction)
-
-# Now there are things in the model
-print('%i reaction in model' % len(cobra_model.reactions))
-print('%i metabolites in model' % len(cobra_model.metabolites))
-print('%i genes in model' % len(cobra_model.genes))
-# Prints:
-# 1 reaction in model
-# 6 metabolites in model
-# 2 genes in model
-
-# We can iterate through the model objects to observe the contents
-
-# Iterate through the the objects in the model
-print("Reactions")
-print("---------")
-for x in cobra_model.reactions:
- print("%s : %s" % (repr(x), x.reaction))
-print("Metabolites")
-print("-----------")
-for x in cobra_model.metabolites:
- print('%s : %s' % (repr(x), x.formula))
-print("Genes")
-print("-----")
-for x in cobra_model.genes:
- reactions_list_str = ", ".join((repr(i) for i in x.reactions))
- print("%s is associated with reactions: %s" % (repr(x), reactions_list_str))
-# Prints:
-# Reactions
-# ---------
-# <Reaction 3OAS140 at 0x4a18b90> : malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c
-# Metabolites
-# -----------
-# <Metabolite co2_c at 0x594ba10> : CO2
-# <Metabolite malACP_c at 0x594ba90> : C14H22N2O10PRS
-# <Metabolite h_c at 0x594bb10> : H
-# <Metabolite 3omrsACP_c at 0x594b950> : C25H45N2O9PRS
-# <Metabolite ACP_c at 0x594b990> : C11H21N2O7PRS
-# <Metabolite ddcaACP_c at 0x594bb90> : C23H43N2O8PRS
-# Genes
-# -----
-# <Gene STM2378 at 0x3739b10> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>
-# <Gene STM1197 at 0x3739b50> is associated with reactions: <Reaction 3OAS140 at 0x4a18b90>
diff --git a/examples/deletions.py b/examples/deletions.py
deleted file mode 100644
index 7ae8130..0000000
--- a/examples/deletions.py
+++ /dev/null
@@ -1,92 +0,0 @@
-
-## Simulating Deletions
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/deletions.ipynb)
-# .
-
-from time import time
-
-
-from cobra.test import create_test_model, salmonella_pickle, ecoli_pickle
-from cobra.flux_analysis import single_deletion
-from cobra.flux_analysis import double_deletion
-
-
-cobra_model = create_test_model(salmonella_pickle)
-
-
-### Single Deletions
-
-# Perform all single gene deletions on a model
-
-start = time() # start timer()
-growth_rates, statuses = single_deletion(cobra_model)
-print("All single gene deletions completed in %.2f sec" % (time() - start))
-# Prints:
-# All single gene deletions completed in 4.01 sec
-
-# These can also be done for only a subset of genes
-
-single_deletion(cobra_model, element_list=cobra_model.genes[:100]);
-
-
-# Single deletions can also be run on reactions
-
-start = time() # start timer()
-growth_rates, statuses = single_deletion(cobra_model, element_type="reaction")
-print("All single reaction deletions completed in %.2f sec" % (time() - start))
-# Prints:
-# All single reaction deletions completed in 7.41 sec
-
-### Double Deletions
-
-# Double deletions run in a similar way
-
-start = time() # start timer()
-double_deletion(cobra_model, element_list_1=cobra_model.genes[:100])
-print("Double gene deletions for 100 genes completed in %.2f sec" % (time() - start))
-# Prints:
-# Double gene deletions for 100 genes completed in 4.94 sec
-
-# By default, the double deletion function will automatically use
-# multiprocessing, splitting the task over up to 4 cores if they are available.
-# The number of cores can be manually sepcified as well. Setting use of a
-# single core will disable use of the multiprocessing library, which often aids
-# debuggging.
-
-start = time() # start timer()
-double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],
- number_of_processes=2)
-t1 = time() - start
-print("Double gene deletions for 100 genes completed in %.2f sec with 2 cores" % t1)
-
-start = time() # start timer()
-double_deletion(cobra_model, element_list_1=cobra_model.genes[:100],
- number_of_processes=1)
-t2 = time() - start
-print("Double gene deletions for 100 genes completed in %.2f sec with 1 core" % t2)
-
-print("Speedup of %.2fx" % (t2/t1))
-# Prints:
-# Double gene deletions for 100 genes completed in 4.02 sec with 2 cores
-# Double gene deletions for 100 genes completed in 6.77 sec with 1 core
-# Speedup of 1.69x
-
-# Double deletions can also be run for reactions
-
-start = time()
-double_deletion(cobra_model, element_list_1=cobra_model.reactions[:100],
- element_type="reaction")
-t = time() - start
-print("Double reaction deletions for 100 reactions completed in %.2f sec" % t)
-# Prints:
-# Double reaction deletions for 100 reactions completed in 0.93 sec
-
-# If pandas is installed, the results can be returned formatted as a
-# pandas.DataFrame
-
-frame = double_deletion(cobra_model, element_list_1=cobra_model.reactions[300:308],
- element_type="reaction", return_frame=True)
-frame[frame < 1e-9] = 0. # round small values to 0
-frame
diff --git a/examples/getting_started.py b/examples/getting_started.py
deleted file mode 100644
index 70ca2bf..0000000
--- a/examples/getting_started.py
+++ /dev/null
@@ -1,250 +0,0 @@
-
-## Getting Started
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/getting_started.
-# ipynb).
-
-# To begin with, cobrapy comes with two bundled models for _Salmonella_ and _E.
-# coli_. To load a test model, type
-
-from __future__ import print_function
-import cobra.test
-model = cobra.test.create_test_model("salmonella")
-
-
-# The reactions, metabolites, and genes attributes of the cobrapy model are are
-# a special type of list called a DictList, and each one is made up of
-# Reaction, Metabolite and Gene objects respectively.
-
-print(len(model.reactions))
-print(len(model.metabolites))
-print(len(model.genes))
-# Prints:
-# 2546
-# 1802
-# 1264
-
-# Just like a regular list, objects in the DictList can be retrived by index.
-# For example, to get the 30th reaction in the model (at index 29 because of
-# [0-indexing](https://en.wikipedia.org/wiki/Z ero-based_numbering)):
-
-model.reactions[29]
-# Output:
-# <Reaction 2AGPA180tipp at 0x7f6d94afc210>
-
-# Addictionally, items can be retrived by their id using the get_by_id()
-# function. For example, to get the cytosolic atp metabolite object (the id is
-# "atp_c"), we can do the following:
-
-model.metabolites.get_by_id("atp_c")
-# Output:
-# <Metabolite atp_c at 0x7f6d94b4c610>
-
-# As an added bonus, users with an interactive shell such as IPython will be
-# able to tab-complete to list elements inside a list. While this is not
-# recommended behavior for most code because of the possibility for characters
-# like "-" inside ids, this is very useful while in an interactive prompt:
-
-model.reactions.EX_glc__D_e.lower_bound
-# Output:
-# 0.0
-
-### Reactions
-
-# We will consider the reaction glucose 6-phosphate isomerase, which
-# interconverts glucose 6-phosphate and fructose 6-phosphate. The reaction id
-# for this reaction in our test model is PGI.
-
-pgi = model.reactions.get_by_id("PGI")
-pgi
-# Output:
-# <Reaction PGI at 0x7f6d93e62110>
-
-# We can view the full name and reaction catalyzed as strings
-
-print(pgi.name)
-print(pgi.reaction)
-# Prints:
-# glucose 6 phosphate isomerase
-# g6p_c <=> f6p_c
-
-# We can also view reaction upper and lower bounds. Because the pgi.lower_bound
-# < 0, and pgi.upper_bound > 0, pgi is reversible
-
-print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
-print(pgi.reversibility)
-# Prints:
-# -1000.0 < pgi < 1000.0
-# True
-
-# We can also ensure the reaction is mass balanced. This function will return
-# elements which violate mass balance. If it comes back empty, then the
-# reaction is mass balanced.
-
-pgi.check_mass_balance()
-# Output:
-# []
-
-# In order to add a metabolite, we pass in a dict with the metabolite object
-# and its coefficient
-
-pgi.add_metabolites({model.metabolites.get_by_id("h_c"): -1})
-pgi.reaction
-# Output:
-# 'g6p_c + h_c <=> f6p_c'
-
-# The reaction is no longer mass balanced
-
-pgi.check_mass_balance()
-# Output:
-# ['PGI', {'C': 0.0, 'H': -1.0, 'O': 0.0, 'P': 0.0}]
-
-# We can remove the metabolite, and the reaction will be balanced once again.
-
-pgi.pop(model.metabolites.get_by_id("h_c"))
-print(pgi.reaction)
-print(pgi.check_mass_balance())
-# Prints:
-# g6p_c <=> f6p_c
-# []
-
-# It is also possible to build the reaction from a string. However, care must
-# be taken when doing this to ensure reaction id's match those in the model.
-# The direction of the arrow is also used to update the upper and lower bounds.
-
-pgi.reaction = "g6p_c --> f6p_c + h_c + green_eggs + ham"
-# Prints:
-# unknown metabolite 'green_eggs' created
-# unknown metabolite 'ham' created
-
-pgi.reaction
-# Output:
-# 'g6p_c --> ham + green_eggs + f6p_c + h_c'
-
-pgi.reaction = "g6p_c <=> f6p_c"
-pgi.reaction
-# Output:
-# 'g6p_c <=> f6p_c'
-
-### Metabolites
-
-# We will consider cytosolic atp as our metabolite, which has the id atp_c in
-# our test model.
-
-atp = model.metabolites.get_by_id("atp_c")
-atp
-# Output:
-# <Metabolite atp_c at 0x7f6d94b4c610>
-
-# We can print out the metabolite name and compartment (cytosol in this case).
-
-print(atp.name)
-print(atp.compartment)
-# Prints:
-# ATP
-# c
-
-# We can see that ATP is a charged molecule in our model.
-
-atp.charge
-# Output:
-# -4
-
-# We can see the chemical formula for the metabolite as well.
-
-print(atp.formula)
-# Prints:
-# C10H12N5O13P3
-
-# The reactions attribute gives a frozenset of all reactions using the given
-# metabolite. We can use this to count the number of reactions which use atp.
-
-len(atp.reactions)
-# Output:
-# 348
-
-# A metabolite like glucose 6-phosphate will participate in fewer reactions.
-
-model.metabolites.get_by_id("g6p_c").reactions
-# Output:
-# frozenset({<Reaction AB6PGH at 0x7f6d93b3d990>,
-# <Reaction TRE6PH at 0x7f6d93d32050>,
-# <Reaction TRE6PS at 0x7f6d93d32310>,
-# <Reaction PGI at 0x7f6d93e62110>,
-# <Reaction PGMT at 0x7f6d93e62690>,
-# <Reaction HEX1 at 0x7f6d940be9d0>,
-# <Reaction GLCptspp at 0x7f6d9412a650>,
-# <Reaction G6PDH2r at 0x7f6d94155790>,
-# <Reaction G6PP at 0x7f6d94155990>,
-# <Reaction G6Pt6_2pp at 0x7f6d94155a50>})
-
-### Genes
-
-# The gene_reaction_rule is a boolean representation of the gene requirements
-# for this reaction to be active as described in [Schellenberger et al 2011
-# Nature Protocols
-# 6(9):1290-307](http://dx.doi.org/doi:10.1038/nprot.2011.308).
-#
-# The GPR is stored as the gene_reaction_rule for a Reaction object as a
-# string.
-
-gpr = pgi.gene_reaction_rule
-gpr
-# Output:
-# 'STM4221'
-
-# Corresponding gene objects also exist. These objects are tracked by the
-# reactions itself, as well as by the model
-
-pgi.genes
-# Output:
-# frozenset({<Gene STM4221 at 0x7f6d93e62190>})
-
-pgi_gene = model.genes.get_by_id("STM4221")
-pgi_gene
-# Output:
-# <Gene STM4221 at 0x7f6d93e62190>
-
-# Each gene keeps track of the reactions it catalyzes
-
-pgi_gene.reactions
-# Output:
-# frozenset({<Reaction PGI at 0x7f6d93e62110>})
-
-# Altering the gene_reaction_rule will create new gene objects if necessary and
-# update all relationships.
-
-pgi.gene_reaction_rule = "(spam or eggs)"
-pgi.genes
-# Output:
-# frozenset({<Gene eggs at 0x7f6d93ad5ad0>, <Gene spam at 0x7f6d93ad5b10>})
-
-pgi_gene.reactions
-# Output:
-# frozenset()
-
-# Newly created genes are also added to the model
-
-model.genes.get_by_id("spam")
-# Output:
-# <Gene spam at 0x7f6d93ad5b10>
-
-# The delete_model_genes function will evaluate the gpr and set the upper and
-# lower bounds to 0 if the reaction is knocked out. This function can preserve
-# existing deletions or reset them using the cumulative_deletions flag.
-
-cobra.manipulation.delete_model_genes(model, ["spam"], cumulative_deletions=True)
-print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
-cobra.manipulation.delete_model_genes(model, ["eggs"], cumulative_deletions=True)
-print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
-# Prints:
-# -1000 < pgi < 1000
-# 0.0 < pgi < 0.0
-
-# The undelete_model_genes can be used to reset a gene deletion
-
-cobra.manipulation.undelete_model_genes(model)
-print(pgi.lower_bound, "< pgi <", pgi.upper_bound)
-# Prints:
-# -1000 < pgi < 1000
diff --git a/examples/io.py b/examples/io.py
deleted file mode 100644
index 88d930b..0000000
--- a/examples/io.py
+++ /dev/null
@@ -1,117 +0,0 @@
-
-## Reading and Writing Models
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/io.ipynb).
-#
-# Functions for reading and writing models to various formats are included with
-# cobrapy. The package also ships with models of *E. coli* and *Salmonella* in
-# various formats for testing purposes. In this example, we will use these
-# functions to read models from these test files in various formats.
-
-import cobra.test
-
-print("E. coli test files: ")
-print(", ".join([i for i in dir(cobra.test) if i.startswith("ecoli")]))
-print("")
-print("Salmonella test files: ")
-print(", ".join([i for i in dir(cobra.test) if i.startswith("salmonella")]))
-
-salmonella_model = cobra.test.create_test_model("salmonella")
-# Prints:
-# E. coli test files:
-# ecoli_json, ecoli_mat, ecoli_pickle, ecoli_sbml
-#
-# Salmonella test files:
-# salmonella_fbc_sbml, salmonella_pickle, salmonella_sbml
-
-### JSON
-
-# cobrapy has a [JSON](https://en.wikipedia.org/wiki/JSON) (JavaScript Object
-# Notation) representation. This is the ideal format for storing a cobra model
-# on a computer, or for interoperability with
-# [escher](https://escher.github.io). Additional fields, however, will not be
-# saved.
-
-cobra.io.load_json_model(cobra.test.ecoli_json)
-# Output:
-# <Model iJO1366 at 0x7f8d2fa20150>
-
-cobra.io.write_sbml_model(salmonella_model, "test.json")
-
-### SBML
-
-# The [Systems Biology Markup Language](http://sbml.org) is an XML-based
-# standard format for distributing models. Cobrapy can use
-# [libsbml](http://sbml.org/Software/libSBML), which must be installed
-# separately (see installation instructions) to read and write SBML files.
-#
-# Initially, the COBRA format for SBML files used the "notes" field in SBML
-# files. More recently, however, the [FBC extension](http://sbml.org/Documents/
-# Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_%28flux%29) to
-# SBML has come into existence, which defines its own fields.
-#
-# Cobrapy can handle both formats (assuming libsbml has been installed
-# correctly). When reading in a model, it will automatically detect whether fbc
-# was used or not. When writing a model, the use_fbc_package can be used.
-
-cobra.io.read_sbml_model(cobra.test.salmonella_sbml)
-# Output:
-# <Model Salmonella_consensus_build_1 at 0x7f8d480ad710>
-
-cobra.io.read_sbml_model(cobra.test.salmonella_fbc_sbml)
-# Output:
-# <Model Salmonella_consensus_build_1 at 0x7f8d480ad5d0>
-
-cobra.io.write_sbml_model(salmonella_model, "test.xml",
- use_fbc_package=False)
-cobra.io.write_sbml_model(salmonella_model, "test_fbc.xml",
- use_fbc_package=True)
-
-
-### MATLAB
-
-# Often, models may be imported and exported soley for the purposes of working
-# with the same models in cobrapy and the [MATLAB cobra
-# toolbox](http://opencobra.github.io/cobratoolbox/). MATLAB has its own ".mat"
-# format for storing variables. Reading and writing to these mat files from
-# python requires scipy, and is generally much faster than using libsbml.
-#
-# A mat file can contain multiple MATLAB variables. Therefore, the variable
-# name of the model in the MATLAB file can be passed into the reading function:
-
-cobra.io.load_matlab_model(cobra.test.ecoli_mat, variable_name="iJO1366")
-# Output:
-# <Model iJO1366 at 0x7f8d48090b50>
-
-# If the mat file contains only a single model, cobra can figure out which
-# variable to read from, and the variable_name paramter is unnecessary.
-
-cobra.io.load_matlab_model(cobra.test.ecoli_mat)
-# Output:
-# <Model iJO1366 at 0x7f8d2d85af10>
-
-# Saving models to mat files is also relatively straightforward
-
-cobra.io.save_matlab_model(ecoli_model, "test_ecoli_model.mat")
-
-### Pickle
-
-# Cobra models can be serialized using the python serialization format,
-# [pickle](https://docs.python.org/2/library/pickle.html). While this will save
-# any extra fields which may have been created, it does not work with any other
-# tools and can break between cobrapy major versions. JSON is generally the
-# preferred format.
-
-from cPickle import load, dump
-
-# read in the test models
-with open(cobra.test.ecoli_pickle, "rb") as infile:
- ecoli_model = load(infile)
-with open(cobra.test.salmonella_pickle, "rb") as infile:
- salmonella_model = load(infile)
-
-# output to a file
-with open("test_output.pickle", "wb") as outfile:
- dump(salmonella_model, outfile)
-
diff --git a/examples/loopless.py b/examples/loopless.py
deleted file mode 100644
index 8cb7746..0000000
--- a/examples/loopless.py
+++ /dev/null
@@ -1,141 +0,0 @@
-
-## Loopless FBA
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/loopless.ipynb).
-#
-# The goal of this procedure is identification of a thermodynamically
-# consistent flux state without loops, as implied by the name.
-#
-# Usually, the model has the following constraints.
-# $$ S \cdot v = 0 $$
-# $$ lb \le v \le ub $$
-#
-# However, this will allow for thermodynamically infeasible loops (referred to
-# as type 3 loops) to occur, where flux flows around a cycle without any net
-# change of metabolites. For most cases, this is not a major issue, as
-# solutions with these loops can usually be converted to equivalent solutions
-# without them. However, if a flux state is desired which does not exhibit any
-# of these loops, loopless FBA can be used. The formulation used here is
-# modified from [Schellenberger et
-# al.](http://dx.doi.org/10.1016/j.bpj.2010.12.3707)
-#
-# We can make the model irreversible, so that all reactions will satisfy
-# $$ 0 \le lb \le v \le ub \le \max(ub) $$
-#
-# We will add in boolean indicators as well, such that
-# $$ \max(ub) i \ge v $$
-# $$ i \in {0, 1} $$
-#
-# We also want to ensure that an entry in the row space of S also exists with
-# negative values wherever v is nonzero. In this expression, $1-i$ acts as a
-# not to indicate inactivity of a reaction.
-#
-# $$ S^\mathsf T x - (1 - i) (\max(ub) + 1) \le -1 $$
-#
-# We will construct an LP integrating both constraints.
-#
-# $$ \left(
-# \begin{matrix}
-# S & 0 & 0\\
-# -I & \max(ub)I & 0 \\
-# 0 & (\max(ub) + 1)I & S^\mathsf T
-# \end{matrix}
-# \right)
-# \cdot
-# \left(
-# \begin{matrix}
-# v \\
-# i \\
-# x
-# \end{matrix}
-# \right)
-# \begin{matrix}
-# &=& 0 \\
-# &\ge& 0 \\
-# &\le& \max(ub)
-# \end{matrix}$$
-#
-# Note that these extra constraints are not applied to boundary reactions which
-# bring metabolites in and out of the system.
-
-import cobra.test
-from cobra import Reaction, Metabolite, Model
-from cobra.flux_analysis.loopless import construct_loopless_model
-from cobra.solvers import get_solver_name
-
-
-# We will demonstrate with a toy model which has a simple loop cycling A -> B
-# -> C -> A, with A allowed to enter the system and C allowed to leave. A
-# graphical view of the system is drawn below:
-
-figure(figsize=(10.5, 4.5), frameon=False)
-gca().axis("off")
-xlim(0.5, 3.5)
-ylim(0.7, 2.2)
-arrow_params = {"head_length": 0.08, "head_width": 0.1, "ec": "k", "fc": "k"}
-text_params = {"fontsize": 25, "horizontalalignment": "center", "verticalalignment": "center"}
-arrow(0.5, 1, 0.85, 0, **arrow_params) # EX_A
-arrow(1.5, 1, 0.425, 0.736, **arrow_params) # v1
-arrow(2.04, 1.82, 0.42, -0.72, **arrow_params) # v2
-arrow(2.4, 1, -0.75, 0, **arrow_params) # v3
-arrow(2.6, 1, 0.75, 0, **arrow_params)
-# reaction labels
-text(0.9, 1.15, "EX_A", **text_params)
-text(1.6, 1.5, r"v$_1$", **text_params)
-text(2.4, 1.5, r"v$_2$", **text_params)
-text(2, 0.85, r"v$_3$", **text_params)
-text(2.9, 1.15, "DM_C", **text_params)
-# metabolite labels
-scatter(1.5, 1, s=250, color='#c994c7')
-text(1.5, 0.9, "A", **text_params)
-scatter(2, 1.84, s=250, color='#c994c7')
-text(2, 1.95, "B", **text_params)
-scatter(2.5, 1, s=250, color='#c994c7')
-text(2.5, 0.9, "C", **text_params);
-
-test_model = Model()
-test_model.add_metabolites(Metabolite("A"))
-test_model.add_metabolites(Metabolite("B"))
-test_model.add_metabolites(Metabolite("C"))
-EX_A = Reaction("EX_A")
-EX_A.add_metabolites({test_model.metabolites.A: 1})
-DM_C = Reaction("DM_C")
-DM_C.add_metabolites({test_model.metabolites.C: -1})
-v1 = Reaction("v1")
-v1.add_metabolites({test_model.metabolites.A: -1, test_model.metabolites.B: 1})
-v2 = Reaction("v2")
-v2.add_metabolites({test_model.metabolites.B: -1, test_model.metabolites.C: 1})
-v3 = Reaction("v3")
-v3.add_metabolites({test_model.metabolites.C: -1, test_model.metabolites.A: 1})
-DM_C.objective_coefficient = 1
-test_model.add_reactions([EX_A, DM_C, v1, v2, v3])
-
-
-# While this model contains a loop, a flux state exists which has no flux
-# through reaction v3, and is identified by loopless FBA.
-
-construct_loopless_model(test_model).optimize()
-# Output:
-# <Solution 1000.00 at 0x62cd250>
-
-# However, if flux is forced through v3, then there is no longer a feasible
-# loopless solution.
-
-v3.lower_bound = 1
-construct_loopless_model(test_model).optimize()
-# Output:
-# <Solution 'infeasible' at 0x62cd5d0>
-
-# Loopless FBA is also possible on genome scale models, but it requires a
-# capable MILP solver.
-
-salmonella = cobra.test.create_test_model()
-construct_loopless_model(salmonella).optimize(solver=get_solver_name(mip=True))
-# Output:
-# <Solution 0.38 at 0x9e67650>
-
-ecoli = cobra.test.create_test_model("ecoli")
-construct_loopless_model(ecoli).optimize(solver=get_solver_name(mip=True))
-# Output:
-# <Solution 0.98 at 0x8e463d0>
diff --git a/examples/milp.py b/examples/milp.py
deleted file mode 100644
index d23cc0d..0000000
--- a/examples/milp.py
+++ /dev/null
@@ -1,217 +0,0 @@
-
-## Mixed-Integer Linear Programming
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/milp.ipynb).
-
-### Ice Cream
-
-# This example was originally contributed by Joshua Lerman.
-#
-# An ice cream stand sells cones and popsicles. It wants to maximize its
-# profit, but is subject to a budget.
-#
-# We can write this problem as a linear program:
-#
-# > **max** cone $\cdot$ cone_margin + popsicle $\cdot$ popsicle margin
-#
-# > *subject to*
-#
-# > cone $\cdot$ cone_cost + popsicle $\cdot$ popsicle_cost $\le$ budget
-
-cone_selling_price = 7.
-cone_production_cost = 3.
-popsicle_selling_price = 2.
-popsicle_production_cost = 1.
-starting_budget = 100.
-
-
-# This problem can be written as a cobra.Model
-
-from cobra import Model, Metabolite, Reaction
-
-cone = Reaction("cone")
-popsicle = Reaction("popsicle")
-
-# constrainted to a budget
-budget = Metabolite("budget")
-budget._constraint_sense = "L"
-budget._bound = starting_budget
-cone.add_metabolites({budget: cone_production_cost})
-popsicle.add_metabolites({budget: popsicle_production_cost})
-
-# objective coefficient is the profit to be made from each unit
-cone.objective_coefficient = cone_selling_price - cone_production_cost
-popsicle.objective_coefficient = popsicle_selling_price - \
- popsicle_production_cost
-
-m = Model("lerman_ice_cream_co")
-m.add_reactions((cone, popsicle))
-
-m.optimize().x_dict
-# Output:
-# {'cone': 33.333333333333336, 'popsicle': 0.0}
-
-# In reality, cones and popsicles can only be sold in integer amounts. We can
-# use the variable kind attribute of a cobra.Reaction to enforce this.
-
-cone.variable_kind = "integer"
-popsicle.variable_kind = "integer"
-m.optimize().x_dict
-# Output:
-# {'cone': 33.0, 'popsicle': 1.0}
-
-# Now the model makes both popsicles and cones.
-
-### Restaurant Order
-
-# To tackle the less immediately obvious problem from the following [XKCD
-# comic](http://xkcd.com/287/):
-
-from IPython.display import Image
-Image(url=r"http://imgs.xkcd.com/comics/np_complete.png")
-
-# We want a solution satisfying the following constraints:
-#
-# $\left(\begin{matrix}2.15&2.75&3.35&3.55&4.20&5.80\end{matrix}\right) \cdot
-# \vec v = 15.05$
-#
-# $\vec v_i \ge 0$
-#
-# $\vec v_i \in \mathbb{Z}$
-#
-# This problem can be written as a COBRA model as well.
-
-total_cost = Metabolite("constraint")
-total_cost._bound = 15.05
-
-costs = {"mixed_fruit": 2.15, "french_fries": 2.75, "side_salad": 3.35,
- "hot_wings": 3.55, "mozarella_sticks": 4.20, "sampler_plate": 5.80}
-
-m = Model("appetizers")
-
-for item, cost in costs.items():
- r = Reaction(item)
- r.add_metabolites({total_cost: cost})
- r.variable_kind = "integer"
- m.add_reaction(r)
-
-# To add to the problem, suppose we don't want to eat all mixed fruit.
-m.reactions.mixed_fruit.objective_coefficient = 1
-
-m.optimize(objective_sense="minimize").x_dict
-# Output:
-# {'french_fries': 0.0,
-# 'hot_wings': 2.0,
-# 'mixed_fruit': 1.0,
-# 'mozarella_sticks': 0.0,
-# 'sampler_plate': 1.0,
-# 'side_salad': 0.0}
-
-# There is another solution to this problem, which would have been obtained if
-# we had maximized for mixed fruit instead of minimizing.
-
-m.optimize(objective_sense="maximize").x_dict
-# Output:
-# {'french_fries': 0.0,
-# 'hot_wings': 0.0,
-# 'mixed_fruit': 7.0,
-# 'mozarella_sticks': 0.0,
-# 'sampler_plate': 0.0,
-# 'side_salad': 0.0}
-
-### Boolean Indicators
-
-# To give a COBRA-related example, we can create boolean variables as integers,
-# which can serve as indicators for a reaction being active in a model. For a
-# reaction flux $v$ with lower bound -1000 and upper bound 1000, we can create
-# a binary variable $b$ with the following constraints:
-#
-# $b \in \{0, 1\}$
-#
-# $-1000 \cdot b \le v \le 1000 \cdot b$
-#
-# To introduce the above constraints into a cobra model, we can rewrite them as
-# follows
-#
-# $v \le b \cdot 1000 \Rightarrow v- 1000\cdot b \le 0$
-#
-# $-1000 \cdot b \le v \Rightarrow v + 1000\cdot b \ge 0$
-
-import cobra.test
-model = cobra.test.create_test_model(cobra.test.ecoli_pickle)
-
-# an indicator for pgi
-pgi = model.reactions.get_by_id("PGI")
-# make a boolean variable
-pgi_indicator = Reaction("indicator_PGI")
-pgi_indicator.lower_bound = 0
-pgi_indicator.upper_bound = 1
-pgi_indicator.variable_kind = "integer"
-# create constraint for v - 1000 b <= 0
-pgi_plus = Metabolite("PGI_plus")
-pgi_plus._constraint_sense = "L"
-# create constraint for v + 1000 b >= 0
-pgi_minus = Metabolite("PGI_minus")
-pgi_minus._constraint_sense = "G"
-
-pgi_indicator.add_metabolites({pgi_plus: -1000, pgi_minus: 1000})
-pgi.add_metabolites({pgi_plus: 1, pgi_minus: 1})
-model.add_reaction(pgi_indicator)
-
-
-# an indicator for zwf
-zwf = model.reactions.get_by_id("G6PDH2r")
-zwf_indicator = Reaction("indicator_ZWF")
-zwf_indicator.lower_bound = 0
-zwf_indicator.upper_bound = 1
-zwf_indicator.variable_kind = "integer"
-# create constraint for v - 1000 b <= 0
-zwf_plus = Metabolite("ZWF_plus")
-zwf_plus._constraint_sense = "L"
-# create constraint for v + 1000 b >= 0
-zwf_minus = Metabolite("ZWF_minus")
-zwf_minus._constraint_sense = "G"
-
-zwf_indicator.add_metabolites({zwf_plus: -1000, zwf_minus: 1000})
-zwf.add_metabolites({zwf_plus: 1, zwf_minus: 1})
-
-# add the indicator reactions to the model
-model.add_reaction(zwf_indicator)
-
-
-# In a model with both these reactions active, the indicators will also be
-# active
-
-solution = model.optimize()
-print("PGI indicator = %d" % solution.x_dict["indicator_PGI"])
-print("ZWF indicator = %d" % solution.x_dict["indicator_ZWF"])
-print("PGI flux = %.2f" % solution.x_dict["PGI"])
-print("ZWF flux = %.2f" % solution.x_dict["G6PDH2r"])
-# Prints:
-# PGI indicator = 1
-# ZWF indicator = 1
-# PGI flux = 5.92
-# ZWF flux = 4.08
-
-# Because these boolean indicators are in the model, additional constraints can
-# be applied on them. For example, we can prevent both reactions from being
-# active at the same time by adding the following constraint:
-#
-# $b_\text{pgi} + b_\text{zwf} = 1$
-
-or_constraint = Metabolite("or")
-or_constraint._bound = 1
-zwf_indicator.add_metabolites({or_constraint: 1})
-pgi_indicator.add_metabolites({or_constraint: 1})
-
-solution = model.optimize()
-print("PGI indicator = %d" % solution.x_dict["indicator_PGI"])
-print("ZWF indicator = %d" % solution.x_dict["indicator_ZWF"])
-print("PGI flux = %.2f" % solution.x_dict["PGI"])
-print("ZWF flux = %.2f" % solution.x_dict["G6PDH2r"])
-# Prints:
-# PGI indicator = 0
-# ZWF indicator = 1
-# PGI flux = 0.00
-# ZWF flux = 3.98
diff --git a/examples/phenotype_phase_plane.py b/examples/phenotype_phase_plane.py
deleted file mode 100644
index d6f282a..0000000
--- a/examples/phenotype_phase_plane.py
+++ /dev/null
@@ -1,53 +0,0 @@
-
-## Phenotype Phase Plane
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/phenotype_phase_
-# plane.ipynb).
-
-# Load iJO1366 as a test model and import cobra
-
-from time import time
-
-import cobra
-from cobra.test import ecoli_pickle, create_test_model
-
-from cobra.flux_analysis.phenotype_phase_plane import \
- calculate_phenotype_phase_plane
-
-model = create_test_model(ecoli_pickle)
-model
-# Output:
-# <Model iJO1366 at 0x5b0abd0>
-
-# We want to make a phenotype phase plane to evaluate uptakes of Glucose and
-# Oxygen.
-#
-# With [matplotlib](http://matplotlib.org) installed, this is as simple as
-
-data = calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e")
-data.plot_matplotlib();
-
-# If [brewer2mpl](https://pypi.python.org/pypi/brewer2mpl/) is installed, other
-# color schemes can be used as well
-
-data.plot_matplotlib("Pastel1")
-data.plot_matplotlib("Dark2");
-
-# The number of points which are plotted in each dimension can also be changed
-
-calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e",
- reaction1_npoints=20,
- reaction2_npoints=20).plot_matplotlib();
-
-# The code can also use multiple processes to speed up calculations
-
-start_time = time()
-calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e", n_processes=1)
-print("took %.2f seconds with 1 process" % (time() - start_time))
-start_time = time()
-calculate_phenotype_phase_plane(model, "EX_glc_e", "EX_o2_e", n_processes=4)
-print("took %.2f seconds with 4 process" % (time() - start_time))
-# Prints:
-# took 5.97 seconds with 1 process
-# took 2.97 seconds with 4 process
diff --git a/examples/qp.py b/examples/qp.py
deleted file mode 100644
index 2c45297..0000000
--- a/examples/qp.py
+++ /dev/null
@@ -1,133 +0,0 @@
-
-## Quadratic Programming
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/qp.ipynb).
-
-# Suppose we want to minimize the Euclidean distance of the solution to the
-# origin while subject to linear constraints. This will require a quadratic
-# objective function. Consider this example problem:
-#
-# > **min** $\frac{1}{2}\left(x^2 + y^2 \right)$
-#
-# > *subject to*
-#
-# > $x + y = 2$
-#
-# > $x \ge 0$
-#
-# > $y \ge 0$
-#
-# This problem can be visualized graphically:
-
-from matplotlib.pyplot import figure, xlim, ylim
-from mpl_toolkits.axes_grid.axislines import SubplotZero
-from numpy import linspace, arange, sqrt, pi, sin, cos, sign
-# axis style
-def make_plot_ax():
- fig = figure(figsize=(6, 5));
- ax = SubplotZero(fig, 111); fig.add_subplot(ax)
- for direction in ["xzero", "yzero"]:
- ax.axis[direction].set_axisline_style("-|>")
- ax.axis[direction].set_visible(True)
- for direction in ["left", "right", "bottom", "top"]:
- ax.axis[direction].set_visible(False)
- xlim(-0.1, 2.1); ylim(xlim())
- ticks = [0.5 * i for i in range(1, 5)]
- labels = [str(i) if i == int(i) else "" for i in ticks]
- ax.set_xticks(ticks); ax.set_yticks(ticks)
- ax.set_xticklabels(labels); ax.set_yticklabels(labels)
- ax.axis["yzero"].set_axis_direction("left")
- return ax
-
-ax = make_plot_ax()
-ax.plot((0, 2), (2, 0), 'b')
-ax.plot([1], [1], 'bo')
-
-# circular grid
-for r in sqrt(2.) + 0.125 * arange(-11, 6):
- t = linspace(0., pi/2., 100)
- ax.plot(r * cos(t), r * sin(t), '-.', color="gray")
-
-# The objective can be rewritten as $\frac{1}{2} v^T \cdot \mathbf Q \cdot v$,
-# where
-# $v = \left(\begin{matrix} x \\ y\end{matrix} \right)$ and
-# $\mathbf Q = \left(\begin{matrix} 1 & 0\\ 0 & 1 \end{matrix}\right)$
-#
-# The matrix $\mathbf Q$ can be passed into a cobra model as the quadratic
-# objective.
-
-import scipy
-
-from cobra import Reaction, Metabolite, Model, solvers
-
-
-# The quadratic objective $\mathbf Q$ should be formatted as a scipy sparse
-# matrix.
-
-Q = scipy.sparse.eye(2).todok()
-Q
-# Output:
-# <2x2 sparse matrix of type '<type 'numpy.float64'>'
-# with 2 stored elements in Dictionary Of Keys format>
-
-# In this case, the quadratic objective is simply the identity matrix
-
-Q.todense()
-# Output:
-# matrix([[ 1., 0.],
-# [ 0., 1.]])
-
-# We need to use a solver that supports quadratic programming, such as gurobi
-# or cplex. If a solver which supports quadratic programming is installed, this
-# function will return its name.
-
-print(solvers.get_solver_name(qp=True))
-# Prints:
-# gurobi
-
-c = Metabolite("c")
-c._bound = 2
-x = Reaction("x")
-y = Reaction("y")
-x.add_metabolites({c: 1})
-y.add_metabolites({c: 1})
-m = Model()
-m.add_reactions([x, y])
-sol = m.optimize(quadratic_component=Q, objective_sense="minimize")
-sol.x_dict
-# Output:
-# {'x': 1.0, 'y': 1.0}
-
-# Suppose we change the problem to have a mixed linear and quadratic objective.
-#
-# > **min** $\frac{1}{2}\left(x^2 + y^2 \right) - y$
-#
-# > *subject to*
-#
-# > $x + y = 2$
-#
-# > $x \ge 0$
-#
-# > $y \ge 0$
-#
-# Graphically, this would be
-
-ax = make_plot_ax()
-ax.plot((0, 2), (2, 0), 'b')
-ax.plot([0.5], [1.5], 'bo')
-
-yrange = linspace(1, 2, 11)
-for r in (yrange ** 2 / 2. - yrange):
- t = linspace(-sqrt(2 * r + 1) + 0.000001, sqrt(2 * r + 1) - 0.000001, 1000)
- ax.plot(abs(t), 1 + sqrt(2 * r + 1 - t ** 2) * sign(t), '-.', color="gray")
-
-# QP solvers in cobrapy will combine linear and quadratic coefficients. The
-# linear portion will be obtained from the same objective_coefficient attribute
-# used with LP's.
-
-y.objective_coefficient = -1
-sol = m.optimize(quadratic_component=Q, objective_sense="minimize")
-sol.x_dict
-# Output:
-# {'x': 0.5, 'y': 1.5}
diff --git a/examples/simulating.py b/examples/simulating.py
deleted file mode 100644
index 897fda9..0000000
--- a/examples/simulating.py
+++ /dev/null
@@ -1,81 +0,0 @@
-
-## Simulating with FBA
-
-# This example is available as an IPython [notebook](http://nbviewer.ipython.or
-# g/github/opencobra/cobrapy/blob/master/documentation_builder/simulating.ipynb
-# ).
-#
-# Simulations using flux balance analysis can be solved using Model.optimize().
-# This will maximize or minimize (maximizing is the default) flux through the
-# objective reactions.
-#
-
-import cobra.test
-model = cobra.test.create_test_model()
-
-
-### Running FBA
-
-model.optimize()
-# Output:
-# <Solution 0.38 at 0x660d990>
-
-# The Model.optimize() function will return a Solution object, which will also
-# be stored at model.solution. A solution object has several attributes:
-#
-# - f: the objective value
-# - status: the status from the linear programming solver
-# - x_dict: a dictionary of {reaction_id: flux_value} (also called "primal")
-# - x: a list for x_dict
-# - y_dict: a dictionary of {metabolite_id: dual_value}.
-# - y: a list for y_dict
-
-# For example, after the last call to model.optimize(), the status should be
-# 'optimal' if the solver returned no errors, and f should be the objective
-# value
-
-model.solution.status
-# Output:
-# 'optimal'
-
-model.solution.f
-# Output:
-# 0.38000797227551136
-
-### Changing the Objectives
-
-# The objective function is determined from the objective_coefficient attribute
-# of the objective reaction(s). Currently in the model, there is only one
-# objective reaction, with an objective coefficient of 1.
-
-{reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
-# Output:
-# {<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}
-
-# The objective function can be changed by using the function
-# Model.change_objective, which will take either a reaction object or just its
-# name.
-
-# change the objective to ATPM
-# the upper bound should be 1000 so we get the actual optimal value
-model.reactions.get_by_id("ATPM").upper_bound = 1000.
-model.change_objective("ATPM")
-{reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
-# Output:
-# {<Reaction ATPM at 0x52cb190>: 1.0}
-
-model.optimize()
-# Output:
-# <Solution 119.67 at 0x4c93110>
-
-# The objective function can also be changed by setting
-# Reaction.objective_coefficient directly.
-
-model.reactions.get_by_id("ATPM").objective_coefficient = 0.
-model.reactions.get_by_id("biomass_iRR1083_metals").objective_coefficient = 1.
-{reaction: reaction.objective_coefficient for reaction in model.reactions
- if reaction.objective_coefficient > 0}
-# Output:
-# {<Reaction biomass_iRR1083_metals at 0x660d350>: 1.0}
diff --git a/ez_setup.py b/ez_setup.py
index 1bcd3e9..6804679 100644
--- a/ez_setup.py
+++ b/ez_setup.py
@@ -1,18 +1,11 @@
#!/usr/bin/env python
-"""Bootstrap setuptools installation
-To use setuptools in your package's setup.py, include this
-file in the same directory and add this to the top of your setup.py::
-
- from ez_setup import use_setuptools
- use_setuptools()
-
-To require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, simply supply
-the appropriate options to ``use_setuptools()``.
+"""
+Setuptools bootstrapping installer.
-This file can also be run as a script to install or upgrade setuptools.
+Run this script to install or upgrade setuptools.
"""
+
import os
import shutil
import sys
@@ -23,6 +16,7 @@ import subprocess
import platform
import textwrap
import contextlib
+import warnings
from distutils import log
@@ -36,11 +30,15 @@ try:
except ImportError:
USER_SITE = None
-DEFAULT_VERSION = "4.0.1"
+DEFAULT_VERSION = "15.2"
DEFAULT_URL = "https://pypi.python.org/packages/source/s/setuptools/"
+DEFAULT_SAVE_DIR = os.curdir
+
def _python_cmd(*args):
"""
+ Execute a command.
+
Return True if the command succeeded.
"""
args = (sys.executable,) + args
@@ -48,6 +46,7 @@ def _python_cmd(*args):
def _install(archive_filename, install_args=()):
+ """Install Setuptools."""
with archive_context(archive_filename):
# installing
log.warn('Installing Setuptools')
@@ -59,6 +58,7 @@ def _install(archive_filename, install_args=()):
def _build_egg(egg, archive_filename, to_dir):
+ """Build Setuptools egg."""
with archive_context(archive_filename):
# building an egg
log.warn('Building a Setuptools egg in %s', to_dir)
@@ -70,9 +70,8 @@ def _build_egg(egg, archive_filename, to_dir):
class ContextualZipFile(zipfile.ZipFile):
- """
- Supplement ZipFile class to support context manager for Python 2.6
- """
+
+ """Supplement ZipFile class to support context manager for Python 2.6."""
def __enter__(self):
return self
@@ -81,9 +80,7 @@ class ContextualZipFile(zipfile.ZipFile):
self.close()
def __new__(cls, *args, **kwargs):
- """
- Construct a ZipFile or ContextualZipFile as appropriate
- """
+ """Construct a ZipFile or ContextualZipFile as appropriate."""
if hasattr(zipfile.ZipFile, '__exit__'):
return zipfile.ZipFile(*args, **kwargs)
return super(ContextualZipFile, cls).__new__(cls)
@@ -91,7 +88,11 @@ class ContextualZipFile(zipfile.ZipFile):
@contextlib.contextmanager
def archive_context(filename):
- # extracting the archive
+ """
+ Unzip filename to a temporary directory, set to the cwd.
+
+ The unzipped target is cleaned up after.
+ """
tmpdir = tempfile.mkdtemp()
log.warn('Extracting in %s', tmpdir)
old_wd = os.getcwd()
@@ -112,6 +113,7 @@ def archive_context(filename):
def _do_download(version, download_base, to_dir, download_delay):
+ """Download Setuptools."""
egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
% (version, sys.version_info[0], sys.version_info[1]))
if not os.path.exists(egg):
@@ -129,41 +131,77 @@ def _do_download(version, download_base, to_dir, download_delay):
setuptools.bootstrap_install_from = egg
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, download_delay=15):
+def use_setuptools(
+ version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=DEFAULT_SAVE_DIR, download_delay=15):
+ """
+ Ensure that a setuptools version is installed.
+
+ Return None. Raise SystemExit if the requested version
+ or later cannot be installed.
+ """
to_dir = os.path.abspath(to_dir)
+
+ # prior to importing, capture the module state for
+ # representative modules.
rep_modules = 'pkg_resources', 'setuptools'
imported = set(sys.modules).intersection(rep_modules)
+
try:
import pkg_resources
- except ImportError:
- return _do_download(version, download_base, to_dir, download_delay)
- try:
pkg_resources.require("setuptools>=" + version)
+ # a suitable version is already installed
return
+ except ImportError:
+ # pkg_resources not available; setuptools is not installed; download
+ pass
except pkg_resources.DistributionNotFound:
- return _do_download(version, download_base, to_dir, download_delay)
+ # no version of setuptools was found; allow download
+ pass
except pkg_resources.VersionConflict as VC_err:
if imported:
- msg = textwrap.dedent("""
- The required version of setuptools (>={version}) is not available,
- and can't be installed while this script is running. Please
- install a more recent version first, using
- 'easy_install -U setuptools'.
+ _conflict_bail(VC_err, version)
+
+ # otherwise, unload pkg_resources to allow the downloaded version to
+ # take precedence.
+ del pkg_resources
+ _unload_pkg_resources()
- (Currently using {VC_err.args[0]!r})
- """).format(VC_err=VC_err, version=version)
- sys.stderr.write(msg)
- sys.exit(2)
+ return _do_download(version, download_base, to_dir, download_delay)
+
+
+def _conflict_bail(VC_err, version):
+ """
+ Setuptools was imported prior to invocation, so it is
+ unsafe to unload it. Bail out.
+ """
+ conflict_tmpl = textwrap.dedent("""
+ The required version of setuptools (>={version}) is not available,
+ and can't be installed while this script is running. Please
+ install a more recent version first, using
+ 'easy_install -U setuptools'.
+
+ (Currently using {VC_err.args[0]!r})
+ """)
+ msg = conflict_tmpl.format(**locals())
+ sys.stderr.write(msg)
+ sys.exit(2)
+
+
+def _unload_pkg_resources():
+ del_modules = [
+ name for name in sys.modules
+ if name.startswith('pkg_resources')
+ ]
+ for mod_name in del_modules:
+ del sys.modules[mod_name]
- # otherwise, reload ok
- del pkg_resources, sys.modules['pkg_resources']
- return _do_download(version, download_base, to_dir, download_delay)
def _clean_check(cmd, target):
"""
- Run the command to download target. If the command fails, clean up before
- re-raising the error.
+ Run the command to download target.
+
+ If the command fails, clean up before re-raising the error.
"""
try:
subprocess.check_call(cmd)
@@ -172,10 +210,13 @@ def _clean_check(cmd, target):
os.unlink(target)
raise
+
def download_file_powershell(url, target):
"""
- Download the file at url to target using Powershell (which will validate
- trust). Raise an exception if the command cannot complete.
+ Download the file at url to target using Powershell.
+
+ Powershell will validate trust.
+ Raise an exception if the command cannot complete.
"""
target = os.path.abspath(target)
ps_cmd = (
@@ -191,7 +232,9 @@ def download_file_powershell(url, target):
]
_clean_check(cmd, target)
+
def has_powershell():
+ """Determine if Powershell is available."""
if platform.system() != 'Windows':
return False
cmd = ['powershell', '-Command', 'echo test']
@@ -201,13 +244,14 @@ def has_powershell():
except Exception:
return False
return True
-
download_file_powershell.viable = has_powershell
+
def download_file_curl(url, target):
cmd = ['curl', url, '--silent', '--output', target]
_clean_check(cmd, target)
+
def has_curl():
cmd = ['curl', '--version']
with open(os.path.devnull, 'wb') as devnull:
@@ -216,13 +260,14 @@ def has_curl():
except Exception:
return False
return True
-
download_file_curl.viable = has_curl
+
def download_file_wget(url, target):
cmd = ['wget', url, '--quiet', '--output-document', target]
_clean_check(cmd, target)
+
def has_wget():
cmd = ['wget', '--version']
with open(os.path.devnull, 'wb') as devnull:
@@ -231,14 +276,11 @@ def has_wget():
except Exception:
return False
return True
-
download_file_wget.viable = has_wget
+
def download_file_insecure(url, target):
- """
- Use Python to download the file, even though it cannot authenticate the
- connection.
- """
+ """Use Python to download the file, without connection authentication."""
src = urlopen(url)
try:
# Read all the data in one block.
@@ -249,9 +291,9 @@ def download_file_insecure(url, target):
# Write all the data in one block to avoid creating a partial file.
with open(target, "wb") as dst:
dst.write(data)
-
download_file_insecure.viable = lambda: True
+
def get_best_downloader():
downloaders = (
download_file_powershell,
@@ -262,13 +304,16 @@ def get_best_downloader():
viable_downloaders = (dl for dl in downloaders if dl.viable())
return next(viable_downloaders, None)
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, delay=15, downloader_factory=get_best_downloader):
+
+def download_setuptools(
+ version=DEFAULT_VERSION, download_base=DEFAULT_URL,
+ to_dir=DEFAULT_SAVE_DIR, delay=15,
+ downloader_factory=get_best_downloader):
"""
- Download setuptools from a specified location and return its filename
+ Download setuptools from a specified location and return its filename.
`version` should be a valid setuptools version number that is available
- as an egg for download under the `download_base` URL (which should end
+ as an sdist for download under the `download_base` URL (which should end
with a '/'). `to_dir` is the directory where the egg will be downloaded.
`delay` is the number of seconds to pause before an actual download
attempt.
@@ -287,16 +332,18 @@ def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
downloader(url, saveto)
return os.path.realpath(saveto)
+
def _build_install_args(options):
"""
- Build the arguments to 'python setup.py install' on the setuptools package
+ Build the arguments to 'python setup.py install' on the setuptools package.
+
+ Returns list of command line arguments.
"""
return ['--user'] if options.user_install else []
+
def _parse_args():
- """
- Parse the command line for options
- """
+ """Parse the command line for options."""
parser = optparse.OptionParser()
parser.add_option(
'--user', dest='user_install', action='store_true', default=False,
@@ -314,18 +361,30 @@ def _parse_args():
'--version', help="Specify which version to download",
default=DEFAULT_VERSION,
)
+ parser.add_option(
+ '--to-dir',
+ help="Directory to save (and re-use) package",
+ default=DEFAULT_SAVE_DIR,
+ )
options, args = parser.parse_args()
# positional arguments are ignored
return options
+
+def _download_args(options):
+ """Return args for download_setuptools function from cmdline args."""
+ return dict(
+ version=options.version,
+ download_base=options.download_base,
+ downloader_factory=options.downloader_factory,
+ to_dir=options.to_dir,
+ )
+
+
def main():
- """Install or upgrade setuptools and EasyInstall"""
+ """Install or upgrade setuptools and EasyInstall."""
options = _parse_args()
- archive = download_setuptools(
- version=options.version,
- download_base=options.download_base,
- downloader_factory=options.downloader_factory,
- )
+ archive = download_setuptools(**_download_args(options))
return _install(archive, _build_install_args(options))
if __name__ == '__main__':
diff --git a/setup.py b/setup.py
index c11c79b..d5327b9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,17 +1,18 @@
+from os.path import isfile, abspath, dirname, join
+from sys import argv, path
+
+# To temporarily modify sys.path
+SETUP_DIR = abspath(dirname(__file__))
+
try:
- import setuptools
+ from setuptools import setup, find_packages
except ImportError:
+ path.insert(0, SETUP_DIR)
import ez_setup
+ path.pop(0)
ez_setup.use_setuptools()
-from setuptools import setup, find_packages
-from sys import argv, path
-from os.path import isfile, abspath, dirname, join
+ from setuptools import setup, find_packages
-# import version to get the version string
-path.insert(0, abspath(join(dirname(__file__), "cobra")))
-from version import get_version, update_release_version
-path.pop(0)
-__version = get_version(pep440=True)
# for running parallel tests due to a bug in python 2.7.3
# http://bugs.python.org/issue15881#msg170215
@@ -20,6 +21,12 @@ try:
except:
None
+# import version to get the version string
+path.insert(0, join(SETUP_DIR, "cobra"))
+from version import get_version, update_release_version
+path.pop(0)
+version = get_version(pep440=True)
+
# If building something for distribution, ensure the VERSION
# file is up to date
if "sdist" in argv or "bdist_wheel" in argv:
@@ -31,13 +38,18 @@ try:
from Cython.Build import cythonize
from distutils.version import StrictVersion
import Cython
- if StrictVersion(Cython.__version__) < StrictVersion("0.21"):
- raise ImportError("Cython version too old to use")
+ try:
+ cython_version = StrictVersion(Cython.__version__)
+ except ValueError:
+ raise ImportError("Cython version not parseable")
+ else:
+ if cython_version < StrictVersion("0.21"):
+ raise ImportError("Cython version too old to use")
except ImportError:
cythonize = None
for k in ["sdist", "develop"]:
if k in argv:
- raise Exception("cython > 0.21 required for " + k)
+ raise Exception("Cython >= 0.21 required for " + k)
# Begin constructing arguments for building
setup_kwargs = {}
@@ -116,24 +128,36 @@ except:
ext_modules = None
extras = {
- 'parallel': ['pp>=1.6.0'],
- 'matlab': ["mlabwrap>=1.1"],
+ 'matlab': ["pymatbridge"],
'sbml': ["python-libsbml-experimental"],
'array': ["numpy>=1.6", "scipy>=11.0"],
'display': ["matplotlib", "brewer2mpl", "pandas"]
}
-all_extras = set()
+all_extras = {'Cython>=0.21'}
for extra in extras.values():
all_extras.update(extra)
extras["all"] = list(all_extras)
+# If using bdist_wininst, the installer will not get dependencies like
+# a setuptools installation does. Therefore, for the one external dependency,
+# which is six.py, we can just download it here and include it in the
+# installer.
+
+# The file six.py will need to be manually downloaded and placed in the
+# same directory as setup.py.
+if "bdist_wininst" in argv:
+ setup_kwargs["py_modules"] = ["six"]
+
+with open("README.md", "r") as infile:
+ setup_kwargs["long_description"] = infile.read()
+
setup(
name="cobra",
- version=__version,
+ version=version,
packages=find_packages(exclude=['cobra.oven', 'cobra.oven*']),
setup_requires=[],
- install_requires=[],
+ install_requires=["six"],
extras_require=extras,
ext_modules=ext_modules,
@@ -147,32 +171,27 @@ setup(
author_email="danielhyduke at gmail.com",
description="COBRApy is a package for constraints-based modeling of "
"biological networks",
- license="GPL V3.0",
+ license="LGPL/GPL v2+",
keywords="metabolism biology linear programming optimization flux"
" balance analysis fba",
url="https://opencobra.github.io/cobrapy",
test_suite="cobra.test.suite",
- long_description="COnstraint-Based Reconstruction and Analysis (COBRA) "
- "methods are widely used for genome-scale modeling of metabolic networks "
- "in both prokaryotes and eukaryotes. COBRApy is a constraint-based "
- "modeling package that is designed to accomodate the biological "
- "complexity of the next generation of COBRA models and provides access to "
- "commonly used COBRA methods, such as flux balance analysis, flux "
- "variability analysis, and gene deletion analyses.",
download_url='https://pypi.python.org/pypi/cobra',
- classifiers=['Development Status :: 5 - Production/Stable',
- 'Environment :: Console',
- 'Intended Audience :: Science/Research',
- 'License :: OSI Approved :: GNU General Public License v3'
- ' or later (GPLv3+)',
- 'Operating System :: OS Independent',
- 'Programming Language :: Python :: 2.7',
- 'Programming Language :: Python :: 3.3',
- 'Programming Language :: Python :: 3.4',
- 'Programming Language :: Python :: Implementation :: CPython',
- 'Programming Language :: Python :: Implementation :: Jython',
- 'Topic :: Scientific/Engineering',
- 'Topic :: Scientific/Engineering :: Bio-Informatics'
- ],
+ classifiers=[
+ 'Development Status :: 5 - Production/Stable',
+ 'Environment :: Console',
+ 'Intended Audience :: Science/Research',
+ 'License :: OSI Approved :: GNU Lesser General Public License v2'
+ ' or later (LGPLv2+)',
+ 'License :: OSI Approved :: GNU General Public License v2'
+ ' or later (GPLv2+)',
+ 'Operating System :: OS Independent',
+ 'Programming Language :: Python :: 2.7',
+ 'Programming Language :: Python :: 3.4',
+ 'Programming Language :: Cython',
+ 'Programming Language :: Python :: Implementation :: CPython',
+ 'Topic :: Scientific/Engineering',
+ 'Topic :: Scientific/Engineering :: Bio-Informatics'
+ ],
platforms="GNU/Linux, Mac OS X >= 10.7, Microsoft Windows >= 7",
**setup_kwargs)
--
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