[med-svn] [transit] 01/02: New upstream version 2.0.2
Andreas Tille
tille at debian.org
Fri Mar 3 13:44:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository transit.
commit c21a7ae64f127d5d7f6a71cb586d848c18cd22d8
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 3 14:37:30 2017 +0100
New upstream version 2.0.2
---
.gitignore | 61 +
.hgignore | 22 +
CHANGELOG.md | 173 +
LICENSE.md | 596 +
MANIFEST.in | 10 +
README.md | 52 +
VERSION | 1 +
setup.cfg | 2 +
setup.py | 121 +
src/pytpp/__init__.py | 1 +
src/pytpp/__main__.py | 126 +
src/pytpp/tpp_gui.py | 304 +
src/pytpp/tpp_tools.py | 794 +
src/pytransit/__init__.py | 6 +
src/pytransit/__main__.py | 71 +
src/pytransit/analysis/__init__.py | 31 +
src/pytransit/analysis/base.py | 341 +
src/pytransit/analysis/binomial.py | 541 +
src/pytransit/analysis/example.py | 240 +
src/pytransit/analysis/griffin.py | 289 +
src/pytransit/analysis/gumbel.py | 511 +
src/pytransit/analysis/hmm.py | 596 +
src/pytransit/analysis/rankproduct.py | 464 +
src/pytransit/analysis/resampling.py | 472 +
src/pytransit/analysis/tn5gaps.py | 416 +
src/pytransit/data/cholesterol_H37Rv_merged.wig | 74607 ++++++++++++++
src/pytransit/data/cholesterol_H37Rv_rep1.wig | 74607 ++++++++++++++
src/pytransit/data/cholesterol_H37Rv_rep2.wig | 74607 ++++++++++++++
src/pytransit/data/cholesterol_H37Rv_rep3.wig | 74607 ++++++++++++++
src/pytransit/data/glycerol_H37Rv_merged.wig | 74607 ++++++++++++++
src/pytransit/data/glycerol_H37Rv_rep1.wig | 74607 ++++++++++++++
src/pytransit/data/glycerol_H37Rv_rep2.wig | 74607 ++++++++++++++
.../gumbel_glycerol_reads_rep1_s10000_b500_t1.dat | 3999 +
src/pytransit/data/hmm_glycerol_sites.dat | 73399 ++++++++++++++
src/pytransit/data/hmm_glycerol_sites_genes.dat | 3992 +
.../data/resampling_results_glyc_chol.dat | 3996 +
src/pytransit/doc/Makefile | 153 +
src/pytransit/doc/images/TPP-screenshot.png | Bin 0 -> 93949 bytes
src/pytransit/doc/images/export_menu.png | Bin 0 -> 120441 bytes
src/pytransit/doc/images/files_list.png | Bin 0 -> 120733 bytes
src/pytransit/doc/images/gumbel_g0g1.png | Bin 0 -> 96454 bytes
src/pytransit/doc/images/hmm_g0g1.png | Bin 0 -> 91756 bytes
src/pytransit/doc/images/main.png | Bin 0 -> 76097 bytes
src/pytransit/doc/images/resampling_g0g1_g2g3.png | Bin 0 -> 113165 bytes
src/pytransit/doc/images/result_table.png | Bin 0 -> 201880 bytes
.../doc/images/result_table_histogram.png | Bin 0 -> 174225 bytes
src/pytransit/doc/images/result_table_menu.png | Bin 0 -> 208781 bytes
src/pytransit/doc/images/result_volcano_graph.png | Bin 0 -> 156387 bytes
src/pytransit/doc/images/scatter.png | Bin 0 -> 142965 bytes
src/pytransit/doc/images/track_view.png | Bin 0 -> 82981 bytes
src/pytransit/doc/images/tutorial_annotation.png | Bin 0 -> 77807 bytes
src/pytransit/doc/images/tutorial_chol_exp.png | Bin 0 -> 112982 bytes
src/pytransit/doc/images/tutorial_glyc_ctrl.png | Bin 0 -> 92076 bytes
src/pytransit/doc/images/tutorial_gumbel_file.png | Bin 0 -> 169429 bytes
src/pytransit/doc/images/tutorial_gumbel_menu.png | Bin 0 -> 95037 bytes
src/pytransit/doc/images/tutorial_hmm_menu.png | Bin 0 -> 97840 bytes
src/pytransit/doc/images/tutorial_hmm_sites.png | Bin 0 -> 125852 bytes
src/pytransit/doc/images/tutorial_resampling.png | Bin 0 -> 115932 bytes
.../doc/images/tutorial_resampling_file.png | Bin 0 -> 191024 bytes
.../doc/images/tutorial_resampling_result.png | Bin 0 -> 123317 bytes
.../doc/images/tutorial_resampling_running.png | Bin 0 -> 119781 bytes
src/pytransit/doc/images/tutorial_scatter.png | Bin 0 -> 142965 bytes
src/pytransit/doc/images/tutorial_track_view.png | Bin 0 -> 82981 bytes
src/pytransit/doc/images/tutorial_view_menu.png | Bin 0 -> 117463 bytes
src/pytransit/doc/images/view_menu.png | Bin 0 -> 117463 bytes
src/pytransit/doc/make.bat | 190 +
src/pytransit/doc/source/Makefile | 230 +
.../doc/source/_images/TPP-screenshot.png | Bin 0 -> 57633 bytes
.../_images/transit_dataset_scatter_graph.png | Bin 0 -> 154623 bytes
.../source/_images/transit_dataset_track_view.png | Bin 0 -> 122323 bytes
.../doc/source/_images/transit_export_options.png | Bin 0 -> 170765 bytes
.../doc/source/_images/transit_gumbel_options.png | Bin 0 -> 179589 bytes
.../doc/source/_images/transit_gumbel_results.png | Bin 0 -> 202479 bytes
.../doc/source/_images/transit_hmm_options.png | Bin 0 -> 176894 bytes
.../doc/source/_images/transit_hmm_results.png | Bin 0 -> 214525 bytes
.../doc/source/_images/transit_interface.png | Bin 0 -> 97208 bytes
src/pytransit/doc/source/_images/transit_logo.png | Bin 0 -> 6590 bytes
.../doc/source/_images/transit_methods_options.png | Bin 0 -> 162446 bytes
.../_images/transit_resampling_histogram_graph.png | Bin 0 -> 158228 bytes
.../doc/source/_images/transit_resampling_menu.png | Bin 0 -> 152824 bytes
.../source/_images/transit_resampling_options.png | Bin 0 -> 186541 bytes
.../source/_images/transit_resampling_results.png | Bin 0 -> 214157 bytes
.../_images/transit_result_volcano_graph.png | Bin 0 -> 156304 bytes
.../source/_images/transit_tutorial_annotation.png | Bin 0 -> 98718 bytes
.../_images/transit_tutorial_control_datasets.png | Bin 0 -> 109145 bytes
.../transit_tutorial_experimental_datasets.png | Bin 0 -> 129905 bytes
.../doc/source/_images/tutorial_glyc_ctrl.png | Bin 0 -> 110792 bytes
src/pytransit/doc/source/conf.py | 383 +
src/pytransit/doc/source/index.rst | 64 +
src/pytransit/doc/source/make.bat | 281 +
src/pytransit/doc/source/pytransit.analysis.rst | 86 +
src/pytransit/doc/source/pytransit.rst | 109 +
src/pytransit/doc/source/tpp.rst | 415 +
src/pytransit/doc/source/transit.rst | 47 +
.../doc/source/transit_comparative_tutorial.rst | 207 +
.../doc/source/transit_essentiality_tutorial.rst | 163 +
.../doc/source/transit_export_tutorial.rst | 56 +
src/pytransit/doc/source/transit_features.rst | 106 +
.../doc/source/transit_genome_tutorial.rst | 163 +
src/pytransit/doc/source/transit_install.rst | 582 +
src/pytransit/doc/source/transit_methods.rst | 541 +
src/pytransit/doc/source/transit_overview.rst | 153 +
src/pytransit/doc/source/transit_running.rst | 249 +
src/pytransit/draw_trash.py | 329 +
src/pytransit/fileDisplay.py | 342 +
src/pytransit/genomes/BCG.fna | 62496 ++++++++++++
src/pytransit/genomes/BCG.prot_table | 3952 +
src/pytransit/genomes/H37Rv.fna | 63023 ++++++++++++
src/pytransit/genomes/H37Rv.prot_table | 3990 +
src/pytransit/genomes/H37RvBD.fna | 63026 ++++++++++++
src/pytransit/genomes/H37RvBD.prot_table | 4036 +
src/pytransit/genomes/H37RvBD_mod3.prot_table | 4036 +
src/pytransit/genomes/H37RvMA2.fna | 63015 ++++++++++++
src/pytransit/genomes/H37RvMA2.prot_table | 4018 +
src/pytransit/genomes/genomes.html | 36 +
src/pytransit/genomes/genomes.html~ | 36 +
src/pytransit/genomes/mc2_155_tamu.fna | 99838 +++++++++++++++++++
src/pytransit/genomes/mc2_155_tamu.prot_table | 6716 ++
src/pytransit/images.py | 278 +
src/pytransit/norm_tools.py | 579 +
src/pytransit/qcDisplay.py | 310 +
src/pytransit/stat_tools.py | 452 +
src/pytransit/tnseq_tools.py | 1299 +
src/pytransit/transit_gui.py | 1894 +
src/pytransit/transit_tools.py | 218 +
src/pytransit/trash.py | 356 +
src/pytransit/view_trash.py | 205 +
src/tpp.py | 27 +
src/transit.fbp | 8810 ++
src/transit.py | 31 +
src/view_files.fbp | 478 +
src/view_trash.fbp | 1883 +
132 files changed, 1013763 insertions(+)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..62e8de6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,61 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+#Data files
+*.wig
+*.dat
+*.prot_table
+*.png
+*.out
+
diff --git a/.hgignore b/.hgignore
new file mode 100644
index 0000000..e3cf528
--- /dev/null
+++ b/.hgignore
@@ -0,0 +1,22 @@
+^output/.*
+^plugins/.*
+^sdk/.*
+^src/.*
+^build/.*
+^dist/.*
+^ObjectListView-1.2/.*
+^backup/.*
+^listctrl_example/.*
+^example/.*
+^source_
+.*\.pyc$
+.*\.swp$
+.*\.png$
+.*\.bat$
+.*\.jpeg$
+.*\.txt$
+.*\.dat$
+.*\.exe$
+.*\.spec$
+.*\.tar.gz$
+^.hgignore~$
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..c4cb15d
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,173 @@
+# Change log
+All notable changes to this project will be documented in this file.
+
+
+## Version 2.0.2 - 2016-08-19
+
+-TRANSIT:
+ - Now accepts GFF3 formatted annotations.
+ - Added ability to specify pseudocounts for resampling.
+ - Added extra columns to resampling output.
+ - Fixed bug with some log2FC calculations.
+ - Export to combined wig format now asks for normalization BEFORE file name.
+ - Fixed bug preventing Quality Control window from opening.
+ - Miscellanous bug fixes.
+ - Updates to Documentation
+
+-TPP:
+ - Now accepts custom primer sequences.
+ - Reporting additional diagnostic statistics for reads mapping to phiMycoMarT7, and Illumina adapters.
+ - Miscellaneous bug fixes.
+
+
+
+## Version 2.0.1 - 2016-07-05
+
+- TRANSIT:
+ - Fixed crash in TPP.
+ - Misc changes for outputs.
+
+
+## Version 2.0.0 - 2016-06-16
+
+- TRANSIT:
+ - Added new method for datasets created with Tn5 transposons.
+ - Added label indicating intended transposons for the methods.
+ - Added textbox with short description of the chosen method.
+ - Changed methods choices to be in menu (on top).
+ - Changed the file display window.
+ - Added Help menu with link to online documentation.
+ - Added new logo.
+ - Added option to export (normalized) datasets to IGV or combined wig format.
+ - Can now select multiple .wig files at the same time (Ctrl + select).
+ - Lots of changes under the hood.
+
+
+## Version 1.4.5 - 2016-01-10
+- TRANSIT:
+ - Added Binomial analysis method as an option to TRANSIT.
+ - Added DE-HMM analysis method as an option to TRANSIT.
+
+
+## Version 1.4.3.1 - 2016-01-02
+- TRANSIT:
+ - Fixed bug causing TRANSIT not to open on some Windows systems.
+
+
+## Version 1.4.3 - 2015-12-04
+- TRANSIT:
+ - Precision of resampling p-values in output file now increases with sample size
+ - Added preliminary Quality Control functionality. Select some datasets and click View -> Quality Control
+ - In resampling, changed logFC to divide by number of replicates
+ - Changed plotting of results files to be more versitile
+ - Fixed bug causing HMM_sites output not to be added to list of files
+ - Fixed bug causing LOESS correction not to work in HMM
+
+
+## Version 1.4.2 - 2015-07-29
+- TRANSIT:
+ - Added Total Trimmed Reads normaliztion (TTR) as the default option. This is the recommended normalization method at this point.
+ - Added BetaGeomtric Correction (betageom) as a normalization option. This is recommended for datasets that are very skewed.
+ - Fixed bug that caused transit to create histograms when not desired.
+ - Added a pseudo-count when calculating log-FC to genes without reads.
+ - Increased size of result windows so that all columns are immediately visible.
+
+
+
+
+## Version 1.4.1 - 2015-06-5
+- TRANSIT:
+ - TRANSIT now accepts read-counts in floating-point precision, not just integers.
+ - Made transit work with most recent versions of matplotlib.
+
+
+## Version 1.4.0 - 2015-05-27
+- TRANSIT:
+ - Added option to correct for genomic position bias (using LOESS)
+ - Added more options for normalization, including zero-inflated negative binomial and quantile normalization.
+
+
+- TPP:
+ - Eliminated soft-clipped reads.
+ - Modified template_counts() to be much more memory efficient (does not need gigabytes of RAM any more to process large datasets)
+ - Added ability to process Tn5 datasets
+
+
+
+
+
+## Version 1.3.0 - 2015-03-31
+- TRANSIT:
+ - Fixed threading issue for volcano plot.
+ - Improved format and quality of the output messages.
+ - Fixed direction of log-fold change in volcano plots.
+ - Added log-fold change column to resampling output file.
+ - Made adaptive resampling work better with custom sample sizes.
+
+
+- TPP:
+ - Fixed genomic portion for single ends.
+ - Added usage help as part of command line arguments.
+
+
+
+## Version 1.2.33 - 2015-03-06
+
+- TRANSIT:
+ - Fixed issue with histograms create using adaptive resampling.
+
+
+
+## Version 1.2.32 - 2015-03-05
+
+- TRANSIT:
+ - Put .pyc files in in new src/ directory.
+ - Fixed error that sometimes occurred when plotting volcano plots.
+ - Made TRANSIT default to the current working directory when opening file dialogs.
+
+- TPP:
+ - TPP can now process files with single-end reads.
+ - TPP can now process *.fasta and compressed files with "*.fastq.gz" extension
+
+
+
+## Version 1.2.7 - 2015-02-25
+
+- TRANSIT:
+ - Fixed error that occured when displaying graphs after running an analysis.
+ - Updated datasets included in the data/ directory.
+
+- TPP:
+ - Removed the requirement for wxPython when running TPP on command-line mode.
+
+
+
+## Version 1.1 - 2015-02-20
+
+- TRANSIT:
+ - Fixed error in HMM results file table, which was not correctly showing breakdown of genes.
+ - Made TRANSIT work from the command-line, without displaying GUI. See documentation for arguments/flags.
+ - Added ability to convert annotation files between several formats (.prot_table, ptt.table, gff3).
+
+- TPP:
+ - User can supply reads in either FastA or FastQ format.
+ - Added an option to specify number of mismatches (default=1) when looking
+ for sequence patterns such as the transposon prefix in read 1.
+ - Added command-line arguments so TPP can be run in batch mode without the GUI.
+ - Number of mapped reads for R1 and R2 independently is also now reported.
+ - Modified how barcodes are extracted from read 2. It now looks for specific
+ sequence patterns, even if they are shifted. This should greatly increase
+ the number of mapped reads (esp. the genomic part of R2) for certain datasets.
+ - Properly handle short fragments, ie. for reads where the insert size is shorter
+ than the read length. In such cases, the adapter from other end appears
+ at the end of read 1, and this suffix is now stripped off so these reads
+ will map too.
+
+
+
+## Version 1.0 - 2015-02-10
+
+- First limited-release version of TRANSIT
+- Released to close collaborators first and presented in teleconference to get feedback.
+
+
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..78f62ad
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,596 @@
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+intact all notices of the absence of any warranty; and give all recipients a copy of
+this License along with the Program.
+
+You may charge any price or no price for each copy that you convey, and you may offer
+support or warranty protection for a fee.
+
+### 5. Conveying Modified Source Versions.
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+the Program, in the form of source code under the terms of section 4, provided that
+you also meet all of these conditions:
+
+* **a)** The work must carry prominent notices stating that you modified it, and giving a
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+* **d)** If the work has interactive user interfaces, each must display Appropriate Legal
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+
+A compilation of a covered work with other separate and independent works, which are
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+it such as to form a larger program, in or on a volume of a storage or distribution
+medium, is called an “aggregate” if the compilation and its resulting
+copyright are not used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work in an aggregate
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+
+### 6. Conveying Non-Source Forms.
+
+You may convey a covered work in object code form under the terms of sections 4 and
+5, provided that you also convey the machine-readable Corresponding Source under the
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+* **a)** Convey the object code in, or embodied in, a physical product (including a
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+* **c)** Convey individual copies of the object code with a copy of the written offer to
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+* **d)** Convey the object code by offering access from a designated place (gratis or for
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+* **e)** Convey the object code using peer-to-peer transmission, provided you inform
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+
+A separable portion of the object code, whose source code is excluded from the
+Corresponding Source as a System Library, need not be included in conveying the
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+
+A “User Product” is either (1) a “consumer product”, which
+means any tangible personal property which is normally used for personal, family, or
+household purposes, or (2) anything designed or sold for incorporation into a
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+“Installation Information” for a User Product means any methods,
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+functioning of the modified object code is in no case prevented or interfered with
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+
+If you convey an object code work under this section in, or with, or specifically for
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+neither you nor any third party retains the ability to install modified object code
+on the User Product (for example, the work has been installed in ROM).
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+The requirement to provide Installation Information does not include a requirement to
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+special password or key for unpacking, reading or copying.
+
+### 7. Additional Terms.
+
+“Additional permissions” are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions. Additional
+permissions that are applicable to the entire Program shall be treated as though they
+were included in this License, to the extent that they are valid under applicable
+law. If additional permissions apply only to part of the Program, that part may be
+used separately under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option remove any
+additional permissions from that copy, or from any part of it. (Additional
+permissions may be written to require their own removal in certain cases when you
+modify the work.) You may place additional permissions on material, added by you to a
+covered work, for which you have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you add to a
+covered work, you may (if authorized by the copyright holders of that material)
+supplement the terms of this License with terms:
+
+* **a)** Disclaiming warranty or limiting liability differently from the terms of
+sections 15 and 16 of this License; or
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+attributions in that material or in the Appropriate Legal Notices displayed by works
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+
+All other non-permissive additional terms are considered “further
+restrictions” within the meaning of section 10. If the Program as you received
+it, or any part of it, contains a notice stating that it is governed by this License
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+license document contains a further restriction but permits relicensing or conveying
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+If you add terms to a covered work in accord with this section, you must place, in
+the relevant source files, a statement of the additional terms that apply to those
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+
+Additional terms, permissive or non-permissive, may be stated in the form of a
+separately written license, or stated as exceptions; the above requirements apply
+either way.
+
+### 8. Termination.
+
+You may not propagate or modify a covered work except as expressly provided under
+this License. Any attempt otherwise to propagate or modify it is void, and will
+automatically terminate your rights under this License (including any patent licenses
+granted under the third paragraph of section 11).
+
+However, if you cease all violation of this License, then your license from a
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+copyright holder explicitly and finally terminates your license, and (b) permanently,
+if the copyright holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+Moreover, your license from a particular copyright holder is reinstated permanently
+if the copyright holder notifies you of the violation by some reasonable means, this
+is the first time you have received notice of violation of this License (for any
+work) from that copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+Termination of your rights under this section does not terminate the licenses of
+parties who have received copies or rights from you under this License. If your
+rights have been terminated and not permanently reinstated, you do not qualify to
+receive new licenses for the same material under section 10.
+
+### 9. Acceptance Not Required for Having Copies.
+
+You are not required to accept this License in order to receive or run a copy of the
+Program. Ancillary propagation of a covered work occurring solely as a consequence of
+using peer-to-peer transmission to receive a copy likewise does not require
+acceptance. However, nothing other than this License grants you permission to
+propagate or modify any covered work. These actions infringe copyright if you do not
+accept this License. Therefore, by modifying or propagating a covered work, you
+indicate your acceptance of this License to do so.
+
+### 10. Automatic Licensing of Downstream Recipients.
+
+Each time you convey a covered work, the recipient automatically receives a license
+from the original licensors, to run, modify and propagate that work, subject to this
+License. You are not responsible for enforcing compliance by third parties with this
+License.
+
+An “entity transaction” is a transaction transferring control of an
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+merging organizations. If propagation of a covered work results from an entity
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+could give under the previous paragraph, plus a right to possession of the
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+has it or can get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the rights granted or
+affirmed under this License. For example, you may not impose a license fee, royalty,
+or other charge for exercise of rights granted under this License, and you may not
+initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging
+that any patent claim is infringed by making, using, selling, offering for sale, or
+importing the Program or any portion of it.
+
+### 11. Patents.
+
+A “contributor” is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The work thus
+licensed is called the contributor's “contributor version”.
+
+A contributor's “essential patent claims” are all patent claims owned or
+controlled by the contributor, whether already acquired or hereafter acquired, that
+would be infringed by some manner, permitted by this License, of making, using, or
+selling its contributor version, but do not include claims that would be infringed
+only as a consequence of further modification of the contributor version. For
+purposes of this definition, “control” includes the right to grant patent
+sublicenses in a manner consistent with the requirements of this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free patent license
+under the contributor's essential patent claims, to make, use, sell, offer for sale,
+import and otherwise run, modify and propagate the contents of its contributor
+version.
+
+In the following three paragraphs, a “patent license” is any express
+agreement or commitment, however denominated, not to enforce a patent (such as an
+express permission to practice a patent or covenant not to sue for patent
+infringement). To “grant” such a patent license to a party means to make
+such an agreement or commitment not to enforce a patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license, and the
+Corresponding Source of the work is not available for anyone to copy, free of charge
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+other readily accessible means, then you must either (1) cause the Corresponding
+Source to be so available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner consistent with
+the requirements of this License, to extend the patent license to downstream
+recipients. “Knowingly relying” means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or your
+recipient's use of the covered work in a country, would infringe one or more
+identifiable patents in that country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or arrangement, you
+convey, or propagate by procuring conveyance of, a covered work, and grant a patent
+license to some of the parties receiving the covered work authorizing them to use,
+propagate, modify or convey a specific copy of the covered work, then the patent
+license you grant is automatically extended to all recipients of the covered work and
+works based on it.
+
+A patent license is “discriminatory” if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on the
+non-exercise of one or more of the rights that are specifically granted under this
+License. You may not convey a covered work if you are a party to an arrangement with
+a third party that is in the business of distributing software, under which you make
+payment to the third party based on the extent of your activity of conveying the
+work, and under which the third party grants, to any of the parties who would receive
+the covered work from you, a discriminatory patent license (a) in connection with
+copies of the covered work conveyed by you (or copies made from those copies), or (b)
+primarily for and in connection with specific products or compilations that contain
+the covered work, unless you entered into that arrangement, or that patent license
+was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied
+license or other defenses to infringement that may otherwise be available to you
+under applicable patent law.
+
+### 12. No Surrender of Others' Freedom.
+
+If conditions are imposed on you (whether by court order, agreement or otherwise)
+that contradict the conditions of this License, they do not excuse you from the
+conditions of this License. If you cannot convey a covered work so as to satisfy
+simultaneously your obligations under this License and any other pertinent
+obligations, then as a consequence you may not convey it at all. For example, if you
+agree to terms that obligate you to collect a royalty for further conveying from
+those to whom you convey the Program, the only way you could satisfy both those terms
+and this License would be to refrain entirely from conveying the Program.
+
+### 13. Use with the GNU Affero General Public License.
+
+Notwithstanding any other provision of this License, you have permission to link or
+combine any covered work with a work licensed under version 3 of the GNU Affero
+General Public License into a single combined work, and to convey the resulting work.
+The terms of this License will continue to apply to the part which is the covered
+work, but the special requirements of the GNU Affero General Public License, section
+13, concerning interaction through a network will apply to the combination as such.
+
+### 14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions of the GNU
+General Public License from time to time. Such new versions will be similar in spirit
+to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that
+a certain numbered version of the GNU General Public License “or any later
+version” applies to it, you have the option of following the terms and
+conditions either of that numbered version or of any later version published by the
+Free Software Foundation. If the Program does not specify a version number of the GNU
+General Public License, you may choose any version ever published by the Free
+Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU
+General Public License can be used, that proxy's public statement of acceptance of a
+version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty.
+
+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
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 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.
+
+### 16. Limitation of Liability.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY 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
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16.
+
+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.
+
+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.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+<<http://www.gnu.org/licenses/>>.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+<<http://www.gnu.org/philosophy/why-not-lgpl.html>>.
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..db131c0
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,10 @@
+include MANIFEST.in
+include README.md
+include LICENSE.md
+include VERSION
+recursive-include src/pytransit/data *
+recursive-include src/pytransit/genomes *
+recursive-include src/pytransit/doc/build/html *.html
+recursive-include src/pytransit/doc/build/html/_images *.png
+recursive-include src/pytransit/doc/build/html/_modules *
+recursive-include src/pytransit/doc/build/html/_static *
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..047a2ab
--- /dev/null
+++ b/README.md
@@ -0,0 +1,52 @@
+# TRANSIT 2.0
+
+
+**New in Version 2.0+**
+ - Support for Tn5 datasets.
+ - New analysis methods.
+ - New way to export normalized datasets.
+
+**Version 2.0.2 changes (August, 2016)**
+- Added support for for custom primers in TPP.
+- Added support for annotations in GFF3 format.
+- Ability to specify pseudocounts in resampling.
+- Misc. Bug fixes
+- **New [mailing list](https://groups.google.com/forum/#!forum/tnseq-transit/join)**
+
+
+
+Welcome! This is the distribution for the TRANSIT and TPP tools developed by the Ioerger Lab.
+
+TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.
+
+
+
+## Mailing List
+
+You can join our mailing list to get announcements of new versions, discuss any bugs, or request features! Just head over to the following site and enter your email address:
+
+https://groups.google.com/forum/#!forum/tnseq-transit/join
+
+
+
+
+## Instructions
+
+For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("doc" folder) or visit the following web page:
+
+
+http://saclab.tamu.edu/essentiality/transit/transit.html
+
+
+## Datasets
+
+The TRANSIT distribution comes with some example .wig files in the data/ directory, as well as an example annotation file (.prot\_table format) in the genomes/ directory. Additional genomes may be found on the following website:
+
+http://saclab.tamu.edu/essentiality/transit/genomes/
+
+
+## Copyright Information
+
+Source code for TRANSIT and TPP are available open source under the terms of the GNU General Public License (Version 3.0) as published by the Free Software Foundation. For more information on this license, please see the included LICENSE.md file or visit their website at:
+
+http://www.gnu.org/licenses/gpl.html
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..c825821
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+version: 2.0.1-58-g0a3b-mod
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..b88034e
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,2 @@
+[metadata]
+description-file = README.md
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..86212ab
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,121 @@
+"""A setuptools based setup module.
+
+See:
+https://packaging.python.org/en/latest/distributing.html
+https://github.com/pypa/sampleproject
+"""
+
+# Always prefer setuptools over distutils
+from setuptools import setup, find_packages
+# To use a consistent encoding
+from codecs import open
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+
+# Get the long description from the README file
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+ long_description = f.read()
+
+# Get current version
+import sys
+sys.path.insert(1, "src/")
+import pytransit
+version = pytransit.__version__[1:] #"2.0.3"
+
+setup(
+ name='tnseq-transit',
+
+ # Versions should comply with PEP440. For a discussion on single-sourcing
+ # the version across setup.py and the project code, see
+ # https://packaging.python.org/en/latest/single_source_version.html
+ version=version,
+
+ description='TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.',
+ long_description=long_description,
+
+ # The project's main homepage.
+ url='https://github.com/mad-lab/transit',
+ download_url='https://github.com/mad-lab/transit',
+
+ # Author details
+ author='Michael A. DeJesus',
+ author_email='mad at cs.tamu.edu',
+
+ # Choose your license
+ license='GNU GPL',
+
+ # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
+ classifiers=[
+ #'Development Status :: 3 - Alpha',
+ 'Development Status :: 5 - Production/Stable',
+ 'Programming Language :: Python :: 2.7',
+ 'Intended Audience :: Science/Research',
+ 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+ 'Operating System :: OS Independent',
+ 'Topic :: Scientific/Engineering :: Bio-Informatics',
+ ],
+
+ # What does your project relate to?
+ keywords=['tnseq', 'analysis', 'biology', 'genome'],
+
+ #package_dir = {'tnseq-transit': 'src/pytransit'},
+
+ # You can just specify the packages manually here if your project is
+ # simple. Or you can use find_packages().
+ packages = find_packages('src', exclude=['contrib', 'tests']),
+ #packages = ['pytransit'],
+ package_dir = {'pytransit': 'src/pytransit', 'pytpp': 'src/pytpp'},
+ include_package_data=True,
+ #py_modules = ['tpp'],
+
+ # Alternatively, if you want to distribute just a my_module.py, uncomment
+ # this:
+ # py_modules=["my_module"],
+
+ # List run-time dependencies here. These will be installed by pip when
+ # your project is installed. For an analysis of "install_requires" vs pip's
+ # requirements files see:
+ # https://packaging.python.org/en/latest/requirements.html
+ install_requires=['setuptools', 'numpy', 'scipy', 'pillow', 'matplotlib>1.2.0,<1.5.0'],
+
+ #dependency_links = [
+ # "git+https://github.com/wxWidgets/wxPython.git#egg=wxPython"
+ #],
+
+ # List additional groups of dependencies here (e.g. development
+ # dependencies). You can install these using the following syntax,
+ # for example:
+ # $ pip install -e .[dev,test]
+ #extras_require={
+ # 'dev': ['check-manifest'],
+ # 'test': ['coverage'],
+ #},
+
+ # If there are data files included in your packages that need to be
+ # installed, specify them here. If using Python 2.6 or less, then these
+ # have to be included in MANIFEST.in as well.
+ package_data={
+ 'pytransit': ['pytransit/data/*', 'pytransit/doc/*.*', 'pytransit/doc/images/*', 'pytransit/genomes/*']
+ },
+
+ #scripts=['src/tpp.py', 'src/transit.py'],
+
+ # Although 'package_data' is the preferred approach, in some case you may
+ # need to place data files outside of your packages. See:
+ # http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files # noqa
+ # In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
+ #data_files=[('transitdata', ['package_data.dat'])],
+
+ # To provide executable scripts, use entry points in preference to the
+ # "scripts" keyword. Entry points provide cross-platform support and allow
+ # pip to create the appropriate form of executable for the target platform.
+ entry_points={
+ 'console_scripts': [
+ 'transit=pytransit.__main__:main',
+ 'tpp=pytpp.__main__:main',
+ ],
+ },
+)
+
diff --git a/src/pytpp/__init__.py b/src/pytpp/__init__.py
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/src/pytpp/__init__.py
@@ -0,0 +1 @@
+
diff --git a/src/pytpp/__main__.py b/src/pytpp/__main__.py
new file mode 100644
index 0000000..de2ee88
--- /dev/null
+++ b/src/pytpp/__main__.py
@@ -0,0 +1,126 @@
+#!/usr/bin/env python
+
+# Copyright 2015.
+# Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
+#
+#
+# This file is part of TRANSIT.
+#
+# TRANSIT 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.
+#
+#
+# TRANSIT 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 TRANSIT. If not, see <http://www.gnu.org/licenses/>.
+
+import sys
+import glob
+import os
+import time
+import math
+import sys
+import re
+import shutil
+import platform
+import gzip
+
+from tpp_tools import *
+from tpp_gui import *
+
+
+def main():
+ # if -nowin is command-line arg, skip the GUI and set filenames in vars
+
+ vars = Globals()
+ #vars.version = "$Revision: 1.5 $".split()[1]
+
+ if len(sys.argv) <= 1 and hasWx:
+ app = wx.App(False)
+ form = MyForm(vars)
+ form.update_dataset_list()
+
+ form.Show()
+ app.MainLoop()
+
+ # vars.action not defined, quit...
+
+ if hasattr(vars, 'action'):
+ if vars.action=="start":
+ verify_inputs(vars)
+ if vars.fq2=="": msg = 'running pre-processing on %s' % (vars.fq1)
+ else: msg = 'running pre-processing on %s and %s' % (vars.fq1,vars.fq2)
+ message(msg)
+ message("transposon type: %s" % vars.transposon)
+ save_config(vars)
+ driver(vars)
+
+ else:
+ pass
+
+ elif len(sys.argv) <= 1 and not hasWx:
+ print "Please install wxPython to run in GUI Mode."
+ print "To run in Console Mode please follow these instructions:"
+ print ""
+ show_help()
+
+ else:
+ flag = False
+ initialize_globals(vars)
+ i,n = 1,len(sys.argv)
+ while i<n:
+ if sys.argv[i] == '-help':
+ show_help()
+ sys.exit()
+ elif sys.argv[i] == '-tn5':
+ vars.transposon = 'Tn5'
+ i += 1
+ elif sys.argv[i] == '-himar1':
+ vars.transposon = 'Himar1'
+ i += 1
+ elif sys.argv[i] == '-primer':
+ vars.prefix = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-reads1':
+ vars.fq1 = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-reads2':
+ flag = True
+ vars.fq2 = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-bwa':
+ vars.bwa = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-ref':
+ vars.ref = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-maxreads':
+ vars.maxreads = int(sys.argv[i+1])
+ i += 2
+ elif sys.argv[i] == '-output':
+ vars.base = sys.argv[i+1]
+ i += 2
+ elif sys.argv[i] == '-mismatches':
+ vars.mm1 = int(sys.argv[i+1])
+ i += 2
+ else:
+ print "error: unrecognized flag:",sys.argv[i]
+ show_help()
+ sys.exit()
+ if flag==False: vars.fq2 = ""
+ if vars.fq2=="": msg = 'running pre-processing on %s' % (vars.fq1)
+ else: msg = 'running pre-processing on %s and %s' % (vars.fq1,vars.fq2)
+ message(msg)
+ message("transposon type: %s" % vars.transposon)
+ verify_inputs(vars)
+ save_config(vars)
+ driver(vars)
+
+if __name__ == "__main__":
+ main()
+
diff --git a/src/pytpp/tpp_gui.py b/src/pytpp/tpp_gui.py
new file mode 100644
index 0000000..82436a4
--- /dev/null
+++ b/src/pytpp/tpp_gui.py
@@ -0,0 +1,304 @@
+#!/usr/bin/env python
+
+# Copyright 2015.
+# Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
+#
+#
+# This file is part of TRANSIT.
+#
+# TRANSIT 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.
+#
+#
+# TRANSIT 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 TRANSIT. If not, see <http://www.gnu.org/licenses/>.
+
+import sys
+import glob
+import os
+import time
+import math
+import re
+import shutil
+import platform
+import gzip
+
+try:
+ import wx
+ import wx.lib.filebrowsebutton
+ hasWx = True
+except Exception as e:
+ hasWx = False
+
+from tpp_tools import *
+
+if hasWx:
+ class MyForm(wx.Frame):
+
+ def __init__(self,vars):
+ self.vars = vars
+ initialize_globals(self.vars)
+
+ wx.Frame.__init__(self, None, wx.ID_ANY, "Tn-Seq PreProcessor") # v%s" % vars.version)
+ # Add a panel so it looks the correct on all platforms
+ panel = wx.Panel(self, wx.ID_ANY)
+ #panel.SetFont(wx.Font(14,wx.DECORATIVE,wx.NORMAL,wx.NORMAL,False,u'times'))
+ # panel.SetFont(wx.Font(14,wx.DECORATIVE,wx.NORMAL,wx.NORMAL,False,u'fixed'))
+ #panel.SetFont(wx.Font(14,wx.DECORATIVE,wx.NORMAL,wx.BOLD,False,u'courier'))
+
+ sizer = wx.BoxSizer(wx.VERTICAL)
+
+ self.list_ctrl = None
+ self.InitMenu()
+ self.InitFiles(panel,sizer)
+
+ buttonrow = wx.BoxSizer(wx.HORIZONTAL)
+
+ btn = wx.Button(panel, label="Start")
+ btn.Bind(wx.EVT_BUTTON, self.map_reads)
+ buttonrow.Add(btn,0,0,0,10)
+
+ btn = wx.Button(panel, label="Quit")
+ btn.Bind(wx.EVT_BUTTON, self.OnQuit)
+ buttonrow.Add(btn,0,0,0,10)
+ sizer.Add(buttonrow,0,0,0)
+
+ self.InitList(panel,sizer)
+
+ panel.SetSizer(sizer)
+ # self.SetSize((1305, 700))
+ self.SetSize((900, 700))
+ #self.SetTitle('Simple menu')
+ self.Centre()
+ #self.Show(True)
+
+ self.pid = None
+
+ '''
+ def initialize_globals(self):
+ vars = self.vars
+ vars.fq1,vars.fq2,vars.ref,vars.bwa,vars.base,vars.maxreads = "","","","","temp",-1
+ read_config(vars)
+ '''
+
+ def InitFiles(self,panel,sizer):
+ vars = self.vars
+ sizer0 = wx.BoxSizer(wx.HORIZONTAL)
+ label0 = wx.StaticText(panel, label='BWA executable:',size=(340,-1))
+ sizer0.Add(label0,0,0,0)
+ print os.path.dirname(vars.bwa)
+ #self.picker0 = wx.FilePickerCtrl(panel, wx.ID_ANY,message="path to BWA",size=(400,30))#,path=os.path.abspath(vars.bwa))
+ #self.picker0.SetDirName('/pacific/home/cambadipudi/chaitra/tpp/')
+ self.picker0 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id = wx.ID_ANY, size=(400,30), dialogTitle='Path to BWA', fileMode=wx.OPEN, fileMask='bwa*', startDirectory=os.path.dirname(vars.bwa), initialValue=vars.bwa, labelText='')
+ sizer0.Add(self.picker0, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer0,0,wx.EXPAND,0)
+
+ sizer3 = wx.BoxSizer(wx.HORIZONTAL)
+ label3 = wx.StaticText(panel, label='Choose a reference genome (FASTA):',size=(340,-1))
+ sizer3.Add(label3,0,0,0)
+ #self.picker3 = wx.FilePickerCtrl(panel, wx.ID_ANY,message="Please select the reference genome", wildcard='*.fna;*.fasta;*.fa', size=(400,30),path=vars.ref)
+ self.picker3 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the reference genome', fileMode=wx.OPEN, fileMask='*.fna;*.fasta;*.fa', size=(400,30), startDirectory=os.path.dirname(vars.ref), initialValue=vars.ref, labelText='')
+ sizer3.Add(self.picker3, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer3,0,wx.EXPAND,0)
+
+
+ sizer1 = wx.BoxSizer(wx.HORIZONTAL)
+ label1 = wx.StaticText(panel, label='Choose the Fastq file for read 1:',size=(340,-1))
+ sizer1.Add(label1,0,0,0)
+ # self.picker1 = wx.FilePickerCtrl(panel, wx.ID_ANY,message="Please select the .fastq file for read 1", wildcard='*.fastq;*.fq;*.reads;*.fasta;*.fa', size=(400,30),path=vars.fq1)
+ self.picker1 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 1', fileMode=wx.OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq1), initialValue=vars.fq1, labelText='',changeCallback=self.OnChanged2)
+ #self.picker1.OnChanged = self.OnChanged(self.picker1.GetValue(), self.base)
+ #self.Bind(wx.EVT_TEXT, self.OnChanged, id=self.picker1.GetId())
+ #self.picker1.Bind(wx.EVT_TEXT, self.OnChanged)
+ sizer1.Add(self.picker1, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer1,0,wx.EXPAND,0)
+
+ sizer2 = wx.BoxSizer(wx.HORIZONTAL)
+ label2 = wx.StaticText(panel, label='Choose the Fastq file for read 2:',size=(340,-1))
+ sizer2.Add(label2,0,0,0)
+ #self.picker2 = wx.FilePickerCtrl(panel, wx.ID_ANY,message="Please select the .fastq file for read 2", wildcard='*.fastq;*.fq;*.reads;*.fasta;*.fa', size=(400,30),path=vars.fq2)
+ self.picker2 = wx.lib.filebrowsebutton.FileBrowseButton(panel, id=wx.ID_ANY, dialogTitle='Please select the .fastq file for read 2', fileMode=wx.OPEN, fileMask='*.fastq;*.fq;*.reads;*.fasta;*.fa;*.fastq.gz', size=(400,30), startDirectory=os.path.dirname(vars.fq2), initialValue=vars.fq2, labelText='', changeCallback=self.OnChanged2)
+ sizer2.Add(self.picker2, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer2,0,wx.EXPAND,0)
+
+ sizer5 = wx.BoxSizer(wx.HORIZONTAL)
+ label5 = wx.StaticText(panel, label='Prefix to use for output filenames:',size=(350,-1))
+ sizer5.Add(label5,0,0,0)
+ self.base = wx.TextCtrl(panel,value=vars.base,size=(400,30))
+ sizer5.Add(self.base, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer5,0,wx.ALL,0)
+
+ sizer8 = wx.BoxSizer(wx.HORIZONTAL)
+ label8 = wx.StaticText(panel, label='Transposon used:',size=(350,-1))
+ sizer8.Add(label8,0,0,0)
+ self.transposon = wx.ComboBox(panel,choices=['Himar1','Tn5'],size=(400,30))
+ self.transposon.SetStringSelection(vars.transposon)
+ sizer8.Add(self.transposon, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer8,0,wx.ALL,0)
+
+ sizer4 = wx.BoxSizer(wx.HORIZONTAL)
+ label4 = wx.StaticText(panel, label='Primer sequence:',size=(350,-1))
+ sizer4.Add(label4,0,0,0)
+ self.prefix = wx.TextCtrl(panel,value="TAAGAGACAG" if self.transposon.GetValue()=="Tn5" else "ACTTATCAGCCAACCTGTTA",size=(400,30))
+ sizer4.Add(self.prefix, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer4,0,wx.ALL,0)
+
+ self.Bind(wx.EVT_COMBOBOX, self.OnTransposonSelection, id=self.transposon.GetId())
+
+ sizer6 = wx.BoxSizer(wx.HORIZONTAL)
+ label6 = wx.StaticText(panel, label='Max reads (leave blank to use all):',size=(350,-1))
+ sizer6.Add(label6,0,0,0)
+ self.maxreads = wx.TextCtrl(panel,size=(400,30))
+ sizer6.Add(self.maxreads, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer6,0,wx.ALL,0)
+
+ sizer7 = wx.BoxSizer(wx.HORIZONTAL)
+ label7 = wx.StaticText(panel, label='Mismatches allowed in Tn prefix:',size=(350,-1))
+ sizer7.Add(label7,0,0,0)
+ self.mismatches = wx.TextCtrl(panel,value=str(vars.mm1),size=(400,30))
+ sizer7.Add(self.mismatches, proportion=1, flag=wx.EXPAND|wx.ALL, border=5)
+ sizer.Add(sizer7,0,wx.ALL,0)
+
+ #self.picker1.OnChanged = self.OnChanged(self.picker1.GetValue())
+
+ def OnTransposonSelection(self, event):
+ if self.transposon.GetValue()=="Tn5": self.prefix.SetValue("TAAGAGACAG")
+ elif self.transposon.GetValue()=="Himar1": self.prefix.SetValue("ACTTATCAGCCAACCTGTTA")
+ else: self.prefix.SetValue("")
+
+ def OnChanged(self, str_path):
+ print "changed"
+ value = os.path.basename(str_path).split('.')[0]
+ if '_R1' in value or '_R2':
+ value = value.split('_')[0]
+ self.base.SetValue(value)
+
+ def OnChanged2(self, event):
+ value2 = os.path.basename(self.picker2.GetValue()).split('.')[0]
+ value1 = os.path.basename(self.picker1.GetValue()).split('.')[0]
+ value = os.path.commonprefix([value1, value2])
+ self.base.SetValue(value)
+ self.base.Refresh()
+
+ def InitList(self,panel,sizer):
+ self.list_ctrl = wx.ListCtrl(panel, size=(500,500), style=wx.LC_HRULES|wx.LC_VRULES|wx.LC_REPORT|wx.BORDER_SUNKEN)
+ self.list_ctrl.InsertColumn(0, 'Dataset (*.tn_stats)',width=300)
+ self.list_ctrl.InsertColumn(1, 'total reads',wx.LIST_FORMAT_RIGHT,width=125)
+ self.list_ctrl.InsertColumn(2, 'TGTTA prefix', wx.LIST_FORMAT_RIGHT,width=125)
+ self.list_ctrl.InsertColumn(3, 'R1_mapped', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(4, 'R2_mapped', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(5, 'mapped\nreads', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(6, 'template\ncount', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(7, 'TAs hit', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(8, 'insertion\ndensity',wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(9, 'NZmean', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(10, 'maxcount', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(11, 'primer', wx.LIST_FORMAT_RIGHT,width=90)
+ self.list_ctrl.InsertColumn(12, 'vector',wx.LIST_FORMAT_RIGHT,width=90)
+ #self.list_ctrl.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.NORMAL))
+ #btn = wx.Button(panel, label="Add Line")
+ #btn.Bind(wx.EVT_BUTTON, self.add_line)
+
+ sizer.Add(self.list_ctrl, 0, wx.ALL|wx.EXPAND, 10)
+ #sizer.Add(btn, 0, wx.ALL|wx.CENTER, 5)
+
+ def InitMenu(self):
+ menubar = wx.MenuBar()
+ fileMenu = wx.Menu()
+
+ #dataset_menuitem = fileMenu.Append(wx.ID_ANY, 'Add New Dataset', 'Analyze New Dataset')
+ #self.Bind(wx.EVT_MENU, self.addNewDataset, dataset_menuitem)
+
+ quit_menuitem = fileMenu.Append(wx.ID_EXIT, 'Quit', 'Quit application')
+ self.Bind(wx.EVT_MENU, self.OnQuit, quit_menuitem)
+
+ menubar.Append(fileMenu, '&File')
+ self.SetMenuBar(menubar)
+
+ def addNewDataset(self, event):
+ dlg = wx.FileDialog(
+ self, message="Choose a file",
+ defaultDir=".",
+ defaultFile="",
+ wildcard="*.wig",
+ style=wx.OPEN | wx.MULTIPLE | wx.CHANGE_DIR
+ )
+ if dlg.ShowModal() == wx.ID_OK:
+ paths = dlg.GetPaths()
+ for path in paths:
+ print "analyzing dataset:",path
+ analyze_dataset(path)
+ dlg.Destroy()
+ self.update_dataset_list()
+
+ def update_dataset_list(self):
+ if self.list_ctrl==None: return
+ self.list_ctrl.DeleteAllItems()
+ self.index = 0
+ datasets = []
+ for fname in glob.glob("*.tn_stats"):
+ filedate = os.path.getmtime(fname)
+ datasets.append((filedate,fname))
+ datasets.sort(reverse=True)
+ for (filedate,fname) in datasets:
+ stats = self.read_stats_file(fname)
+
+ vals = [stats.get("total_reads","?"),stats.get("TGTTA_reads","?"),stats.get("reads1_mapped", "?"),stats.get("reads2_mapped","?"),stats.get("mapped_reads","?"),stats.get("template_count","?"), stats.get("TAs_hit","?"), stats.get("density", "?"), stats.get("NZ_mean", "?"), stats.get("max_count", "?"), stats.get("primer_matches:","?"),stats.get("vector_matches:","?")]
+
+ #dataset = "[%s] %s" % (time.strftime("%m/%d/%y",time.localtime(os.path.getmtime(fname))),fname[:fname.rfind('.')])
+ dsname = "[%s] %s" % (time.strftime("%m/%d/%y",time.localtime(filedate)),fname[:fname.rfind('.')])
+ self.add_data(dsname, vals)
+
+ def read_stats_file(self,fname):
+ stats = {}
+ for line in open(fname):
+ w = line.rstrip().split()
+ val = ""
+ if len(w)>2: val = w[2]
+ stats[w[1]] = val
+ return stats
+
+ def add_data(self, dataset,vals):
+ self.list_ctrl.InsertStringItem(self.index, dataset)
+ for i in range(1, len(vals)+1):
+ self.list_ctrl.SetStringItem(self.index, i, vals[i-1])
+ self.index += 1
+
+ def OnQuit(self, e):
+ print "Quitting TPP. Good bye."
+ self.vars.action = "quit"
+ self.Close()
+ return 0
+
+ def map_reads(self,event):
+ # add bwa path, prefix
+ # bwapath = self.picker0.GetPath()
+ bwapath = self.picker0.GetValue()
+ #fq1,fq2,ref,base,maxreads = self.picker1.GetPath(),self.picker2.GetPath(),self.picker3.GetPath(),self.base.GetValue(),self.maxreads.GetValue()
+ fq1, fq2, ref, base, prefix, maxreads = self.picker1.GetValue(), self.picker2.GetValue(), self.picker3.GetValue(), self.base.GetValue(), self.prefix.GetValue(), self.maxreads.GetValue()
+
+ mm1 = self.mismatches.GetValue()
+ try: mm1 = int(mm1)
+ except Exception: mm1 = 1
+
+ self.vars.transposon = self.transposon.GetStringSelection()
+
+ self.vars.bwa = bwapath
+ self.vars.fq1 = fq1
+ self.vars.fq2 = fq2
+ self.vars.ref = ref
+ self.vars.base = base
+ self.vars.mm1 = mm1
+ if maxreads == '': self.vars.maxreads = -1
+ else: self.vars.maxreads = int(maxreads)
+
+ self.vars.action = "start"
+ self.Close()
+ return 0
+
diff --git a/src/pytpp/tpp_tools.py b/src/pytpp/tpp_tools.py
new file mode 100644
index 0000000..1a44434
--- /dev/null
+++ b/src/pytpp/tpp_tools.py
@@ -0,0 +1,794 @@
+#!/usr/bin/env python
+
+# Copyright 2015.
+# Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
+#
+#
+# This file is part of TRANSIT.
+#
+# TRANSIT 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.
+#
+#
+# TRANSIT 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 TRANSIT. If not, see <http://www.gnu.org/licenses/>.
+
+
+import glob,os,sys,time,math
+import sys, re, shutil
+import platform
+import gzip
+import subprocess
+
+
+
+def analyze_dataset(wigfile):
+ data = []
+ TAs,ins,reads = 0,0,0
+ for line in open(wigfile):
+ if line[0]=='#': continue
+ if line[:3]=='var': continue # variableStep
+ w = line.rstrip().split()
+ TAs += 1
+ cnt = int(w[1])
+ if cnt>1: ins += 1
+ reads += cnt
+ data.append((cnt,w[0]))
+
+ output = open(wigfile+".stats","w")
+ output.write("total TAs: %d, insertions: %d (%0.1f%%), total reads: %d\n" % (TAs,ins,100*(ins/float(TAs)),reads))
+ output.write("mean read count per non-zero site: %0.1f\n" % (reads/float(ins)))
+ output.write("5 highest counts:\n")
+ data.sort(reverse=True)
+ for cnt,coord in data[:5]:
+ output.write("coord=%s, count=%s\n" % (coord,cnt))
+ output.close()
+
+#############################################################################
+
+def fastq2reads(infile,outfile,maxreads):
+ output = open(outfile,"w")
+ cnt,tot = 0,0
+ for line in open(infile):
+ if cnt==0 and line[0]=='@':
+ tot += 1
+ if tot%1000000==0: message("%s reads processed" % tot)
+ if maxreads > -1:
+ if tot > maxreads:
+ break
+ if cnt==0:
+ h = line[1:] # strip off '@'
+ #h = h.replace(' ','_')
+ output.write(">%s" % h)
+ if cnt==1: output.write(line)
+ cnt = (cnt+1)%4
+ output.close()
+
+# the headers for each pair must be identical up to /1 and /2 at the ends
+# if the variable character with the read number occurs in the middle, move it to the end
+
+def fix_paired_headers_for_bwa(reads1,reads2):
+ a = open(reads1)
+ b = open(reads2)
+ temp1 = "temp."+reads1
+ temp2 = "temp."+reads2
+ c = open(temp1,"w")
+ d = open(temp2,"w")
+ tot = 0
+ try:
+ while True:
+ e = a.readline().rstrip()
+ f = b.readline().rstrip()
+ if len(e)<=2 or len(f)<=2: break
+ if e[0]=='>':
+ tot += 1
+ if tot%1000000==0: message("%s reads processed" % tot)
+ # find first position where there is a difference
+ i,n = 0,len(e)
+ if len(f)!=n: raise Exception('Error: unexpected format of headers in .fastq files')
+ while i<n and e[i]==f[i]: i += 1
+ if i==n: raise Exception('Error: unexpected format of headers in .fastq files')
+ e = e.replace(' ','_')
+ f = f.replace(' ','_')
+ e = e.replace('/','_') # this was neceesary for bwa 0.7.10 but not 0.7.12
+ f = f.replace('/','_')
+ #if i<n-1:
+ if e[i+1:]!=f[i+1:]: raise Exception('Error: unexpected format of headers in .fastq files')
+ e,f = e[:-1],f[:-1] # strip EOL
+ # needed for bwa 0.7.12? which apparently trims off last 2 chars to make ids identical
+ # "/[1|2]" are automatically trimmed, but not /3
+ e = e[:i]+e[i+1:]
+ f = f[:i]+f[i+1:]
+ c.write(e+"\n")
+ d.write(f+"\n")
+ except Exception as ex:
+ a.close(); b.close(); c.close(); d.close()
+ error(ex.args[0])
+ a.close(); b.close(); c.close(); d.close()
+
+ if(os.path.exists(reads1)): os.remove(reads1)
+ if(os.path.exists(reads2)): os.remove(reads2)
+ os.rename(temp1, reads1)
+ os.rename(temp2, reads2)
+
+ '''
+ if platform.platform == 'win32':
+ os.system("move %s %s" % (temp1,reads1))
+ os.system("move %s %s" % (temp2,reads2))
+ else:
+ os.system("mv %s %s"%(temp1, reads1))
+ os.system("mv %s %s" % (temp2, reads2))
+ '''
+
+def mmfind(G,n,H,m,max): # lengths; assume n>m
+ for i in range(0,n-m):
+ cnt = 0
+ for k in range(m):
+ if G[i+k]!=H[k]: cnt += 1
+ if cnt>max: break
+ if cnt<=max: return i
+ return -1
+
+def extract_staggered(infile,outfile,vars):
+ Tn = vars.prefix
+ message("prefix sequence: %s" % vars.prefix)
+ lenTn = len(Tn)
+ ADAPTER2 = "TACCACGACCA"
+ lenADAP = len(ADAPTER2)
+
+ #P,Q = 5,10 # 1-based inclusive positions to look for start of Tn prefix
+ P,Q = 0,15
+
+ vars.tot_tgtta = 0
+ vars.truncated_reads = 0
+ output = open(outfile,"w")
+ tot = 0
+ for line in open(infile):
+ line = line.rstrip()
+ if line[0]=='>': header = line; continue
+ tot += 1
+ if tot%1000000==0: message("%s reads processed" % tot)
+ readlen = len(line)
+ a = mmfind(line,readlen,Tn,lenTn,vars.mm1) # allow some mismatches
+ b = mmfind(line,readlen,ADAPTER2,lenADAP, 1) # look for end of short frags
+ if a>=P and a<=Q:
+ gstart,gend = a+lenTn,readlen
+ if b!=-1: gend = b; vars.truncated_reads += 1
+ if gend-gstart<20: continue # too short
+ output.write(header+"\n")
+ output.write(line[gstart:gend]+"\n")
+ vars.tot_tgtta += 1
+ output.close()
+ if vars.tot_tgtta == 0:
+ raise ValueError("Error: Input files did not contain any reads matching prefix sequence with %d mismatches" % vars.mm1)
+
+
+
+
+def message(s):
+ print "[tn_preprocess]",s
+ sys.stdout.flush()
+
+def get_id(line):
+ a,b = line.find(":")+1,line.rfind("#")
+ if b==-1: b = line.rfind("_")
+ return line[a:b]
+
+# select the reads from infile that have headers occuring in goodreads
+
+def select_reads(goodreads,infile,outfile):
+ hash = {}
+ for line in open(goodreads):
+ if line[0]=='>':
+ #id = line[line.find(":")+1:line.rfind("#")]
+ id = get_id(line)
+ hash[id] = 1
+
+ output = open(outfile,"w")
+ for line in open(infile):
+ if line[0]=='>':
+ header = line
+ id = get_id(line)
+ else:
+ if hash.has_key(id):
+ output.write(header)
+ output.write(line)
+ output.close()
+
+def replace_ids(infile1,infile2,outfile):
+ f = open(infile1)
+ g = open(infile2)
+ h = open(outfile,"w")
+
+ while True:
+ a = f.readline()
+ b = g.readline()
+ if len(a)<2: break
+ if a[0]=='>': header = a
+ else:
+ h.write(header)
+ h.write(b)
+ f.close()
+ g.close()
+ h.close()
+
+# indexes i and j are 1-based and inclusive (could be -1)
+
+def select_cycles(infile,i,j,outfile):
+ output = open(outfile,"w")
+ for line in open(infile):
+ if line[0]=='>': header = line
+ else:
+ output.write(header)
+ output.write(line[i-1:j]+"\n")
+ output.close()
+
+def read_genome(filename):
+ s = ""
+ for line in open(filename):
+ if line[0]=='>': continue # skip fasta header
+ else: s += line[:-1]
+ return s
+
+# convert to bistring (8 bits; bit 0 is low-order bit)
+#
+# Bit Description
+# 0 0x1 template having multiple segments in sequencing
+# 1 0x2 each segment properly aligned according to the aligner
+# 2 0x4 segment unmapped
+# 3 0x8 next segment in the template unmapped
+# 4 0x10 SEQ being reverse complemented
+# 5 0x20 SEQ of the next segment in the template being reversed
+# 6 0x40 the first segment in the template
+# 7 0x80 the last segment in the template
+#
+# code[6]=1 means read1
+# code[4]=1 means reverse strand
+
+def samcode(num): return bin(int(num))[2:].zfill(8)[::-1]
+
+def template_counts(ref,sam,bcfile,vars):
+ genome = read_genome(ref)
+ barcodes = {}
+
+
+ fil1 = open(bcfile)
+ fil2 = open(sam)
+
+ idx=1
+ for line in fil1:
+ if idx==1: break
+ idx+=1
+
+ idx=1
+ for line in fil2:
+ if idx==2: break
+ idx+=1
+
+ '''
+ for line in open(bcfile):
+ line = line.rstrip()
+ if line[0]=='>': id = line[1:]
+ else: barcodes[id] = line
+ '''
+ hits = {}
+ vars.tot_tgtta,vars.mapped = 0,0
+ vars.r1 = vars.r2 = 0
+
+ #for line in open(sam):
+ bcline=''
+ for line in fil2:
+ try:
+ bcline = fil1.next().rstrip()
+ if bcline[0] !='>': bc = bcline
+ except StopIteration:
+ pass
+ if line[0]=='@': continue
+ else:
+ w = line.split('\t')
+ code = samcode(w[1])
+ if 'S' in w[5]: continue #elimate softclipped reads
+ if code[6]=="1": # previously checked for for reads1's via w[1]<128
+ vars.tot_tgtta += 1
+ if code[2]=="0": vars.r1 += 1
+ if code[7]=="1" and code[2]=="0": vars.r2 += 1
+ # include "improperly mapped reads, which might just be short frags
+ #if w[1]=="99" or w[1]=="83" or w[1]=="97" or w[1]=="81":
+ if code[6]=="1" and code[2]=="0" and code[3]=="0": # both reads mapped (proper or not)
+ vars.mapped += 1
+ readlen = len(w[9])
+ pos,size = int(w[3]),int(w[8]) # note: size could be negative
+ strand,delta = 'F',-2
+ if code[4]=="1": strand,delta = 'R',readlen
+
+ pos += delta
+ #bc = barcodes[w[0]]
+ if pos not in hits: hits[pos] = []
+ hits[pos].append((strand,size,bc))
+
+ sites = []
+ for i in range(len(genome)-1):
+ if genome[i:i+2]=="TA":
+ pos = i+1
+ h = hits.get(pos,[])
+ f = filter(lambda x: x[0]=='F',h)
+ r = filter(lambda x: x[0]=='R',h)
+ h.sort()
+ unique = {}
+ for (strand,size,bc) in h:
+ #print strand,bc,size
+ s = "%s-%s-%s" % (strand,bc,size)
+ unique[s] = 1
+ u = unique.keys()
+ uf = filter(lambda x: x[0]=='F',u)
+ ur = filter(lambda x: x[0]=='R',u)
+ data = [pos,len(f),len(uf),len(r),len(ur),len(f)+len(r),len(uf)+len(ur)]
+ sites.append(data)
+
+ return sites # (coord, Fwd_Rd_Ct, Fwd_Templ_Ct, Rev_Rd_Ct, Rev_Templ_Ct, Tot_Rd_Ct, Tot_Templ_Ct)
+
+# pretend that all reads count as unique templates
+
+def read_counts(ref,sam,vars):
+ genome = read_genome(ref)
+ hits = {}
+ vars.tot_tgtta,vars.mapped = 0,0
+ vars.r1 = vars.r2 = 0
+ for line in open(sam):
+ if line[0]=='@': continue
+ else:
+ w = line.split('\t')
+ code,icode = samcode(w[1]),int(w[1])
+ vars.tot_tgtta += 1
+ if icode==0 or icode==16:
+ vars.r1 += 1
+ vars.mapped += 1
+ readlen = len(w[9])
+ pos = int(w[3])
+ strand,delta = 'F',-2
+ if code[4]=="1": strand,delta = 'R',readlen
+ pos += delta
+ if pos not in hits: hits[pos] = []
+ hits[pos].append(strand)
+
+ sites = []
+ for i in range(len(genome)-1):
+ if genome[i:i+2]=="TA" or vars.transposon=='Tn5':
+ pos = i+1
+ h = hits.get(pos,[])
+ lenf,lenr = h.count('F'),h.count('R')
+ data = [pos,lenf,lenf,lenr,lenr,lenf+lenr,lenf+lenr]
+ sites.append(data)
+
+ return sites # (coord, Fwd_Rd_Ct, Fwd_Templ_Ct, Rev_Rd_Ct, Rev_Templ_Ct, Tot_Rd_Ct, Tot_Templ_Ct)
+
+def driver(vars):
+ vars.reads1 = vars.base+".reads1"
+ vars.reads2 = vars.base+".reads2"
+ vars.tgtta1 = vars.base+".tgtta1"
+ vars.tgtta2 = vars.base+".tgtta2"
+ vars.barcodes1 = vars.base+".barcodes1"
+ vars.barcodes2 = vars.base+".barcodes2"
+ vars.genomic2 = vars.base+".genomic2"
+ vars.sai1 = vars.base+".sai1"
+ vars.sai2 = vars.base+".sai2"
+ vars.sam = vars.base+".sam"
+ vars.tc = vars.base+".counts"
+ vars.wig = vars.base+".wig"
+ vars.stats = vars.base+".tn_stats"
+
+ if vars.prefix==None:
+ if vars.transposon=="Tn5": vars.prefix = "TAAGAGACAG"
+ elif vars.transposon=="Himar1": vars.prefix = "ACTTATCAGCCAACCTGTTA"
+
+ try:
+ extract_reads(vars)
+
+ run_bwa(vars)
+
+ generate_output(vars)
+
+ except ValueError as err:
+ message("")
+ message("%s" % " ".join(err.args))
+ message("Exiting.")
+ sys.exit()
+
+ except IOError as err:
+ message("")
+ message("%s" % " ".join(err.args))
+ message("Make sure you have read/write access in the directories containing the necessary files.")
+ message("Note: If TPP cannot find index files for the FASTA sequence (i.e. *.fna.bwt, *.fna.pac, *.fna.ann, *.fna.sa), it will attempt to create them.")
+ message("Exiting.")
+ sys.exit()
+
+
+ message("Done.")
+
+def uncompress(filename):
+ outfil = open(filename[0:-3], "w+")
+ for line in gzip.open(filename):
+ outfil.write(line)
+ return filename[0:-3]
+
+def extract_reads(vars):
+ message("extracting reads...")
+
+ flag = ['','']
+ for idx, name in enumerate([vars.fq1, vars.fq2]):
+ if idx==1 and vars.single_end==True: continue
+ fil = open(name)
+ for line in fil:
+ if line[0] == '>':
+ flag[idx] = 'FASTA'
+ break
+ flag[idx] = 'FASTQ'
+ break
+ fil.close()
+
+ if vars.fq1.endswith('.gz'):
+ vars.fq1 = uncompress(vars.fq1)
+
+ if vars.fq2.endswith('.gz'):
+ vars.fq2 = uncompress(vars.fq2)
+
+ if(flag[0] == 'FASTQ'):
+ message("fastq2reads: %s -> %s" % (vars.fq1,vars.reads1))
+ fastq2reads(vars.fq1,vars.reads1,vars.maxreads)
+ else:
+ shutil.copyfile(vars.fq1, vars.reads1)
+
+ if vars.single_end==True:
+ message("assuming single-ended reads")
+ message("creating %s" % vars.tgtta1)
+ extract_staggered(vars.reads1,vars.tgtta1,vars)
+
+ return
+
+ if(flag[1] == 'FASTQ'):
+ message("fastq2reads: %s -> %s" % (vars.fq2,vars.reads2))
+ fastq2reads(vars.fq2,vars.reads2,vars.maxreads)
+ else:
+ shutil.copyfile(vars.fq2, vars.reads2)
+
+ message("fixing headers of paired reads for bwa...")
+ fix_paired_headers_for_bwa(vars.reads1,vars.reads2)
+
+ message("extracting barcodes and genomic parts of reads...")
+
+ message("creating %s" % vars.tgtta1)
+ extract_staggered(vars.reads1,vars.tgtta1,vars)
+
+ message("creating %s" % vars.tgtta2)
+ select_reads(vars.tgtta1,vars.reads2,vars.tgtta2)
+ #message("creating %s" % vars.barcodes2)
+ #select_cycles(vars.tgtta2,22,30,vars.barcodes2)
+ #message("creating %s" % vars.genomic2)
+ #select_cycles(vars.tgtta2,43,-1,vars.genomic2)
+
+ # instead of using select_cycles, do these both in one shot by looking for constant seqs
+ message("creating %s" % vars.barcodes2)
+ message("creating %s" % vars.genomic2)
+ extract_barcodes(vars.tgtta2,vars.barcodes2,vars.genomic2, vars.mm1)
+
+ message("creating %s" % vars.barcodes1)
+ replace_ids(vars.tgtta1,vars.barcodes2,vars.barcodes1)
+
+# pattern for read 2...
+# TAGTGGATGATGGCCGGTGGATTTGTG GTAATTACCA TGGTCGTGGTAT CCCAGCGCGACTTCTTCGGCGCACACACC TAACAGGTTGGCTGATAAGTCCCCG?AGAT AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGT
+# -----const1---------------- --barcode- ---const2--- ------genomic---------------- ------const3--------------------------------------------------------------
+# const suffix might appear if fragment is shorter than read length; if so, truncate
+# if genomic part is too short, just output at least 20bp of const so as not to mess up BWA
+# could the start of these be shifted slightly?
+
+def extract_barcodes(fn_tgtta2,fn_barcodes2,fn_genomic2,mm1):
+ const1 = "GATGGCCGGTGGATTTGTG"
+ const2 = "TGGTCGTGGTAT"
+ const3 = "TAACAGGTTGGCTGATAAG"
+ nconst1,nconst2,nconst3 = len(const1),len(const2),len(const3)
+ fl_barcodes2 = open(fn_barcodes2,"w")
+ fl_genomic2 = open(fn_genomic2,"w")
+ tot,DEBUG = 0,0
+ for line in open(fn_tgtta2):
+ line = line.rstrip()
+ if line[0]=='>': header = line
+ else:
+ tot += 1
+ if tot%1000000==0: message("%s reads processed" % tot)
+ #a = line.find(const1)
+ #b = line.find(const2)
+ #c = line.find(const3)
+ a = mmfind(line,len(line),const1,nconst1, mm1)
+ b = mmfind(line,len(line),const2,nconst2, mm1)
+ c = mmfind(line,len(line),const3,nconst3, mm1)
+ bstart,bend = a+nconst1,b
+ gstart,gend = b+nconst2,len(line)
+ if c!=-1 and c-gstart>20: gend = c
+ if a==-1 or bend<bstart+5 or bend>bstart+15:
+ # you can't just reject these, beacuse they are paired with R1
+ # but setting the genomic part to the first 20 cycles should prevent it from mapping
+ bstart,bend = 0,10
+ gstart,gend = 0,20
+ barcode,genomic = "XXXXXXXXXX","XXXXXXXXXX"
+ else: barcode,genomic = line[bstart:bend],line[gstart:gend]
+ if DEBUG==1:
+ fl_barcodes2.write(header+"\n")
+ fl_barcodes2.write(line+"\n")
+ #fl_barcodes2.write((" "*bstart)+line[bstart:bend]+"\n")
+ fl_barcodes2.write((" "*bstart)+barcode+"\n")
+ fl_genomic2.write(header+"\n")
+ fl_genomic2.write(line+"\n")
+ #fl_genomic2.write((" "*gstart)+line[gstart:gend]+"\n")
+ fl_genomic2.write((" "*gstart)+genomic+"\n")
+ else:
+ fl_barcodes2.write(header+"\n")
+ #fl_barcodes2.write(line[bstart:bend]+"\n")
+ fl_barcodes2.write(barcode+"\n")
+ fl_genomic2.write(header+"\n")
+ #fl_genomic2.write(line[gstart:gend]+"\n")
+ fl_genomic2.write(genomic+"\n")
+ fl_barcodes2.close()
+ fl_genomic2.close()
+ if DEBUG==1: sys.exit(0)
+
+
+
+def bwa_subprocess(command, outfile):
+ commandstr = " ".join(command)
+ if outfile.name != "<stdout>":
+ commandstr += " > %s" % outfile.name
+ message(commandstr)
+ process = subprocess.Popen(command, stdout=outfile, stderr=subprocess.PIPE)
+ for line in iter(process.stderr.readline, ''):
+ if "Permission denied" in line:
+ raise IOError("Error: BWA encountered a permissions error: \n\n%s" % line)
+ sys.stderr.write("%s\n" % line.strip())
+
+
+
+
+def run_bwa(vars):
+ message("mapping reads using BWA...(this takes a couple of minutes)")
+
+ if not os.path.exists(vars.ref+".amb"):
+ cmd = [vars.bwa, "index", vars.ref]
+ bwa_subprocess(cmd, sys.stdout)
+
+
+ cmd = [vars.bwa, "aln", vars.ref, vars.tgtta1]
+ outfile = open(vars.sai1, "w")
+ bwa_subprocess(cmd, outfile)
+
+
+ if vars.single_end==True:
+ cmd = [vars.bwa, "samse", vars.ref, vars.sai1, vars.tgtta1]
+ outfile = open(vars.sam, "w")
+ bwa_subprocess(cmd, outfile)
+
+ else:
+ cmd = [vars.bwa, "aln", vars.ref, vars.genomic2]
+ outfile = open(vars.sai2, "w")
+ bwa_subprocess(cmd, outfile)
+
+ cmd = [vars.bwa, "sampe", vars.ref, vars.sai1, vars.sai2, vars.tgtta1, vars.genomic2]
+ outfile = open(vars.sam, "w")
+ bwa_subprocess(cmd, outfile)
+
+
+
+def stats(vals):
+ sum,ss = 0,0
+ for x in vals: sum += x; ss += x*x
+ N = float(len(vals))
+ mean = sum/N
+ var = ss/N-mean*mean
+ stdev = math.sqrt(var)
+ return mean,stdev
+
+def corr(X,Y):
+ muX,sdX = stats(X)
+ muY,sdY = stats(Y)
+
+ if sdX == 0 or sdY == 0:
+ raise ValueError("Warning: Standard deviations of counts is zero.")
+
+ cX = [x-muX for x in X]
+ cY = [y-muY for y in Y]
+ s = sum([x*y for (x,y) in zip(cX,cY)])
+ return s/(float(len(X))*sdX*sdY)
+
+def get_read_length(filename):
+ fil = open(filename)
+ i = 0
+ for line in fil:
+ if i == 1:
+ #print "reads1 line: " + line
+ return len(line.strip())
+ i+=1
+
+def get_genomic_portion(filename):
+ fil = open(filename)
+ i = 0
+ tot_len = 0.0
+ n = 1
+ for line in fil:
+ if i%2 == 1:
+ tot_len += len(line.strip())
+ n += 1
+ i+=1
+ return tot_len/n
+
+
+def generate_output(vars):
+ message("tabulating template counts and statistics...")
+ if vars.single_end==True: counts = read_counts(vars.ref,vars.sam,vars) # return read counts copied as template counts
+ else: counts = template_counts(vars.ref,vars.sam,vars.barcodes1,vars)
+ tcfile = open(vars.tc,"w")
+ tcfile.write('\t'.join("coord Fwd_Rd_Ct Fwd_Templ_Ct Rev_Rd_Ct Rev_Templ_Ct Tot_Rd_Ct Tot_Templ_Ct".split())+"\n")
+ for data in counts: tcfile.write('\t'.join([str(x) for x in data])+"\n")
+ tcfile.close()
+
+ if vars.mapped == 0:
+ raise ValueError('Error: BWA was unable to map any reads to the genome.')
+
+ message("writing %s" % vars.wig)
+ output = open(vars.wig,"w")
+
+ read1 = os.path.basename(vars.fq1)
+ read2 = os.path.basename(vars.fq2)
+ fi = re.split(r'\.', os.path.basename(vars.ref))[0]
+ output.write("# Generated by tpp from " + read1 + " and " + read2 + "\n")
+ output.write("variableStep chrom="+ fi + "\n")
+ for data in counts: output.write("%s %s\n" % (data[0],data[-1]))
+ output.close()
+
+ primer = "CTAGAGGGCCCAATTCGCCCTATAGTGAGT"
+ vector = "CTAGACCGTCCAGTCTGGCAGGCCGGAAAC"
+ adapter = "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
+ Himar1 = "ACTTATCAGCCAACCTGTTA"
+
+ tot_reads,nprimer,nvector,nadapter,misprimed = 0,0,0,0,0
+ for line in open(vars.reads1):
+ if line[0]=='>': tot_reads += 1; continue
+ if primer in line: nprimer += 1
+ if vector in line: nvector += 1
+ if adapter in line: nadapter += 1
+ if Himar1[:-5] in line and Himar1 not in line: misprimed += 1
+
+
+
+
+ rcounts = [x[5] for x in counts]
+ tcounts = [x[6] for x in counts]
+ rc,tc = sum(rcounts),sum(tcounts)
+ ratio = rc/float(tc)
+ ta_sites = len(rcounts)
+ tas_hit = len(filter(lambda x: x>0,rcounts))
+ density = tas_hit/float(ta_sites)
+ counts.sort(key=lambda x: x[-1])
+ max_tc = counts[-1][6]
+ max_coord = counts[-1][0]
+ NZmean = tc/float(tas_hit)
+
+ try:
+ FR_corr = corr([x[1] for x in counts],[x[3] for x in counts])
+ except ValueError:
+ FR_corr = float("nan")
+ try:
+ BC_corr = corr([x for x in rcounts if x!=0],[x for x in tcounts if x!=0])
+ except ValueError:
+ BC_corr = float("nan")
+
+
+ read_length = get_read_length(vars.base + ".reads1")
+ mean_r1_genomic = get_genomic_portion(vars.base + ".tgtta1")
+ if vars.single_end==False: mean_r2_genomic = get_genomic_portion(vars.base + ".genomic2")
+
+ output = open(vars.stats,"w")
+ version = "1.0"
+ #output.write("# title: Tn-Seq Pre-Processor, version %s\n" % vars.version)
+ output.write("# title: Tn-Seq Pre-Processor\n")
+ output.write("# date: %s\n" % time.strftime("%m/%d/%Y %H:%M:%S"))
+ output.write("# command: python ")
+ output.write(' '.join(sys.argv)+"\n")
+ output.write('# transposon type: %s\n' % vars.transposon)
+ output.write('# read1: %s\n' % vars.fq1)
+ output.write('# read2: %s\n' % vars.fq2)
+ output.write('# ref_genome: %s\n' % vars.ref)
+ output.write("# total_reads %s (or read pairs)\n" % tot_reads)
+ #output.write("# truncated_reads %s (fragments shorter than the read length; ADAP2 appears in read1)\n" % vars.truncated_reads)
+ output.write("# TGTTA_reads %s (reads with valid Tn prefix, and insert size>20bp)\n" % vars.tot_tgtta)
+ output.write("# reads1_mapped %s\n" % vars.r1)
+ output.write("# reads2_mapped %s\n" % vars.r2)
+ output.write("# mapped_reads %s (both R1 and R2 map into genome)\n" % vars.mapped)
+ output.write("# read_count %s (TA sites only, for Himar1)\n" % rc)
+ output.write("# template_count %s\n" % tc)
+ output.write("# template_ratio %0.2f (reads per template)\n" % ratio)
+ output.write("# TA_sites %s\n" % ta_sites)
+ output.write("# TAs_hit %s\n" % tas_hit)
+ output.write("# density %0.3f\n" % density)
+ output.write("# max_count %s (among templates)\n" % max_tc)
+ output.write("# max_site %s (coordinate)\n" % max_coord)
+ output.write("# NZ_mean %0.1f (among templates)\n" % NZmean)
+ output.write("# FR_corr %0.3f (Fwd templates vs. Rev templates)\n" % FR_corr)
+ output.write("# BC_corr %0.3f (reads vs. templates, summed over both strands)\n" % BC_corr)
+ output.write("# primer_matches: %s reads (%0.1f%%) contain %s (Himar1)\n" % (nprimer,nprimer*100/float(tot_reads),primer))
+ output.write("# vector_matches: %s reads (%0.1f%%) contain %s (phiMycoMarT7)\n" % (nvector,nvector*100/float(tot_reads),vector))
+ output.write("# adapter_matches: %s reads (%0.1f%%) contain %s (Illumina/TruSeq index)\n" % (nadapter,nadapter*100/float(tot_reads),adapter))
+ output.write("# misprimed_reads: %s reads (%0.1f%%) contain Himar1 prefix but don't end in TGTTA\n" % (misprimed,misprimed*100/float(tot_reads)))
+ output.write("# read_length: %s bp\n" % read_length)
+ output.write("# mean_R1_genomic_length: %0.1f bp\n" % mean_r1_genomic)
+ if vars.single_end==False: output.write("# mean_R2_genomic_length: %0.1f bp\n" % mean_r2_genomic)
+
+ #output.write("# most_abundant_prefix: %s reads start with %s\n" % (temp[0][1],temp[0][0]))
+ # since these are reads (within Tn prefix stripped off), I expect ~1/4 to match Tn prefix
+ vals = [vars.fq1,vars.fq2,tot_reads,vars.tot_tgtta,vars.r1,vars.r2,vars.mapped,rc,tc,ratio,ta_sites,tas_hit,max_tc,density,max_coord,NZmean,FR_corr,BC_corr,nprimer,nvector,nadapter,misprimed]
+ output.write('\t'.join([str(x) for x in vals])+"\n")
+ output.close()
+
+ message("writing %s" % vars.stats)
+ #os.system("grep '#' %s" % vars.stats)
+ infile = open(vars.stats)
+ for line in infile:
+ if '#' in line:
+ print line.rstrip()
+ infile.close()
+
+#############################################################################
+
+def error(s):
+ print "error:",s
+ sys.exit(0)
+
+def verify_inputs(vars):
+ if not os.path.exists(vars.fq1): error("file not found: "+vars.fq1)
+ vars.single_end = False
+ if vars.fq2=="": vars.single_end = True
+ elif not os.path.exists(vars.fq2): error("file not found: "+vars.fq2)
+ if not os.path.exists(vars.ref): error("file not found: "+vars.ref)
+ if vars.base == '': error("prefix cannot be empty")
+ if vars.fq1 == vars.fq2: error('fastq files cannot be identical')
+
+def initialize_globals(vars):
+ vars.fq1,vars.fq2,vars.ref,vars.bwa,vars.base,vars.maxreads = "","","","","temp",-1
+ vars.mm1 = 1 # mismatches allowed in Tn prefix
+ vars.transposon = 'Himar1'
+ vars.prefix = None
+ read_config(vars)
+
+def read_config(vars):
+ if not os.path.exists("tpp.cfg"): return
+ for line in open("tpp.cfg"):
+ w = line.split()
+ if len(w)>=2 and w[0]=='reads1': vars.fq1 = w[1]
+ if len(w)>=2 and w[0]=='reads2': vars.fq2 = w[1]
+ if len(w)>=2 and w[0]=='ref': vars.ref = w[1]
+ if len(w)>=2 and w[0]=='bwa': vars.bwa = w[1]
+ if len(w)>=2 and w[0]=='prefix': vars.base = w[1]
+ if len(w)>=2 and w[0]=='mismatches1': vars.mm1 = int(w[1])
+ if len(w)>=2 and w[0]=='transposon': vars.transposon = w[1]
+
+def save_config(vars):
+ f = open("tpp.cfg","w")
+ f.write("reads1 %s\n" % vars.fq1)
+ f.write("reads2 %s\n" % vars.fq2)
+ f.write("ref %s\n" % vars.ref)
+ f.write("bwa %s\n" % vars.bwa)
+ f.write("prefix %s\n" % vars.base)
+ f.write("mismatches1 %s\n" % vars.mm1)
+ f.write("transposon %s\n" % vars.transposon)
+ f.close()
+
+def show_help():
+ print 'usage: python PATH/src/tpp.pyc -bwa <PATH_TO_EXECUTABLE> -ref <REF_SEQ> -reads1 <FASTQ_OR_FASTA_FILE> [-reads2 <FASTQ_OR_FASTA_FILE>] -output <BASE_FILENAME> [-maxreads <N>] [-mismatches <N>] [-tn5|-himar1] [-primer <seq>]'
+
+class Globals:
+ pass
+
+
diff --git a/src/pytransit/__init__.py b/src/pytransit/__init__.py
new file mode 100644
index 0000000..1f1d4de
--- /dev/null
+++ b/src/pytransit/__init__.py
@@ -0,0 +1,6 @@
+__all__ = []
+
+#__all__ = ["transit_tools", "tnseq_tools", "norm_tools", "stat_tools"]
+
+__version__ = "v2.0.2"
+prefix = "[TRANSIT]"
diff --git a/src/pytransit/__main__.py b/src/pytransit/__main__.py
new file mode 100644
index 0000000..24d2001
--- /dev/null
+++ b/src/pytransit/__main__.py
@@ -0,0 +1,71 @@
+
+import sys
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+
+import pytransit
+import pytransit.transit_tools as transit_tools
+import pytransit.analysis
+
+method_wrap_width = 250
+methods = pytransit.analysis.methods
+
+
+wildcard = "Python source (*.py)|*.py|" \
+ "All files (*.*)|*.*"
+transit_prefix = "[TRANSIT]"
+
+
+def main(args=None):
+ #If no arguments, show GUI:
+ if len(sys.argv) == 1 and hasWx:
+ import pytransit.transit_gui as transit_gui
+
+
+ transit_tools.transit_message("Running in GUI Mode")
+
+ app = wx.App(False)
+
+ #create an object of CalcFrame
+ frame = transit_gui.TnSeekFrame(None)
+ #show the frame
+ frame.Show(True)
+ #start the applications
+ app.MainLoop()
+ elif len(sys.argv) == 1 and not hasWx:
+ print "Please install wxPython to run in GUI Mode."
+ print "To run in Console Mode please follow these instructions:"
+ print ""
+ print "Usage: python %s <method>" % sys.argv[0]
+ print "List of known methods:"
+ for m in methods:
+ print "\t - %s" % m
+ else:
+ method_name = sys.argv[1]
+ if method_name not in methods:
+ print "Error: The '%s' method is unknown." % method_name
+ print "Please use one of the known methods (or see documentation to add a new one):"
+ for m in methods:
+ print "\t - %s" % m
+ print "Usage: python %s <method>" % sys.argv[0]
+ else:
+ methodobj = methods[method_name].method.fromconsole()
+ methodobj.Run()
+
+
+
+if __name__ == "__main__":
+ main()
+
+
diff --git a/src/pytransit/analysis/__init__.py b/src/pytransit/analysis/__init__.py
new file mode 100644
index 0000000..3f3ed35
--- /dev/null
+++ b/src/pytransit/analysis/__init__.py
@@ -0,0 +1,31 @@
+#__all__ = []
+
+from os.path import dirname, basename, isfile
+import glob
+modules = glob.glob(dirname(__file__)+"/*.py")
+__all__ = [ basename(f)[:-3] for f in modules if isfile(f)]
+
+import base
+
+import gumbel
+#import example
+import tn5gaps
+import binomial
+import griffin
+import resampling
+import hmm
+import rankproduct
+
+
+methods = {}
+#methods["example"] = example.ExampleAnalysis()
+methods["gumbel"] = gumbel.GumbelAnalysis()
+methods["binomial"] = binomial.BinomialAnalysis()
+methods["griffin"] = griffin.GriffinAnalysis()
+methods["hmm"] = hmm.HMMAnalysis()
+methods["resampling"] = resampling.ResamplingAnalysis()
+methods["tn5gaps"] = tn5gaps.Tn5GapsAnalysis()
+methods["rankproduct"] = rankproduct.RankProductAnalysis()
+
+
+
diff --git a/src/pytransit/analysis/base.py b/src/pytransit/analysis/base.py
new file mode 100644
index 0000000..8ca34a8
--- /dev/null
+++ b/src/pytransit/analysis/base.py
@@ -0,0 +1,341 @@
+#__all__ = []
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import traceback
+import datetime
+import pytransit.transit_tools as transit_tools
+
+file_prefix = "[FileDisplay]"
+
+class TransitFile:
+ #TODO write docstring
+
+ def __init__(self, identifier="#Unknown", colnames=[]):
+ #TODO write docstring
+ self.identifier = identifier
+ self.colnames = colnames
+
+ def getData(self, path, colnames):
+ #TODO write docstring
+ row = 0
+ data = []
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.split("\t")
+ tmp[-1] = tmp[-1].strip()
+ rowdict = dict([(colnames[i], tmp[i]) for i in range(len(colnames))])
+ data.append((row, rowdict))
+ row+=1
+ return data
+
+ def getHeader(self, path):
+ #TODO write docstring
+ return "Generic Transit File Type."
+
+
+ def getMenus(self):
+ menus = [("Display in Track View", self.displayInTrackView)]
+ return menus
+
+ def displayInTrackView(self, displayFrame, event):
+
+ #print "Self:", self
+ #print "Frame:", displayFrame
+ #print "Event:", event
+ #print "Frame parent:", displayFrame.parent
+ try:
+ gene = displayFrame.grid.GetCellValue(displayFrame.row, 0)
+ displayFrame.parent.allViewFunc(displayFrame, gene)
+ except Exception as e:
+ print file_prefix, "Error occurred: %s" % e
+
+class AnalysisGUI:
+
+ def __init__(self):
+ self.wxobj = None
+ self.panel = None
+
+ def Hide(self):
+ self.panel.Hide()
+
+ def Show(self):
+ self.panel.Show()
+
+ def Enable(self):
+ self.panel.Enable()
+
+
+
+ def definePanel(self, wxobj):
+ #TODO: write docstring
+
+ self.wxobj = wxobj
+ wPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ Section = wx.BoxSizer( wx.VERTICAL )
+
+ Label = wx.StaticText(wPanel, id=wx.ID_ANY, label=str("Options"), pos=wx.DefaultPosition, size=wx.DefaultSize, style=0 )
+ Label.Wrap( -1 )
+ Section.Add( Label, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ Sizer1 = wx.BoxSizer( wx.HORIZONTAL )
+ Section.Add( Sizer1, 1, wx.EXPAND, 5 )
+
+ Button = wx.Button( wPanel, wx.ID_ANY, u"Run", wx.DefaultPosition, wx.DefaultSize, 0 )
+ Section.Add( Button, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ wPanel.SetSizer( Section )
+ wPanel.Layout()
+ Section.Fit( wPanel )
+
+ #Connect events
+ Button.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+ self.panel = wPanel
+
+
+
+class AnalysisMethod:
+ '''
+ Basic class for analysis methods. Inherited by SingleMethod and ComparisonMethod.
+ '''
+
+ def __init__(self, short_name, long_name, description, output, annotation_path, wxobj=None):
+ self.short_name = short_name
+ self.long_name = long_name
+ self.description = description
+ self.output = output
+ self.annotation_path = annotation_path
+
+ self.newWx = newWx
+ self.wxobj = wxobj
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ #TODO: write docstring
+ raise NotImplementedError
+
+ @classmethod
+ def fromargs(self, rawargs):
+ #TODO: write docstring
+ raise NotImplementedError
+
+ @classmethod
+ def fromconsole(self):
+ #TODO: write docstring
+ try:
+ return self.fromargs(sys.argv[2:])
+ except IndexError as e:
+ traceback.print_exc()
+ print self.usage_string()
+ except TypeError as e:
+ print "Error: %s" % str(e)
+ traceback.print_exc()
+ print self.usage_string()
+ except ValueError as e:
+ print "Error: %s" % str(e)
+ traceback.print_exc()
+ print self.usage_string()
+ except Exception as e:
+ print "Error: %s" % str(e)
+ traceback.print_exc()
+ print self.usage_string()
+ sys.exit()
+
+ @classmethod
+ def usage_string(self):
+ #TODO: write docstring
+ raise NotImplementedError
+
+ def Run(self):
+ #TODO write docstring
+ raise NotImplementedError
+
+
+ def print_members(self):
+ #TODO: write docstring
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ for m in members:
+ print "%s = %s" % (m, getattr(self, m))
+
+
+ def add_file(self, path=None, filetype=None):
+
+ #TODO: write docstring
+ if not path:
+ path = self.output.name
+ if not filetype:
+ filetype = self.short_name
+
+ data = {"path":path, "type":filetype, "date": datetime.datetime.today().strftime("%B %d, %Y %I:%M%p")}
+
+ if self.wxobj:
+ if newWx:
+ wx.CallAfter(pub.sendMessage, "file", data=data)
+ else:
+ wx.CallAfter(pub.sendMessage, "file", data)
+
+ def finish(self):
+ #TODO: write docstring
+ if self.wxobj:
+ if newWx:
+ wx.CallAfter(pub.sendMessage,"finish", msg=self.short_name.lower())
+ else:
+ wx.CallAfter(pub.sendMessage,"finish", self.short_name.lower())
+
+ def progress_update(self, text, count):
+ #TODO: write docstring
+ if self.wxobj:
+ if newWx:
+ wx.CallAfter(pub.sendMessage, "progress", msg=(self.short_name, count))
+ else:
+ wx.CallAfter(pub.sendMessage, "progress", (self.short_name, count))
+ wx.Yield()
+
+ def progress_range(self, count):
+ #TODO: write docstring
+ if self.wxobj:
+ if newWx:
+ wx.CallAfter(pub.sendMessage, "progressrange", msg=count)
+ else:
+ wx.CallAfter(pub.sendMessage, "progressrange", count)
+ wx.Yield()
+
+
+
+ def status_message(self, text):
+ #TODO: write docstring
+ if self.wxobj:
+ if newWx:
+ wx.CallAfter(pub.sendMessage, "status", msg=(self.short_name, text))
+ else:
+ wx.CallAfter(pub.sendMessage, "status", (self.short_name, text))
+ wx.Yield()
+
+ def console_message(self, text):
+ #TODO: write docstring
+ sys.stdout.write("[%s] %s\n" % (self.short_name, text))
+
+ def console_message_inplace(self, text):
+ #TODO: write docstring
+ sys.stdout.write("[%s] %s \r" % (self.short_name, text) )
+ sys.stdout.flush()
+
+ def transit_message(self, text):
+ #TODO: write docstring
+ self.console_message(text)
+ self.status_message(text)
+
+ def transit_message_inplace(self, text):
+ #TODO: write docstring
+ self.console_message_inplace(text)
+ self.status_message(text)
+
+
+ def transit_error(self,text):
+ self.transit_message(text)
+ if self.wxobj:
+ transit_tools.ShowError(text)
+
+ def transit_warning(self,text):
+ self.transit_message(text)
+ if self.wxobj:
+ transit_tools.ShowWarning(text)
+
+
+class SingleConditionMethod(AnalysisMethod):
+ '''
+ Class to be inherited by analysis methods that determine essentiality in a single condition (e.g. Gumbel, Binomial, HMM).
+ '''
+
+ def __init__(self, short_name, long_name, description, ctrldata, annotation_path, output, replicates="Sum", normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
+ AnalysisMethod.__init__(self, short_name, long_name, description, output, annotation_path, wxobj)
+ self.ctrldata = ctrldata
+ self.replicates = replicates
+ self.normalization = normalization
+ self.LOESS = LOESS
+ self.ignoreCodon = ignoreCodon
+ self.NTerminus = NTerminus
+ self.CTerminus = CTerminus
+
+
+
+class DualConditionMethod(AnalysisMethod):
+ '''
+ Class to be inherited by analysis methods that determine changes in essentiality between two conditions (e.g. Resampling, DEHMM).
+ '''
+
+ def __init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output, normalization, replicates="Sum", LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None):
+ AnalysisMethod.__init__(self, short_name, long_name, description, output, annotation_path, wxobj)
+ self.ctrldata = ctrldata
+ self.expdata = expdata
+ self.normalization = normalization
+ self.replicates = replicates
+ self.LOESS = LOESS
+ self.ignoreCodon = ignoreCodon
+ self.NTerminus = NTerminus
+ self.CTerminus = CTerminus
+
+
+
+class TransitAnalysis:
+ def __init__(self, sn, ln, desc, tn, method_class=AnalysisMethod, gui_class=AnalysisGUI, filetypes=[TransitFile]):
+ self.short_name = sn
+ self.long_name = ln
+ self.description = desc
+ self.transposons = tn
+ self.method = method_class
+ self.gui = gui_class()
+ self.filetypes = filetypes
+
+
+ def __str__(self):
+ return """Analysis Method:
+ Short Name: %s
+ Long Name: %s
+ Description: %s
+ Method: %s
+ GUI: %s""" % (self.short_name, self.long_name, self.description, self.method, self.gui)
+
+
+ def fullname(self):
+ return "[%s] - %s" % (self.short_name, self.long_name)
+
+ def getInstructionsText(self):
+ return ""
+
+ def getDescriptionText(self):
+ return self.description
+
+ def getTransposonsText(self):
+ if len(self.transposons) == 0:
+ return "Tn attribute missing!"
+ elif len(self.transposons) == 1:
+ return "Intended for %s only" % self.transposons[0]
+ elif len(self.transposons) == 2:
+ return "Intended for %s && %s" % tuple(self.transposons)
+ else:
+ return "Intended for " + ", ".join(self.transposons[:-1]) + ", and " + self.transposons[-1]
+
+
+
+if __name__ == "__main__":
+ pass
+
+
+
diff --git a/src/pytransit/analysis/binomial.py b/src/pytransit/analysis/binomial.py
new file mode 100644
index 0000000..308c3a6
--- /dev/null
+++ b/src/pytransit/analysis/binomial.py
@@ -0,0 +1,541 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+#method_name = "binomial"
+
+############# GUI ELEMENTS ##################
+
+short_name = "binomial"
+long_name = "Hierarchical binomial model of essentiality with individual frequencies."
+description = """Hierarchical bayesian model of essentiality based on the binomial distribution. Estimates individual probabilities for insertion, leading to more conservative predictions.
+
+Reference: DeJesus and Ioerger (2014; IEEE TCBB)
+"""
+transposons = ["himar1"]
+columns = ["Orf","Name","Description","Mean Insertion","Sites per Replicate","Total Insertions","Total Sites","thetabar", "zbar", "Call"]
+
+############# Analysis Method ##############
+
+class BinomialAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, BinomialMethod, BinomialGUI, [BinomialFile])
+
+
+################## FILE ###################
+
+class BinomialFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Binomial", columns)
+
+ def getHeader(self, path):
+ ess=0; unc=0; non=0; short=0
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if tmp[-1] == "Essential": ess+=1
+ if tmp[-1] == "Uncertain": unc+=1
+ if tmp[-1] == "Non-Essential": non+=1
+
+ text = """Results:
+ Essentials: %s
+ Uncertain: %s
+ Non-Essential: %s
+ """ % (ess, unc, non)
+ return text
+
+
+################## GUI ###################
+
+class BinomialGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ binomialPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ binomialSection = wx.BoxSizer( wx.VERTICAL )
+
+ binomialLabel = wx.StaticText( binomialPanel, wx.ID_ANY, u"Binomial Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialLabel.Wrap( -1 )
+ binomialSection.Add( binomialLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ binomialSizer1 = wx.BoxSizer( wx.HORIZONTAL )
+ binomialSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+ binomialLabelSizer = wx.BoxSizer( wx.VERTICAL )
+ binomialControlSizer = wx.BoxSizer( wx.VERTICAL )
+
+ #Samples
+ binomialSampleLabel = wx.StaticText( binomialPanel, wx.ID_ANY, u"Samples", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialSampleLabel.Wrap(-1)
+ binomialLabelSizer.Add(binomialSampleLabel, 1, wx.ALL, 5)
+ self.wxobj.binomialSampleText = wx.TextCtrl( binomialPanel, wx.ID_ANY, u"10000", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialControlSizer.Add(self.wxobj.binomialSampleText, 0, wx.ALL|wx.EXPAND, 5)
+
+ #Burnin
+ binomialBurnLabel = wx.StaticText( binomialPanel, wx.ID_ANY, u"Burn-in", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialBurnLabel.Wrap(-1)
+ binomialLabelSizer.Add(binomialBurnLabel, 1, wx.ALL, 5)
+ self.wxobj.binomialBurnText = wx.TextCtrl( binomialPanel, wx.ID_ANY, u"500", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialControlSizer.Add(self.wxobj.binomialBurnText, 0, wx.ALL|wx.EXPAND, 5)
+
+
+ binomialSizer2.Add(binomialLabelSizer, 1, wx.EXPAND, 5)
+ binomialSizer2.Add(binomialControlSizer, 1, wx.EXPAND, 5)
+ binomialSizer1.Add(binomialSizer2, 1, wx.EXPAND, 5 )
+
+
+ binomialSection.Add( binomialSizer1, 1, wx.EXPAND, 5 )
+
+ binomialButton = wx.Button( binomialPanel, wx.ID_ANY, u"Run binomial", wx.DefaultPosition, wx.DefaultSize, 0 )
+ binomialSection.Add( binomialButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ binomialPanel.SetSizer( binomialSection )
+ binomialPanel.Layout()
+ binomialSection.Fit( binomialPanel )
+
+ #Connect events
+ binomialButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = binomialPanel
+
+
+
+
+
+########## CLASS #######################
+
+class BinomialMethod(base.SingleConditionMethod):
+ """
+ binomial
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ samples=10000,
+ burnin=500,
+ replicates="Sum",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0,
+ pi0=0.5,
+ pi1=0.5,
+ M0=1.0,
+ M1=1.0,
+ a0=10.0,
+ a1=10.0,
+ b0=1.0,
+ b1=1.0,
+ alpha_w=0.5,
+ beta_w=0.5,
+ wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+ self.samples = samples
+ self.burnin = burnin
+
+ self.pi0 = pi0
+ self.pi1 = pi1
+ self.M0 = M0
+ self.M1 = M1
+ self.a0 = a0
+ self.a1 = a1
+ self.b0 = b0
+ self.b1 = b1
+ self.alpha_w = alpha_w
+ self.beta_w = beta_w
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata, transposons):
+ return None
+
+
+
+ #Read the parameters from the wxPython widgets
+ samples = int(wxobj.binomialSampleText.GetValue())
+ burnin = int(wxobj.binomialBurnText.GetValue())
+ ignoreCodon = True
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ replicates = "Sum"
+ normalization = None
+ LOESS = False
+
+
+
+ #Get output path
+ name = transit_tools.basename(ctrldata[0])
+ defaultFileName = "binomial_output.dat"
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ samples=samples,
+ burnin=burnin,
+ replicates=replicates,
+ normalization=normalization,
+ LOESS=LOESS,
+ ignoreCodon=ignoreCodon,
+ NTerminus=NTerminus,
+ CTerminus=CTerminus,
+ wxobj=wxobj)
+
+
+ @classmethod
+ def fromargs(self, rawargs):
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ samples = int(kwargs.get("s", 10000))
+ burnin = int(kwargs.get("b", 500))
+ replicates = "Sum"
+ normalization = None
+ LOESS = False
+ ignoreCodon = True
+ NTerminus = float(kwargs.get("iN", 0.0))
+ CTerminus = float(kwargs.get("iC", 0.0))
+
+ pi0 = float(kwargs.get("pi0", 0.5))
+ pi1 = float(kwargs.get("pi1", 0.5))
+ M0 = float(kwargs.get("M0", 1.0))
+ M1 = float(kwargs.get("M1", 1.0))
+ a0 = float(kwargs.get("a0", 10.0))
+ a1 = float(kwargs.get("a1", 10.0))
+ b0 = float(kwargs.get("b0", 1.0))
+ b1 = float(kwargs.get("b1", 1.0))
+ alpha_w = float(kwargs.get("aw", 0.5))
+ beta_w = float(kwargs.get("bw", 0.5))
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ samples=samples,
+ burnin=burnin,
+ replicates=replicates,
+ normalization=normalization,
+ LOESS=LOESS,
+ ignoreCodon=ignoreCodon,
+ NTerminus=NTerminus,
+ CTerminus=CTerminus,
+ pi0=pi0,
+ pi1=pi1,
+ M0=M0,
+ M1=M1,
+ a0=a0,
+ a1=a1,
+ b0=b0,
+ b1=b1,
+ alpha_w=alpha_w,
+ beta_w=beta_w)
+
+
+ def Run(self):
+
+ self.transit_message("Starting Binomial Method")
+ start_time = time.time()
+
+ self.progress_range(self.samples+self.burnin)
+
+ #Get orf data
+ self.transit_message("Getting Data")
+ G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+
+ #Parameters
+ self.transit_message("Setting Parameters")
+ w1 = 0.15
+ w0 = 1.0 - w1
+ mu_c = 0
+
+ Ngenes = len(G)
+ sample_size = self.samples+self.burnin
+ numReps = len(self.ctrldata)
+
+ theta = numpy.zeros((Ngenes, sample_size))
+ theta[:,0] = 0.10
+
+ rho0 = numpy.zeros(sample_size); rho0[0] = 0.5; Kp0 = numpy.zeros(sample_size); Kp0[0] = 10;
+ rho1 = numpy.zeros(sample_size); rho1[0] = 0.10; Kp1 = numpy.zeros(sample_size); Kp1[0] = 3;
+
+ Z = numpy.zeros((Ngenes, sample_size))
+ pz1 = numpy.zeros(sample_size);
+ n1 = 0
+
+ w1 = scipy.stats.beta.rvs(self.alpha_w, self.beta_w)
+ W1 = numpy.zeros(sample_size); W1[0] = w1
+
+
+
+ #
+ self.transit_message("Setting Initial Values")
+ K = numpy.array([sum([1 for x in gene.reads.flatten() if x> 0]) for gene in G])
+ N = numpy.array([len(gene.reads.flatten()) for gene in G])
+
+ for g,gene in enumerate(G):
+ if N[g] == 0: theta[g][0] = 0.5
+ elif K[g]/float(N[g]) == 0: theta[g][0] = 0.001
+ elif K[g]/float(N[g]) == 1: theta[g][0] = 0.001
+ else: theta[g][0] = K[g]/float(N[g])
+
+ #print g, ORF[g], K[g], N[g], theta[g][0]
+ Z[g][0] = scipy.stats.bernoulli.rvs(1-theta[g][0])
+
+
+ acc_p0 = 0; acc_k0 = 0;
+ acc_p1 = 0; acc_k1 = 0;
+
+
+ rho0c_std = 0.010
+ kp0c_std = 1.40
+ rho1c_std = 0.009
+ kp1c_std = 1.1
+
+
+ for i in range(1, sample_size):
+
+ i0 = Z[:,i-1] == 0; n0 = numpy.sum(i0);
+ i1 = Z[:,i-1] == 1; n1 = numpy.sum(i1);
+
+ theta[i0,i] = scipy.stats.beta.rvs(Kp0[i-1]*rho0[i-1] + K[i0], Kp0[i-1]*(1-rho0[i-1]) + N[i0] - K[i0])
+ theta[i1,i] = scipy.stats.beta.rvs(Kp1[i-1]*rho1[i-1] + K[i1], Kp1[i-1]*(1-rho1[i-1]) + N[i1] - K[i1])
+
+ rho0_c = rho0[i-1] + scipy.stats.norm.rvs(0, rho0c_std)
+ Kp0_c = Kp0[i-1] + scipy.stats.norm.rvs(0, kp0c_std)
+
+
+ if rho0_c <= 0: rho0[i] = rho0[i-1]
+ else:
+ fc = numpy.log(scipy.stats.beta.pdf(rho0_c, self.M0*self.pi0, self.M0*(1.0-self.pi0)))
+ f0 = numpy.log(scipy.stats.beta.pdf(rho0[i-1], self.M0*self.pi0, self.M0*(1.0-self.pi0)))
+ fc += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i0,i], Kp0[i-1]*rho0_c, Kp0[i-1]*(1-rho0_c))))
+ f0 += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i0,i], Kp0[i-1]*rho0[i-1], Kp0[i-1]*(1-rho0[i-1]))))
+
+ if numpy.log(scipy.stats.uniform.rvs()) < fc - f0:
+ rho0[i] = rho0_c
+ acc_p0+=1
+ else: rho0[i] = rho0[i-1]
+
+
+ if Kp0_c <= 0: Kp0[i] = Kp0[i-1]
+ else:
+ fc = numpy.log(scipy.stats.gamma.pdf(Kp0_c, self.a0, self.b0));
+ f0 = numpy.log(scipy.stats.gamma.pdf(Kp0[i-1], self.a0, self.b0));
+ fc += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i0,i], Kp0_c*rho0[i], Kp0_c*(1-rho0[i]))))
+ f0 += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i0,i], Kp0[i-1]*rho0[i], Kp0[i-1]*(1-rho0[i]))))
+
+ if numpy.log(scipy.stats.uniform.rvs()) < fc - f0:
+ Kp0[i] = Kp0_c
+ acc_k0+=1
+ else: Kp0[i] = Kp0[i-1]
+
+ rho1_c = rho1[i-1] + scipy.stats.norm.rvs(0, rho1c_std)
+ Kp1_c = Kp1[i-1] + scipy.stats.norm.rvs(0, kp1c_std)
+
+
+ if rho1_c <= 0:
+ rho1[i] = rho1[i-1]
+ else:
+ fc = numpy.log(scipy.stats.beta.pdf(rho1_c, self.M1*self.pi1, self.M1*(1-self.pi1)))
+ f1 = numpy.log(scipy.stats.beta.pdf(rho1[i-1], self.M1*self.pi1, self.M1*(1-self.pi1)))
+ fc += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i1,i], Kp1[i-1]*rho1_c, Kp1[i-1]*(1-rho1_c))))
+ f1 += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i1,i], Kp1[i-1]*rho1[i-1], Kp1[i-1]*(1-rho1[i-1]))))
+
+ if numpy.log(scipy.stats.uniform.rvs()) < fc - f1:
+ rho1[i] = rho1_c
+ acc_p1+=1
+ else: rho1[i] = rho1[i-1]
+
+ if Kp1_c <= 0: Kp1[i] = Kp1[i-1]
+ else:
+ fc = numpy.log(scipy.stats.gamma.pdf(Kp1_c, self.a1, self.b1));
+ f1 = numpy.log(scipy.stats.gamma.pdf(Kp1[i-1], self.a1, self.b1));
+ fc += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i1,i], Kp1_c*rho1[i], Kp1_c*(1-rho1[i]))))
+ f1 += numpy.sum(numpy.log(scipy.stats.beta.pdf(theta[i1,i], Kp1[i-1]*rho1[i], Kp1[i-1]*(1-rho1[i]))))
+
+ if numpy.log(scipy.stats.uniform.rvs()) < fc - f1:
+ Kp1[i] = Kp1_c
+ acc_k1+=1
+ else: Kp1[i] = Kp1[i-1]
+
+
+ g0 = scipy.stats.beta.pdf(theta[:,i], Kp0[i]*rho0[i], Kp0[i]*(1-rho0[i])) * (1-w1)
+ g1 = scipy.stats.beta.pdf(theta[:,i], Kp1[i]*rho1[i], Kp1[i]*(1-rho1[i])) * (w1)
+ p1 = g1/(g0+g1)
+ p1 = numpy.nan_to_num(p1)
+
+
+ try:
+ Z[:,i] = scipy.stats.bernoulli.rvs(p1)
+ except:
+ inan = numpy.isnan(p1)
+ print >> sys.stderr, "K=\t", K[inan]
+ print >> sys.stderr, "N=\t", N[inan]
+ print >> sys.stderr, "theta=", theta[inan,i]
+ sys.exit()
+ pz1[i] = p1[0]
+
+
+ i1 = Z[:,i] == 1; n1 = numpy.sum(i1);
+ #w1 = 0.15
+ w1 = scipy.stats.beta.rvs(self.alpha_w + n1, self.beta_w + Ngenes - n1)
+ W1[i] = w1
+
+
+ #Update progress
+ text = "Running Gumbel Method... %2.0f%%" % (100.0*(i+1)/(sample_size))
+ self.progress_update(text, i)
+ self.transit_message_inplace(text)
+
+
+ z_bar = numpy.apply_along_axis(numpy.mean, 1, Z[:, self.burnin:])
+ theta_bar = numpy.apply_along_axis(numpy.mean, 1, theta[:, self.burnin:])
+ #(ess_threshold, noness_threshold) = stat_tools.fdr_post_prob(z_bar)
+ (ess_threshold, noness_threshold) = stat_tools.bayesian_ess_thresholds(z_bar)
+
+ self.output.write("#Binomial\n")
+ #output.write("#Command: %s\n" % " ".join(["%s=%s" %(key,val) for (key,val) in kwargs.items()]))
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s, samples=%s, burnin=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output.name, self.samples, self.burnin))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Thresholds: (%1.5f, %1.5f)\n" % (ess_threshold,noness_threshold))
+ self.output.write("#rho0 Acceptance Rate:\t%f%%\n" % ((100.0*acc_p0)/sample_size))
+ self.output.write("#Kp0 Acceptance Rate:\t%f%%\n" % ((100.0*acc_k0)/sample_size))
+ self.output.write("#rho1 Acceptance Rate:\t%f%%\n" % ((100.0*acc_p1)/sample_size))
+ self.output.write("#Kp1 Acceptance Rate:\t%f%%\n" % ((100.0*acc_k1)/sample_size))
+ self.output.write("#Hyperparameters rho: \t%1.2f\t%3.1f\t%1.2f\t%3.1f\n" % (self.pi0, self.M0, self.pi1, self.M1))
+ self.output.write("#Hyperparameters Kp: \t%3.1f\t%3.1f\t%3.1f\t%3.1f\n" % (self.a0, self.b0, self.a1, self.b1))
+ self.output.write("#Hyperparameters W: \t%1.3f\t%1.3f\n" % (self.alpha_w, self.beta_w))
+
+
+ self.output.write("#%s\n" % "\t".join(columns))
+
+ data = []
+ for g,gene in enumerate(G):
+ c = "Uncertain"
+ if z_bar[g] > ess_threshold:
+ c = "Essential"
+ if z_bar[g] < noness_threshold:
+ c = "Non-Essential"
+ data.append("%s\t%s\t%s\t%1.1f\t%d\t%d\t%d\t%f\t%f\t%s" % (gene.orf, gene.name, gene.desc, K[g]/float(numReps), N[g]/numReps, K[g], N[g], theta_bar[g], z_bar[g], c))
+
+ data.sort()
+ for row in data:
+ self.output.write("%s\n" % row)
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Binomial")
+ self.finish()
+ self.transit_message("Finished Binomial Method")
+
+
+
+
+ @classmethod
+ def usage_string(self):
+ return """python %s binomial <comma-separated .wig files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]
+
+ Optional Arguments:
+ -s <int> := Number of samples to take. Default: -s 10000
+ -b <int> := Number of burn-in samples to take. Default: -b 500
+ -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
+ -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
+
+ Hyper-parameters:
+ -pi0 <float> := Hyper-parameters for rho, non-essential genes. Default: -pi0 0.5
+ -pi1 <float> := Hyper-parameters for rho, essential genes. Default: -pi1 0.5
+ -M0 <float> := Hyper-parameters for rho, non-essential genes. Default: -M0 1.0
+ -M1 <float> := Hyper-parameters for rho, essential genes. Default: -M1 1.0
+
+ -a0 <float> := Hyper-parameters for kappa, non-essential genes. Default: -a0 10
+ -a1 <float> := Hyper-parameters for kappa, essential genes. Default: -a1 10
+ -b0 <float> := Hyper-parameters for kappa, non-essential genes. Default: -b0 1.0
+ -b1 <float> := Hyper-parameters for kappa, essential genes. Default: -b1 1.0
+
+ -aw <float> := Hyper-parameters for prior prob of gene being essential. Default: -aw 0.5
+ -bw <float> := Hyper-parameters for prior prob of gene being essential. Default: -bw 0.5
+
+
+ """ % (sys.argv[0])
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+ G = BinomialMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/example.py b/src/pytransit/analysis/example.py
new file mode 100644
index 0000000..b12eec7
--- /dev/null
+++ b/src/pytransit/analysis/example.py
@@ -0,0 +1,240 @@
+import sys
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+
+############# Description ##################
+
+short_name = "example"
+long_name = "Example method that calculates mean read-counts per gene."
+description = "A method made to serve as an example to implementing other methods."
+transposons = ["himar1", "tn5"]
+columns = ["Orf","Name","Desc","k","n","mean","nzmean"]
+
+############# Analysis Method ##############
+
+class ExampleAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, ExampleMethod, ExampleGUI, [ExampleFile])
+
+
+################## FILE ###################
+
+class ExampleFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Example", columns)
+
+ def getHeader(self, path):
+ text = """This is file contains mean counts for each gene. Nzmean is mean accross non-zero sites."""
+ return text
+
+
+################# GUI ##################
+
+class ExampleGUI(base.AnalysisGUI):
+
+ def __init__(self):
+ base.AnalysisGUI.__init__(self)
+
+########## METHOD #######################
+
+class ExampleMethod(base.SingleConditionMethod):
+ """
+ Example
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ replicates="Sum",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata, transposons):
+ return None
+
+ #Read the parameters from the wxPython widgets
+ ignoreCodon = True
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ replicates="Sum"
+ normalization = None
+ LOESS = False
+
+ #Get output path
+ defaultFileName = "example_output.dat"
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+ print "ARGS:", args
+ print "KWARGS:", kwargs
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ replicates = "Sum"
+ normalization = None
+ LOESS = False
+ ignoreCodon = True
+ NTerminus = 0.0
+ CTerminus = 0.0
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+ def Run(self):
+
+ self.transit_message("Starting Example Method")
+ start_time = time.time()
+
+ #Get orf data
+ self.transit_message("Getting Data")
+ G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+ data = []
+ N = len(G)
+ count = 0
+ self.progress_range(N)
+ for gene in G:
+ count+=1
+ mean = numpy.mean(gene.reads)
+ if gene.k == 0:
+ nzmean = 0.0
+ else:
+ nzmean = numpy.sum(gene.reads)/float(gene.k)
+
+ data.append("%s\t%s\t%s\t%s\t%s\t%1.2f\t%1.2f\n" % (gene.orf, gene.name, gene.desc, gene.k, gene.n, mean, nzmean))
+
+
+ self.progress_update("gumbel", count)
+ self.transit_message_inplace("Running Example Method... %1.1f%%" % (100.0*count/N))
+
+
+ self.output.write("#Example\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Annotation path: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#%s\n" % "\t".join(columns))
+
+ data.sort()
+ for line in data:
+ self.output.write(line)
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Example")
+ self.finish()
+ self.transit_message("Finished Example Method")
+
+ @classmethod
+ def usage_string(self):
+ return """python %s example <comma-separated .wig files> <annotation .prot_table> <output file>""" % (sys.argv[0])
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv[1:])
+
+ print "ARGS:", args
+ print "KWARGS:", kwargs
+
+ G = Example.fromargs(sys.argv[1:])
+
+ print G
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/griffin.py b/src/pytransit/analysis/griffin.py
new file mode 100644
index 0000000..1afe43c
--- /dev/null
+++ b/src/pytransit/analysis/griffin.py
@@ -0,0 +1,289 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+#method_name = "griffin"
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "griffin"
+long_name = "Basic frequentist analysis of essentiality using gaps."
+description = "Analysis of gaps used in Griffin et al. 2011"
+transposons = ["himar1"]
+columns = ["Orf","Name","Desc","k","n","r","s","t","Expected Run","p-value", "p-adjusted"]
+
+
+
+############# Analysis Method ##############
+
+class GriffinAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, GriffinMethod, GriffinGUI, [GriffinFile])
+
+
+################## FILE ###################
+
+class GriffinFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Griffin", columns)
+
+ def getHeader(self, path):
+ ess=0; unc=0; non=0; short=0
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if float(tmp[-1]) < 0.05:
+ ess+=1
+ else:
+ non+=1
+
+ text = """Results:
+ Essentials: %s
+ Non-Essential: %s
+ """ % (ess,non)
+ return text
+
+
+################## GUI ###################
+
+class GriffinGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ griffinPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ griffinSection = wx.BoxSizer( wx.VERTICAL )
+
+ griffinLabel = wx.StaticText( griffinPanel, wx.ID_ANY, u"griffin Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ griffinLabel.Wrap( -1 )
+ griffinSection.Add( griffinLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ griffinSizer1 = wx.BoxSizer( wx.HORIZONTAL )
+
+ griffinSection.Add( griffinSizer1, 1, wx.EXPAND, 5 )
+
+ griffinButton = wx.Button( griffinPanel, wx.ID_ANY, u"Run griffin", wx.DefaultPosition, wx.DefaultSize, 0 )
+ griffinSection.Add( griffinButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ griffinPanel.SetSizer( griffinSection )
+ griffinPanel.Layout()
+ griffinSection.Fit( griffinPanel )
+
+ #Connect events
+ griffinButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = griffinPanel
+
+
+
+
+
+########## CLASS #######################
+
+class GriffinMethod(base.SingleConditionMethod):
+ """
+ griffin
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ replicates="Sum",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata, transposons):
+ return None
+
+
+ #Read the parameters from the wxPython widgets
+ ignoreCodon = True
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ replicates = "Sum"
+ normalization = None
+ LOESS = False
+
+ #Get output path
+ name = transit_tools.basename(ctrldata[0])
+ defaultFileName = "griffin_output.dat"
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ replicates = "Sum"
+ normalization = None
+ LOESS = False
+ ignoreCodon = True
+ NTerminus = 0.0
+ CTerminus = 0.0
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+ def Run(self):
+
+ self.transit_message("Starting Griffin Method")
+ start_time = time.time()
+
+
+ #Get orf data
+ self.transit_message("Getting Data")
+ G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+ N = len(G)
+ self.progress_range(N)
+ count = 0
+ pins = G.global_theta()
+ pnon = 1.0 - pins
+ results = []
+ for gene in G:
+ if gene.n == 0:
+ results.append([gene, 0.0, 1.000])
+ else:
+ B = 1.0/math.log(1.0/pnon)
+ u = math.log(gene.n*pins, 1.0/pnon)
+ exprun = tnseq_tools.ExpectedRuns(gene.n, pnon)
+ pval = 1.0 - tnseq_tools.GumbelCDF(gene.r, u, B)
+ results.append([gene, exprun, pval])
+
+ text = "Running Griffin Method... %2.0f%%" % (100.0*(count+1)/(N))
+ self.progress_update(text, count)
+ self.transit_message_inplace(text)
+ count+=1
+
+
+ pval = [row[-1] for row in results]
+ padj = stat_tools.BH_fdr_correction(pval)
+ for i in range(len(results)):
+ results[i].append(padj[i])
+ results.sort()
+
+ self.output.write("#Griffin\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output.name))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Annotation path: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#%s\n" % "\t".join(columns))
+
+ for (gene, exprun, pval, padj) in results:
+ self.output.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%1.1f\t%1.5f\t%1.5f\n" % (gene.orf, gene.name, gene.desc, gene.k, gene.n, gene.r, gene.s, gene.t, exprun, pval, padj))
+
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Griffin")
+ self.finish()
+ self.transit_message("Finished Griffin Method")
+
+ @classmethod
+ def usage_string(self):
+ return """python %s griffin <comma-separated .wig files> <annotation .prot_table> <output file>""" % (sys.argv[0])
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+
+ G = GriffinMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/gumbel.py b/src/pytransit/analysis/gumbel.py
new file mode 100644
index 0000000..15e5632
--- /dev/null
+++ b/src/pytransit/analysis/gumbel.py
@@ -0,0 +1,511 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "gumbel"
+long_name = "Bayesian analysis of essentiality based on long gaps."
+description = """Bayesian methods of analyzing longest runs of non-insertions in a row. Estimates the parameters using the MCMC sampling, and estimates posterior probabilities of essentiality.
+
+Reference: DeJesus et al. (2013; Bioinformatics)"""
+transposons = ["himar1"]
+columns = ["Orf","Name","Desc","k","n","r","s","zbar", "Call"]
+
+
+############# Analysis Method ##############
+
+class GumbelAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, GumbelMethod, GumbelGUI, [GumbelFile])
+
+
+################## FILE ###################
+
+class GumbelFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Gumbel", columns)
+
+ def getHeader(self, path):
+ ess=0; unc=0; non=0; short=0
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if tmp[-1] == "E": ess+=1
+ if tmp[-1] == "U": unc+=1
+ if tmp[-1] == "NE": non+=1
+ if tmp[-1] == "S": short+=1
+
+ text = """Results:
+ Essentials: %s
+ Uncertain: %s
+ Non-Essential: %s
+ Short: %s
+ """ % (ess, unc, non, short)
+ return text
+
+
+
+
+################# GUI ##################
+
+class GumbelGUI(base.AnalysisGUI):
+
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ gumbelPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+ #wxobj.gumbelPanel.SetMinSize( wx.Size( 50,1 ) )
+ #wxobj.gumbelPanel.SetMaxSize( wx.Size( 250,-1 ) )
+
+ gumbelSection = wx.BoxSizer( wx.VERTICAL )
+
+ gumbelLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Gumbel Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelLabel.Wrap( -1 )
+ gumbelSection.Add( gumbelLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ mainSizer1 = wx.BoxSizer( wx.HORIZONTAL )
+
+ mainSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+
+ labelSizer = wx.BoxSizer( wx.VERTICAL )
+
+ gumbelSampleLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Samples", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelSampleLabel.Wrap( -1 )
+ labelSizer.Add( gumbelSampleLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ gumbelBurninLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Burn-In", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelBurninLabel.Wrap( -1 )
+ labelSizer.Add( gumbelBurninLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ gumbelTrimLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Trim", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelTrimLabel.Wrap( -1 )
+ labelSizer.Add( gumbelTrimLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ gumbelReadLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Minimum Read", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelReadLabel.Wrap( -1 )
+ labelSizer.Add( gumbelReadLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ gumbelRepLabel = wx.StaticText( gumbelPanel, wx.ID_ANY, u"Replicates", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelRepLabel.Wrap( -1 )
+ labelSizer.Add( gumbelRepLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ mainSizer2.Add( labelSizer, 1, wx.EXPAND, 5 )
+
+ widgetSizer = wx.BoxSizer( wx.VERTICAL )
+
+ self.wxobj.gumbelSampleText = wx.TextCtrl( gumbelPanel, wx.ID_ANY, u"10000", wx.DefaultPosition, wx.DefaultSize, 0 )
+ widgetSizer.Add( self.wxobj.gumbelSampleText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ self.wxobj.gumbelBurninText = wx.TextCtrl( gumbelPanel, wx.ID_ANY, u"500", wx.DefaultPosition, wx.DefaultSize, 0 )
+ widgetSizer.Add( self.wxobj.gumbelBurninText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ self.wxobj.gumbelTrimText = wx.TextCtrl( gumbelPanel, wx.ID_ANY, u"1", wx.DefaultPosition, wx.DefaultSize, 0 )
+ widgetSizer.Add( self.wxobj.gumbelTrimText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ gumbelReadChoiceChoices = [ u"1", u"2", u"3", u"4", u"5" ]
+ self.wxobj.gumbelReadChoice = wx.Choice( gumbelPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, gumbelReadChoiceChoices, 0 )
+ self.wxobj.gumbelReadChoice.SetSelection( 0 )
+ widgetSizer.Add( self.wxobj.gumbelReadChoice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ gumbelRepChoiceChoices = [ u"Sum", u"Mean" ]
+ self.wxobj.gumbelRepChoice = wx.Choice( gumbelPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, gumbelRepChoiceChoices, 0 )
+ self.wxobj.gumbelRepChoice.SetSelection( 0 )
+ widgetSizer.Add( self.wxobj.gumbelRepChoice, 0, wx.ALL|wx.EXPAND, 5 )
+
+ mainSizer2.Add( widgetSizer, 1, wx.EXPAND, 5 )
+
+ mainSizer1.Add( mainSizer2, 1, wx.EXPAND, 5 )
+
+ gumbelSection.Add( mainSizer1, 1, wx.EXPAND, 5 )
+
+ gumbelButton = wx.Button( gumbelPanel, wx.ID_ANY, u"Run Gumbel", wx.DefaultPosition, wx.DefaultSize, 0 )
+ gumbelSection.Add( gumbelButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ gumbelPanel.SetSizer( gumbelSection )
+ gumbelPanel.Layout()
+ gumbelSection.Fit( gumbelPanel )
+
+
+ #Connect events
+ gumbelButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = gumbelPanel
+
+
+
+
+
+
+########## METHOD #######################
+
+ALPHA = 1
+BETA = 1
+class GumbelMethod(base.SingleConditionMethod):
+ """
+ Gumbel
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ samples=10000,
+ burnin=500,
+ trim=1,
+ minread=1,
+ replicates="Sum",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+ self.samples = samples
+ self.burnin = burnin
+ self.trim = trim
+ self.minread = minread
+
+
+ self.cache_nn = {}
+
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata, transposons):
+ return None
+
+
+ #Read the parameters from the wxPython widgets
+ minread = int(wxobj.gumbelReadChoice.GetString(wxobj.gumbelReadChoice.GetCurrentSelection()))
+ samples = int(wxobj.gumbelSampleText.GetValue())
+ burnin = int(wxobj.gumbelBurninText.GetValue())
+ trim = int(wxobj.gumbelTrimText.GetValue())
+ replicates = wxobj.gumbelRepChoice.GetString(wxobj.gumbelRepChoice.GetCurrentSelection())
+ ignoreCodon = True
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ normalization = None
+ LOESS = False
+
+ #Get output path
+ name = transit_tools.basename(ctrldata[0])
+ defaultFileName = "gumbel_%s_s%d_b%d_t%d.dat" % (".".join(name.split(".")[:-1]), samples, burnin, trim)
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ samples,
+ burnin,
+ trim,
+ minread,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self,rawargs):
+
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ samples = int(kwargs.get("s", 10000))
+ burnin = int(kwargs.get("b", 500))
+ trim = int(kwargs.get("t", 1))
+ minread = int(kwargs.get("m", 1))
+ replicates = kwargs.get("r", "Sum")
+ normalization = None
+ LOESS = False
+ ignoreCodon = True
+ NTerminus = float(kwargs.get("iN", 0.0))
+ CTerminus = float(kwargs.get("iC", 0.0))
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ samples,
+ burnin,
+ trim,
+ minread,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+ def Run(self):
+
+ self.status_message("Starting Gumbel Method")
+
+ #Set Default parameter values
+ w1 = 0.15
+ w0 = 1.0 - w1
+ ALPHA = 1
+ BETA = 1
+ ALPHA_w = 600
+ BETA_w = 3400
+ mu_c = 0
+ acctot = 0.0
+ phi_start = 0.3
+ sigma_c = 0.01
+
+ start_time = time.time()
+
+ self.progress_range(self.samples+self.burnin)
+
+ #Get orf data
+ self.transit_message("Reading Annotation")
+ self.transit_message("Getting Data")
+
+
+
+ G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, minread=self.minread, reps=self.replicates, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+ ii_good = numpy.array([self.good_orf(g) for g in G]) # Gets index of the genes that can be analyzed
+
+ K = G.local_insertions()[ii_good]
+ N = G.local_sites()[ii_good]
+ R = G.local_runs()[ii_good]
+ S = G.local_gap_span()[ii_good]
+ T = G.local_gene_span()[ii_good]
+
+ self.transit_message("Doing Regression")
+ mu_s, temp, sigma_s = stat_tools.regress(R, S) # Linear regression to estimate mu_s, sigma_s for span data
+ mu_r, temp, sigma_r = stat_tools.regress(S, R) # Linear regression to estimate mu_r, sigma_r for run data
+
+ N_GENES = len(G)
+ N_GOOD = sum(ii_good)
+
+ self.transit_message("Setting Initial Class")
+ Z_sample = numpy.zeros((N_GOOD, self.samples))
+ Z = [self.classify(g.n, g.r, 0.5) for g in G if self.good_orf(g)]
+ Z_sample[:,0] = Z
+ N_ESS = numpy.sum(Z_sample[:,0] == 1)
+
+ phi_sample = numpy.zeros(self.samples) #[]
+ phi_sample[0] = phi_start
+ phi_old = phi_start
+ phi_new = 0.00
+
+ SIG = numpy.array([self.sigmoid(g.s, g.t) * scipy.stats.norm.pdf(g.r, mu_r*g.s, sigma_r) for g in G if self.good_orf(g)])
+
+
+ i = 1; count = 0;
+ while i < self.samples:
+
+ # PHI
+ acc = 1.0
+ phi_new = phi_old + random.gauss(mu_c, sigma_c)
+ i0 = Z_sample[:,i-1] == 0
+ if phi_new > 1 or phi_new <= 0 or (self.F_non(phi_new, N[i0], R[i0]) - self.F_non(phi_old, N[i0], R[i0])) < math.log(random.uniform(0,1)):
+ phi_new = phi_old
+ acc = 0.0
+ flag = 0
+
+ # Z
+ Z = self.sample_Z(phi_new, w1, N, R, S, T, mu_s, sigma_s, SIG)
+
+ # w1
+ N_ESS = sum(Z == 1)
+ w1 = scipy.stats.beta.rvs(N_ESS + ALPHA_w, N_GOOD - N_ESS + BETA_w)
+
+ count +=1
+ acctot+=acc
+
+ if (count > self.burnin) and (count % self.trim == 0):
+ phi_sample[i] = phi_new
+ Z_sample[:,i] = Z
+ i+=1
+
+ phi_old = phi_new
+ #Update progress
+ text = "Running Gumbel Method... %2.0f%%" % (100.0*(count+1)/(self.samples+self.burnin))
+ self.progress_update(text, count)
+ self.transit_message_inplace(text)
+
+
+ ZBAR = numpy.apply_along_axis(numpy.mean, 1, Z_sample)
+ (ess_t, non_t) = stat_tools.bayesian_ess_thresholds(ZBAR)
+
+ #Orf k n r s zbar
+ self.output.write("#Gumbel\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s, samples=%s, minread=%s, trim=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output.name, self.samples, self.minread, self.trim))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Annotation path: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#FDR Corrected thresholds: %f, %f\n" % (ess_t, non_t))
+ self.output.write("#MH Acceptance-Rate:\t%2.2f%%\n" % (100.0*acctot/count))
+ self.output.write("#Total Iterations Performed:\t%d\n" % count)
+ self.output.write("#Sample Size:\t%d\n" % i)
+ self.output.write("#phi estimate:\t%f\n" % numpy.average(phi_sample))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#%s\n" % "\t".join(columns))
+ i = 0
+ data = []
+ for g in G:
+ if not self.good_orf(g):
+ zbar = -1.0
+ else:
+ zbar = ZBAR[i]
+ i+=1
+ if zbar > ess_t:
+ call = "E"
+ elif non_t <= zbar <= ess_t:
+ call = "U"
+ elif 0 <= zbar < non_t:
+ call = "NE"
+ else:
+ call = "S"
+ data.append("%s\t%s\t%s\t%d\t%d\t%d\t%d\t%f\t%s\n" % (g.orf, g.name, g.desc, g.k, g.n, g.r, g.s, zbar, call))
+ data.sort()
+ for line in data:
+ self.output.write(line)
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Gumbel")
+ self.finish()
+ self.transit_message("Finished Gumbel Method")
+
+ @classmethod
+ def usage_string(self):
+ return """python %s gumbel <comma-separated .wig files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]
+
+ Optional Arguments:
+ -s <integer> := Number of samples. Default: -s 10000
+ -b <integer> := Number of Burn-in samples. Default -b 500
+ -m <integer> := Smallest read-count to consider. Default: -m 1
+ -t <integer> := Trims all but every t-th value. Default: -t 1
+ -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum
+ -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
+ -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
+ """ % (sys.argv[0])
+
+ def good_orf(self, gene):
+ return (gene.n >= 3 and gene.t >= 150)
+
+ def classify(self, n,r,p):
+ if n == 0: return 0
+ q = 1-p; B = 1/math.log(1/p); u = math.log(n*q,1/p);
+ pval = 1 - scipy.stats.gumbel_r.cdf(r,u,B)
+ if pval < 0.05: return(1)
+ else: return(0)
+
+ def F_non(self, p, N, R):
+ q = 1.0 - p
+ total = numpy.log(scipy.stats.beta.pdf(p,ALPHA,BETA))
+ mu = numpy.log(N*q) / numpy.log(1/p)
+ sigma = 1/math.log(1/p);
+ total+= numpy.sum(numpy.log(scipy.stats.gumbel_r.pdf(R, mu, sigma)))
+ return(total)
+
+ def sample_Z(self, p, w1, N, R, S, T, mu_s, sigma_s, SIG):
+ G = len(N)
+ q = 1.0-p
+ mu = numpy.log(N*q) / numpy.log(1.0/p)
+ sigma = 1.0/math.log(1.0/p);
+ h0 = ((scipy.stats.gumbel_r.pdf(R,mu,sigma)) * scipy.stats.norm.pdf(S, mu_s*R, sigma_s) * (1-w1))
+ h1 = SIG * w1
+ p_z1 = h1/(h0+h1)
+ return scipy.stats.binom.rvs(1, p_z1, size=G)
+
+ def sigmoid(self,d,n):
+ Kn = 0.1
+ MEAN_DOMAIN_SPAN = 300
+
+ if d == 0: return(0.00)
+ f = 1./(1.+math.exp(Kn*(MEAN_DOMAIN_SPAN-d)))
+ #if n in self.cache_nn: return f/self.cache_nn[n]
+ tot = 0
+ N = int(n+1)
+ for i in range(1,N): tot += 1.0/(1.0+math.exp(Kn*(MEAN_DOMAIN_SPAN-i)))
+ self.cache_nn[n] = tot
+ return f/tot
+
+
+
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+
+ G = GumbelMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/hmm.py b/src/pytransit/analysis/hmm.py
new file mode 100644
index 0000000..35da86b
--- /dev/null
+++ b/src/pytransit/analysis/hmm.py
@@ -0,0 +1,596 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+#method_name = "hmm"
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "hmm"
+long_name = "Analysis of genomic regions using a Hidden Markov Model"
+description = """Analysis of essentiality in the entire genome using a Hidden Markov Model. Capable of determining regions with different levels of essentiality representing Essential, Growth-Defect, Non-Essential and Growth-Advantage regions.
+
+Reference: DeJesus et al. (2013; BMC Bioinformatics)
+"""
+transposons = ["himar1"]
+columns_sites = ["Location","Read Count","Probability - ES","Probability - GD","Probability - NE","Probability - GA","State","Gene"]
+columns_genes = ["Orf","Name","Description","Total Sites","Num. ES","Num. GD","Num. NE","Num. GA", "Avg. Insertions", "Avg. Reads", "State Call"]
+
+
+############# Analysis Method ##############
+
+class HMMAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, HMMMethod, HMMGUI, [HMMSitesFile, HMMGenesFile])
+
+
+################## FILE ###################
+
+class HMMSitesFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#HMM - Sites", columns_sites)
+
+ def getHeader(self, path):
+ es=0; gd=0; ne=0; ga=0; T=0;
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if len(tmp) == 7:
+ col = -1
+ else:
+ col = -2
+ if tmp[col] == "ES": es+=1
+ elif tmp[col] == "GD": gd+=1
+ elif tmp[col] == "NE": ne+=1
+ elif tmp[col] == "GA": ga+=1
+ else: print tmp
+ T+=1
+
+ text = """Results:
+ Essential: %1.1f%%
+ Growth-Defect: %1.1f%%
+ Non-Essential: %1.1f%%
+ Growth-Advantage: %1.1f%%
+ """ % (100.0*es/T, 100.0*gd/T, 100.0*ne/T, 100.0*ga/T)
+ return text
+
+
+
+class HMMGenesFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#HMM - Genes", columns_genes)
+
+ def getHeader(self, path):
+ es=0; gd=0; ne=0; ga=0; T=0;
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if len(tmp) < 5: continue
+ if tmp[-1] == "ES": es+=1
+ if tmp[-1] == "GD": gd+=1
+ if tmp[-1] == "NE": ne+=1
+ if tmp[-1] == "GA": ga+=1
+
+ text = """Results:
+ Essential: %s
+ Growth-Defect: %s
+ Non-Essential: %s
+ Growth-Advantage: %s
+ """ % (es, gd, ne, ga)
+
+ return text
+
+
+############# GUI ##################
+
+class HMMGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ hmmPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ hmmSection = wx.BoxSizer( wx.VERTICAL )
+
+ hmmLabel = wx.StaticText( hmmPanel, wx.ID_ANY, u"HMM Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ hmmLabel.Wrap( -1 )
+ hmmSection.Add( hmmLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ hmmSizer1 = wx.BoxSizer( wx.HORIZONTAL )
+ hmmSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+ hmmLabelSizer = wx.BoxSizer( wx.VERTICAL )
+ hmmControlSizer = wx.BoxSizer( wx.VERTICAL )
+
+
+ hmmRepLabel = wx.StaticText( hmmPanel, wx.ID_ANY, u"Replicates", wx.DefaultPosition, wx.DefaultSize, 0 )
+ hmmRepLabel.Wrap(-1)
+ hmmLabelSizer.Add(hmmRepLabel, 1, wx.ALL, 5)
+
+
+ hmmRepChoiceChoices = [ u"Sum", u"Mean", "TTRMean" ]
+ self.wxobj.hmmRepChoice = wx.Choice( hmmPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, hmmRepChoiceChoices, 0 )
+ self.wxobj.hmmRepChoice.SetSelection( 2 )
+
+ hmmControlSizer.Add(self.wxobj.hmmRepChoice, 0, wx.ALL|wx.EXPAND, 5)
+
+
+ hmmSizer2.Add(hmmLabelSizer, 1, wx.EXPAND, 5)
+ hmmSizer2.Add(hmmControlSizer, 1, wx.EXPAND, 5)
+
+ hmmSizer1.Add(hmmSizer2, 1, wx.EXPAND, 5 )
+
+
+ hmmSection.Add( hmmSizer1, 1, wx.EXPAND, 5 )
+
+ hmmButton = wx.Button( hmmPanel, wx.ID_ANY, u"Run HMM", wx.DefaultPosition, wx.DefaultSize, 0 )
+ hmmSection.Add( hmmButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+
+ hmmPanel.SetSizer( hmmSection )
+ hmmPanel.Layout()
+ hmmSection.Fit( hmmPanel )
+
+ #Connect events
+ hmmButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = hmmPanel
+
+
+
+########## CLASS #######################
+
+class HMMMethod(base.SingleConditionMethod):
+ """
+ HMM
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ replicates="TTRMean",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+ try:
+ T = len([1 for line in open(ctrldata[0]).readlines() if not line.startswith("#")])
+ self.maxiterations = T*4 + 1
+ except:
+ self.self.maxiterations = 100
+ self.count = 1
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata, transposons):
+ return None
+
+
+ #Read the parameters from the wxPython widgets
+ replicates = wxobj.hmmRepChoice.GetString(wxobj.hmmRepChoice.GetCurrentSelection())
+ ignoreCodon = True
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ normalization = None
+ LOESS = False
+
+ #Get output path
+ name = transit_tools.basename(ctrldata[0])
+ defaultFileName = "hmm_output.dat"
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ replicates = kwargs.get("r", "TTRMean")
+ normalization = None
+ LOESS = kwargs.get("l", False)
+ ignoreCodon = True
+ NTerminus = float(kwargs.get("iN", 0.0))
+ CTerminus = float(kwargs.get("iC", 0.0))
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+ def Run(self):
+
+ self.transit_message("Starting HMM Method")
+ start_time = time.time()
+
+ #Get orf data
+ self.transit_message("Getting Data")
+ (data, position) = tnseq_tools.get_data(self.ctrldata)
+ hash = transit_tools.get_pos_hash(self.annotation_path)
+ rv2info = transit_tools.get_gene_info(self.annotation_path)
+ self.transit_message("Combining Replicates as '%s'" % self.replicates)
+
+ O = tnseq_tools.combine_replicates(data, method=self.replicates) + 1 # Adding 1 to because of shifted geometric in scipy
+
+ #Parameters
+ Nstates = 4
+ label = {0:"ES", 1:"GD", 2:"NE",3:"GA"}
+
+ reads = O-1
+ reads_nz = sorted(reads[reads !=0 ])
+ size = len(reads_nz)
+ mean_r = numpy.average(reads_nz[:int(0.95 * size)])
+ mu = numpy.array([1/0.99, 0.01 * mean_r + 2, mean_r, mean_r*5.0])
+ #mu = numpy.array([1/0.99, 0.1 * mean_r + 2, mean_r, mean_r*5.0])
+ L = 1.0/mu
+ B = [] # Emission Probability Distributions
+ for i in range(Nstates):
+ B.append(scipy.stats.geom(L[i]).pmf)
+
+ pins = self.calculate_pins(O-1)
+ pins_obs = sum([1 for rd in O if rd >=2])/float(len(O))
+ pnon = 1.0 - pins
+ pnon_obs = 1.0 - pins_obs
+
+ for r in range(100):
+ if pnon ** r < 0.01: break
+
+ A = numpy.zeros((Nstates,Nstates))
+ a = math.log1p(-B[int(Nstates/2)](1)**r)
+ b = r*math.log(B[int(Nstates/2)](1)) + math.log(1.0/3) # change to Nstates-1?
+ for i in range(Nstates):
+ A[i] = [b]*Nstates
+ A[i][i] = a
+
+ PI = numpy.zeros(Nstates) # Initial state distribution
+ PI[0] = 0.7; PI[1:] = 0.3/(Nstates-1);
+
+
+ self.progress_range(self.maxiterations)
+
+
+ ###############
+ ### VITERBI ###
+ (Q_opt, delta, Q) = self.viterbi(A, B, PI, O)
+ ###############
+
+ ##################
+ ### ALPHA PASS ###
+ (log_Prob_Obs, alpha, C) = self.forward_procedure(numpy.exp(A), B, PI, O)
+ ##################
+
+ #################
+ ### BETA PASS ###
+ beta = self.backward_procedure(numpy.exp(A), B, PI, O, C)
+ #################
+
+ T = len(O); total=0; state2count = dict.fromkeys(range(Nstates),0)
+ for t in xrange(T):
+ state = Q_opt[t]
+ state2count[state] +=1
+ total+=1
+
+
+
+ self.output.write("#HMM - Sites\n")
+ self.output.write("# Tn-HMM\n")
+
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output.name))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("# \n")
+ self.output.write("# Mean:\t%2.2f\n" % (numpy.average(reads_nz)))
+ self.output.write("# Median:\t%2.2f\n" % numpy.median(reads_nz))
+ self.output.write("# pins (obs):\t%f\n" % pins_obs)
+ self.output.write("# pins (est):\t%f\n" % pins)
+ self.output.write("# Run length (r):\t%d\n" % r)
+ self.output.write("# State means:\n")
+ self.output.write("# %s\n" % " ".join(["%s: %8.4f" % (label[i], mu[i]) for i in range(Nstates)]))
+ self.output.write("# Self-Transition Prob:\n")
+ self.output.write("# %s\n" % " ".join(["%s: %2.4e" % (label[i], A[i][i]) for i in range(Nstates)]))
+ self.output.write("# State Emission Parameters (theta):\n")
+ self.output.write("# %s\n" % " ".join(["%s: %1.4f" % (label[i], L[i]) for i in range(Nstates)]))
+ self.output.write("# State Distributions:")
+ self.output.write("# %s\n" % " ".join(["%s: %2.2f%%" % (label[i], state2count[i]*100.0/total) for i in range(Nstates)]))
+
+
+ states = [int(Q_opt[t]) for t in range(T)]
+ last_orf = ""
+ for t in xrange(T):
+ s_lab = label.get(states[t], "Unknown State")
+ gamma_t = (alpha[:,t] * beta[:,t])/numpy.sum(alpha[:,t] * beta[:,t])
+ genes_at_site = hash.get(position[t], [""])
+ genestr = ""
+ if not (len(genes_at_site) == 1 and not genes_at_site[0]):
+ genestr = ",".join(["%s_(%s)" % (g,rv2info.get(g, "-")[0]) for g in genes_at_site])
+
+ self.output.write("%s\t%s\t%s\t%s\t%s\n" % (int(position[t]), int(O[t])-1, "\t".join(["%-9.2e" % g for g in gamma_t]), s_lab, genestr))
+
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Finished HMM - Sites Method")
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="HMM - Sites")
+
+ #Gene Files
+ self.transit_message("Creating HMM Genes Level Output")
+ genes_path = ".".join(self.output.name.split(".")[:-1]) + "_genes." + self.output.name.split(".")[-1]
+
+ tempObs = numpy.zeros((1,len(O)))
+ tempObs[0,:] = O - 1
+ self.post_process_genes(tempObs, position, states, genes_path)
+
+
+ self.transit_message("Adding File: %s" % (genes_path))
+ self.add_file(path=genes_path, filetype="HMM - Genes")
+ self.finish()
+ self.transit_message("Finished HMM Method")
+
+
+ @classmethod
+ def usage_string(self):
+ return """python %s hmm <comma-separated .wig files> <annotation .prot_table or GFF3> <output file>
+
+ Optional Arguments:
+ -r <string> := How to handle replicates. Sum, Mean, TTRMean. Default: -r TTRMean
+ -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
+ -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
+ -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
+ """ % (sys.argv[0])
+
+
+
+ def forward_procedure(self, A, B, PI, O):
+ T = len(O)
+ N = len(B)
+ alpha = numpy.zeros((N, T))
+ C = numpy.zeros(T)
+
+ alpha[:,0] = PI * [B[i](O[0]) for i in range(N)]
+
+ C[0] = 1.0/numpy.sum(alpha[:,0])
+ alpha[:,0] = C[0] * alpha[:,0]
+
+ for t in xrange(1, T):
+ #B[i](O[:,t]) => numpy.prod(B[i](O[:,t]))
+ #b_o = numpy.array([numpy.prod(B[i](O[:,t])) for i in range(N)])
+ b_o = [B[i](O[t]) for i in range(N)]
+
+ alpha[:,t] = numpy.dot(alpha[:,t-1], A) * b_o
+
+ C[t] = numpy.nan_to_num(1.0/numpy.sum(alpha[:,t]))
+ alpha[:,t] = numpy.nan_to_num(alpha[:,t] * C[t])
+
+ if numpy.sum(alpha[:,t]) == 0:
+ alpha[:,t] = 0.0000000000001
+
+ self.progress_update("hmm", self.count)
+ self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+ self.count+=1
+ #print t, O[:,t], alpha[:,t]
+
+ log_Prob_Obs = - (numpy.sum(numpy.log(C)))
+ return(( log_Prob_Obs, alpha, C ))
+
+ def backward_procedure(self, A, B, PI, O, C=None):
+
+ N = len(B)
+ T = len(O)
+ beta = numpy.zeros((N,T))
+
+ beta[:,T-1] = 1.0
+ if C!=None: beta[:,T-1] = beta[:,T-1] * C[T-1]
+
+ for t in xrange(T-2, -1, -1):
+ #B[i](O[:,t]) => numpy.prod(B[i](O[:,t]))
+ #b_o = numpy.array([numpy.prod(B[i](O[:,t])) for i in range(N)])
+ b_o = [B[i](O[t]) for i in range(N)]
+
+ beta[:,t] = numpy.nan_to_num(numpy.dot(A, (b_o * beta[:,t+1] ) ))
+
+ if sum(beta[:,t]) == 0:
+ beta[:,t] = 0.0000000000001
+
+ if C!=None:
+ beta[:,t] = beta[:,t] * C[t]
+
+ self.progress_update("hmm", self.count)
+ self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+ self.count+=1
+
+ return(beta)
+
+
+
+ def viterbi(self, A, B, PI, O):
+ N=len(B)
+ T = len(O)
+ delta = numpy.zeros((N, T))
+
+ b_o = [B[i](O[0]) for i in range(N)]
+ delta[:,0] = numpy.log(PI) + numpy.log(b_o)
+
+ Q = numpy.zeros((N, T))
+
+ for t in xrange(1, T):
+ b_o = [B[i](O[t]) for i in range(N)]
+ #nus = delta[:, t-1] + numpy.log(A)
+ nus = delta[:, t-1] + A
+ delta[:,t] = nus.max(1) + numpy.log(b_o)
+ Q[:,t] = nus.argmax(1)
+ self.progress_update("hmm", self.count)
+ self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+ self.count+=1
+
+ Q_opt = [numpy.argmax(delta[:,T-1])]
+ for t in xrange(T-2, -1, -1):
+ Q_opt.insert(0, Q[Q_opt[0],t+1])
+ self.progress_update("hmm", self.count)
+ self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+ self.count+=1
+
+ self.progress_update("hmm", self.count)
+ self.transit_message_inplace("Running HMM Method... %1.1f%%" % (100.0*self.count/self.maxiterations))
+
+ return((Q_opt, delta, Q))
+
+
+ def calculate_pins(self, reads):
+ non_ess_reads = []
+ temp = []
+ for rd in reads:
+
+ if rd >=1:
+ if len(temp) < 10: non_ess_reads.extend(temp)
+ non_ess_reads.append(rd)
+ temp = []
+ else:
+ temp.append(rd)
+
+ return(sum([1 for rd in non_ess_reads if rd >= 1])/float(len(non_ess_reads)) )
+
+
+
+ def post_process_genes(self, data, position, states, output_path):
+
+ output = open(output_path, "w")
+ pos2state = dict([(position[t],states[t]) for t in range(len(states))])
+ theta = numpy.mean(data > 0)
+ G = tnseq_tools.Genes(self.ctrldata, self.annotation_path, data=data, position=position)
+
+ num2label = {0:"ES", 1:"GD", 2:"NE", 3:"GA"}
+ output.write("#HMM - Genes\n")
+ for gene in G:
+
+ reads_nz = [c for c in gene.reads.flatten() if c > 0]
+ avg_read_nz = 0
+ if len(reads_nz) > 0:
+ avg_read_nz = numpy.average(reads_nz)
+
+ # State
+ genestates = [pos2state[p] for p in gene.position]
+ statedist = {}
+ for st in genestates:
+ if st not in statedist: statedist[st] = 0
+ statedist[st] +=1
+
+ # State counts
+ n0 = statedist.get(0, 0); n1 = statedist.get(1, 0);
+ n2 = statedist.get(2, 0); n3 = statedist.get(3, 0);
+
+
+ if gene.n > 0:
+ E = tnseq_tools.ExpectedRuns(gene.n, 1.0 - theta)
+ V = tnseq_tools.VarR(gene.n, 1.0 - theta)
+ if n0 == gene.n: S = "ES"
+ elif n0 >= int(E+(3*math.sqrt(V))): S = "ES"
+ else:
+ temp = max([(statedist.get(s, 0), s) for s in [0, 1, 2, 3]])[1]
+ S = num2label[temp]
+ else:
+ E = 0.0
+ V = 0.0
+ S = "N/A"
+ output.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%1.4f\t%1.2f\t%s\n" % (gene.orf, gene.name, gene.desc, gene.n, n0, n1, n2, n3, gene.theta(), avg_read_nz, S))
+
+ output.close()
+
+
+
+
+
+
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+
+ G = HMMMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/rankproduct.py b/src/pytransit/analysis/rankproduct.py
new file mode 100644
index 0000000..fac2e97
--- /dev/null
+++ b/src/pytransit/analysis/rankproduct.py
@@ -0,0 +1,464 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import matplotlib.pyplot as plt
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "rankproduct"
+long_name = "Rank Product test for determining conditional essentiality."
+description = "Differential Comparison based on ranks"
+transposons = ["himar1", "tn5"]
+columns = ["Orf","Name","Desc","Sites","Mean Ctrl","Mean Exp","log2FC","Obs RP","pvalue","adj. pvalue"]
+
+
+
+############# Analysis Method ##############
+
+class RankProductAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, RankProductMethod, RankProductGUI, [RankProductFile])
+
+
+################## FILE ###################
+
+class RankProductFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#RankProduct", columns)
+
+
+############# GUI ##################
+
+class RankProductGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ rankproductPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ rankproductSizer = wx.BoxSizer( wx.VERTICAL )
+
+ rankproductLabel = wx.StaticText( rankproductPanel, wx.ID_ANY, u"rankproduct Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ rankproductLabel.Wrap( -1 )
+ rankproductSizer.Add( rankproductLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ rankproductTopSizer = wx.BoxSizer( wx.HORIZONTAL )
+
+ rankproductTopSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+
+ rankproductLabelSizer = wx.BoxSizer( wx.VERTICAL )
+
+ rankproductSampleLabel = wx.StaticText( rankproductPanel, wx.ID_ANY, u"Samples", wx.DefaultPosition, wx.DefaultSize, 0 )
+ rankproductSampleLabel.Wrap( -1 )
+ rankproductLabelSizer.Add( rankproductSampleLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ rankproductNormLabel = wx.StaticText( rankproductPanel, wx.ID_ANY, u"Normalization", wx.DefaultPosition, wx.DefaultSize, 0 )
+ rankproductNormLabel.Wrap( -1 )
+ rankproductLabelSizer.Add( rankproductNormLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ rankproductTopSizer2.Add( rankproductLabelSizer, 1, wx.EXPAND, 5 )
+
+ rankproductControlSizer = wx.BoxSizer( wx.VERTICAL )
+
+ self.wxobj.rankproductSampleText = wx.TextCtrl( rankproductPanel, wx.ID_ANY, u"10000", wx.DefaultPosition, wx.DefaultSize, 0 )
+ rankproductControlSizer.Add( self.wxobj.rankproductSampleText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ rankproductNormChoiceChoices = [ u"TTR", u"nzmean", u"totreads", u'zinfnb', u'quantile', u"betageom", u"nonorm" ]
+ self.wxobj.rankproductNormChoice = wx.Choice( rankproductPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, rankproductNormChoiceChoices, 0 )
+ self.wxobj.rankproductNormChoice.SetSelection( 0 )
+ rankproductControlSizer.Add( self.wxobj.rankproductNormChoice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+
+ rankproductTopSizer2.Add( rankproductControlSizer, 1, wx.EXPAND, 5 )
+
+ rankproductTopSizer.Add( rankproductTopSizer2, 1, wx.EXPAND, 5 )
+
+ rankproductSizer.Add( rankproductTopSizer, 1, wx.EXPAND, 5 )
+
+ rankproductButton = wx.Button( rankproductPanel, wx.ID_ANY, u"Run rankproduct", wx.DefaultPosition, wx.DefaultSize, 0 )
+ rankproductSizer.Add( rankproductButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+
+ rankproductPanel.SetSizer( rankproductSizer )
+ rankproductPanel.Layout()
+ rankproductSizer.Fit( rankproductPanel )
+
+ #Connect events
+ rankproductButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = rankproductPanel
+
+
+
+########## CLASS #######################
+
+class RankProductMethod(base.DualConditionMethod):
+ """
+ rankproduct
+
+ """
+ def __init__(self,
+ ctrldata,
+ expdata,
+ annotation_path,
+ output_file,
+ normalization="TTR",
+ samples=10000,
+ adaptive=False,
+ doHistogram=False,
+ replicates="Sum",
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.DualConditionMethod.__init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+ self.samples = samples
+ self.adaptive = adaptive
+ self.doHistogram = doHistogram
+
+
+
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ expdata = wxobj.expSelected()
+ if not transit_tools.validate_both_datasets(ctrldata, expdata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata+expdata, transposons):
+ return None
+
+
+
+ #Read the parameters from the wxPython widgets
+ ignoreCodon = True
+ samples = int(wxobj.rankproductSampleText.GetValue())
+ normalization = wxobj.rankproductNormChoice.GetString(wxobj.rankproductNormChoice.GetCurrentSelection())
+ replicates="Sum"
+ adaptive = False
+ doHistogram = False
+
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ LOESS = False
+
+ #Get output path
+ defaultFileName = "rankproduct_output.dat"
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+ return self(ctrldata,
+ expdata,
+ annotationPath,
+ output_file,
+ normalization,
+ samples,
+ adaptive,
+ doHistogram,
+ replicates,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+
+ ctrldata = args[0].split(",")
+ expdata = args[1].split(",")
+ annotationPath = args[2]
+ output_path = args[3]
+ output_file = open(output_path, "w")
+
+ normalization = kwargs.get("n", "TTR")
+ samples = int(kwargs.get("s", 100))
+ adaptive = kwargs.get("a", False)
+ doHistogram = kwargs.get("h", False)
+ replicates = kwargs.get("r", "Sum")
+
+
+ LOESS = kwargs.get("l", False)
+ ignoreCodon = True
+ NTerminus = float(kwargs.get("iN", 0.00))
+ CTerminus = float(kwargs.get("iC", 0.00))
+
+ return self(ctrldata,
+ expdata,
+ annotationPath,
+ output_file,
+ normalization,
+ samples,
+ adaptive,
+ doHistogram,
+ replicates,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+
+
+ def Run(self):
+
+ self.transit_message("Starting rankproduct Method")
+ start_time = time.time()
+
+
+
+ Kctrl = len(self.ctrldata)
+ Kexp = len(self.expdata)
+ #Get orf data
+ self.transit_message("Getting Data")
+ (data, position) = tnseq_tools.get_data(self.ctrldata+self.expdata)
+ if self.normalization != "none":
+ self.transit_message("Normalizing using: %s" % self.normalization)
+
+ (data, factors) = norm_tools.normalize_data(data, self.normalization, self.ctrldata+self.expdata, self.annotation_path)
+
+
+ Gctrl= tnseq_tools.Genes(self.ctrldata + self.expdata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus, data=data[:Kctrl,:], position=position)
+
+ Gexp= tnseq_tools.Genes(self.ctrldata + self.expdata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus, data=data[Kctrl:,:], position=position)
+
+
+ Ngenes = len(Gctrl)
+
+
+ #print numpy.log2(30/10)
+
+
+ """
+
+ types_list = set([])
+ for x in [numpy.mean(g.reads+1.0,1) for g in Gctrl]:
+ types_list.add(type(x[0]))
+
+ print [numpy.mean(g.reads+1.0,1) for g in Gctrl]
+ print "FLORF", types_list
+ """
+
+ #print Gctrl[0].reads.shape
+ #print numpy.ones((Kctrl,1)).shape
+
+ T = numpy.ones((Kctrl,1))
+
+ meanCtrl = numpy.zeros((Kctrl, Ngenes))
+ meanExp = numpy.zeros((Kexp, Ngenes))
+
+ for i in range(Ngenes):
+ if numpy.any(Gctrl[i].reads):
+ meanCtrl[:,i] = numpy.mean(Gctrl[i].reads,1)
+ else:
+ meanCtrl[:,i] = numpy.zeros(Kctrl)
+
+ if numpy.any(Gexp[i].reads):
+ meanExp[:,i] = numpy.mean(Gexp[i].reads,1)
+ else:
+ meanExp[:,i] = numpy.zeros(Kexp)
+
+
+ #meanCtrl = numpy.array([numpy.mean(numpy.concatenate((g.reads, numpy.ones((Kctrl,1))),1),1) for g in Gctrl])
+ #meanExp = numpy.array([numpy.mean(numpy.concatenate((g.reads, numpy.ones((Kexp,1))),1),1) for g in Gexp])
+
+ #meanExp = numpy.nan_to_num(numpy.array([numpy.mean(g.reads+1.0,1) for g in Gexp]))
+
+ #meanCtrl[numpy.isnan(meanCtrl)]
+
+ #print type(meanCtrl[0][0])
+ #print type(meanExp[0][0])
+ #print type(meanExp[0][0]/meanCtrl[0][0])
+
+ #print numpy.log2(meanExp[0][0]/meanCtrl[0][0])
+
+ """
+ logFC2 = numpy.zeros((Ngenes, len(meanCtrl[0])))
+ for i,ratio in enumerate(meanExp/meanCtrl):
+ #print i, ratio, numpy.log2(ratio)
+ logFC2[i] = numpy.log2(ratio)
+ """
+
+ #print "meanCtrl"
+ #print meanCtrl
+
+
+ #print "meanExp"
+ #print meanExp
+
+
+ logFC2 = numpy.log2((meanExp+0.0001)/(meanCtrl+0.0001))
+ rank = numpy.array([scipy.stats.rankdata(Lvec)/float(Ngenes) for Lvec in logFC2])
+ obsRP = numpy.prod(rank,0)
+
+
+ #print "logFC2"
+ #print logFC2
+
+ #print "rank"
+ #print numpy.array([scipy.stats.rankdata(Lvec) for Lvec in logFC2])
+
+
+ #print "obsRP"
+ #print obsRP
+
+
+ permutations = numpy.zeros((self.samples, Ngenes))
+ tempranks = scipy.array([numpy.arange(1,Ngenes+1) for rep in range(Kctrl)])
+ for s in range(self.samples):
+ rankperm = numpy.array([numpy.random.permutation(tr)/float(Ngenes) for tr in tempranks])
+ #print numpy.prod(rankperm,0)
+ permutations[s] = numpy.prod(rankperm,0)
+
+
+ #print "permutations"
+ #print permutations
+
+
+ rankRP = scipy.stats.rankdata(obsRP)
+
+
+
+
+ #rankproduct
+ data = []
+ count = 0
+ self.progress_range(Ngenes)
+ for i,gene in enumerate(Gctrl):
+ count+=1
+ #print gene, obsRP[i]
+
+ meanctrl = numpy.mean(Gctrl[i].reads)
+ meanexp = numpy.mean(Gexp[i].reads)
+ log2fc = numpy.log2((meanexp+0.0001)/(meanctrl+0.0001))
+ #countbetter = numpy.sum(permutations < obsRP[i])
+ countbetter = numpy.sum(permutations < obsRP[i])
+
+ pval = countbetter/float(self.samples*Ngenes)
+ q_paper = pval/rankRP[i]
+
+ data.append([gene.orf, gene.name, gene.desc, gene.n, meanctrl, meanexp, log2fc, obsRP[i], q_paper, pval])
+ self.progress_update("rankproduct", count)
+ self.transit_message_inplace("Running rankproduct Method... %1.1f%%" % (100.0*count/Ngenes))
+
+
+ #
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Performing Benjamini-Hochberg Correction")
+ data.sort()
+ qval = stat_tools.BH_fdr_correction([row[-1] for row in data])
+
+
+ self.output.write("#RankProduct\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Annotation path: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#%s\n" % (columns))
+
+ for i,row in enumerate(data):
+ (orf, name, desc, n, mean1, mean2, log2FCgene, obsRPgene, q_paper, pval_2tail) = row
+ self.output.write("%s\t%s\t%s\t%d\t%1.1f\t%1.1f\t%1.2f\t%1.7f\t%1.7f\t%1.7f\n" % (orf, name, desc, n, mean1, mean2,log2FCgene, obsRPgene, pval_2tail, qval[i]))
+ self.output.close()
+
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="RankProduct")
+ self.finish()
+ self.transit_message("Finished rankproduct Method")
+
+
+ @classmethod
+ def usage_string(self):
+ return """python %s rankproduct <comma-separated .wig control files> <comma-separated .wig experimental files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]
+
+ Optional Arguments:
+ -s <integer> := Number of samples. Default: -s 100
+ -n <string> := Normalization method. Default: -n TTR
+ -h := Output histogram of the permutations for each gene. Default: Turned Off.
+ -a := Perform adaptive rankproduct. Default: Turned Off.
+ -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Turned Off.
+ -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
+ -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
+ """ % (sys.argv[0])
+
+
+
+
+
+
+
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+ #TODO: Figure out issue with inputs (transit requires initial method name, running as script does not !!!!)
+
+ G = RankProductMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/resampling.py b/src/pytransit/analysis/resampling.py
new file mode 100644
index 0000000..55ed247
--- /dev/null
+++ b/src/pytransit/analysis/resampling.py
@@ -0,0 +1,472 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import ntpath
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import matplotlib.pyplot as plt
+
+import base
+import pytransit
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "resampling"
+long_name = "Resampling test of conditional essentiality between two conditions"
+description = """Method for determining conditional essentiality based on resampling (i.e. permutation test). Identifies significant changes in mean read-counts for each gene after normalization."""
+
+transposons = ["himar1", "tn5"]
+columns = ["Orf","Name","Desc","Sites","Mean Ctrl","Mean Exp","Sum Ctrl", "Sum Exp", "Delta Sum","log2FC","p-value","Adj. p-value"]
+
+class ResamplingAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, ResamplingMethod, ResamplingGUI, [ResamplingFile])
+
+
+
+############# FILE ##################
+
+class ResamplingFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Resampling", columns)
+
+ def getHeader(self, path):
+ DE=0; poslogfc=0; neglogfc=0;
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if float(tmp[-1]) < 0.05:
+ DE +=1
+ if float(tmp[-3]) > 0:
+ poslogfc+=1
+ else:
+ neglogfc+=1
+
+ text = """Results:
+ Conditionally - Essentials: %s
+ More Essential in Experimental datasets: %s
+ Less Essential in Experimental datasets: %s
+ """ % (DE, poslogfc, neglogfc)
+ return text
+
+
+ def getMenus(self):
+ menus = []
+ menus.append(("Display in Track View", self.displayInTrackView))
+ menus.append(("Display Histogram", self.displayHistogram))
+ return menus
+
+ def displayHistogram(self, displayFrame, event):
+ gene = displayFrame.grid.GetCellValue(displayFrame.row, 0)
+ filepath = os.path.join(ntpath.dirname(displayFrame.path), transit_tools.fetch_name(displayFrame.path))
+ filename = os.path.join(filepath, gene+".png")
+ if os.path.exists(filename):
+ imgWindow = pytransit.fileDisplay.ImgFrame(None, filename)
+ imgWindow.Show()
+ else:
+ transit_tools.ShowError(MSG="Error Displaying File. Histogram image not found. Make sure results were obtained with the histogram option turned on.")
+ print "Error Displaying File. Histogram image does not exist."
+
+
+
+
+############# GUI ##################
+
+class ResamplingGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ resamplingPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ resamplingSizer = wx.BoxSizer( wx.VERTICAL )
+
+ resamplingLabel = wx.StaticText( resamplingPanel, wx.ID_ANY, u"resampling Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ resamplingLabel.Wrap( -1 )
+ resamplingSizer.Add( resamplingLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ resamplingTopSizer = wx.BoxSizer( wx.HORIZONTAL )
+
+ resamplingTopSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+
+ resamplingLabelSizer = wx.BoxSizer( wx.VERTICAL )
+
+ # Samples Label
+ resamplingSampleLabel = wx.StaticText( resamplingPanel, wx.ID_ANY, u"Samples", wx.DefaultPosition, wx.DefaultSize, 0 )
+ resamplingSampleLabel.Wrap( -1 )
+ resamplingLabelSizer.Add( resamplingSampleLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+
+ # Pseudocount Label
+ resamplingPseudocountLabel = wx.StaticText(resamplingPanel, wx.ID_ANY, u"Pseudocount", wx.DefaultPosition, wx.DefaultSize, 0)
+ resamplingPseudocountLabel.Wrap( -1 )
+ resamplingLabelSizer.Add( resamplingPseudocountLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+
+ # Norm Label
+ resamplingNormLabel = wx.StaticText( resamplingPanel, wx.ID_ANY, u"Normalization", wx.DefaultPosition, wx.DefaultSize, 0 )
+ resamplingNormLabel.Wrap( -1 )
+ resamplingLabelSizer.Add( resamplingNormLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+
+ resamplingTopSizer2.Add( resamplingLabelSizer, 1, wx.EXPAND, 5 )
+
+ resamplingControlSizer = wx.BoxSizer( wx.VERTICAL )
+
+ # Samples Text
+ self.wxobj.resamplingSampleText = wx.TextCtrl( resamplingPanel, wx.ID_ANY, u"10000", wx.DefaultPosition, wx.DefaultSize, 0 )
+ resamplingControlSizer.Add( self.wxobj.resamplingSampleText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+
+ # Pseudocounts
+ self.wxobj.resamplingPseudocountText = wx.TextCtrl(resamplingPanel, wx.ID_ANY, u"0.0", wx.DefaultPosition, wx.DefaultSize, 0)
+ resamplingControlSizer.Add( self.wxobj.resamplingPseudocountText, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+
+ # Norm Choices
+ resamplingNormChoiceChoices = [ u"TTR", u"nzmean", u"totreads", u'zinfnb', u'quantile', u"betageom", u"nonorm" ]
+ self.wxobj.resamplingNormChoice = wx.Choice( resamplingPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, resamplingNormChoiceChoices, 0 )
+ self.wxobj.resamplingNormChoice.SetSelection( 0 )
+ resamplingControlSizer.Add( self.wxobj.resamplingNormChoice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+
+ # Adaptive Check
+ self.wxobj.resamplingAdaptiveCheckBox = wx.CheckBox(resamplingPanel, label = 'Adaptive Resampling (Faster)')
+
+ # Histogram Check
+ self.wxobj.resamplingHistogramCheckBox = wx.CheckBox(resamplingPanel, label = 'Generate Resampling Histograms')
+
+ # Zeros Check
+ self.wxobj.resamplingZeroCheckBox = wx.CheckBox(resamplingPanel, label = 'Include sites with all zeros')
+
+
+ resamplingTopSizer2.Add( resamplingControlSizer, 1, wx.EXPAND, 5 )
+
+ resamplingTopSizer.Add( resamplingTopSizer2, 1, wx.EXPAND, 5 )
+
+
+
+ resamplingSizer.Add( resamplingTopSizer, 1, wx.EXPAND, 5 )
+ resamplingSizer.Add( self.wxobj.resamplingAdaptiveCheckBox, 0, wx.EXPAND, 5 )
+ resamplingSizer.Add( self.wxobj.resamplingHistogramCheckBox, 0, wx.EXPAND, 5 )
+ resamplingSizer.Add( self.wxobj.resamplingZeroCheckBox, 0, wx.EXPAND, 5 )
+
+ resamplingButton = wx.Button( resamplingPanel, wx.ID_ANY, u"Run resampling", wx.DefaultPosition, wx.DefaultSize, 0 )
+ resamplingSizer.Add( resamplingButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+
+ resamplingPanel.SetSizer( resamplingSizer )
+ resamplingPanel.Layout()
+ resamplingSizer.Fit( resamplingPanel )
+
+ #Connect events
+ resamplingButton.Bind( wx.EVT_BUTTON, self.wxobj.RunMethod )
+
+ self.panel = resamplingPanel
+
+
+
+########## CLASS #######################
+
+class ResamplingMethod(base.DualConditionMethod):
+ """
+ resampling
+
+ """
+ def __init__(self,
+ ctrldata,
+ expdata,
+ annotation_path,
+ output_file,
+ normalization="TTR",
+ samples=10000,
+ adaptive=False,
+ doHistogram=False,
+ includeZeros=False,
+ pseudocount=0.0,
+ replicates="Sum",
+ LOESS=False,
+ ignoreCodon=True,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.DualConditionMethod.__init__(self, short_name, long_name, description, ctrldata, expdata, annotation_path, output_file, normalization=normalization, replicates=replicates, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+
+ self.samples = samples
+ self.adaptive = adaptive
+ self.doHistogram = doHistogram
+ self.includeZeros = includeZeros
+ self.pseudocount = pseudocount
+
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ expdata = wxobj.expSelected()
+ if not transit_tools.validate_both_datasets(ctrldata, expdata):
+ return None
+
+ #Validate transposon types
+ if not transit_tools.validate_filetypes(ctrldata+expdata, transposons):
+ return None
+
+
+ #Read the parameters from the wxPython widgets
+ ignoreCodon = True
+ samples = int(wxobj.resamplingSampleText.GetValue())
+ normalization = wxobj.resamplingNormChoice.GetString(wxobj.resamplingNormChoice.GetCurrentSelection())
+ replicates="Sum"
+ adaptive = wxobj.resamplingAdaptiveCheckBox.GetValue()
+ doHistogram = wxobj.resamplingHistogramCheckBox.GetValue()
+
+ includeZeros = wxobj.resamplingZeroCheckBox.GetValue()
+ pseudocount = float(wxobj.resamplingPseudocountText.GetValue())
+
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ LOESS = False
+
+ #Get output path
+ defaultFileName = "resampling_output_s%d_pc%1.2f" % (samples, pseudocount)
+ if adaptive: defaultFileName+= "_adaptive"
+ if includeZeros: defaultFileName+= "_iz"
+ defaultFileName+=".dat"
+
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+ return self(ctrldata,
+ expdata,
+ annotationPath,
+ output_file,
+ normalization,
+ samples,
+ adaptive,
+ doHistogram,
+ includeZeros,
+ pseudocount,
+ replicates,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+ ctrldata = args[0].split(",")
+ expdata = args[1].split(",")
+ annotationPath = args[2]
+ output_path = args[3]
+ output_file = open(output_path, "w")
+
+ normalization = kwargs.get("n", "TTR")
+ samples = int(kwargs.get("s", 10000))
+ adaptive = kwargs.get("a", False)
+ doHistogram = kwargs.get("h", False)
+ replicates = kwargs.get("r", "Sum")
+ includeZeros = kwargs.get("iz", False)
+ pseudocount = float(kwargs.get("pc", 0.00))
+
+
+ LOESS = kwargs.get("l", False)
+ ignoreCodon = True
+ NTerminus = float(kwargs.get("iN", 0.00))
+ CTerminus = float(kwargs.get("iC", 0.00))
+
+ return self(ctrldata,
+ expdata,
+ annotationPath,
+ output_file,
+ normalization,
+ samples,
+ adaptive,
+ doHistogram,
+ includeZeros,
+ pseudocount,
+ replicates,
+ LOESS,
+ ignoreCodon,
+ NTerminus,
+ CTerminus)
+
+
+
+ def Run(self):
+
+ self.transit_message("Starting resampling Method")
+ start_time = time.time()
+
+
+ if self.doHistogram:
+ histPath = os.path.join(os.path.dirname(self.output.name), transit_tools.fetch_name(self.output.name)+"_histograms")
+ if not os.path.isdir(histPath):
+ os.makedirs(histPath)
+ else:
+ histPath = ""
+
+
+
+
+ Kctrl = len(self.ctrldata)
+ Kexp = len(self.expdata)
+ #Get orf data
+ self.transit_message("Getting Data")
+ if self.normalization != "nonorm":
+ self.transit_message("Normalizing using: %s" % self.normalization)
+ G = tnseq_tools.Genes(self.ctrldata+self.expdata, self.annotation_path, norm=self.normalization, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+
+ #Resampling
+ data = []
+ N = len(G)
+ count = 0
+ self.progress_range(N)
+ for gene in G:
+ count+=1
+ if gene.k == 0 or gene.n == 0:
+ (test_obs, mean1, mean2, log2FC, pval_ltail, pval_utail, pval_2tail, testlist, data1, data2) = (0, 0, 0, 0, 1.00, 1.00, 1.00, [], [0], [0])
+ else:
+
+ if not self.includeZeros:
+ ii = numpy.sum(gene.reads,0) > 0
+ else:
+ ii = numpy.ones(gene.n) == 1
+
+
+ data1 = gene.reads[:Kctrl,ii].flatten()+self.pseudocount
+ data2 = gene.reads[Kctrl:,ii].flatten()+self.pseudocount
+
+ (test_obs, mean1, mean2, log2FC, pval_ltail, pval_utail, pval_2tail, testlist) = stat_tools.resampling(data1, data2, S=self.samples, testFunc=stat_tools.F_sum_diff_flat, adaptive=self.adaptive)
+
+
+ if self.doHistogram:
+ if testlist:
+ n, bins, patches = plt.hist(testlist, normed=1, facecolor='c', alpha=0.75, bins=100)
+ else:
+ n, bins, patches = plt.hist([0], normed=1, facecolor='c', alpha=0.75, bins=100)
+ plt.xlabel('Delta Sum')
+ plt.ylabel('Probability')
+ plt.title('%s - Histogram of Delta Sum' % gene.orf)
+ plt.axvline(test_obs, color='r', linestyle='dashed', linewidth=3)
+ plt.grid(True)
+ genePath = os.path.join(histPath, gene.orf +".png")
+ plt.savefig(genePath)
+ plt.clf()
+
+
+ sum1 = numpy.sum(data1)
+ sum2 = numpy.sum(data2)
+ data.append([gene.orf, gene.name, gene.desc, gene.n, mean1, mean2, sum1, sum2, test_obs, log2FC, pval_2tail])
+ self.progress_update("resampling", count)
+ self.transit_message_inplace("Running Resampling Method... %1.1f%%" % (100.0*count/N))
+
+
+ #
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Performing Benjamini-Hochberg Correction")
+ data.sort()
+ qval = stat_tools.BH_fdr_correction([row[-1] for row in data])
+
+
+ self.output.write("#Resampling\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: norm=%s, samples=%s, pseudocounts=%1.2f, adaptive=%s, histogram=%s, includeZeros=%s, output=%s\n" % (self.normalization, self.samples, self.pseudocount, self.adaptive, self.doHistogram, self.includeZeros, self.output.name))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+ self.output.write("#Control Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Experimental Data: %s\n" % (",".join(self.expdata)))
+ self.output.write("#Annotation path: %s\n" % (self.annotation_path))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#%s\n" % "\t".join(columns))
+
+ for i,row in enumerate(data):
+ (orf, name, desc, n, mean1, mean2, sum1, sum2, test_obs, log2FC, pval_2tail) = row
+ self.output.write("%s\t%s\t%s\t%d\t%1.1f\t%1.1f\t%1.1f\t%1.1f\t%1.2f\t%1.2f\t%1.5f\t%1.5f\n" % (orf, name, desc, n, mean1, mean2, sum1, sum2, test_obs, log2FC, pval_2tail, qval[i]))
+ self.output.close()
+
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Resampling")
+ self.finish()
+ self.transit_message("Finished resampling Method")
+
+
+ @classmethod
+ def usage_string(self):
+ return """python %s resampling <comma-separated .wig control files> <comma-separated .wig experimental files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]
+
+ Optional Arguments:
+ -s <integer> := Number of samples. Default: -s 10000
+ -n <string> := Normalization method. Default: -n TTR
+ -h := Output histogram of the permutations for each gene. Default: Turned Off.
+ -a := Perform adaptive resampling. Default: Turned Off.
+ -iz := Include rows with zero accross conditions.
+ -pc := Pseudocounts to be added at each site.
+ -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Turned Off.
+ -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
+ -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
+ """ % (sys.argv[0])
+
+
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv)
+
+ #TODO: Figure out issue with inputs (transit requires initial method name, running as script does not !!!!)
+
+ G = ResamplingMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/analysis/tn5gaps.py b/src/pytransit/analysis/tn5gaps.py
new file mode 100644
index 0000000..73d11b0
--- /dev/null
+++ b/src/pytransit/analysis/tn5gaps.py
@@ -0,0 +1,416 @@
+import sys
+
+try:
+ import wx
+ hasWx = True
+ #Check if wx is the newest 3.0+ version:
+ try:
+ from wx.lib.pubsub import pub
+ pub.subscribe
+ newWx = True
+ except AttributeError as e:
+ from wx.lib.pubsub import Publisher as pub
+ newWx = False
+except Exception as e:
+ hasWx = False
+ newWx = False
+
+import os
+import time
+import math
+import random
+import numpy
+import scipy.stats
+import datetime
+
+import base
+import pytransit.transit_tools as transit_tools
+import pytransit.tnseq_tools as tnseq_tools
+import pytransit.norm_tools as norm_tools
+import pytransit.stat_tools as stat_tools
+
+#method_name = "example"
+
+
+############# GUI ELEMENTS ##################
+
+short_name = "tn5gaps"
+long_name = "Analysis of essentiality on gaps in entire genome (Tn5)."
+description = "A analysis method based on the extreme value (Gumbel) distribution that considers longest runs over the whole genome instead of individual genes."
+transposons = ["tn5"]
+columns = ["Orf","Name","Desc","k","n","r","ovr","lenovr","pval","padj","call"]
+
+
+
+############# Analysis Method ##############
+
+class Tn5GapsAnalysis(base.TransitAnalysis):
+ def __init__(self):
+ base.TransitAnalysis.__init__(self, short_name, long_name, description, transposons, Tn5GapsMethod, Tn5GapsGUI, [Tn5GapsFile])
+
+
+################## FILE ###################
+
+class Tn5GapsFile(base.TransitFile):
+
+ def __init__(self):
+ base.TransitFile.__init__(self, "#Tn5 Gaps", columns)
+
+ def getHeader(self, path):
+ ess=0; unc=0; non=0; short=0
+ for line in open(path):
+ if line.startswith("#"): continue
+ tmp = line.strip().split("\t")
+ if tmp[-1] == "Essential": ess+=1
+ if tmp[-1] == "Non-essential": non+=1
+
+ text = """Results:
+ Essentials: %s
+ Non-Essential: %s
+ """ % (ess, non)
+ return text
+
+
+################## GUI ###################
+
+class Tn5GapsGUI(base.AnalysisGUI):
+
+ def definePanel(self, wxobj):
+ self.wxobj = wxobj
+ tn5GapsPanel = wx.Panel( self.wxobj.optionsWindow, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL )
+
+ tn5GapsSection = wx.BoxSizer( wx.VERTICAL )
+
+ tn5GapsLabel = wx.StaticText( tn5GapsPanel, wx.ID_ANY, u"Tn5 Gaps Options", wx.DefaultPosition, wx.DefaultSize, 0 )
+ tn5GapsLabel.Wrap( -1 )
+ tn5GapsSection.Add( tn5GapsLabel, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+ tn5GapsSizer1 = wx.BoxSizer( wx.HORIZONTAL )
+
+ # Min read option
+ tn5GapsSizer2 = wx.BoxSizer( wx.HORIZONTAL )
+
+ tn5GapsSizer2_1 = wx.BoxSizer( wx.VERTICAL )
+ tn5GapsReadLabel = wx.StaticText( tn5GapsPanel, wx.ID_ANY, u"Minimum Read", wx.DefaultPosition, wx.DefaultSize, 0 )
+ tn5GapsReadLabel.Wrap( -1 )
+ tn5GapsSizer2_1.Add( tn5GapsReadLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ tn5GapsSizer2_2 = wx.BoxSizer( wx.VERTICAL )
+ tn5GapsReadChoiceChoices = [ u"1", u"2", u"3", u"4", u"5" ]
+ self.wxobj.tn5GapsReadChoice = wx.Choice( tn5GapsPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, tn5GapsReadChoiceChoices, 0 )
+ self.wxobj.tn5GapsReadChoice.SetSelection( 0 )
+ tn5GapsSizer2_2.Add( self.wxobj.tn5GapsReadChoice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ tn5GapsSizer2.Add(tn5GapsSizer2_1, 1, wx.EXPAND, 5)
+ tn5GapsSizer2.Add(tn5GapsSizer2_2, 1, wx.EXPAND, 5)
+
+ # Replicates option
+ tn5GapsSizer3 = wx.BoxSizer( wx.HORIZONTAL )
+
+ tn5GapsSizer3_1 = wx.BoxSizer( wx.VERTICAL )
+ tn5GapsRepLabel = wx.StaticText( tn5GapsPanel, wx.ID_ANY, u"Replicates", wx.DefaultPosition, wx.DefaultSize, 0 )
+ tn5GapsRepLabel.Wrap( -1 )
+ tn5GapsSizer3_1.Add( tn5GapsRepLabel, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5 )
+
+ tn5GapsSizer3_2 = wx.BoxSizer( wx.VERTICAL )
+ tn5GapsRepChoiceChoices = [ u"Sum", u"Mean" ]
+ self.wxobj.tn5GapsRepChoice = wx.Choice( tn5GapsPanel, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, tn5GapsRepChoiceChoices, 0 )
+ self.wxobj.tn5GapsRepChoice.SetSelection( 0 )
+ tn5GapsSizer3_2.Add( self.wxobj.tn5GapsRepChoice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL|wx.EXPAND, 5 )
+
+ tn5GapsSizer3.Add(tn5GapsSizer3_1, 1, wx.EXPAND, 5)
+ tn5GapsSizer3.Add(tn5GapsSizer3_2, 1, wx.EXPAND, 5)
+
+ tn5GapsSection.Add( tn5GapsSizer1, 1, wx.EXPAND, 5 )
+ tn5GapsSection.Add( tn5GapsSizer2, 1, wx.EXPAND, 5 )
+ tn5GapsSection.Add( tn5GapsSizer3, 1, wx.EXPAND, 5 )
+
+ tn5GapsButton = wx.Button( tn5GapsPanel, wx.ID_ANY, u"Run Tn5Gaps", wx.DefaultPosition, wx.DefaultSize, 0 )
+ tn5GapsSection.Add( tn5GapsButton, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5 )
+
+
+ tn5GapsPanel.SetSizer( tn5GapsSection )
+ tn5GapsPanel.Layout()
+ tn5GapsSection.Fit( tn5GapsPanel )
+
+ #Connect events
+ tn5GapsButton.Bind( wx.EVT_BUTTON, wxobj.RunMethod )
+
+
+ self.panel = tn5GapsPanel
+
+
+
+
+########## CLASS #######################
+
+class Tn5GapsMethod(base.SingleConditionMethod):
+ """
+ Example
+
+ """
+ def __init__(self,
+ ctrldata,
+ annotation_path,
+ output_file,
+ replicates="Sum",
+ normalization=None,
+ LOESS=False,
+ ignoreCodon=True,
+ minread=1,
+ NTerminus=0.0,
+ CTerminus=0.0, wxobj=None):
+
+ base.SingleConditionMethod.__init__(self, short_name, long_name, description, ctrldata, annotation_path, output_file, replicates=replicates, normalization=normalization, LOESS=LOESS, NTerminus=NTerminus, CTerminus=CTerminus, wxobj=wxobj)
+ self.minread = minread
+
+
+
+ @classmethod
+ def fromGUI(self, wxobj):
+ """ """
+ #Get Annotation file
+ annotationPath = wxobj.annotation
+ if not transit_tools.validate_annotation(annotationPath):
+ return None
+
+ #Get selected files
+ ctrldata = wxobj.ctrlSelected()
+ if not transit_tools.validate_control_datasets(ctrldata):
+ return None
+
+ #Validate transposon types
+ types = tnseq_tools.get_file_types(ctrldata)
+ if 'himar1' in types:
+ answer = transit_tools.ShowAskWarning("Warning: One of the selected wig files looks like a Himar1 dataset. This method is designed to work on Tn5 wig files. Proceeding will fill in missing data with zeroes. Click OK to continue.")
+ if answer == wx.ID_CANCEL:
+ return None
+
+
+ #Read the parameters from the wxPython widgets
+ ignoreCodon = True
+ minread = int(wxobj.tn5GapsReadChoice.GetString(wxobj.tn5GapsReadChoice.GetCurrentSelection()))
+ NTerminus = float(wxobj.globalNTerminusText.GetValue())
+ CTerminus = float(wxobj.globalCTerminusText.GetValue())
+ replicates= wxobj.tn5GapsRepChoice.GetString(wxobj.tn5GapsRepChoice.GetCurrentSelection())
+ normalization = None
+ LOESS = False
+
+ #Get output path
+ name = transit_tools.basename(ctrldata[0])
+ defaultFileName = "tn5_gaps_output_m%d_r%s.dat" % (minread, replicates)
+
+
+ defaultDir = os.getcwd()
+ output_path = wxobj.SaveFile(defaultDir, defaultFileName)
+ if not output_path: return None
+ output_file = open(output_path, "w")
+
+
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ minread,
+ NTerminus,
+ CTerminus, wxobj)
+
+ @classmethod
+ def fromargs(self, rawargs):
+ (args, kwargs) = transit_tools.cleanargs(rawargs)
+
+ ctrldata = args[0].split(",")
+ annotationPath = args[1]
+ outpath = args[2]
+ output_file = open(outpath, "w")
+
+ replicates = kwargs.get("r", "Sum")
+ minread = int(kwargs.get("m", 1))
+ normalization = None
+ LOESS = False
+ ignoreCodon = True
+ NTerminus = 0.0
+ CTerminus = 0.0
+
+ return self(ctrldata,
+ annotationPath,
+ output_file,
+ replicates,
+ normalization,
+ LOESS,
+ ignoreCodon,
+ minread,
+ NTerminus,
+ CTerminus)
+
+
+
+
+ def Run(self):
+ self.transit_message("Starting Tn5 gaps method")
+ start_time = time.time()
+
+ self.transit_message("Getting data (May take a while)")
+ genes_obj = tnseq_tools.Genes(self.ctrldata, self.annotation_path, ignoreCodon=self.ignoreCodon, nterm=self.NTerminus, cterm=self.CTerminus)
+
+ # Combine all wigs
+ (data,position) = tnseq_tools.get_data_zero_fill(self.ctrldata)
+ combined = tnseq_tools.combine_replicates(data, method=self.replicates)
+ combined[combined < self.minread] = 0
+ counts = combined
+ counts[counts > 0] = 1
+ num_sites = counts.size
+
+ pins = numpy.mean(counts)
+ pnon = 1.0 - pins
+
+ # Calculate stats of runs
+ exprunmax = tnseq_tools.ExpectedRuns(num_sites, pnon)
+ varrun = tnseq_tools.VarR(num_sites, pnon)
+ stddevrun = math.sqrt(varrun)
+ exp_cutoff = exprunmax + 2*stddevrun
+
+ # Get the runs
+ self.transit_message("Getting non-insertion runs in genome")
+ run_arr = tnseq_tools.runs_w_info(counts)
+ pos_hash = transit_tools.get_pos_hash(self.annotation_path)
+
+ # Finally, calculate the results
+ self.transit_message("Running Tn5 gaps method")
+ results_per_gene = {}
+ for gene in genes_obj.genes:
+ results_per_gene[gene.orf] = [gene.orf, gene.name, gene.desc, gene.k, gene.n, gene.r, 0, 0, 1]
+
+ N = len(run_arr)
+ count = 0
+ accum = 0
+ self.progress_range(N)
+ for run in run_arr:
+ accum += run['length']
+ count += 1
+ genes = tnseq_tools.get_genes_in_range(pos_hash, run['start'], run['end'])
+ for gene_orf in genes:
+ gene = genes_obj[gene_orf]
+ inter_sz = self.intersect_size([run['start'], run['end']], [gene.start, gene.end]) + 1
+ percent_overlap = self.calc_overlap([run['start'], run['end']], [gene.start, gene.end])
+ run_len = run['length']
+ B = 1.0/math.log(1.0/pnon)
+ u = math.log(num_sites*pins, 1.0/pnon)
+ pval = 1.0 - tnseq_tools.GumbelCDF(run['length'], u, B)
+
+ curr_val = results_per_gene[gene.orf]
+ curr_inter_sz = curr_val[6]
+ curr_len = curr_val[7]
+ if inter_sz > curr_inter_sz:
+ results_per_gene[gene.orf] = [gene.orf, gene.name, gene.desc, gene.k, gene.n, gene.r, inter_sz, run_len, pval]
+ self.progress_update("tn5gaps", count)
+ self.transit_message_inplace("Running Tn5Gaps method... %1.1f%%" % (100.0*count/N))
+
+ data = list(results_per_gene.values())
+ exp_run_len = float(accum)/N
+
+ min_sig_len = float('inf')
+ sig_genes_count = 0
+ pval = [row[-1] for row in data]
+ padj = stat_tools.BH_fdr_correction(pval)
+ for i in range(len(data)):
+ if padj[i] < 0.05:
+ sig_genes_count += 1
+ min_sig_len = min(min_sig_len, data[i][-2])
+ data[i].append(padj[i]);
+ data[i].append('Essential' if padj[i] < 0.05 else 'Non-essential');#(data[i][0], data[i][1], data[i][2], data[i][3], data[i][4], data[i][5], data[i][6], data[i][7], data[i][8], padj[i], 'Essential' if padj[i] < 0.05 else 'Non-essential')
+ data.sort(key=lambda l: l[0])
+
+ # Output results
+ self.output.write("#Tn5 Gaps\n")
+ if self.wxobj:
+ members = sorted([attr for attr in dir(self) if not callable(getattr(self,attr)) and not attr.startswith("__")])
+ memberstr = ""
+ for m in members:
+ memberstr += "%s = %s, " % (m, getattr(self, m))
+ self.output.write("#GUI with: ctrldata=%s, annotation=%s, output=%s\n" % (",".join(self.ctrldata), self.annotation_path, self.output.name))
+ else:
+ self.output.write("#Console: python %s\n" % " ".join(sys.argv))
+
+ self.output.write("#Data: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Annotation path: %s\n" % (",".join(self.ctrldata)))
+ self.output.write("#Time: %s\n" % (time.time() - start_time))
+ self.output.write("#Essential gene count: %d\n" % (sig_genes_count))
+ self.output.write("#Minimum reads: %d\n" % (self.minread))
+ self.output.write("#Replicate combination method: %s\n" % (self.replicates))
+ self.output.write("#Minimum significant run length: %d\n" % (min_sig_len))
+ self.output.write("#Expected run length: %1.5f\n" % (exp_run_len))
+ self.output.write("#Expected max run length: %s\n" % (exprunmax))
+ self.output.write("#%s\n" % "\t".join(columns))
+ #self.output.write("#Orf\tName\tDesc\tk\tn\tr\tovr\tlenovr\tpval\tpadj\tcall\n")
+
+ for res in data:
+ self.output.write("%s\t%s\t%s\t%s\t%s\t%s\t%d\t%d\t%1.5f\t%1.5f\t%s\n" % (res[0], res[1], res[2], res[3], res[4], res[5], res[6], res[7], res[8], res[9], res[10]))
+ self.output.close()
+
+ self.transit_message("") # Printing empty line to flush stdout
+ self.transit_message("Adding File: %s" % (self.output.name))
+ self.add_file(filetype="Tn5 Gaps")
+ self.finish()
+ self.transit_message("Finished Tn5Gaps Method")
+
+
+ @classmethod
+ def usage_string(self):
+ return """python %s resampling <comma-separated .wig control files> <comma-separated .wig experimental files> <annotation .prot_table or GFF3> <output file> [Optional Arguments]
+
+ Optional Arguments:
+ -m <integer> := Smallest read-count to consider. Default: -m 1
+ -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum
+ """ % (sys.argv[0])
+
+
+
+
+
+
+ def intersect_size(self, intv1, intv2):
+ first = intv1 if intv1[0] < intv2[0] else intv2
+ second = intv1 if first == intv2 else intv2
+
+ if first[1] < second[0]:
+ return 0
+
+ right_ovr = min(first[1], second[1])
+ left_ovr = max(first[0], second[0])
+
+ return right_ovr - left_ovr
+
+
+ def calc_overlap(self, run_interv, gene_interv):
+ first = run_interv if run_interv[0] < gene_interv[0] else gene_interv
+ second = run_interv if first == gene_interv else gene_interv
+
+ if second[0] > first[0] and second[1] < first[1]:
+ return 1.0
+
+ intersect = self.intersect_size(run_interv, gene_interv)
+ return float(intersect)/(gene_interv[1] - gene_interv[0])
+
+
+
+
+if __name__ == "__main__":
+
+ (args, kwargs) = transit_tools.cleanargs(sys.argv[1:])
+
+ G = Tn5GapsMethod.fromargs(sys.argv[1:])
+
+ G.console_message("Printing the member variables:")
+ G.print_members()
+
+ print ""
+ print "Running:"
+
+ G.Run()
+
+
diff --git a/src/pytransit/data/cholesterol_H37Rv_merged.wig b/src/pytransit/data/cholesterol_H37Rv_merged.wig
new file mode 100644
index 0000000..f74c151
--- /dev/null
+++ b/src/pytransit/data/cholesterol_H37Rv_merged.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/cholesterol_H37Rv_rep1.wig b/src/pytransit/data/cholesterol_H37Rv_rep1.wig
new file mode 100644
index 0000000..40f081b
--- /dev/null
+++ b/src/pytransit/data/cholesterol_H37Rv_rep1.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/cholesterol_H37Rv_rep2.wig b/src/pytransit/data/cholesterol_H37Rv_rep2.wig
new file mode 100644
index 0000000..6ffb99b
--- /dev/null
+++ b/src/pytransit/data/cholesterol_H37Rv_rep2.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/cholesterol_H37Rv_rep3.wig b/src/pytransit/data/cholesterol_H37Rv_rep3.wig
new file mode 100644
index 0000000..18dac2c
--- /dev/null
+++ b/src/pytransit/data/cholesterol_H37Rv_rep3.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/glycerol_H37Rv_merged.wig b/src/pytransit/data/glycerol_H37Rv_merged.wig
new file mode 100644
index 0000000..66d6a07
--- /dev/null
+++ b/src/pytransit/data/glycerol_H37Rv_merged.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
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diff --git a/src/pytransit/data/glycerol_H37Rv_rep1.wig b/src/pytransit/data/glycerol_H37Rv_rep1.wig
new file mode 100644
index 0000000..4f03d34
--- /dev/null
+++ b/src/pytransit/data/glycerol_H37Rv_rep1.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/glycerol_H37Rv_rep2.wig b/src/pytransit/data/glycerol_H37Rv_rep2.wig
new file mode 100644
index 0000000..b05df70
--- /dev/null
+++ b/src/pytransit/data/glycerol_H37Rv_rep2.wig
@@ -0,0 +1,74607 @@
+# from Griffin et al, (2011). PLOS Pathogens, e1002251.
+variableStep chrom=H37Rv
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diff --git a/src/pytransit/data/gumbel_glycerol_reads_rep1_s10000_b500_t1.dat b/src/pytransit/data/gumbel_glycerol_reads_rep1_s10000_b500_t1.dat
new file mode 100644
index 0000000..ae28e77
--- /dev/null
+++ b/src/pytransit/data/gumbel_glycerol_reads_rep1_s10000_b500_t1.dat
@@ -0,0 +1,3999 @@
+#Gumbel
+#Command used: python transit.py
+#FDR Corrected thresholds: 0.989800, 0.038400
+#MH Acceptance-Rate: 45.72%
+#Total Iterations Performed: 10499
+#Sample Size: 10000
+#phi estimate: 0.280561
+#Time: 143.290342808
+#Orf Name Desc k n r s zbar Call
+Rv0001 dnaA chromosomal replication initiation protein 0 29 29 1323 1.000000 E
+Rv0002 dnaN DNA polymerase III subunit beta 0 27 27 1006 1.000000 E
+Rv0003 recF recombination protein F 11 33 7 71 0.000000 NE
+Rv0004 - hypothetical protein Rv0004 0 5 5 299 0.992800 E
+Rv0005 gyrB DNA gyrase subunit B 0 38 38 1822 1.000000 E
+Rv0006 gyrA DNA gyrase subunit A 0 42 42 2156 1.000000 E
+Rv0007 - POSSIBLE CONSERVED MEMBRANE PROTEIN 3 10 5 393 0.721300 U
+Rv0008c - POSSIBLE MEMBRANE PROTEIN 3 4 1 2 0.000000 NE
+Rv0009 ppiA PROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) 6 6 0 0 0.000000 NE
+Rv0010c - PROBABLE CONSERVED MEMBRANE PROTEIN 6 10 3 29 0.000000 NE
+Rv0011c - putative septation inhibitor protein 0 3 3 133 -1.000000 S
+Rv0012 - PROBABLE CONSERVED MEMBRANE PROTEIN 10 14 3 89 0.000000 NE
+Rv0013 trpG para-aminobenzoate synthase component II 0 13 13 610 0.999900 E
+Rv0014c pknB TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) 0 22 22 1562 1.000000 E
+Rv0015c pknA TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) 0 13 13 1109 1.000000 E
+Rv0016c pbpA PROBABLE PENICILLIN-BINDING PROTEIN PBPA 11 34 6 133 0.000000 NE
+Rv0017c rodA PROBABLE CELL DIVISION PROTEIN RODA 11 23 4 149 0.000000 NE
+Rv0018c ppp POSSIBLE SERINE/THREONINE PHOSPHATASE PPP 8 23 10 641 0.995800 E
+Rv0019c - hypothetical protein Rv0019c 7 12 2 20 0.000000 NE
+Rv0020c TB39.8 hypothetical protein Rv0020c 6 50 42 1015 1.000000 E
+Rv0021c - hypothetical protein Rv0021c 16 18 1 2 0.000000 NE
+Rv0022c whiB5 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 8 8 0 0 0.000000 NE
+Rv0023 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 0 12 12 582 1.000000 E
+Rv0024 - PUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN 9 11 1 2 0.000000 NE
+Rv0025 - hypothetical protein Rv0025 7 7 0 0 0.000000 NE
+Rv0026 - hypothetical protein Rv0026 8 12 1 2 0.000000 NE
+Rv0027 - hypothetical protein Rv0027 2 5 2 31 0.000000 NE
+Rv0028 - hypothetical protein Rv0028 2 4 2 19 -1.000000 S
+Rv0029 - hypothetical protein Rv0029 14 17 1 2 0.000000 NE
+Rv0030 - hypothetical protein Rv0030 1 5 3 86 0.000900 NE
+Rv0031 - POSSIBLE REMNANT OF A TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv0032 bioF2 POSSIBLE 8-AMINO-7-OXONONANOATE SYNTHASE BIOF2 (AONS) (8-AMINO-7-KETOPELARGONATE SYNTHASE) (7-KETO-8-AMINO-PELARGONIC ACID SYNTHETASE) (7-KAP SYNTHETASE) (L-ALANINE--PIMELYL CoA LIGASE) 23 50 12 231 0.166800 U
+Rv0033 acpA PROBABLE ACYL CARRIER PROTEIN ACPA (ACP) 3 3 0 0 -1.000000 S
+Rv0034 - hypothetical protein Rv0034 4 5 1 2 -1.000000 S
+Rv0035 fadD34 PROBABLE FATTY-ACID-CoA LIGASE FADD34 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 22 24 1 2 0.000000 NE
+Rv0036c - hypothetical protein Rv0036c 4 4 0 0 0.000000 NE
+Rv0037c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 10 17 4 335 0.212900 U
+Rv0038 - hypothetical protein Rv0038 5 7 1 2 0.000000 NE
+Rv0039c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 2 4 2 25 0.000000 NE
+Rv0040c mtc28 SECRETED PROLINE RICH PROTEIN MTC28 (PROLINE RICH 28 KDA ANTIGEN) 5 8 1 2 0.000000 NE
+Rv0041 leuS leucyl-tRNA synthetase 0 66 66 2526 1.000000 E
+Rv0042c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MARR-FAMILY) 3 5 1 2 0.000000 NE
+Rv0043c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) 6 7 1 2 0.000000 NE
+Rv0044c - POSSIBLE OXIDOREDUCTASE 16 19 1 2 0.000000 NE
+Rv0045c - POSSIBLE HYDROLASE 6 6 0 0 0.000000 NE
+Rv0046c ino1 MYO-INOSITOL-1-PHOSPHATE SYNTHASE INO1 (Inositol 1-phosphate synthetase) (D-glucose 6-phosphate cycloaldolase) (Glucose 6-phosphate cyclase) (Glucocycloaldolase) 0 15 15 923 1.000000 E
+Rv0047c - hypothetical protein Rv0047c 3 7 2 56 0.000000 NE
+Rv0048c - POSSIBLE MEMBRANE PROTEIN 13 14 1 2 0.000000 NE
+Rv0049 - hypothetical protein Rv0049 4 6 1 2 0.000000 NE
+Rv0050 ponA1 PROBABLE BIFUNCTIONAL PENICILLIN-BINDING PROTEIN 1A/1B PONA1 (MUREIN POLYMERASE) (PBP1): PENICILLIN-INSENSITIVE TRANSGLYCOSYLASE (PEPTIDOGLYCAN TGASE) + PENICILLIN-SENSITIVE TRANSPEPTIDASE (DD-TRANSPEPTIDASE) 10 33 5 188 0.000000 NE
+Rv0051 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 19 33 2 22 0.000000 NE
+Rv0052 - hypothetical protein Rv0052 5 6 1 2 0.000000 NE
+Rv0053 rpsF 30S ribosomal protein S6 0 5 5 215 0.994200 E
+Rv0054 ssb single-strand DNA-binding protein 0 5 5 218 0.994100 E
+Rv0055 rpsR 30S ribosomal protein S18 1 4 3 69 0.000000 NE
+Rv0056 rplI 50S ribosomal protein L9 5 7 2 108 0.000000 NE
+Rv0057 - hypothetical protein Rv0057 7 15 2 14 0.000000 NE
+Rv0058 dnaB replicative DNA helicase 0 36 36 2292 1.000000 E
+Rv0059 - hypothetical protein Rv0059 12 16 1 2 0.000000 NE
+Rv0060 - hypothetical protein Rv0060 0 21 21 893 1.000000 E
+Rv0061 - hypothetical protein Rv0061 3 6 2 10 0.000000 NE
+Rv0062 celA1 POSSIBLE CELLULASE CELA1 (ENDOGLUCANASE) (ENDO-1,4-BETA-GLUCANASE) (FI-CMCASE) (CARBOXYMETHYL CELLULASE) 18 19 1 2 0.000000 NE
+Rv0063 - POSSIBLE OXIDOREDUCTASE 17 21 3 22 0.000000 NE
+Rv0064 - hypothetical protein Rv0064 36 64 3 147 0.000000 NE
+Rv0065 - hypothetical protein Rv0065 4 7 1 2 0.000000 NE
+Rv0066c icd2 PROBABLE ISOCITRATE DEHYDROGENASE 1 33 22 1601 1.000000 E
+Rv0067c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 3 11 5 327 0.837400 U
+Rv0068 - short chain dehydrogenase 8 11 1 2 0.000000 NE
+Rv0069c sdaA PROBABLE L-SERINE DEHYDRATASE SDAA (L-SERINE DEAMINASE) (SDH) (L-SD) 6 11 2 99 0.000000 NE
+Rv0070c glyA2 PROBABLE SERINE HYDROXYMETHYLTRANSFERASE GLYA2 (SERINE METHYLASE 2) (SHMT 2) 10 16 2 89 0.000000 NE
+Rv0071 - POSSIBLE MATURASE 5 8 3 36 0.000000 NE
+Rv0072 - PROBABLE GLUTAMINE-TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER 13 16 2 36 0.000000 NE
+Rv0073 - PROBABLE GLUTAMINE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 12 13 1 2 0.000000 NE
+Rv0074 - hypothetical protein Rv0074 8 14 2 100 0.000000 NE
+Rv0075 - PROBABLE AMINOTRANSFERASE 17 22 1 2 0.000000 NE
+Rv0076c - PROBABLE MEMBRANE PROTEIN 3 3 0 0 -1.000000 S
+Rv0077c - PROBABLE OXIDOREDUCTASE 7 11 3 197 0.000000 NE
+Rv0078 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 7 2 91 0.000000 NE
+Rv0078A - hypothetical protein Rv0078A 8 9 1 2 0.000000 NE
+Rv0079 - hypothetical protein Rv0079 10 13 1 2 0.000000 NE
+Rv0080 - hypothetical protein Rv0080 2 3 1 2 -1.000000 S
+Rv0081 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 4 5 1 2 0.000000 NE
+Rv0082 - PROBABLE OXIDOREDUCTASE 4 7 3 35 0.000000 NE
+Rv0083 - PROBABLE OXIDOREDUCTASE 15 20 3 77 0.000000 NE
+Rv0084 hycD POSSIBLE FORMATE HYDROGENLYASE HYCD (FHL) 6 7 1 2 0.000000 NE
+Rv0085 hycP POSSIBLE HYDROGENASE HYCP 1 3 2 171 0.000000 NE
+Rv0086 hycQ POSSIBLE HYDROGENASE HYCQ 8 14 1 2 0.000000 NE
+Rv0087 hycE POSSIBLE FORMATE HYDROGENASE HYCE (FHL) 7 22 6 231 0.001500 NE
+Rv0088 - hypothetical protein Rv0088 3 11 7 238 0.063500 U
+Rv0089 - POSSIBLE METHYLTRANSFERASE/METHYLASE 7 9 1 2 0.000000 NE
+Rv0090 - POSSIBLE MEMBRANE PROTEIN 8 12 1 2 0.000000 NE
+Rv0091 mtn PROBABLE BIFUNCTIONAL MTA/SAH NUCLEOSIDASE MTN: 5'-METHYLTHIOADENOSINE NUCLEOSIDASE (METHYLTHIOADENOSINE METHYLTHIORIBOHYDROLASE) + S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE (S-ADENOSYL-L-HOMOCYSTEINE HOMOCYSTEINYLRIBOHYDROLASE) 8 11 2 56 0.000000 NE
+Rv0092 ctpA PROBABLE CATION TRANSPORTER P-TYPE ATPASE A CTPA 21 27 3 140 0.000000 NE
+Rv0093c - PROBABLE CONSERVED MEMBRANE PROTEIN 4 7 1 2 0.000000 NE
+Rv0094c - hypothetical protein Rv0094c 0 0 0 0 -1.000000 S
+Rv0095c - hypothetical protein Rv0095c 1 6 5 227 0.976900 U
+Rv0096 PPE1 PPE FAMILY PROTEIN 19 30 3 106 0.000000 NE
+Rv0097 - POSSIBLE OXIDOREDUCTASE 14 24 2 8 0.000000 NE
+Rv0098 - hypothetical protein Rv0098 7 10 1 2 0.000000 NE
+Rv0099 fadD10 acyl-CoA synthetase 11 30 7 416 0.796000 U
+Rv0100 - hypothetical protein Rv0100 2 3 1 2 -1.000000 S
+Rv0101 nrp PROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE) 59 103 5 362 0.017600 NE
+Rv0102 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 0 38 38 1711 1.000000 E
+Rv0103c ctpB PROBABLE CATION-TRANSPORTER P-TYPE ATPASE B CTPB 24 28 2 12 0.000000 NE
+Rv0104 - hypothetical protein Rv0104 18 25 3 52 0.000000 NE
+Rv0105c rpmB 50S ribosomal protein L28 3 5 1 2 -1.000000 S
+Rv0106 - hypothetical protein Rv0106 8 10 1 2 0.000000 NE
+Rv0107c ctpI PROBABLE CATION-TRANSPORTER ATPASE I CTPI 29 59 9 287 0.414100 U
+Rv0108c - hypothetical protein Rv0108c 2 2 0 0 -1.000000 S
+Rv0109 PE_PGRS1 PE-PGRS FAMILY PROTEIN 11 25 3 92 0.000000 NE
+Rv0110 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 11 13 1 2 0.000000 NE
+Rv0111 - POSSIBLE TRANSMEMBRANE ACYLTRANSFERASE 28 40 2 63 0.000000 NE
+Rv0112 gca POSSIBLE GDP-MANNOSE 4,6-DEHYDRATASE GCA (GDP-D-MANNOSE DEHYDRATASE) 7 29 7 135 0.000000 NE
+Rv0113 gmhA PROBABLE SEDOHEPTULOSE-7-PHOSPHATE ISOMERASE GMHA (PHOSPHOHEPTOSE ISOMERASE) 3 12 4 167 0.000000 NE
+Rv0114 gmhB POSSIBLE D-ALPHA,BETA-D-HEPTOSE-1,7-BIPHOSPHATE PHOSPHATASE GMHB (D-GLYCERO-D-MANNO-HEPTOSE 7-PHOSPHATE KINASE) 7 9 1 2 0.000000 NE
+Rv0115 hddA POSSIBLE D-ALPHA-D-HEPTOSE-7-PHOSPHATE KINASE HDDA 16 17 1 2 0.000000 NE
+Rv0116c - POSSIBLE CONSERVED MEMBRANE PROTEIN 14 15 1 2 0.000000 NE
+Rv0117 oxyS OXIDATIVE STRESS RESPONSE REGULATORY PROTEIN OXYS 8 16 4 170 0.000000 NE
+Rv0118c oxcA putative oxalyl-CoA decarboxylase 11 25 8 483 0.931000 U
+Rv0119 fadD7 acyl-CoA synthetase 1 13 9 469 0.993800 E
+Rv0120c fusA2 elongation factor G 11 25 6 354 0.460900 U
+Rv0121c - hypothetical protein Rv0121c 6 10 3 39 0.000000 NE
+Rv0122 - hypothetical protein Rv0122 4 9 3 13 0.000000 NE
+Rv0123 - hypothetical protein Rv0123 0 7 7 303 0.999100 E
+Rv0124 PE_PGRS2 PE-PGRS FAMILY PROTEIN 7 11 2 101 0.000000 NE
+Rv0125 pepA PROBABLE SERINE PROTEASE PEPA (SERINE PROTEINASE) (MTB32A) 8 9 1 2 0.000000 NE
+Rv0126 treS TREHALOSE SYNTHASE TRES 7 29 9 357 0.957700 U
+Rv0127 - hypothetical protein Rv0127 0 28 28 1189 1.000000 E
+Rv0128 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 16 17 1 2 0.000000 NE
+Rv0129c fbpC SECRETED ANTIGEN 85-C FBPC (85C) (ANTIGEN 85 COMPLEX C) (AG58C) (MYCOLYL TRANSFERASE 85C) (FIBRONECTIN-BINDING PROTEIN C) 10 27 6 102 0.000000 NE
+Rv0130 - hypothetical protein Rv0130 3 3 0 0 -1.000000 S
+Rv0131c fadE1 PROBABLE ACYL-CoA DEHYDROGENASE FADE1 15 17 1 2 0.000000 NE
+Rv0132c fgd2 PUTATIVE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD2 10 14 1 2 0.000000 NE
+Rv0133 - PROBABLE ACETYLTRANSFERASE 6 6 0 0 0.000000 NE
+Rv0134 ephF POSSIBLE EPOXIDE HYDROLASE EPHF (EPOXIDE HYDRATASE) (ARENE-OXIDE HYDRATASE) 10 11 1 2 0.000000 NE
+Rv0135c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 6 11 2 46 0.000000 NE
+Rv0136 cyp138 PROBABLE CYTOCHROME P450 138 CYP138 18 22 1 2 0.000000 NE
+Rv0137c msrA methionine sulfoxide reductase A 8 11 1 2 0.000000 NE
+Rv0138 - hypothetical protein Rv0138 6 6 0 0 0.000000 NE
+Rv0139 - POSSIBLE OXIDOREDUCTASE 11 12 1 2 0.000000 NE
+Rv0140 - hypothetical protein Rv0140 9 14 3 41 0.000000 NE
+Rv0141c - hypothetical protein Rv0141c 5 8 2 106 0.000000 NE
+Rv0142 - hypothetical protein Rv0142 4 5 1 2 0.000000 NE
+Rv0143c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 18 25 2 22 0.000000 NE
+Rv0144 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 12 14 1 2 0.000000 NE
+Rv0145 - hypothetical protein Rv0145 11 14 1 2 0.000000 NE
+Rv0146 - hypothetical protein Rv0146 12 15 1 2 0.000000 NE
+Rv0147 - PROBABLE ALDEHYDE DEHYDROGENASE (NAD+) DEPENDENT 21 23 1 2 0.000000 NE
+Rv0148 - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 14 15 1 2 0.000000 NE
+Rv0149 - POSSIBLE QUINONE OXIDOREDUCTASE (NADPH:QUINONE OXIDOREDUCTASE) (ZETA-CRYSTALLIN) 12 19 5 163 0.000000 NE
+Rv0150c - hypothetical protein Rv0150c 3 4 1 2 0.000000 NE
+Rv0151c PE1 PE FAMILY PROTEIN 34 40 2 41 0.000000 NE
+Rv0152c PE2 PE FAMILY PROTEIN 30 35 1 2 0.000000 NE
+Rv0153c ptbB PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPB (PROTEIN-TYROSINE-PHOSPHATASE) (PTPase) 5 11 3 103 0.000000 NE
+Rv0154c fadE2 PROBABLE ACYL-CoA DEHYDROGENASE FADE2 7 11 3 336 0.119900 U
+Rv0155 pntAa PROBABLE NAD(P) TRANSHYDROGENASE (SUBUNIT ALPHA) PNTAA 6 10 2 12 0.000000 NE
+Rv0156 pntAb PROBABLE NAD(P) TRANSHYDROGENASE (SUBUNIT ALPHA) PNTAB 0 0 0 0 -1.000000 S
+Rv0157 pntB PROBABLE NAD(P) TRANSHYDROGENASE (SUBUNIT BETA) PNTB 6 10 2 83 0.000000 NE
+Rv0158 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 13 15 1 2 0.000000 NE
+Rv0159c PE3 PE FAMILY PROTEIN 41 48 2 17 0.000000 NE
+Rv0160c PE4 PE FAMILY PROTEIN 33 41 2 22 0.000000 NE
+Rv0161 - POSSIBLE OXIDOREDUCTASE 7 16 2 45 0.000000 NE
+Rv0162c adhE1 PROBABLE ZINC-TYPE ALCOHOL DEHYDROGENASE (E SUBUNIT) ADHE 8 15 2 210 0.000000 NE
+Rv0163 - hypothetical protein Rv0163 9 9 0 0 0.000000 NE
+Rv0164 TB18.5 hypothetical protein Rv0164 1 8 7 141 0.229300 U
+Rv0165c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) 5 6 1 2 0.000000 NE
+Rv0166 fadD5 acyl-CoA synthetase 18 23 2 102 0.000000 NE
+Rv0167 yrbE1A CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE1A 5 6 1 2 0.000000 NE
+Rv0168 yrbE1B CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE1B 12 13 1 2 0.000000 NE
+Rv0169 mce1A MCE-FAMILY PROTEIN MCE1A 27 33 2 38 0.000000 NE
+Rv0170 mce1B MCE-FAMILY PROTEIN MCE1B 12 16 2 19 0.000000 NE
+Rv0171 mce1C MCE-FAMILY PROTEIN MCE1C 20 23 1 2 0.000000 NE
+Rv0172 mce1D MCE-FAMILY PROTEIN MCE1D 25 31 1 2 0.000000 NE
+Rv0173 lprK POSSIBLE MCE-FAMILY LIPOPROTEIN LPRK (MCE-FAMILY LIPOPROTEIN MCE1E) 10 15 2 87 0.000000 NE
+Rv0174 mce1F MCE-FAMILY PROTEIN MCE1F 22 28 2 10 0.000000 NE
+Rv0175 - PROBABLE CONSERVED MCE ASSOCIATED MEMBRANE PROTEIN 7 9 1 2 0.000000 NE
+Rv0176 - PROBABLE CONSERVED MCE ASSOCIATED TRANSMEMBRANE PROTEIN 12 15 1 2 0.000000 NE
+Rv0177 - PROBABLE CONSERVED MCE ASSOCIATED PROTEIN 8 11 1 2 0.000000 NE
+Rv0178 - PROBABLE CONSERVED MCE ASSOCIATED MEMBRANE PROTEIN 8 11 1 2 0.000000 NE
+Rv0179c lprO POSSIBLE LIPOPROTEIN LPRO 17 22 2 13 0.000000 NE
+Rv0180c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 16 27 2 45 0.000000 NE
+Rv0181c - hypothetical protein Rv0181c 10 14 1 2 0.000000 NE
+Rv0182c sigG RNA polymerase factor sigma-70 17 19 1 2 0.000000 NE
+Rv0183 - POSSIBLE LYSOPHOSPHOLIPASE 13 14 1 2 0.000000 NE
+Rv0184 - hypothetical protein Rv0184 6 11 2 16 0.000000 NE
+Rv0185 - hypothetical protein Rv0185 3 9 3 79 0.000000 NE
+Rv0186 bglS PROBABLE BETA-GLUCOSIDASE BGLS (GENTIOBIASE) (CELLOBIASE) (BETA-D-GLUCOSIDE GLUCOHYDROLASE) 16 32 7 416 0.694100 U
+Rv0187 - PROBABLE O-METHYLTRANSFERASE 4 7 3 199 0.000000 NE
+Rv0188 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 6 8 1 2 0.000000 NE
+Rv0189c ilvD dihydroxy-acid dehydratase 0 18 18 1197 1.000000 E
+Rv0190 - hypothetical protein Rv0190 3 3 0 0 -1.000000 S
+Rv0191 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 15 17 1 2 0.000000 NE
+Rv0192 - hypothetical protein Rv0192 11 11 0 0 0.000000 NE
+Rv0192A - CONSERVED SECRETED PROTEIN 2 2 0 0 -1.000000 S
+Rv0193c - hypothetical protein Rv0193c 27 32 2 86 0.000000 NE
+Rv0194 - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 40 48 1 2 0.000000 NE
+Rv0195 - POSSIBLE TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LUXR-FAMILY) 6 6 0 0 0.000000 NE
+Rv0196 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 7 7 0 0 0.000000 NE
+Rv0197 - POSSIBLE OXIDOREDUCTASE 16 31 3 218 0.000000 NE
+Rv0198c - PROBABLE ZINC METALLOPROTEASE 18 39 8 195 0.000100 NE
+Rv0199 - PROBABLE CONSERVED MEMBRANE PROTEIN 7 12 2 23 0.000000 NE
+Rv0200 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 2 7 3 94 0.000000 NE
+Rv0201c - hypothetical protein Rv0201c 7 7 0 0 0.000000 NE
+Rv0202c mmpL11 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL11 18 36 4 394 0.048400 U
+Rv0203 - POSSIBLE EXPORTED PROTEIN 3 3 0 0 0.000000 NE
+Rv0204c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 7 19 9 327 0.985800 U
+Rv0205 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 7 12 2 27 0.000000 NE
+Rv0206c mmpL3 POSSIBLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL3 1 27 26 1974 1.000000 E
+Rv0207c - hypothetical protein Rv0207c 6 9 2 135 0.000000 NE
+Rv0208c trmB tRNA (guanine-N(7))-methyltransferase 2 10 4 153 0.000000 NE
+Rv0209 - hypothetical protein Rv0209 11 14 1 2 0.000000 NE
+Rv0210 - hypothetical protein Rv0210 8 12 2 36 0.000000 NE
+Rv0211 pckA phosphoenolpyruvate carboxykinase 0 22 22 1529 1.000000 E
+Rv0212c nadR POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN NADR (PROBABLY ASNC-FAMILY) 6 6 0 0 0.000000 NE
+Rv0213c - POSSIBLE METHYLTRANSFERASE (METHYLASE) 25 30 1 2 0.000000 NE
+Rv0214 fadD4 acyl-CoA synthetase 23 31 2 22 0.000000 NE
+Rv0215c fadE3 PROBABLE ACYL-CoA DEHYDROGENASE FADE3 10 14 1 2 0.000000 NE
+Rv0216 - hypothetical protein Rv0216 10 19 4 62 0.000000 NE
+Rv0217c lipW POSSIBLE ESTERASE LIPW 13 19 2 43 0.000000 NE
+Rv0218 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 14 18 2 24 0.000000 NE
+Rv0219 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 7 11 1 2 0.000000 NE
+Rv0220 lipC PROBABLE ESTERASE LIPC 11 22 5 76 0.000000 NE
+Rv0221 - hypothetical protein Rv0221 17 25 2 38 0.000000 NE
+Rv0222 echA1 enoyl-CoA hydratase 4 8 2 234 0.000200 NE
+Rv0223c - PROBABLE ALDEHYDE DEHYDROGENASE 11 22 5 125 0.000000 NE
+Rv0224c - POSSIBLE METHYLTRANSFERASE (METHYLASE) 0 14 14 605 1.000000 E
+Rv0225 - POSSIBLE CONSERVED PROTEIN 0 20 20 988 1.000000 E
+Rv0226c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 23 23 1445 1.000000 E
+Rv0227c - PROBABLE CONSERVED MEMBRANE PROTEIN 0 21 21 1007 1.000000 E
+Rv0228 - PROBABLE INTEGRAL MEMBRANE ACYLTRANSFERASE 0 13 13 936 1.000000 E
+Rv0229c - POSSIBLE CONSERVED MEMBRANE PROTEIN 8 16 4 65 0.000000 NE
+Rv0230c php PROBABLE PHOSPHOTRIESTERASE PHP (PARATHION HYDROLASE) (PTE) (ARYLDIALKYLPHOSPHATASE) (PARAOXONASE) (A-ESTERASE) (ARYLTRIPHOSPHATASE) (PARAOXON HYDROLASE) 11 13 2 36 0.000000 NE
+Rv0231 fadE4 PROBABLE ACYL-CoA DEHYDROGENASE FADE4 30 33 1 2 0.000000 NE
+Rv0232 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR/ACRR-FAMILY) 9 9 0 0 0.000000 NE
+Rv0233 nrdB ribonucleotide-diphosphate reductase subunit beta 11 11 0 0 0.000000 NE
+Rv0234c gabD1 succinic semialdehyde dehydrogenase 10 19 2 31 0.000000 NE
+Rv0235c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 11 22 8 291 0.804800 U
+Rv0236A - SMALL SECRETED PROTEIN 0 2 2 7 -1.000000 S
+Rv0236c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 34 34 3658 1.000000 E
+Rv0237 lpqI PROBABLE CONSERVED LIPOPROTEIN LPQI 5 12 2 17 0.000000 NE
+Rv0238 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 1 11 5 220 0.001800 NE
+Rv0239 - hypothetical protein Rv0239 2 2 0 0 -1.000000 S
+Rv0240 - hypothetical protein Rv0240 5 6 1 2 0.000000 NE
+Rv0241c - hypothetical protein Rv0241c 3 13 4 152 0.000000 NE
+Rv0242c fabG 3-ketoacyl-(acyl-carrier-protein) reductase 3 11 4 728 0.494500 U
+Rv0243 fadA2 acetyl-CoA acetyltransferase 11 18 2 33 0.000000 NE
+Rv0244c fadE5 PROBABLE ACYL-CoA DEHYDROGENASE FADE5 17 21 1 2 0.000000 NE
+Rv0245 - POSSIBLE OXIDOREDUCTASE 4 4 0 0 0.000000 NE
+Rv0246 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 19 29 4 51 0.000000 NE
+Rv0247c - fumarate reductase iron-sulfur subunit 0 9 9 589 0.998800 E
+Rv0248c sdhA succinate dehydrogenase flavoprotein subunit 4 33 21 1018 1.000000 E
+Rv0249c - PROBABLE SUCCINATE DEHYDROGENASE 3 22 14 370 0.999900 E
+Rv0250c - hypothetical protein Rv0250c 2 3 1 2 -1.000000 S
+Rv0251c hsp HEAT SHOCK PROTEIN HSP (HEAT-STRESS-INDUCED RIBOSOME-BINDING PROTEIN A) 5 5 0 0 0.000000 NE
+Rv0252 nirB PROBABLE NITRITE REDUCTASE 24 38 5 252 0.000900 NE
+Rv0253 nirD PROBABLE NITRITE REDUCTASE 5 6 1 2 0.000000 NE
+Rv0254c cobU PROBABLE BIFUNCTIONAL COBALAMIN BIOSYNTHESIS PROTEIN COBU: COBINAMIDE KINASE + COBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE 4 5 1 2 0.000000 NE
+Rv0255c cobQ1 cobyric acid synthase 11 13 1 2 0.000000 NE
+Rv0256c PPE2 PPE FAMILY PROTEIN 24 31 4 212 0.000000 NE
+Rv0257 - hypothetical protein Rv0257 3 3 0 0 0.000000 NE
+Rv0258c - hypothetical protein Rv0258c 2 6 2 77 0.000000 NE
+Rv0259c - hypothetical protein Rv0259c 4 7 1 2 0.000000 NE
+Rv0260c - bifunctional uroporphyrinogen-III synthetase/response regulator domain protein 7 18 9 385 0.990000 E
+Rv0261c narK3 PROBABLE INTEGRAL MEMBRANE NITRITE EXTRUSION PROTEIN NARK3 (NITRITE FACILITATOR) 11 22 7 175 0.000000 NE
+Rv0262c aac AMINOGLYCOSIDE 2'-N-ACETYLTRANSFERASE AAC (AAC(2')-IC) 4 6 2 29 0.000000 NE
+Rv0263c - hypothetical protein Rv0263c 9 15 1 2 0.000000 NE
+Rv0264c - hypothetical protein Rv0264c 8 9 1 2 0.000000 NE
+Rv0265c - PROBABLE PERIPLASMIC IRON-TRANSPORT LIPOPROTEIN 8 9 1 2 0.000000 NE
+Rv0266c oplA PROBABLE 5-OXOPROLINASE OPLA (5-OXO-L-PROLINASE) (PYROGLUTAMASE) (5-OPASE) 31 38 2 77 0.000000 NE
+Rv0267 narU PROBABLE INTEGRAL MEMBRANE NITRITE EXTRUSION PROTEIN NARU (NITRITE FACILITATOR) 10 11 1 2 0.000000 NE
+Rv0268c - hypothetical protein Rv0268c 10 12 1 2 0.000000 NE
+Rv0269c - hypothetical protein Rv0269c 8 10 1 2 0.000000 NE
+Rv0270 fadD2 acyl-CoA synthetase 18 21 1 2 0.000000 NE
+Rv0271c fadE6 PROBABLE ACYL-CoA DEHYDROGENASE FADE6 20 25 1 2 0.000000 NE
+Rv0272c - hypothetical protein Rv0272c 10 15 2 22 0.000000 NE
+Rv0273c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 8 15 3 61 0.000000 NE
+Rv0274 - hypothetical protein Rv0274 5 8 2 25 0.000000 NE
+Rv0275c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 4 7 2 30 0.000000 NE
+Rv0276 - hypothetical protein Rv0276 14 17 1 2 0.000000 NE
+Rv0277c - hypothetical protein Rv0277c 3 5 1 2 0.000000 NE
+Rv0278c PE_PGRS3 PE-PGRS FAMILY PROTEIN 13 23 5 324 0.156100 U
+Rv0279c PE_PGRS4 PE-PGRS FAMILY PROTEIN 14 16 1 2 0.000000 NE
+Rv0280 PPE3 PPE FAMILY PROTEIN 23 26 3 148 0.000000 NE
+Rv0281 - hypothetical protein Rv0281 11 12 1 2 0.000000 NE
+Rv0282 - hypothetical protein Rv0282 0 19 19 1596 1.000000 E
+Rv0283 - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 22 22 1312 1.000000 E
+Rv0284 - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 57 57 3462 1.000000 E
+Rv0285 PE5 PE FAMILY PROTEIN 0 5 5 186 0.993100 E
+Rv0286 PPE4 PPE FAMILY PROTEIN 0 28 28 1203 1.000000 E
+Rv0287 esxG ESAT-6 LIKE PROTEIN ESXG (CONSERVED HYPOTHETICAL PROTEIN TB9.8) 0 3 3 228 0.961900 U
+Rv0288 esxH LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4) 0 7 7 191 0.999300 E
+Rv0289 - hypothetical protein Rv0289 0 13 13 582 1.000000 E
+Rv0290 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 18 18 1198 1.000000 E
+Rv0291 mycP3 PROBABLE MEMBRANE-ANCHORED MYCOSIN MYCP3 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-3) 0 12 12 900 0.999900 E
+Rv0292 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 2 17 15 685 1.000000 E
+Rv0293c - hypothetical protein Rv0293c 15 26 3 23 0.000000 NE
+Rv0294 tam PROBABLE TRANS-ACONITATE METHYLTRANSFERASE TAM 8 13 3 38 0.000000 NE
+Rv0295c - hypothetical protein Rv0295c 5 7 2 9 0.000000 NE
+Rv0296c - PROBABLE SULFATASE 28 42 5 67 0.000000 NE
+Rv0297 PE_PGRS5 PE-PGRS FAMILY PROTEIN 7 14 4 236 0.000400 NE
+Rv0298 - hypothetical protein Rv0298 4 5 1 2 -1.000000 S
+Rv0299 - hypothetical protein Rv0299 1 2 1 2 -1.000000 S
+Rv0300 - hypothetical protein Rv0300 4 4 0 0 0.000000 NE
+Rv0301 - hypothetical protein Rv0301 7 7 0 0 0.000000 NE
+Rv0302 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR/ACRR-FAMILY) 6 8 1 2 0.000000 NE
+Rv0303 - PROBABLE DEHYDROGENASE/REDUCTASE 12 12 0 0 0.000000 NE
+Rv0304c PPE5 PPE FAMILY PROTEIN 74 119 6 163 0.000000 NE
+Rv0305c PPE6 PPE FAMILY PROTEIN 29 52 6 284 0.040700 U
+Rv0306 - PUTATIVE OXIDOREDUCTASE 4 6 1 2 0.000000 NE
+Rv0307c - hypothetical protein Rv0307c 6 8 2 66 0.000000 NE
+Rv0308 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 8 15 3 48 0.000000 NE
+Rv0309 - POSSIBLE CONSERVED EXPORTED PROTEIN 6 11 4 82 0.000000 NE
+Rv0310c - hypothetical protein Rv0310c 6 12 2 8 0.000000 NE
+Rv0311 - hypothetical protein Rv0311 8 15 6 360 0.752400 U
+Rv0312 - CONSERVED HYPOTHETICAL PROLINE AND THREONINE RICH PROTEIN 5 19 5 265 0.010700 NE
+Rv0313 - hypothetical protein Rv0313 3 4 1 2 -1.000000 S
+Rv0314c - POSSIBLE CONSERVED MEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv0315 - POSSIBLE BETA-1,3-GLUCANASE PRECURSOR 6 8 2 61 0.000000 NE
+Rv0316 - POSSIBLE MUCONOLACTONE ISOMERASE 6 8 1 2 0.000000 NE
+Rv0317c glpQ2 POSSIBLE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE GLPQ2 (GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE) 12 13 1 2 0.000000 NE
+Rv0318c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 6 6 0 0 0.000000 NE
+Rv0319 pcp pyrrolidone-carboxylate peptidase 5 7 1 2 0.000000 NE
+Rv0320 - POSSIBLE CONSERVED EXPORTED PROTEIN 11 12 1 2 0.000000 NE
+Rv0321 dcd deoxycytidine triphosphate deaminase 3 4 1 2 0.000000 NE
+Rv0322 udgA PROBABLE UDP-GLUCOSE 6-DEHYDROGENASE UDGA (UDP-GLC DEHYDROGENASE) (UDP-GLCDH) (UDPGDH) 13 21 2 72 0.000000 NE
+Rv0323c - hypothetical protein Rv0323c 5 11 2 10 0.000000 NE
+Rv0324 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY) 5 11 3 28 0.000000 NE
+Rv0325 - hypothetical protein Rv0325 6 6 0 0 0.000000 NE
+Rv0326 - hypothetical protein Rv0326 4 9 4 110 0.000000 NE
+Rv0327c cyp135A1 POSSIBLE CYTOCHROME P450 135A1 CYP135A1 8 21 9 218 0.012700 NE
+Rv0328 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR/ACRR-FAMILY) 7 11 3 76 0.000000 NE
+Rv0329c - hypothetical protein Rv0329c 4 8 2 18 0.000000 NE
+Rv0330c - hypothetical protein Rv0330c 8 9 1 2 0.000000 NE
+Rv0331 - POSSIBLE DEHYDROGENASE/REDUCTASE 14 18 2 30 0.000000 NE
+Rv0332 - hypothetical protein Rv0332 7 8 1 2 0.000000 NE
+Rv0333 - hypothetical protein Rv0333 3 4 1 2 0.000000 NE
+Rv0334 rmlA ALPHA-D-GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE RMLA (DTDP-GLUCOSE SYNTHASE) (DTDP-GLUCOSE PYROPHOSPHORYLASE) 0 15 15 538 1.000000 E
+Rv0335c PE6 PE FAMILY PROTEIN 0 1 1 2 -1.000000 S
+Rv0336 - CONSERVED 13E12 REPEAT FAMILY PROTEIN 0 1 1 2 -1.000000 S
+Rv0337c aspC aminotransferase AlaT 0 20 20 989 1.000000 E
+Rv0338c - PROBABLE IRON-SULFUR-BINDING REDUCTASE 1 35 34 2247 1.000000 E
+Rv0339c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 16 26 2 298 0.011800 NE
+Rv0340 - hypothetical protein Rv0340 1 4 3 357 0.649200 U
+Rv0341 iniB ISONIAZID INDUCTIBLE GENE PROTEIN INIB 6 15 4 194 0.000000 NE
+Rv0342 iniA ISONIAZID INDUCTIBLE GENE PROTEIN INIA 18 24 3 47 0.000000 NE
+Rv0343 iniC ISONIAZID INDUCTIBLE GENE PROTEIN INIC 8 10 1 2 0.000000 NE
+Rv0344c lpqJ PROBABLE LIPOPROTEIN LPQJ 7 10 1 2 0.000000 NE
+Rv0345 - hypothetical protein Rv0345 6 7 1 2 0.000000 NE
+Rv0346c ansP2 POSSIBLE L-ASPARAGINE PERMEASE ANSP2 (L-ASPARAGINE TRANSPORT PROTEIN) 13 26 4 185 0.000000 NE
+Rv0347 - PROBABLE CONSERVED MEMBRANE PROTEIN 0 15 15 695 1.000000 E
+Rv0348 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 5 16 7 434 0.967700 U
+Rv0349 - hypothetical protein Rv0349 5 8 2 33 0.000000 NE
+Rv0350 dnaK molecular chaperone DnaK 0 17 17 1510 1.000000 E
+Rv0351 grpE PROBABLE GRPE PROTEIN (HSP-70 COFACTOR) 0 9 9 612 0.998300 E
+Rv0352 dnaJ1 PROBABLE CHAPERONE PROTEIN DNAJ1 1 12 11 972 0.999800 E
+Rv0353 hspR PROBABLE HEAT SHOCK PROTEIN TRANSCRIPTIONAL REPRESSOR HSPR (MERR FAMILY) 5 6 1 2 0.000000 NE
+Rv0354c PPE7 PPE FAMILY PROTEIN 3 4 1 2 0.000000 NE
+Rv0355c PPE8 PPE FAMILY PROTEIN 110 149 4 157 0.000000 NE
+Rv0356c - hypothetical protein Rv0356c 7 8 1 2 0.000000 NE
+Rv0357c purA adenylosuccinate synthetase 0 23 23 1094 1.000000 E
+Rv0358 - hypothetical protein Rv0358 0 11 11 531 0.999700 E
+Rv0359 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 10 10 0 0 0.000000 NE
+Rv0360c - hypothetical protein Rv0360c 6 8 1 2 0.000000 NE
+Rv0361 - PROBABLE CONSERVED MEMBRANE PROTEIN 5 8 2 29 0.000000 NE
+Rv0362 mgtE POSSIBLE Mg2+ TRANSPORT TRANSMEMBRANE PROTEIN MGTE 12 14 1 2 0.000000 NE
+Rv0363c fba fructose-bisphosphate aldolase 0 14 14 887 1.000000 E
+Rv0364 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 1 12 11 581 0.999800 E
+Rv0365c - hypothetical protein Rv0365c 15 19 2 8 0.000000 NE
+Rv0366c - hypothetical protein Rv0366c 4 5 1 2 0.000000 NE
+Rv0367c - hypothetical protein Rv0367c 2 2 0 0 -1.000000 S
+Rv0368c - hypothetical protein Rv0368c 13 17 2 178 0.000000 NE
+Rv0369c - POSSIBLE MEMBRANE OXIDOREDUCTASE 4 7 2 122 0.000000 NE
+Rv0370c - POSSIBLE OXIDOREDUCTASE 8 19 6 405 0.791800 U
+Rv0371c - hypothetical protein Rv0371c 1 6 5 482 0.921400 U
+Rv0372c - hypothetical protein Rv0372c 2 6 3 166 0.000500 NE
+Rv0373c - PROBABLE CARBON MONOXYDE DEHYDROGENASE (LARGE CHAIN) 17 37 9 222 0.003400 NE
+Rv0374c - PROBABLE CARBON MONOXYDE DEHYDROGENASE (SMALL CHAIN) 3 4 1 2 0.000000 NE
+Rv0375c - PROBABLE CARBON MONOXYDE DEHYDROGENASE (MEDIUM CHAIN) 5 8 2 169 0.000000 NE
+Rv0376c - hypothetical protein Rv0376c 11 18 2 189 0.000000 NE
+Rv0377 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LYSR-FAMILY) 4 8 2 31 0.000000 NE
+Rv0378 - CONSERVED HYPOTHETICAL GLYCINE RICH PROTEIN 1 3 2 56 -1.000000 S
+Rv0379 secE2 POSSIBLE PROTEIN TRANSPORT PROTEIN SECE2 1 2 1 2 -1.000000 S
+Rv0380c - POSSIBLE RNA METHYLTRANSFERASE (RNA METHYLASE) 4 10 4 169 0.000000 NE
+Rv0381c - hypothetical protein Rv0381c 14 17 1 2 0.000000 NE
+Rv0382c pyrE orotate phosphoribosyltransferase 0 12 12 404 1.000000 E
+Rv0383c - POSSIBLE CONSERVED SECRETED PROTEIN 0 8 8 633 0.996000 E
+Rv0384c clpB PROBABLE ENDOPEPTIDASE ATP BINDING PROTEIN (CHAIN B) CLPB (CLPB PROTEIN) (HEAT SHOCK PROTEIN F84.1) 0 21 21 2274 1.000000 E
+Rv0385 - hypothetical protein Rv0385 16 19 2 22 0.000000 NE
+Rv0386 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LUXR/UHPA-FAMILY) 31 41 3 254 0.000200 NE
+Rv0387c - hypothetical protein Rv0387c 9 11 1 2 0.000000 NE
+Rv0388c PPE9 PPE FAMILY PROTEIN 6 8 1 2 0.000000 NE
+Rv0389 purT phosphoribosylglycinamide formyltransferase 2 6 7 1 2 0.000000 NE
+Rv0390 - hypothetical protein Rv0390 3 6 2 23 0.000000 NE
+Rv0391 metZ O-succinylhomoserine sulfhydrylase 8 20 6 396 0.762400 U
+Rv0392c ndhA PROBABLE MEMBRANE NADH DEHYDROGENASE NDHA 10 15 2 32 0.000000 NE
+Rv0393 - CONSERVED 13E12 REPEAT FAMILY PROTEIN 9 10 1 2 0.000000 NE
+Rv0394c - POSSIBLE SECRETED PROTEIN 6 9 2 99 0.000000 NE
+Rv0395 - hypothetical protein Rv0395 5 6 1 2 0.000000 NE
+Rv0396 - hypothetical protein Rv0396 2 4 2 9 -1.000000 S
+Rv0397 - CONSERVED 13E12 REPEAT FAMILY PROTEIN 2 3 1 2 0.000000 NE
+Rv0398c - POSSIBLE SECRETED PROTEIN 2 4 2 155 0.000000 NE
+Rv0399c lpqK POSSIBLE CONSERVED LIPOPROTEIN LPQK 11 23 7 136 0.000000 NE
+Rv0400c fadE7 ACYL-CoA DEHYDROGENASE FADE7 5 10 3 31 0.000000 NE
+Rv0401 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 2 3 1 2 -1.000000 S
+Rv0402c mmpL1 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL1 36 48 3 133 0.000000 NE
+Rv0403c mmpS1 PROBABLE CONSERVED MEMBRANE PROTEIN MMPS1 5 7 1 2 0.000000 NE
+Rv0404 fadD30 acyl-CoA synthetase 21 80 22 425 1.000000 E
+Rv0405 pks6 PROBABLE MEMBRANE BOUND POLYKETIDE SYNTHASE PKS6 36 103 17 303 0.999900 E
+Rv0406c - BETA LACTAMASE LIKE PROTEIN 11 13 1 2 0.000000 NE
+Rv0407 fgd1 PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1 15 18 2 189 0.000000 NE
+Rv0408 pta phosphate acetyltransferase 21 38 5 164 0.000000 NE
+Rv0409 ackA acetate kinase 10 16 2 8 0.000000 NE
+Rv0410c pknG SERINE/THREONINE-PROTEIN KINASE PKNG (PROTEIN KINASE G) (STPK G) 0 29 29 1630 1.000000 E
+Rv0411c glnH PROBABLE GLUTAMINE-BINDING LIPOPROTEIN GLNH (GLNBP) 0 8 8 509 0.996600 E
+Rv0412c - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 21 21 971 1.000000 E
+Rv0413 mutT3 POSSIBLE MUTATOR PROTEIN MUTT3 (7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE) (8-OXO-DGTPASE) (DGTP PYROPHOSPHOHYDROLASE) 4 5 1 2 0.000000 NE
+Rv0414c thiE thiamine-phosphate pyrophosphorylase 0 9 9 493 0.998400 E
+Rv0415 thiO POSSIBLE THIAMINE BIOSYNTHESIS OXIDOREDUCTASE THIO 0 11 11 761 0.999900 E
+Rv0416 thiS sulfur carrier protein ThiS 0 4 4 85 -1.000000 S
+Rv0417 thiG thiazole synthase 0 14 14 633 1.000000 E
+Rv0418 lpqL PROBABLE LIPOPROTEIN AMINOPEPTIDASE LPQL 18 27 3 67 0.000000 NE
+Rv0419 lpqM POSSIBLE LIPOPROTEIN PEPTIDASE LPQM 14 18 2 20 0.000000 NE
+Rv0420c - POSSIBLE TRANSMEMBRANE PROTEIN 7 7 0 0 0.000000 NE
+Rv0421c - hypothetical protein Rv0421c 2 8 4 238 0.012900 NE
+Rv0422c thiD phosphomethylpyrimidine kinase 0 14 14 678 1.000000 E
+Rv0423c thiC thiamine biosynthesis protein ThiC 0 19 19 1428 1.000000 E
+Rv0424c - hypothetical protein Rv0424c 6 8 1 2 0.000000 NE
+Rv0425c ctpH POSSIBLE METAL CATION TRANSPORTING P-TYPE ATPASE CTPH 23 35 3 261 0.000100 NE
+Rv0426c - POSSIBLE TRANSMEMBRANE PROTEIN 2 2 0 0 -1.000000 S
+Rv0427c xthA PROBABLE EXODEOXYRIBONUCLEASE III PROTEIN XTHA (EXONUCLEASE III) (EXO III) (AP ENDONUCLEASE VI) 9 13 2 31 0.000000 NE
+Rv0428c - hypothetical protein Rv0428c 7 12 2 212 0.000000 NE
+Rv0429c def peptide deformylase 0 8 8 457 0.996600 E
+Rv0430 - hypothetical protein Rv0430 0 3 3 66 -1.000000 S
+Rv0431 - PUTATIVE TUBERCULIN RELATED PEPTIDE 0 9 9 386 0.999600 E
+Rv0432 sodC PROBABLE PERIPLASMIC SUPEROXIDE DISMUTASE 11 12 1 2 0.000000 NE
+Rv0433 - hypothetical protein Rv0433 16 22 3 108 0.000000 NE
+Rv0434 - hypothetical protein Rv0434 10 13 1 2 0.000000 NE
+Rv0435c - PUTATIVE CONSERVED ATPASE 18 21 1 2 0.000000 NE
+Rv0436c pssA PROBABLE CDP-DIACYLGLYCEROL--SERINE O-PHOSPHATIDYLTRANSFERASE PSSA (PS SYNTHASE) (PHOSPHATIDYLSERINE SYNTHASE) 5 16 8 282 0.836600 U
+Rv0437c psd phosphatidylserine decarboxylase 2 8 6 446 0.966400 U
+Rv0438c moeA2 PROBABLE MOLYBDOPTERIN BIOSYNTHESIS PROTEIN MOEA2 10 13 1 2 0.000000 NE
+Rv0439c - short chain dehydrogenase 13 18 2 28 0.000000 NE
+Rv0440 groEL chaperonin GroEL 0 11 11 1253 0.999900 E
+Rv0441c - hypothetical protein Rv0441c 7 7 0 0 0.000000 NE
+Rv0442c PPE10 PPE FAMILY PROTEIN 15 22 2 56 0.000000 NE
+Rv0443 - hypothetical protein Rv0443 10 12 2 23 0.000000 NE
+Rv0444c - hypothetical protein Rv0444c 4 7 1 2 0.000000 NE
+Rv0445c sigK RNA polymerase sigma factor SigK 8 10 1 2 0.000000 NE
+Rv0446c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 13 15 1 2 0.000000 NE
+Rv0447c ufaA1 PROBABLE CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE UFAA1 (CYCLOPROPANE FATTY ACID SYNTHASE) (CFA SYNTHASE) 22 25 1 2 0.000000 NE
+Rv0448c - hypothetical protein Rv0448c 13 13 0 0 0.000000 NE
+Rv0449c - hypothetical protein Rv0449c 19 23 2 33 0.000000 NE
+Rv0450c mmpL4 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL4 35 77 9 157 0.000000 NE
+Rv0451c mmpS4 PROBABLE CONSERVED MEMBRANE PROTEIN MMPS4 3 14 6 144 0.000000 NE
+Rv0452 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 9 9 0 0 0.000000 NE
+Rv0453 PPE11 PPE FAMILY PROTEIN 15 21 2 107 0.000000 NE
+Rv0454 - hypothetical protein Rv0454 6 6 0 0 0.000000 NE
+Rv0455c - hypothetical protein Rv0455c 0 10 10 298 0.999700 E
+Rv0456A - hypothetical protein Rv0456A 3 4 1 2 -1.000000 S
+Rv0456c echA2 enoyl-CoA hydratase 7 9 1 2 0.000000 NE
+Rv0457c - PROBABLE PEPTIDASE 19 34 7 174 0.000000 NE
+Rv0458 - PROBABLE ALDEHYDE DEHYDROGENASE 14 18 1 2 0.000000 NE
+Rv0459 - hypothetical protein Rv0459 4 5 1 2 0.000000 NE
+Rv0460 - CONSERVED HYDROPHOBIC PROTEIN 1 2 1 2 -1.000000 S
+Rv0461 - PROBABLE TRANSMEMBRANE PROTEIN 13 15 1 2 0.000000 NE
+Rv0462 lpd dihydrolipoamide dehydrogenase 0 25 25 1113 1.000000 E
+Rv0463 - PROBABLE CONSERVED MEMBRANE PROTEIN 2 3 1 2 -1.000000 S
+Rv0464c - hypothetical protein Rv0464c 10 14 2 97 0.000000 NE
+Rv0465c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 20 24 1 2 0.000000 NE
+Rv0466 - hypothetical protein Rv0466 6 8 1 2 0.000000 NE
+Rv0467 icl isocitrate lyase 4 18 9 342 0.982000 U
+Rv0468 fadB2 3-hydroxybutyryl-CoA dehydrogenase 8 10 1 2 0.000000 NE
+Rv0469 umaA POSSIBLE MYCOLIC ACID SYNTHASE UMAA 15 21 3 100 0.000000 NE
+Rv0470A - hypothetical protein Rv0470A 10 11 1 2 0.000000 NE
+Rv0470c pcaA MYCOLIC ACID SYNTHASE PCAA (CYCLOPROPANE SYNTHASE) 8 10 2 185 0.000000 NE
+Rv0471c - hypothetical protein Rv0471c 11 12 1 2 0.000000 NE
+Rv0472c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 6 9 2 8 0.000000 NE
+Rv0473 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 9 14 1 2 0.000000 NE
+Rv0474 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 7 7 0 0 0.000000 NE
+Rv0475 hbhA IRON-REGULATED HEPARIN BINDING HEMAGGLUTININ HBHA (ADHESIN) 7 9 2 19 0.000000 NE
+Rv0476 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 5 5 0 0 0.000000 NE
+Rv0477 - POSSIBLE CONSERVED SECRETED PROTEIN 4 5 1 2 0.000000 NE
+Rv0478 deoC deoxyribose-phosphate aldolase 3 3 0 0 0.000000 NE
+Rv0479c - PROBABLE CONSERVED MEMBRANE PROTEIN 1 12 11 595 0.999100 E
+Rv0480c - POSSIBLE AMIDOHYDROLASE 12 14 1 2 0.000000 NE
+Rv0481c - hypothetical protein Rv0481c 9 11 1 2 0.000000 NE
+Rv0482 murB UDP-N-acetylenolpyruvoylglucosamine reductase 0 10 10 666 0.999100 E
+Rv0483 lprQ PROBABLE CONSERVED LIPOPROTEIN LPRQ 22 24 1 2 0.000000 NE
+Rv0484c - PROBABLE SHORT-CHAIN TYPE OXIDOREDUCTASE 5 8 1 2 0.000000 NE
+Rv0485 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 17 21 2 110 0.000000 NE
+Rv0486 - MANNOSYLTRANSFERASE 1 11 10 1112 1.000000 E
+Rv0487 - hypothetical protein Rv0487 9 9 0 0 0.000000 NE
+Rv0488 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 8 9 1 2 0.000000 NE
+Rv0489 gpm1 phosphoglyceromutase 0 11 11 538 0.999900 E
+Rv0490 senX3 PUTATIVE TWO COMPONENT SENSOR HISTIDINE KINASE SENX3 10 16 4 36 0.000000 NE
+Rv0491 regX3 TWO COMPONENT SENSORY TRANSDUCTION PROTEIN REGX3 (TRANSCRIPTIONAL REGULATORY PROTEIN) (PROBABLY LUXR-FAMILY) 6 8 1 2 0.000000 NE
+Rv0492A - hypothetical protein Rv0492A 4 4 0 0 0.000000 NE
+Rv0492c - PROBABLE OXIDOREDUCTASE GMC-TYPE 11 14 1 2 0.000000 NE
+Rv0493c - hypothetical protein Rv0493c 13 16 2 53 0.000000 NE
+Rv0494 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) 5 6 1 2 0.000000 NE
+Rv0495c - hypothetical protein Rv0495c 8 11 2 19 0.000000 NE
+Rv0496 - hypothetical protein Rv0496 5 8 3 242 0.001500 NE
+Rv0497 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 1 12 9 476 0.995600 E
+Rv0498 - hypothetical protein Rv0498 9 11 1 2 0.000000 NE
+Rv0499 - hypothetical protein Rv0499 5 5 0 0 0.000000 NE
+Rv0500 proC pyrroline-5-carboxylate reductase 0 11 11 672 0.999800 E
+Rv0500A - hypothetical protein Rv0500A 2 3 1 2 0.000000 NE
+Rv0500B - hypothetical protein Rv0500B 1 1 0 0 -1.000000 S
+Rv0501 galE2 POSSIBLE UDP-GLUCOSE 4-EPIMERASE GALE2 (GALACTOWALDENASE) (UDP-GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHATE GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHO-GALACTOSE 4-EPIMERASE) 16 23 2 37 0.000000 NE
+Rv0502 - hypothetical protein Rv0502 9 16 5 67 0.000000 NE
+Rv0503c cmaA2 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2 CMAA2 (CYCLOPROPANE FATTY ACID SYNTHASE) (CFA SYNTHASE) (CYCLOPROPANE MYCOLIC ACID SYNTHASE 2) (MYCOLIC ACID TRANS-CYCLOPROPANE SYNTHETASE) 18 19 1 2 0.000000 NE
+Rv0504c - hypothetical protein Rv0504c 1 8 7 265 0.861900 U
+Rv0505c serB1 POSSIBLE PHOSPHOSERINE PHOSPHATASE SERB1 (PSP) (O-PHOSPHOSERINE PHOSPHOHYDROLASE) (PSPASE) 2 19 14 693 1.000000 E
+Rv0506 mmpS2 PROBABLE CONSERVED MEMBRANE PROTEIN MMPS2 8 8 0 0 0.000000 NE
+Rv0507 mmpL2 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL2 39 79 13 200 0.010800 NE
+Rv0508 - hypothetical protein Rv0508 4 6 1 2 0.000000 NE
+Rv0509 hemA glutamyl-tRNA reductase 0 19 19 1155 1.000000 E
+Rv0510 hemC porphobilinogen deaminase 0 10 10 318 0.999900 E
+Rv0511 hemD PROBABLE UROPORPHYRIN-III C-METHYLTRANSFERASE HEMD (UROPORPHYRINOGEN III METHYLASE) (UROGEN III METHYLASE) (SUMT) (UROGEN III METHYLASE) (UROM) 0 16 16 1400 1.000000 E
+Rv0512 hemB delta-aminolevulinic acid dehydratase 0 18 18 773 1.000000 E
+Rv0513 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 4 6 2 148 0.000000 NE
+Rv0514 - POSSIBLE TRANSMEMBRANE PROTEIN 1 1 0 0 -1.000000 S
+Rv0515 - CONSERVED 13E12 REPEAT FAMILY PROTEIN 0 1 1 2 -1.000000 S
+Rv0516c - hypothetical protein Rv0516c 7 7 0 0 0.000000 NE
+Rv0517 - POSSIBLE MEMBRANE ACYLTRANSFERASE 17 17 0 0 0.000000 NE
+Rv0518 - POSSIBLE EXPORTED PROTEIN 9 10 1 2 0.000000 NE
+Rv0519c - POSSIBLE CONSERVED MEMBRANE PROTEIN 6 8 1 2 0.000000 NE
+Rv0520 - POSSIBLE METHYLTRANSFERASE/METHYLASE (FRAGMENT) 4 4 0 0 0.000000 NE
+Rv0521 - POSSIBLE METHYLTRANSFERASE/METHYLASE (FRAGMENT) 4 4 0 0 0.000000 NE
+Rv0522 gabP PROBABLE GABA PERMEASE GABP (4-AMINO BUTYRATE TRANSPORT CARRIER) (GAMA-AMINOBUTYRATE PERMEASE) 16 19 1 2 0.000000 NE
+Rv0523c - hypothetical protein Rv0523c 4 8 3 72 0.000000 NE
+Rv0524 hemL glutamate-1-semialdehyde aminotransferase 0 20 20 1180 1.000000 E
+Rv0525 - hypothetical protein Rv0525 0 9 9 504 0.998100 E
+Rv0526 - POSSIBLE THIOREDOXIN PROTEIN (THIOL-DISULFIDE INTERCHANGE PROTEIN) 0 7 7 427 0.991500 E
+Rv0527 ccdA POSSIBLE CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCDA 0 5 5 508 0.930100 U
+Rv0528 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 15 15 1320 1.000000 E
+Rv0529 ccsA POSSIBLE CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCSA 0 15 15 663 1.000000 E
+Rv0530 - hypothetical protein Rv0530 14 16 1 2 0.000000 NE
+Rv0531 - POSSIBLE CONSERVED MEMBRANE PROTEIN 1 3 2 10 0.000000 NE
+Rv0532 PE_PGRS6 PE-PGRS FAMILY PROTEIN 9 14 2 77 0.000000 NE
+Rv0533c fabH 3-oxoacyl-(acyl carrier protein) synthase III 11 14 1 2 0.000000 NE
+Rv0534c menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase 0 11 11 633 0.999600 E
+Rv0535 pnp 5'-methylthioadenosine phosphorylase 4 9 4 191 0.000000 NE
+Rv0536 galE3 PROBABLE UDP-GLUCOSE 4-EPIMERASE GALE3 (GALACTOWALDENASE) (UDP-GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHATE GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHO-GALACTOSE 4-EPIMERASE) 10 12 1 2 0.000000 NE
+Rv0537c - PROBABLE INTEGRAL MEMBRANE PROTEIN 15 18 1 2 0.000000 NE
+Rv0538 - POSSIBLE CONSERVED MEMBRANE PROTEIN 11 14 1 2 0.000000 NE
+Rv0539 - PROBABLE DOLICHYL-PHOSPHATE SUGAR SYNTHASE (DOLICHOL-PHOSPHATE SUGAR SYNTHETASE) (DOLICHOL-PHOSPHATE SUGAR TRANSFERASE) (SUGAR PHOSPHORYLDOLICHOL SYNTHASE) 3 6 1 2 0.000000 NE
+Rv0540 - hypothetical protein Rv0540 6 10 2 50 0.000000 NE
+Rv0541c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 0 17 17 1037 1.000000 E
+Rv0542c menE O-succinylbenzoic acid--CoA ligase 0 14 14 911 1.000000 E
+Rv0543c - hypothetical protein Rv0543c 0 2 2 91 -1.000000 S
+Rv0544c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 5 6 1 2 0.000000 NE
+Rv0545c pitA PROBABLE LOW-AFFINITY INORGANIC PHOSPHATE TRANSPORTER INTEGRAL MEMBRANE PROTEIN PITA 9 14 2 8 0.000000 NE
+Rv0546c - hypothetical protein Rv0546c 6 7 1 2 0.000000 NE
+Rv0547c - short chain dehydrogenase 7 10 1 2 0.000000 NE
+Rv0548c menB naphthoate synthase 0 10 10 746 0.999900 E
+Rv0549c - hypothetical protein Rv0549c 3 4 1 2 0.000000 NE
+Rv0550c - hypothetical protein Rv0550c 1 3 2 14 -1.000000 S
+Rv0551c fadD8 acyl-CoA synthetase 25 28 1 2 0.000000 NE
+Rv0552 - hypothetical protein Rv0552 11 18 3 55 0.000000 NE
+Rv0553 menC O-succinylbenzoate synthase 0 7 7 520 0.988100 U
+Rv0554 bpoC POSSIBLE PEROXIDASE BPOC (NON-HAEM PEROXIDASE) 11 13 2 72 0.000000 NE
+Rv0555 menD 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase 0 15 15 1346 1.000000 E
+Rv0556 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 12 12 397 0.999900 E
+Rv0557 pimB MANNOSYLTRANSFERASE PIMB 4 13 5 407 0.567800 U
+Rv0558 ubiE ubiquinone/menaquinone biosynthesis methyltransferase 0 13 13 591 1.000000 E
+Rv0559c - POSSIBLE CONSERVED SECRETED PROTEIN 6 6 0 0 0.000000 NE
+Rv0560c - POSSIBLE BENZOQUINONE METHYLTRANSFERASE (METHYLASE) 9 12 1 2 0.000000 NE
+Rv0561c - POSSIBLE OXIDOREDUCTASE 14 18 2 43 0.000000 NE
+Rv0562 grcC1 PROBABLE POLYPRENYL-DIPHOSPHATE SYNTHASE GRCC1 (POLYPRENYL PYROPHOSPHATE SYNTHETASE) 0 13 13 657 0.999900 E
+Rv0563 htpX heat shock protein HtpX 1 11 10 538 0.999700 E
+Rv0564c gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 8 11 1 2 0.000000 NE
+Rv0565c - PROBABLE MONOOXYGENASE 26 34 2 69 0.000000 NE
+Rv0566c - nucleotide-binding protein 2 4 1 2 -1.000000 S
+Rv0567 - PROBABLE METHYLTRANSFERASE/METHYLASE 13 16 2 63 0.000000 NE
+Rv0568 cyp135B1 POSSIBLE CYTOCHROME P450 135B1 CYP135B1 9 12 1 2 0.000000 NE
+Rv0569 - hypothetical protein Rv0569 3 3 0 0 -1.000000 S
+Rv0570 nrdZ PROBABLE RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE (LARGE SUBUNIT) NRDZ (RIBONUCLEOTIDE REDUCTASE) 26 34 4 126 0.000000 NE
+Rv0571c - hypothetical protein Rv0571c 10 12 1 2 0.000000 NE
+Rv0572c - hypothetical protein Rv0572c 7 7 0 0 0.000000 NE
+Rv0573c - nicotinate phosphoribosyltransferase 10 14 2 8 0.000000 NE
+Rv0574c - hypothetical protein Rv0574c 14 19 2 19 0.000000 NE
+Rv0575c - hypothetical protein Rv0575c 8 11 1 2 0.000000 NE
+Rv0576 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY ARSR-FAMILY) 10 18 2 14 0.000000 NE
+Rv0577 TB27.3 hypothetical protein Rv0577 9 12 2 10 0.000000 NE
+Rv0578c PE_PGRS7 PE-PGRS FAMILY PROTEIN 11 23 3 203 0.000000 NE
+Rv0579 - hypothetical protein Rv0579 7 11 2 88 0.000000 NE
+Rv0580c - hypothetical protein Rv0580c 4 7 2 97 0.000000 NE
+Rv0581 - hypothetical protein Rv0581 4 4 0 0 -1.000000 S
+Rv0582 - hypothetical protein Rv0582 4 9 3 169 0.000000 NE
+Rv0583c lpqN PROBABLE CONSERVED LIPOPROTEIN LPQN 7 7 0 0 0.000000 NE
+Rv0584 - POSSIBLE CONSERVED EXPORTED PROTEIN 38 56 4 25 0.000000 NE
+Rv0585c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 16 34 7 229 0.000900 NE
+Rv0586 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (GNTR-FAMILY) 5 10 3 37 0.000000 NE
+Rv0587 yrbE2A CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE2A 4 11 3 70 0.000000 NE
+Rv0588 yrbE2B CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE2B 8 13 2 169 0.000000 NE
+Rv0589 mce2A MCE-FAMILY PROTEIN MCE2A 12 23 4 103 0.000000 NE
+Rv0590 mce2B MCE-FAMILY PROTEIN MCE2B 8 9 1 2 0.000000 NE
+Rv0590A - MCE-FAMILY RELATED PROTEIN 4 7 2 20 0.000000 NE
+Rv0591 mce2C MCE-FAMILY PROTEIN MCE2C 18 21 2 5 0.000000 NE
+Rv0592 mce2D MCE-FAMILY PROTEIN MCE2D 18 27 3 57 0.000000 NE
+Rv0593 lprL POSSIBLE MCE-FAMILY LIPOPROTEIN LPRL (MCE-FAMILY LIPOPROTEIN MCE2E) 13 17 3 240 0.000500 NE
+Rv0594 mce2F MCE-FAMILY PROTEIN MCE2F 24 28 1 2 0.000000 NE
+Rv0595c - hypothetical protein Rv0595c 6 6 0 0 0.000000 NE
+Rv0596c - hypothetical protein Rv0596c 0 4 4 180 0.984100 U
+Rv0597c - hypothetical protein Rv0597c 8 11 2 107 0.000000 NE
+Rv0598c - hypothetical protein Rv0598c 5 7 2 12 0.000000 NE
+Rv0599c - hypothetical protein Rv0599c 3 6 2 56 0.000100 NE
+Rv0600c - PROBABLE TWO COMPONENT SENSOR KINASE -SECOND PART 1 2 1 2 -1.000000 S
+Rv0601c - PROBABLE TWO COMPONENT SENSOR KINASE -FIRST PART 2 4 2 32 0.000000 NE
+Rv0602c tcrA PROBABLE TWO COMPONENT DNA BINDING TRANSCRIPTIONAL REGULATORY PROTEIN TCRA 8 11 1 2 0.000000 NE
+Rv0603 - POSSIBLE EXPORTED PROTEIN 1 1 0 0 -1.000000 S
+Rv0604 lpqO PROBABLE CONSERVED LIPOPROTEIN LPQO 4 5 1 2 0.000000 NE
+Rv0605 - POSSIBLE RESOLVASE 8 8 0 0 0.000000 NE
+Rv0606 - POSSIBLE TRANSPOSASE (FRAGMENT) 5 8 2 55 0.000000 NE
+Rv0607 - hypothetical protein Rv0607 1 1 0 0 -1.000000 S
+Rv0608 - hypothetical protein Rv0608 1 2 1 2 -1.000000 S
+Rv0609 - hypothetical protein Rv0609 4 7 3 69 0.000000 NE
+Rv0609A - hypothetical protein Rv0609A 1 2 1 2 -1.000000 S
+Rv0610c - hypothetical protein Rv0610c 6 7 1 2 0.000000 NE
+Rv0611c - hypothetical protein Rv0611c 9 12 1 2 0.000000 NE
+Rv0612 - hypothetical protein Rv0612 6 6 0 0 0.000000 NE
+Rv0613c - hypothetical protein Rv0613c 14 16 1 2 0.000000 NE
+Rv0614 - hypothetical protein Rv0614 11 13 1 2 0.000000 NE
+Rv0615 - PROBABLE INTEGRAL MEMBRANE PROTEIN 2 3 1 2 -1.000000 S
+Rv0616c - hypothetical protein Rv0616c 3 5 1 2 0.000000 NE
+Rv0617 - hypothetical protein Rv0617 2 3 1 2 -1.000000 S
+Rv0618 galTa PROBABLE GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE GALTA 5 6 1 2 0.000000 NE
+Rv0619 galTb PROBABLE GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE GALTB 7 12 4 188 0.000000 NE
+Rv0620 galK galactokinase 2 7 3 130 0.000000 NE
+Rv0621 - POSSIBLE MEMBRANE PROTEIN 5 9 3 97 0.000000 NE
+Rv0622 - POSSIBLE MEMBRANE PROTEIN 5 11 3 185 0.000000 NE
+Rv0623 - hypothetical protein Rv0623 0 2 2 141 -1.000000 S
+Rv0624 - hypothetical protein Rv0624 5 6 1 2 0.000000 NE
+Rv0625c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 8 10 1 2 0.000000 NE
+Rv0626 - hypothetical protein Rv0626 3 4 1 2 0.000000 NE
+Rv0627 - hypothetical protein Rv0627 0 1 1 2 -1.000000 S
+Rv0628c - hypothetical protein Rv0628c 2 3 1 2 0.000000 NE
+Rv0629c recD PROBABLE EXONUCLEASE V (ALPHA CHAIN) RECD (EXODEOXYRIBONUCLEASE V ALPHA CHAIN) (EXODEOXYRIBONUCLEASE V POLYPEPTIDE) 10 15 2 23 0.000000 NE
+Rv0630c recB PROBABLE EXONUCLEASE V (BETA CHAIN) RECB (EXODEOXYRIBONUCLEASE V BETA CHAIN)(EXODEOXYRIBONUCLEASE V POLYPEPTIDE) (CHI-SPECIFIC ENDONUCLEASE) 19 31 6 143 0.000000 NE
+Rv0631c recC PROBABLE EXONUCLEASE V (GAMMA CHAIN) RECC (EXODEOXYRIBONUCLEASE V GAMMA CHAIN)(EXODEOXYRIBONUCLEASE V POLYPEPTIDE) 12 17 2 42 0.000000 NE
+Rv0632c echA3 enoyl-CoA hydratase 5 10 4 117 0.000000 NE
+Rv0633c - POSSIBLE EXPORTED PROTEIN 10 12 1 2 0.000000 NE
+Rv0634A - hypothetical protein Rv0634A 3 6 3 89 0.006200 NE
+Rv0634B rpmG 50S ribosomal protein L33 0 3 3 57 -1.000000 S
+Rv0634c - POSSIBLE GLYOXALASE II (HYDROXYACYLGLUTATHIONE HYDROLASE) (GLX II) 11 12 1 2 0.000000 NE
+Rv0635 - hypothetical protein Rv0635 0 14 14 385 1.000000 E
+Rv0636 - hypothetical protein Rv0636 0 6 6 319 0.995300 E
+Rv0637 - hypothetical protein Rv0637 0 6 6 377 0.988100 U
+Rv0638 secE preprotein translocase subunit SecE 0 9 9 355 0.999300 E
+Rv0639 nusG transcription antitermination protein NusG 0 11 11 527 0.999500 E
+Rv0640 rplK 50S ribosomal protein L11 0 5 5 268 0.994100 E
+Rv0641 rplA 50S ribosomal protein L1 0 6 6 563 0.971300 U
+Rv0642c mmaA4 METHOXY MYCOLIC ACID SYNTHASE 4 MMAA4 (METHYL MYCOLIC ACID SYNTHASE 4) (MMA4) (HYDROXY MYCOLIC ACID SYNTHASE) 5 16 5 182 0.000000 NE
+Rv0643c mmaA3 METHOXY MYCOLIC ACID SYNTHASE 3 MMAA3 (METHYL MYCOLIC ACID SYNTHASE 3) (MMA3) (HYDROXY MYCOLIC ACID SYNTHASE) 15 19 2 8 0.000000 NE
+Rv0644c mmaA2 METHOXY MYCOLIC ACID SYNTHASE 2 MMAA2 (METHYL MYCOLIC ACID SYNTHASE 2) (MMA2) (HYDROXY MYCOLIC ACID SYNTHASE) 8 9 1 2 0.000000 NE
+Rv0645c mmaA1 METHOXY MYCOLIC ACID SYNTHASE 1 MMAA1 (METHYL MYCOLIC ACID SYNTHASE 1) (MMA1) (HYDROXY MYCOLIC ACID SYNTHASE) 14 15 1 2 0.000000 NE
+Rv0646c lipG PROBABLE LIPASE/ESTERASE LIPG 9 9 0 0 0.000000 NE
+Rv0647c - hypothetical protein Rv0647c 0 11 11 1189 1.000000 E
+Rv0648 - ALPHA-MANNOSIDASE 27 35 2 114 0.000000 NE
+Rv0649 fabD2 POSSIBLE MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE FABD2 (MCT) 2 4 2 140 0.000000 NE
+Rv0650 - POSSIBLE SUGAR KINASE 4 5 1 2 0.000000 NE
+Rv0651 rplJ 50S ribosomal protein L10 0 5 5 315 0.987700 U
+Rv0652 rplL 50S ribosomal protein L7/L12 0 0 0 0 -1.000000 S
+Rv0653c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 6 10 2 102 0.000000 NE
+Rv0654 - PROBABLE DIOXYGENASE 20 25 2 49 0.000000 NE
+Rv0655 mkl POSSIBLE RIBONUCLEOTIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER MKL 7 11 2 48 0.000000 NE
+Rv0656c - hypothetical protein Rv0656c 4 4 0 0 0.000000 NE
+Rv0657c - hypothetical protein Rv0657c 1 1 0 0 -1.000000 S
+Rv0658c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 10 14 1 2 0.000000 NE
+Rv0659c - hypothetical protein Rv0659c 3 4 1 2 0.000000 NE
+Rv0660c - hypothetical protein Rv0660c 2 2 0 0 -1.000000 S
+Rv0661c - hypothetical protein Rv0661c 4 4 0 0 0.000000 NE
+Rv0662c - hypothetical protein Rv0662c 4 4 0 0 -1.000000 S
+Rv0663 atsD POSSIBLE ARYLSULFATASE ATSD (ARYL-SULFATE SULPHOHYDROLASE) (ARYLSULPHATASE) 25 43 9 195 0.000500 NE
+Rv0664 - hypothetical protein Rv0664 2 3 1 2 -1.000000 S
+Rv0665 - hypothetical protein Rv0665 4 5 1 2 0.000000 NE
+Rv0666 - POSSIBLE MEMBRANE PROTEIN 0 0 0 0 -1.000000 S
+Rv0667 rpoB DNA-directed RNA polymerase subunit beta 0 32 32 3038 1.000000 E
+Rv0668 rpoC DNA-directed RNA polymerase subunit beta' 0 35 35 3415 1.000000 E
+Rv0669c - POSSIBLE HYDROLASE 28 32 2 47 0.000000 NE
+Rv0670 end endonuclease IV 4 5 1 2 0.000000 NE
+Rv0671 lpqP POSSIBLE CONSERVED LIPOPROTEIN LPQP 10 12 1 2 0.000000 NE
+Rv0672 fadE8 PROBABLE ACYL-CoA DEHYDROGENASE FADE8 16 23 3 21 0.000000 NE
+Rv0673 echA4 enoyl-CoA hydratase 6 8 1 2 0.000000 NE
+Rv0674 - hypothetical protein Rv0674 2 6 3 203 0.000000 NE
+Rv0675 echA5 enoyl-CoA hydratase 1 4 3 405 0.522600 U
+Rv0676c mmpL5 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL5 22 31 2 44 0.000000 NE
+Rv0677c mmpS5 POSSIBLE CONSERVED MEMBRANE PROTEIN MMPS5 5 6 1 2 0.000000 NE
+Rv0678 - hypothetical protein Rv0678 4 5 1 2 0.000000 NE
+Rv0679c - CONSERVED HYPOTHETICAL THREONINE RICH PROTEIN 4 6 1 2 0.000000 NE
+Rv0680c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 3 3 0 0 -1.000000 S
+Rv0681 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY TETR-FAMILY) 7 11 2 79 0.000000 NE
+Rv0682 rpsL 30S ribosomal protein S12 0 7 7 300 0.998200 E
+Rv0683 rpsG 30S ribosomal protein S7 0 4 4 269 0.984100 U
+Rv0684 fusA1 elongation factor G 0 29 29 1872 1.000000 E
+Rv0685 tuf elongation factor Tu 0 11 11 909 1.000000 E
+Rv0686 - PROBABLE MEMBRANE PROTEIN 8 8 0 0 0.000000 NE
+Rv0687 fabG 3-ketoacyl-(acyl-carrier-protein) reductase 6 15 5 129 0.000000 NE
+Rv0688 - PUTATIVE FERREDOXIN REDUCTASE 10 17 2 53 0.000000 NE
+Rv0689c - hypothetical protein Rv0689c 2 3 1 2 -1.000000 S
+Rv0690c - hypothetical protein Rv0690c 13 17 2 8 0.000000 NE
+Rv0691c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 6 9 1 2 0.000000 NE
+Rv0692 - hypothetical protein Rv0692 5 6 1 2 0.000000 NE
+Rv0693 pqqE PROBABLE COENZYME PQQ SYNTHESIS PROTEIN E PQQE (COENZYME PQQ SYNTHESIS PROTEIN III) 9 17 3 57 0.000000 NE
+Rv0694 lldD1 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 7 16 3 107 0.000000 NE
+Rv0695 - hypothetical protein Rv0695 7 10 3 149 0.000000 NE
+Rv0696 - PROBABLE MEMBRANE SUGAR TRANSFERASE 11 23 7 304 0.725300 U
+Rv0697 - PROBABLE DEHYDROGENASE 4 25 11 555 0.997600 E
+Rv0698 - hypothetical protein Rv0698 4 11 6 174 0.000000 NE
+Rv0699 - hypothetical protein Rv0699 2 2 0 0 -1.000000 S
+Rv0700 rpsJ 30S ribosomal protein S10 0 6 6 137 -1.000000 S
+Rv0701 rplC 50S ribosomal protein L3 0 15 15 515 1.000000 E
+Rv0702 rplD 50S ribosomal protein L4 0 11 11 563 0.999900 E
+Rv0703 rplW 50S ribosomal protein L23 0 4 4 158 0.982500 U
+Rv0704 rplB 50S ribosomal protein L2 0 16 16 717 1.000000 E
+Rv0705 rpsS 30S ribosomal protein S19 0 2 2 113 -1.000000 S
+Rv0706 rplV 50S ribosomal protein L22 0 4 4 256 0.985400 U
+Rv0707 rpsC 30S ribosomal protein S3 0 14 14 676 1.000000 E
+Rv0708 rplP 50S ribosomal protein L16 0 8 8 304 0.999300 E
+Rv0709 rpmC 50S ribosomal protein L29 0 4 4 95 -1.000000 S
+Rv0710 rpsQ 30S ribosomal protein S17 0 9 9 245 1.000000 E
+Rv0711 atsA POSSIBLE ARYLSULFATASE ATSA (ARYL-SULFATE SULPHOHYDROLASE) (ARYLSULPHATASE) 33 42 2 119 0.000000 NE
+Rv0712 - hypothetical protein Rv0712 9 18 3 51 0.000000 NE
+Rv0713 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 11 16 3 30 0.000000 NE
+Rv0714 rplN 50S ribosomal protein L14 0 4 4 241 0.985600 U
+Rv0715 rplX 50S ribosomal protein L24 0 5 5 242 0.994200 E
+Rv0716 rplE 50S ribosomal protein L5 0 4 4 390 0.903800 U
+Rv0717 rpsN 30S ribosomal protein S14 0 2 2 41 -1.000000 S
+Rv0718 rpsH 30S ribosomal protein S8 0 9 9 314 0.999900 E
+Rv0719 rplF 50S ribosomal protein L6 0 12 12 417 1.000000 E
+Rv0720 rplR 50S ribosomal protein L18 0 4 4 25 -1.000000 S
+Rv0721 rpsE 30S ribosomal protein S5 0 9 9 453 0.998800 E
+Rv0722 rpmD 50S ribosomal protein L30 1 1 0 0 -1.000000 S
+Rv0723 rplO 50S ribosomal protein L15 0 2 2 21 -1.000000 S
+Rv0724 sppA POSSIBLE PROTEASE IV SPPA (ENDOPEPTIDASE IV) (SIGNAL PEPTIDE PEPTIDASE) 19 28 2 124 0.000000 NE
+Rv0724A - hypothetical protein Rv0724A 4 5 1 2 0.000000 NE
+Rv0725c - hypothetical protein Rv0725c 9 14 3 196 0.000000 NE
+Rv0726c - hypothetical protein Rv0726c 9 14 2 22 0.000000 NE
+Rv0727c fucA L-fuculose-phosphate aldolase 8 10 1 2 0.000000 NE
+Rv0728c serA2 POSSIBLE D-3-PHOSPHOGLYCERATE DEHYDROGENASE SERA2 (PHOSPHOGLYCERATE DEHYDROGENASE) (PGDH) 4 8 2 128 0.000000 NE
+Rv0729 xylB POSSIBLE D-XYLULOSE KINASE XYLB (XYLULOKINASE) (XYLULOSE KINASE) 13 17 1 2 0.000000 NE
+Rv0730 - hypothetical protein Rv0730 0 1 1 2 -1.000000 S
+Rv0731c - hypothetical protein Rv0731c 7 9 1 2 0.000000 NE
+Rv0732 secY preprotein translocase subunit SecY 0 26 26 1150 1.000000 E
+Rv0733 adk adenylate kinase 0 5 5 311 0.990100 E
+Rv0734 mapA methionine aminopeptidase 5 8 2 90 0.000000 NE
+Rv0735 sigL RNA polymerase sigma factor SigL 6 6 0 0 0.000000 NE
+Rv0736 - PROBABLE CONSERVED MEMBRANE PROTEIN 0 6 6 482 0.975300 U
+Rv0737 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 4 1 2 -1.000000 S
+Rv0738 - hypothetical protein Rv0738 1 1 0 0 -1.000000 S
+Rv0739 - hypothetical protein Rv0739 15 17 1 2 0.000000 NE
+Rv0740 - hypothetical protein Rv0740 3 7 2 42 0.000000 NE
+Rv0741 - PROBABLE TRANSPOSASE (FRAGMENT) 2 3 1 2 -1.000000 S
+Rv0742 PE_PGRS8 PE-PGRS FAMILY PROTEIN 3 5 2 69 0.000000 NE
+Rv0743c - hypothetical protein Rv0743c 7 8 1 2 0.000000 NE
+Rv0744c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 4 9 3 186 0.000000 NE
+Rv0745 - hypothetical protein Rv0745 6 7 1 2 0.000000 NE
+Rv0746 PE_PGRS9 PE-PGRS FAMILY PROTEIN 7 14 3 188 0.000000 NE
+Rv0747 PE_PGRS10 PE-PGRS FAMILY PROTEIN 8 12 2 329 0.027100 NE
+Rv0748 - hypothetical protein Rv0748 2 2 0 0 -1.000000 S
+Rv0749 - hypothetical protein Rv0749 3 3 0 0 0.000000 NE
+Rv0749A - hypothetical protein Rv0749A 1 1 0 0 -1.000000 S
+Rv0750 - hypothetical protein Rv0750 0 1 1 2 -1.000000 S
+Rv0751c mmsB PROBABLE 3-HYDROXYISOBUTYRATE DEHYDROGENASE MMSB (HIBADH) 4 6 1 2 0.000000 NE
+Rv0752c fadE9 PROBABLE ACYL-CoA DEHYDROGENASE FADE9 9 14 2 57 0.000000 NE
+Rv0753c mmsA PROBABLE METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE MMSA (METHYLMALONIC ACID SEMIALDEHYDE DEHYDROGENASE) (MMSDH) 14 18 1 2 0.000000 NE
+Rv0754 PE_PGRS11 PE-PGRS FAMILY PROTEIN 18 27 6 251 0.006400 NE
+Rv0755A - PUTATIVE TRANSPOSASE (FRAGMENT) 4 5 1 2 -1.000000 S
+Rv0755c PPE12 PPE FAMILY PROTEIN 11 50 18 434 1.000000 E
+Rv0756c - hypothetical protein Rv0756c 6 6 0 0 0.000000 NE
+Rv0757 phoP POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP 1 10 7 219 0.010700 NE
+Rv0758 phoR POSSIBLE TWO COMPONENT SYSTEM RESPONSE SENSOR KINASE MEMBRANE ASSOCIATED PHOR 10 16 2 17 0.000000 NE
+Rv0759c - hypothetical protein Rv0759c 0 2 2 110 -1.000000 S
+Rv0760c - hypothetical protein Rv0760c 4 5 1 2 0.000000 NE
+Rv0761c adhB POSSIBLE ZINC-CONTAINING ALCOHOL DEHYDROGENASE NAD DEPENDENT ADHB 8 12 2 71 0.000000 NE
+Rv0762c - hypothetical protein Rv0762c 10 12 1 2 0.000000 NE
+Rv0763c - POSSIBLE FERREDOXIN 1 1 0 0 -1.000000 S
+Rv0764c cyp51 CYTOCHROME P450 51 CYP51 (CYPL1) (P450-L1A1) (STEROL 14-ALPHA DEMETHYLASE) (LANOSTEROL 14-ALPHA DEMETHYLASE) (P450-14DM) 11 16 3 377 0.085200 U
+Rv0765c - short chain dehydrogenase 5 9 1 2 0.000000 NE
+Rv0766c cyp123 PROBABLE CYTOCHROME P450 123 CYP123 12 23 5 136 0.000000 NE
+Rv0767c - hypothetical protein Rv0767c 8 11 2 191 0.000000 NE
+Rv0768 aldA PROBABLE ALDEHYDE DEHYDROGENASE NAD DEPENDENT ALDA (ALDEHYDE DEHYDROGENASE 10 22 4 184 0.000000 NE
+Rv0769 - short chain dehydrogenase 11 16 3 75 0.000000 NE
+Rv0770 - PROBABLE DEHYDROGENASE/REDUCTASE 6 7 1 2 0.000000 NE
+Rv0771 - POSSIBLE 4-CARBOXYMUCONOLACTONE DECARBOXYLASE (CMD) 5 9 2 33 0.000000 NE
+Rv0772 purD phosphoribosylamine--glycine ligase 0 20 20 1099 1.000000 E
+Rv0773c ggtA PROBABLE BIFUNCTIONAL ACYLASE GGTA: CEPHALOSPORIN ACYLASE (GL-7ACA ACYLASE) + GAMMA-GLUTAMYLTRANSPEPTIDASE (GGT) 11 19 3 137 0.000000 NE
+Rv0774c - PROBABLE CONSERVED EXPORTED PROTEIN 5 9 2 31 0.000000 NE
+Rv0775 - hypothetical protein Rv0775 9 9 0 0 0.000000 NE
+Rv0776c - hypothetical protein Rv0776c 12 14 2 79 0.000000 NE
+Rv0777 purB adenylosuccinate lyase 0 14 14 1028 1.000000 E
+Rv0778 cyp126 POSSIBLE CYTOCHROME P450 126 CYP126 11 17 2 51 0.000000 NE
+Rv0779c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 3 6 3 212 0.000200 NE
+Rv0780 hemH phosphoribosylaminoimidazole-succinocarboxamide synthase 0 23 23 785 1.000000 E
+Rv0781 ptrBa PROBABLE PROTEASE II PTRBA 5 24 8 209 0.003900 NE
+Rv0782 ptrBb PROBABLE PROTEASE II PTRBB 15 38 7 206 0.000100 NE
+Rv0783c emrB POSSIBLE MULTIDRUG RESISTANCE INTEGRAL MEMBRANE EFFLUX PROTEIN EMRB 10 23 6 340 0.544600 U
+Rv0784 - hypothetical protein Rv0784 4 8 1 2 0.000000 NE
+Rv0785 - putative FAD-binding dehydrogenase 16 30 3 76 0.000000 NE
+Rv0786c - hypothetical protein Rv0786c 5 11 3 33 0.000000 NE
+Rv0787 - hypothetical protein Rv0787 13 14 1 2 0.000000 NE
+Rv0787A - phosphoribosylformylglycinamidine synthase subunit PurS 0 2 2 48 -1.000000 S
+Rv0788 purQ phosphoribosylformylglycinamidine synthase subunit I 0 11 11 384 1.000000 E
+Rv0789c - hypothetical protein Rv0789c 6 7 1 2 0.000000 NE
+Rv0790c - hypothetical protein Rv0790c 13 20 2 32 0.000000 NE
+Rv0791c - hypothetical protein Rv0791c 9 12 1 2 0.000000 NE
+Rv0792c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) 12 17 2 21 0.000000 NE
+Rv0793 - hypothetical protein Rv0793 6 8 1 2 0.000000 NE
+Rv0794c - PROBABLE OXIDOREDUCTASE 8 15 2 60 0.000000 NE
+Rv0795 - PUTATIVE TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS6110 (FRAGMENT) 0 0 0 0 -1.000000 S
+Rv0796 - PUTATIVE TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS6110 0 1 1 2 -1.000000 S
+Rv0797 - IS1547 transposase 0 0 0 0 -1.000000 S
+Rv0798c cfp29 29 KDa ANTIGEN CFP29 4 14 5 139 0.000000 NE
+Rv0799c - hypothetical protein Rv0799c 3 9 3 201 0.000000 NE
+Rv0800 pepC putative aminopeptidase 2 10 13 1 2 0.000000 NE
+Rv0801 - hypothetical protein Rv0801 0 0 0 0 -1.000000 S
+Rv0802c - hypothetical protein Rv0802c 7 15 5 55 0.000000 NE
+Rv0803 purL phosphoribosylformylglycinamidine synthase II 0 32 32 1878 1.000000 E
+Rv0804 - hypothetical protein Rv0804 4 6 1 2 0.000000 NE
+Rv0805 - hypothetical protein Rv0805 10 15 2 129 0.000000 NE
+Rv0806c cpsY POSSIBLE UDP-GLUCOSE-4-EPIMERASE CPSY (GALACTOWALDENASE) (UDP-GALACTOSE-4-EPIMERASE) (URIDINE DIPHOSPHATE GALACTOSE-4-EPIMERASE) (URIDINE DIPHOSPHO-GALACTOSE-4-EPIMERASE) 31 41 2 39 0.000000 NE
+Rv0807 - hypothetical protein Rv0807 1 2 1 2 -1.000000 S
+Rv0808 purF amidophosphoribosyltransferase 0 25 25 1335 1.000000 E
+Rv0809 purM phosphoribosylaminoimidazole synthetase 0 11 11 831 0.999300 E
+Rv0810c - hypothetical protein Rv0810c 0 4 4 95 -1.000000 S
+Rv0811c - hypothetical protein Rv0811c 0 15 15 731 1.000000 E
+Rv0812 - 4-amino-4-deoxychorismate lyase 0 15 15 562 1.000000 E
+Rv0813c - hypothetical protein Rv0813c 13 13 0 0 0.000000 NE
+Rv0814c sseC2 CONSERVED HYPOTHETICAL PROTEIN SSEC2 0 0 0 0 -1.000000 S
+Rv0815c cysA2 PROBABLE THIOSULFATE SULFURTRANSFERASE CYSA2 (RHODANESE-LIKE PROTEIN) (THIOSULFATE CYANIDE TRANSSULFURASE) (THIOSULFATE THIOTRANSFERASE) 3 4 1 2 0.000000 NE
+Rv0816c thiX PROBABLE THIOREDOXIN THIX 3 3 0 0 0.000000 NE
+Rv0817c - PROBABLE CONSERVED EXPORTED PROTEIN 0 14 14 670 1.000000 E
+Rv0818 - TRANSCRIPTIONAL REGULATORY PROTEIN 7 8 1 2 0.000000 NE
+Rv0819 - hypothetical protein Rv0819 0 10 10 790 0.999500 E
+Rv0820 phoT PROBABLE PHOSPHATE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER PHOT 9 10 1 2 0.000000 NE
+Rv0821c phoY2 PROBABLE PHOSPHATE-TRANSPORT SYSTEM TRANSCRIPTIONAL REGULATORY PROTEIN PHOY2 2 5 3 295 0.238800 U
+Rv0822c - hypothetical protein Rv0822c 22 27 2 17 0.000000 NE
+Rv0823c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 12 17 3 130 0.000000 NE
+Rv0824c desA1 PROBABLE ACYL- 0 18 18 889 1.000000 E
+Rv0825c - hypothetical protein Rv0825c 8 10 1 2 0.000000 NE
+Rv0826 - hypothetical protein Rv0826 15 18 1 2 0.000000 NE
+Rv0827c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 3 0 0 0.000000 NE
+Rv0828c - POSSIBLE DEAMINASE 10 10 0 0 0.000000 NE
+Rv0829 - POSSIBLE TRANSPOSASE (FRAGMENT) 1 1 0 0 -1.000000 S
+Rv0830 - hypothetical protein Rv0830 15 18 2 32 0.000000 NE
+Rv0831c - hypothetical protein Rv0831c 15 18 1 2 0.000000 NE
+Rv0832 PE_PGRS12 PE-PGRS FAMILY PROTEIN 2 3 1 2 0.000000 NE
+Rv0833 PE_PGRS13 PE-PGRS FAMILY PROTEIN 3 11 4 110 0.000000 NE
+Rv0834c PE_PGRS14 PE-PGRS FAMILY PROTEIN 18 24 2 257 0.000700 NE
+Rv0835 lpqQ POSSIBLE LIPOPROTEIN LPQQ 11 14 2 13 0.000000 NE
+Rv0836c - hypothetical protein Rv0836c 7 8 1 2 0.000000 NE
+Rv0837c - hypothetical protein Rv0837c 18 22 1 2 0.000000 NE
+Rv0838 lpqR PROBABLE CONSERVED LIPOPROTEIN LPQR 5 7 2 112 0.000000 NE
+Rv0839 - hypothetical protein Rv0839 9 10 1 2 0.000000 NE
+Rv0840c pip PROBABLE PROLINE IMINOPEPTIDASE PIP (PROLYL AMINOPEPTIDASE) (PAP) 6 8 1 2 0.000000 NE
+Rv0841 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 2 3 1 2 -1.000000 S
+Rv0842 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 13 21 5 211 0.000100 NE
+Rv0843 - PROBABLE DEHYDROGENASE 13 17 1 2 0.000000 NE
+Rv0844c narL POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL 8 9 1 2 0.000000 NE
+Rv0845 - POSSIBLE TWO COMPONENT SENSOR KINASE 15 23 5 64 0.000000 NE
+Rv0846c - PROBABLE OXIDASE 17 28 3 68 0.000000 NE
+Rv0847 lpqS PROBABLE LIPOPROTEIN LPQS 4 6 1 2 0.000000 NE
+Rv0848 cysK2 POSSIBLE CYSTEINE SYNTHASE A CYSK2 (O-ACETYLSERINE SULFHYDRYLASE) (O-ACETYLSERINE (THIOL)-LYASE) (CSASE) 17 26 2 29 0.000000 NE
+Rv0849 - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 16 21 1 2 0.000000 NE
+Rv0850 - PUTATIVE TRANSPOSASE (FRAGMENT) 7 9 2 35 0.000000 NE
+Rv0851c - short chain dehydrogenase 8 9 1 2 0.000000 NE
+Rv0852 fadD16 POSSIBLE FATTY-ACID-CoA LIGASE FADD16 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 8 13 3 59 0.000000 NE
+Rv0853c pdc PROBABLE PYRUVATE OR INDOLE-3-PYRUVATE DECARBOXYLASE PDC 12 23 3 31 0.000000 NE
+Rv0854 - hypothetical protein Rv0854 5 6 1 2 0.000000 NE
+Rv0855 far PROBABLE FATTY-ACID-CoA RACEMASE FAR 9 12 2 30 0.000000 NE
+Rv0856 - hypothetical protein Rv0856 3 5 1 2 0.000000 NE
+Rv0857 - hypothetical protein Rv0857 4 6 1 2 0.000000 NE
+Rv0858c - aminotransferase 14 19 1 2 0.000000 NE
+Rv0859 fadA acetyl-CoA acetyltransferase 3 7 2 43 0.000000 NE
+Rv0860 fadB PROBABLE FATTY OXIDATION PROTEIN FADB 5 21 7 577 0.859500 U
+Rv0861c ercc3 PROBABLE DNA HELICASE ERCC3 12 22 5 466 0.343000 U
+Rv0862c - hypothetical protein Rv0862c 12 27 5 275 0.016000 NE
+Rv0863 - hypothetical protein Rv0863 5 6 1 2 0.000000 NE
+Rv0864 moaC molybdenum cofactor biosynthesis protein C 10 11 1 2 0.000000 NE
+Rv0865 mog PROBABLE MOLYBDOPTERIN BIOSYNTHESIS MOG PROTEIN 5 8 2 23 0.000000 NE
+Rv0866 moaE2 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E2 MOAE2 (MOLYBDOPTERIN CONVERTING FACTOR LARGE SUBUNIT) (MOLYBDOPTERIN 3 3 0 0 0.000000 NE
+Rv0867c rpfA POSSIBLE RESUSCITATION-PROMOTING FACTOR RPFA 7 8 1 2 0.000000 NE
+Rv0868c moaD2 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D 2 MOAD2 (MOLYBDOPTERIN CONVERTING FACTOR SMALL SUBUNIT) (MOLYBDOPTERIN 5 6 1 2 0.000000 NE
+Rv0869c moaA molybdenum cofactor biosynthesis protein A 11 14 1 2 0.000000 NE
+Rv0870c - hypothetical protein Rv0870c 4 4 0 0 0.000000 NE
+Rv0871 cspB PROBABLE COLD SHOCK-LIKE PROTEIN B CSPB 3 4 1 2 0.000000 NE
+Rv0872c PE_PGRS15 PE-PGRS FAMILY PROTEIN 19 25 2 50 0.000000 NE
+Rv0873 fadE10 PROBABLE ACYL-CoA DEHYDROGENASE FADE10 25 33 2 227 0.000000 NE
+Rv0874c - hypothetical protein Rv0874c 6 9 2 30 0.000000 NE
+Rv0875c - POSSIBLE CONSERVED EXPORTED PROTEIN 1 11 10 362 0.999900 E
+Rv0876c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 12 24 6 176 0.000000 NE
+Rv0877 - hypothetical protein Rv0877 12 15 1 2 0.000000 NE
+Rv0878c PPE13 PPE FAMILY PROTEIN 15 15 0 0 0.000000 NE
+Rv0879c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 2 3 1 2 0.000000 NE
+Rv0880 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY MARR-FAMILY) 0 1 1 2 -1.000000 S
+Rv0881 - POSSIBLE RRNA METHYLTRANSFERASE (RRNA METHYLASE) 10 14 1 2 0.000000 NE
+Rv0882 - PROBABLE TRANSMEMBRANE PROTEIN 1 1 0 0 -1.000000 S
+Rv0883c - hypothetical protein Rv0883c 0 6 6 596 0.974700 U
+Rv0884c serC phosphoserine aminotransferase 0 12 12 800 0.999900 E
+Rv0885 - hypothetical protein Rv0885 6 12 2 31 0.000000 NE
+Rv0886 fprB PROBABLE NADPH:ADRENODOXIN OXIDOREDUCTASE FPRB (ADRENODOXIN REDUCTASE) (AR) (FERREDOXIN-NADP(+) REDUCTASE) 14 22 5 567 0.427000 U
+Rv0887c - hypothetical protein Rv0887c 3 4 1 2 0.000000 NE
+Rv0888 - PROBABLE EXPORTED PROTEIN 19 26 4 143 0.000000 NE
+Rv0889c citA citrate synthase 2 9 10 1 2 0.000000 NE
+Rv0890c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LUXR-FAMILY) 36 44 2 9 0.000000 NE
+Rv0891c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 19 23 2 69 0.000000 NE
+Rv0892 - PROBABLE MONOOXYGENASE 14 37 4 76 0.000000 NE
+Rv0893c - hypothetical protein Rv0893c 6 21 11 423 0.998900 E
+Rv0894 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (POSSIBLY LUXR-FAMILY) 9 14 3 101 0.000000 NE
+Rv0895 - hypothetical protein Rv0895 21 26 1 2 0.000000 NE
+Rv0896 gltA type II citrate synthase 0 23 23 954 1.000000 E
+Rv0897c - PROBABLE OXIDOREDUCTASE 10 18 3 236 0.000000 NE
+Rv0898c - hypothetical protein Rv0898c 0 0 0 0 -1.000000 S
+Rv0899 ompA OUTER MEMBRANE PROTEIN A OMPA 6 18 6 444 0.818100 U
+Rv0900 - POSSIBLE MEMBRANE PROTEIN 2 2 0 0 -1.000000 S
+Rv0901 - POSSIBLE CONSERVED EXPORTED OR MEMBRANE PROTEIN 6 9 2 11 0.000000 NE
+Rv0902c prrB TWO COMPONENT SENSOR HISTIDINE KINASE PRRB 0 12 12 890 0.999900 E
+Rv0903c prrA TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN PRRA 0 9 9 585 0.998800 E
+Rv0904c accD3 PUTATIVE ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE (SUBUNIT BETA) ACCD3 (ACCASE BETA CHAIN) 14 19 2 159 0.000000 NE
+Rv0905 echA6 enoyl-CoA hydratase 5 8 2 41 0.000000 NE
+Rv0906 - hypothetical protein Rv0906 8 14 4 280 0.037500 NE
+Rv0907 - hypothetical protein Rv0907 12 33 8 293 0.738400 U
+Rv0908 ctpE PROBABLE METAL CATION TRANSPORTER ATPASE P-TYPE CTPE 21 29 2 58 0.000000 NE
+Rv0909 - hypothetical protein Rv0909 2 2 0 0 -1.000000 S
+Rv0910 - hypothetical protein Rv0910 5 7 2 52 0.000000 NE
+Rv0911 - hypothetical protein Rv0911 8 12 2 142 0.000000 NE
+Rv0912 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 3 4 1 2 -1.000000 S
+Rv0913c - POSSIBLE DIOXYGENASE 11 38 11 369 0.996200 E
+Rv0914c - acetyl-CoA acetyltransferase 14 15 1 2 0.000000 NE
+Rv0915c PPE14 PPE FAMILY PROTEIN 10 15 2 20 0.000000 NE
+Rv0916c PE7 PE FAMILY PROTEIN 3 5 1 2 0.000000 NE
+Rv0917 betP POSSIBLE GLYCINE BETAINE TRANSPORT INTEGRAL MEMBRANE PROTEIN BETP 25 40 3 88 0.000000 NE
+Rv0918 - hypothetical protein Rv0918 7 8 1 2 0.000000 NE
+Rv0919 - hypothetical protein Rv0919 7 8 1 2 0.000000 NE
+Rv0920c - PROBABLE TRANSPOSASE 16 21 1 2 0.000000 NE
+Rv0921 - POSSIBLE RESOLVASE 5 7 1 2 0.000000 NE
+Rv0922 - POSSIBLE TRANSPOSASE 13 16 1 2 0.000000 NE
+Rv0923c - hypothetical protein Rv0923c 11 16 2 9 0.000000 NE
+Rv0924c mntH manganese transport protein MntH 13 17 2 64 0.000000 NE
+Rv0925c - hypothetical protein Rv0925c 11 15 1 2 0.000000 NE
+Rv0926c - hypothetical protein Rv0926c 11 18 2 47 0.000000 NE
+Rv0927c - short chain dehydrogenase 4 5 1 2 0.000000 NE
+Rv0928 pstS3 PERIPLASMIC PHOSPHATE-BINDING LIPOPROTEIN PSTS3 (PBP-3) (PSTS3) (PHOS1) 13 21 5 335 0.402500 U
+Rv0929 pstC2 PHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTC2 7 16 3 80 0.000000 NE
+Rv0930 pstA1 PROBABLE PHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTA1 11 15 2 10 0.000000 NE
+Rv0931c pknD TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE D PKND (PROTEIN KINASE D) (STPK D) 35 40 1 2 0.000000 NE
+Rv0932c pstS2 PERIPLASMIC PHOSPHATE-BINDING LIPOPROTEIN PSTS2 (PBP-2) (PSTS2) 19 23 3 30 0.000000 NE
+Rv0933 pstB PHOSPHATE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER PSTB 7 12 4 205 0.000000 NE
+Rv0934 pstS1 PERIPLASMIC PHOSPHATE-BINDING LIPOPROTEIN PSTS1 (PBP-1) (PSTS1) 16 19 1 2 0.000000 NE
+Rv0935 pstC1 PHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTC1 11 12 1 2 0.000000 NE
+Rv0936 pstA2 PHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTA2 15 19 2 7 0.000000 NE
+Rv0937c - hypothetical protein Rv0937c 5 12 4 305 0.313600 U
+Rv0938 - ATP-dependent DNA ligase 9 38 14 478 0.999700 E
+Rv0939 - POSSIBLE BIFUNCTIONAL ENZYME: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) + CYCLASE/DEHYDRASE 14 27 4 158 0.000000 NE
+Rv0940c - POSSIBLE OXIDOREDUCTASE 7 13 4 95 0.000000 NE
+Rv0941c - hypothetical protein Rv0941c 7 8 1 2 0.000000 NE
+Rv0942 - hypothetical protein Rv0942 6 7 1 2 0.000000 NE
+Rv0943c - PROBABLE MONOOXYGENASE 14 16 1 2 0.000000 NE
+Rv0944 - POSSIBLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FAPY-DNA GLYCOSYLASE) 4 7 2 64 0.000000 NE
+Rv0945 - short chain dehydrogenase 3 7 3 314 0.501200 U
+Rv0946c pgi glucose-6-phosphate isomerase 0 17 17 1416 1.000000 E
+Rv0948c - hypothetical protein Rv0948c 1 6 5 150 0.050800 U
+Rv0949 uvrD1 PROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 2 44 38 1671 1.000000 E
+Rv0950c - hypothetical protein Rv0950c 5 18 6 449 0.833700 U
+Rv0951 sucC succinyl-CoA synthetase subunit beta 0 14 14 758 1.000000 E
+Rv0952 sucD succinyl-CoA synthetase subunit alpha 0 10 10 668 0.999500 E
+Rv0953c - POSSIBLE OXIDOREDUCTASE 9 10 1 2 0.000000 NE
+Rv0954 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 15 25 4 52 0.000000 NE
+Rv0955 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 0 17 17 1133 1.000000 E
+Rv0956 purN phosphoribosylglycinamide formyltransferase 0 12 12 518 1.000000 E
+Rv0957 purH bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 0 20 20 974 1.000000 E
+Rv0958 - POSSIBLE MAGNESIUM CHELATASE 8 11 2 26 0.000000 NE
+Rv0959 - hypothetical protein Rv0959 5 14 5 196 0.000100 NE
+Rv0960 - hypothetical protein Rv0960 3 5 2 79 -1.000000 S
+Rv0961 - PROBABLE INTEGRAL MEMBRANE PROTEIN 5 7 1 2 0.000000 NE
+Rv0962c lprP POSSIBLE LIPOPROTEIN LPRP 13 14 1 2 0.000000 NE
+Rv0963c - hypothetical protein Rv0963c 7 10 1 2 0.000000 NE
+Rv0964c - hypothetical protein Rv0964c 4 5 1 2 0.000000 NE
+Rv0965c - hypothetical protein Rv0965c 5 6 1 2 0.000000 NE
+Rv0966c - hypothetical protein Rv0966c 7 9 1 2 0.000000 NE
+Rv0967 - hypothetical protein Rv0967 1 1 0 0 -1.000000 S
+Rv0968 - hypothetical protein Rv0968 5 6 1 2 0.000000 NE
+Rv0969 ctpV PROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV 15 19 3 493 0.048700 U
+Rv0970 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 4 12 3 77 0.000000 NE
+Rv0971c echA7 enoyl-CoA hydratase 4 5 1 2 0.000000 NE
+Rv0972c fadE12 PROBABLE ACYL-CoA DEHYDROGENASE FADE12 7 16 3 160 0.000000 NE
+Rv0973c accA2 PROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) 4 20 7 546 0.865400 U
+Rv0974c accD2 PROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 4 19 7 344 0.826400 U
+Rv0975c fadE13 PROBABLE ACYL-CoA DEHYDROGENASE FADE13 10 18 2 10 0.000000 NE
+Rv0976c - hypothetical protein Rv0976c 13 17 2 71 0.000000 NE
+Rv0977 PE_PGRS16 PE-PGRS FAMILY PROTEIN 16 26 5 719 0.332300 U
+Rv0978c PE_PGRS17 PE-PGRS FAMILY PROTEIN 2 2 0 0 -1.000000 S
+Rv0979A rpmF 50S ribosomal protein L32 0 2 2 131 -1.000000 S
+Rv0979c - hypothetical protein Rv0979c 0 1 1 2 -1.000000 S
+Rv0980c PE_PGRS18 PE-PGRS FAMILY PROTEIN 9 11 1 2 0.000000 NE
+Rv0981 mprA MYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) 7 9 2 111 0.000000 NE
+Rv0982 mprB PROBABLE TWO COMPONENT SENSOR KINASE MPRB 0 20 20 1247 1.000000 E
+Rv0983 pepD PROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) 8 13 2 35 0.000000 NE
+Rv0984 moaB2 POSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) 2 5 3 157 0.000000 NE
+Rv0985c mscL large-conductance mechanosensitive channel 8 9 1 2 0.000000 NE
+Rv0986 - PROBABLE ADHESION COMPONENT TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 4 21 16 467 1.000000 E
+Rv0987 - PROBABLE ADHESION COMPONENT TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER 24 85 15 321 0.999300 E
+Rv0988 - POSSIBLE CONSERVED EXPORTED PROTEIN 6 37 12 304 0.997700 E
+Rv0989c grcC2 PROBABLE POLYPRENYL-DIPHOSPHATE SYNTHASE GRCC2 (POLYPRENYL PYROPHOSPHATE SYNTHETASE) 14 17 1 2 0.000000 NE
+Rv0990c - hypothetical protein Rv0990c 5 8 1 2 0.000000 NE
+Rv0991c - CONSERVED HYPOTHETICAL SERINE RICH PROTEIN 1 1 0 0 -1.000000 S
+Rv0992c - hypothetical protein Rv0992c 4 6 1 2 0.000000 NE
+Rv0993 galU PROBABLE UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE GALU (UDP-GLUCOSE PYROPHOSPHORYLASE) (UDPGP) (ALPHA-D-GLUCOSYL-1-PHOSPHATE URIDYLYLTRANSFERASE) (URIDINE DIPHOSPHOGLUCOSE PYROPHOSPHORYLASE) 0 12 12 807 1.000000 E
+Rv0994 moeA1 PROBABLE MOLYBDOPTERIN BIOSYNTHESIS PROTEIN MOEA1 8 11 1 2 0.000000 NE
+Rv0995 rimJ POSSIBLE RIBOSOMAL-PROTEIN-ALANINE ACETYLTRANSFERASE RIMJ (ACETYLATING ENZYME FOR N-TERMINAL OF RIBOSOMAL PROTEIN S5) 5 5 0 0 0.000000 NE
+Rv0996 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 12 14 1 2 0.000000 NE
+Rv0997 - hypothetical protein Rv0997 3 4 1 2 0.000000 NE
+Rv0998 - hypothetical protein Rv0998 7 11 3 256 0.003200 NE
+Rv0999 - hypothetical protein Rv0999 9 10 1 2 0.000000 NE
+Rv1000c - hypothetical protein Rv1000c 7 7 0 0 0.000000 NE
+Rv1001 arcA arginine deiminase 15 18 1 2 0.000000 NE
+Rv1002c - hypothetical protein Rv1002c 0 21 21 1229 1.000000 E
+Rv1003 - hypothetical protein Rv1003 5 8 2 63 0.000000 NE
+Rv1004c - PROBABLE MEMBRANE PROTEIN 6 9 1 2 0.000000 NE
+Rv1005c pabB para-aminobenzoate synthase component I 1 21 20 980 1.000000 E
+Rv1006 - hypothetical protein Rv1006 25 37 3 42 0.000000 NE
+Rv1007c metG methionyl-tRNA synthetase 0 23 23 1353 1.000000 E
+Rv1008 tatD PROBABLE DEOXYRIBONUCLEASE TATD (YJJV PROTEIN) 9 11 1 2 0.000000 NE
+Rv1009 rpfB Probable resuscitation-promoting factor rpfB 4 9 4 542 0.533600 U
+Rv1010 ksgA dimethyladenosine transferase 4 12 5 142 0.000000 NE
+Rv1011 ispE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 0 12 12 675 0.999900 E
+Rv1012 - hypothetical protein Rv1012 5 6 1 2 0.000000 NE
+Rv1013 pks16 acyl-CoA synthetase 9 21 2 23 0.000000 NE
+Rv1014c pth peptidyl-tRNA hydrolase 0 11 11 481 0.999700 E
+Rv1015c rplY 50S ribosomal protein L25/general stress protein Ctc 0 9 9 568 0.998400 E
+Rv1016c lpqT PROBABLE CONSERVED LIPOPROTEIN LPQT 4 6 1 2 0.000000 NE
+Rv1017c prsA ribose-phosphate pyrophosphokinase 0 10 10 545 0.999100 E
+Rv1018c glmU Probable UDP-N-acetylglucosamine pyrophosphorylase glmU 0 23 23 1176 1.000000 E
+Rv1019 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 7 7 0 0 0.000000 NE
+Rv1020 mfd PROBABLE TRANSCRIPTION-REPAIR COUPLING FACTOR MFD (TRCF) 27 33 3 458 0.020800 NE
+Rv1021 - nucleoside triphosphate pyrophosphohydrolase 7 12 5 138 0.000000 NE
+Rv1022 lpqU PROBABLE CONSERVED LIPOPROTEIN LPQU 4 13 5 79 0.000000 NE
+Rv1023 eno phosphopyruvate hydratase 0 13 13 1116 1.000000 E
+Rv1024 - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 8 8 292 0.999400 E
+Rv1025 - hypothetical protein Rv1025 0 6 6 363 0.988500 U
+Rv1026 - hypothetical protein Rv1026 2 6 4 351 0.646900 U
+Rv1027c kdpE PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN KDPE 4 10 3 32 0.000000 NE
+Rv1028A kdpF Probable membrane protein kdpF 2 3 1 2 -1.000000 S
+Rv1028c kdpD PROBABLE SENSOR PROTEIN KDPD 10 21 3 235 0.000000 NE
+Rv1029 kdpA potassium-transporting ATPase subunit A 16 25 4 521 0.147400 U
+Rv1030 kdpB potassium-transporting ATPase subunit B 9 12 2 233 0.000000 NE
+Rv1031 kdpC Probable Potassium-transporting ATPase C chain KDPC (Potassium-translocating ATPase C chain) (ATP phosphohydrolase 5 9 3 55 0.000000 NE
+Rv1032c trcS TWO COMPONENT SENSOR HISTIDINE KINASE TRCS 21 23 1 2 0.000000 NE
+Rv1033c trcR TWO COMPONENT TRANSCRIPTIONAL REGULATOR TRCR 12 13 1 2 0.000000 NE
+Rv1034c - PROBABLE TRANSPOSASE (FRAGMENT) 2 2 0 0 -1.000000 S
+Rv1035c - PROBABLE TRANSPOSASE (FRAGMENT) 1 4 3 226 0.000900 NE
+Rv1036c - truncated IS1560 transposase 4 5 1 2 0.000000 NE
+Rv1037c esxI PUTATIVE ESAT-6 LIKE PROTEIN ESXI (ESAT-6 LIKE PROTEIN 1) 0 0 0 0 -1.000000 S
+Rv1038c esxJ ESAT-6 LIKE PROTEIN ESXJ (ESAT-6 LIKE PROTEIN 2) 1 1 0 0 -1.000000 S
+Rv1039c PPE15 PPE FAMILY PROTEIN 14 20 4 140 0.000000 NE
+Rv1040c PE8 PE FAMILY PROTEIN 7 8 1 2 0.000000 NE
+Rv1041c - PROBABLE IS LIKE-2 TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv1042c - PROBABLE IS LIKE-2 TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv1043c - hypothetical protein Rv1043c 11 14 1 2 0.000000 NE
+Rv1044 - hypothetical protein Rv1044 1 9 8 447 0.993700 E
+Rv1045 - hypothetical protein Rv1045 9 10 1 2 0.000000 NE
+Rv1046c - hypothetical protein Rv1046c 4 4 0 0 0.000000 NE
+Rv1047 - PROBABLE TRANSPOSASE 0 2 2 44 -1.000000 S
+Rv1048c - hypothetical protein Rv1048c 15 21 4 25 0.000000 NE
+Rv1049 - PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN 4 4 0 0 0.000000 NE
+Rv1050 - PROBABLE OXIDOREDUCTASE 9 10 1 2 0.000000 NE
+Rv1051c - hypothetical protein Rv1051c 3 8 4 263 0.032500 NE
+Rv1052 - hypothetical protein Rv1052 4 4 0 0 0.000000 NE
+Rv1053c - hypothetical protein Rv1053c 4 6 1 2 0.000000 NE
+Rv1054 - PROBABLE INTEGRASE (FRAGMENT) 2 5 2 54 0.000000 NE
+Rv1055 - POSSIBLE INTEGRASE (FRAGMENT) 1 3 2 13 -1.000000 S
+Rv1056 - hypothetical protein Rv1056 15 20 2 93 0.000000 NE
+Rv1057 - hypothetical protein Rv1057 14 16 1 2 0.000000 NE
+Rv1058 fadD14 acyl-CoA synthetase 13 26 5 147 0.000000 NE
+Rv1059 - hypothetical protein Rv1059 2 9 7 503 0.973500 U
+Rv1060 - hypothetical protein Rv1060 3 5 1 2 0.000000 NE
+Rv1061 - hypothetical protein Rv1061 8 13 2 79 0.000000 NE
+Rv1062 - hypothetical protein Rv1062 4 4 0 0 0.000000 NE
+Rv1063c - hypothetical protein Rv1063c 9 15 4 308 0.203900 U
+Rv1064c lpqV POSSIBLE LIPOPROTEIN LPQV 3 5 1 2 0.000000 NE
+Rv1065 - hypothetical protein Rv1065 9 9 0 0 0.000000 NE
+Rv1066 - hypothetical protein Rv1066 3 4 1 2 0.000000 NE
+Rv1067c PE_PGRS19 PE-PGRS FAMILY PROTEIN 7 12 4 347 0.181400 U
+Rv1068c PE_PGRS20 PE-PGRS FAMILY PROTEIN 4 9 4 359 0.312500 U
+Rv1069c - hypothetical protein Rv1069c 17 19 1 2 0.000000 NE
+Rv1070c echA8 enoyl-CoA hydratase 6 7 1 2 0.000000 NE
+Rv1071c echA9 enoyl-CoA hydratase 10 11 1 2 0.000000 NE
+Rv1072 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 13 13 740 1.000000 E
+Rv1073 - hypothetical protein Rv1073 16 19 1 2 0.000000 NE
+Rv1074c fadA3 acetyl-CoA acetyltransferase 9 11 1 2 0.000000 NE
+Rv1075c - CONSERVED EXPORTED PROTEIN 16 18 1 2 0.000000 NE
+Rv1076 lipU POSSIBLE LIPASE LIPU 6 17 11 406 0.999300 E
+Rv1077 cbs Probable cystathionine beta-synthase CBS (Serine sulfhydrase) (Beta-thionase) (Hemoprotein H-450) 17 22 2 50 0.000000 NE
+Rv1078 pra Probable Proline-rich antigen homolog pra 1 17 11 284 0.996700 E
+Rv1079 metB cystathionine gamma-synthase 8 17 3 116 0.000000 NE
+Rv1080c greA transcription elongation factor GreA 0 7 7 321 0.997600 E
+Rv1081c - PROBABLE CONSERVED MEMBRANE PROTEIN 0 6 6 356 0.989300 U
+Rv1082 mca Mycothiol conjugate amidase Mca (Mycothiol S-conjugate amidase) 10 13 1 2 0.000000 NE
+Rv1083 - hypothetical protein Rv1083 2 3 1 2 -1.000000 S
+Rv1084 - hypothetical protein Rv1084 13 19 2 204 0.000000 NE
+Rv1085c - POSSIBLE HEMOLYSIN-LIKE PROTEIN 2 10 5 134 0.000000 NE
+Rv1086 - SHORT (C15) CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHASE (Z-FPP SYNTHASE) (Z-FARNESYL DIPHOSPHATE SYNTHASE) (Z-FPP SYNTHETASE) (Z-FARNESYL DIPHOSPHATE SYNTHETASE) (GERANYLTRANSTRANSFERASE) (FARNESYL PYROPHOSPHATE SYNTHETASE) 3 12 7 428 0.961300 U
+Rv1087 PE_PGRS21 PE-PGRS FAMILY PROTEIN 16 19 1 2 0.000000 NE
+Rv1087A - hypothetical protein Rv1087A 6 6 0 0 0.000000 NE
+Rv1088 PE9 PE FAMILY PROTEIN 2 4 2 26 -1.000000 S
+Rv1089 PE10 PE FAMILY PROTEIN 3 5 2 70 -1.000000 S
+Rv1089A celA2a PROBABLE CELLULASE CELA2A (ENDO-1,4-BETA-GLUCANASE) (ENDOGLUCANASE) (CARBOXYMETHYL CELLULASE) 1 1 0 0 -1.000000 S
+Rv1090 celA2b PROBABLE CELLULASE CELA2B (ENDO-1,4-BETA-GLUCANASE) (ENDOGLUCANASE) (CARBOXYMETHYL CELLULASE) 6 6 0 0 0.000000 NE
+Rv1091 PE_PGRS22 PE-PGRS FAMILY PROTEIN 15 26 3 230 0.000000 NE
+Rv1092c coaA pantothenate kinase 0 16 16 705 1.000000 E
+Rv1093 glyA serine hydroxymethyltransferase 0 12 12 1098 1.000000 E
+Rv1094 desA2 POSSIBLE ACYL- 0 12 12 642 0.999700 E
+Rv1095 phoH2 PROBABLE PHOH-LIKE PROTEIN PHOH2 (PHOSPHATE STARVATION-INDUCIBLE PROTEIN PSIH) 8 11 1 2 0.000000 NE
+Rv1096 - POSSIBLE GLYCOSYL HYDROLASE 8 16 3 85 0.000000 NE
+Rv1097c - PROBABLE MEMBRANE GLYCINE AND PROLINE RICH PROTEIN 5 14 5 86 0.000000 NE
+Rv1098c fumC fumarate hydratase 0 11 11 1132 1.000000 E
+Rv1099c glpX fructose 1,6-bisphosphatase II 1 12 8 549 0.986000 U
+Rv1100 - hypothetical protein Rv1100 6 9 2 11 0.000000 NE
+Rv1101c - hypothetical protein Rv1101c 14 18 2 218 0.000000 NE
+Rv1102c - hypothetical protein Rv1102c 5 7 1 2 0.000000 NE
+Rv1103c - hypothetical protein Rv1103c 6 6 0 0 0.000000 NE
+Rv1104 - POSSIBLE PARA-NITROBENZYL ESTERASE (FRAGMENT) 6 9 2 54 0.000000 NE
+Rv1105 - POSSIBLE PARA-NITROBENZYL ESTERASE (FRAGMENT) 7 11 1 2 0.000000 NE
+Rv1106c - PROBABLE CHOLESTEROL DEHYDROGENASE 14 17 1 2 0.000000 NE
+Rv1107c xseB exodeoxyribonuclease VII small subunit 2 2 0 0 -1.000000 S
+Rv1108c xseA exodeoxyribonuclease VII large subunit 8 9 1 2 0.000000 NE
+Rv1109c - hypothetical protein Rv1109c 4 6 1 2 0.000000 NE
+Rv1110 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 0 13 13 855 1.000000 E
+Rv1111c - hypothetical protein Rv1111c 8 22 11 456 0.998500 E
+Rv1112 - translation-associated GTPase 3 8 4 267 0.022700 NE
+Rv1113 - hypothetical protein Rv1113 2 2 0 0 -1.000000 S
+Rv1114 - hypothetical protein Rv1114 3 3 0 0 0.000000 NE
+Rv1115 - POSSIBLE EXPORTED PROTEIN 9 14 2 45 0.000000 NE
+Rv1116 - hypothetical protein Rv1116 0 2 2 105 -1.000000 S
+Rv1116A - CONSERVED HYPOTHETICAL PROTEIN (FRAGMENT) 2 5 2 88 0.000100 NE
+Rv1117 - hypothetical protein Rv1117 3 3 0 0 -1.000000 S
+Rv1118c - hypothetical protein Rv1118c 9 10 1 2 0.000000 NE
+Rv1119c - hypothetical protein Rv1119c 1 3 2 42 -1.000000 S
+Rv1120c - hypothetical protein Rv1120c 1 4 2 258 0.014900 NE
+Rv1121 zwf1 glucose-6-phosphate 1-dehydrogenase 12 23 7 193 0.000200 NE
+Rv1122 gnd2 6-phosphogluconate dehydrogenase-like protein 0 11 11 735 0.999900 E
+Rv1123c bpoB POSSIBLE PEROXIDASE BPOB (NON-HAEM PEROXIDASE) 4 7 3 98 0.000000 NE
+Rv1124 ephC PROBABLE EPOXIDE HYDROLASE EPHC (EPOXIDE HYDRATASE) 5 12 2 90 0.000000 NE
+Rv1125 - hypothetical protein Rv1125 15 21 3 148 0.000000 NE
+Rv1126c - hypothetical protein Rv1126c 1 8 5 167 0.000100 NE
+Rv1127c ppdK pyruvate phosphate dikinase 4 18 7 649 0.924400 U
+Rv1128c - hypothetical protein Rv1128c 8 26 7 214 0.000600 NE
+Rv1129c - PROBABLE TRANSCRIPTIONAL REGULATOR PROTEIN 9 22 5 159 0.000000 NE
+Rv1130 - hypothetical protein Rv1130 15 24 3 41 0.000000 NE
+Rv1131 gltA1 methylcitrate synthase 5 14 3 86 0.000000 NE
+Rv1132 - hypothetical protein Rv1132 19 25 2 23 0.000000 NE
+Rv1133c metE 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 0 31 31 1942 1.000000 E
+Rv1134 - hypothetical protein Rv1134 3 4 1 2 -1.000000 S
+Rv1135A - POSSIBLE ACETYL-CoA ACETYLTRANSFERASE (ACETOACETYL-CoA THIOLASE) 3 6 2 9 0.000000 NE
+Rv1135c PPE16 PPE FAMILY PROTEIN 18 24 1 2 0.000000 NE
+Rv1136 - POSSIBLE ENOYL-CoA HYDRATASE 2 2 0 0 -1.000000 S
+Rv1137c - hypothetical protein Rv1137c 2 2 0 0 -1.000000 S
+Rv1138c - POSSIBLE OXIDOREDUCTASE 7 13 4 157 0.000000 NE
+Rv1139c - hypothetical protein Rv1139c 5 9 2 19 0.000000 NE
+Rv1140 - PROBABLE INTEGRAL MEMBRANE PROTEIN 5 10 2 66 0.000000 NE
+Rv1141c echA11 enoyl-CoA hydratase 10 13 1 2 0.000000 NE
+Rv1142c echA10 enoyl-CoA hydratase 6 7 1 2 0.000000 NE
+Rv1143 mcr PROBABLE ALPHA-METHYLACYL-CoA RACEMASE MCR (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) 12 15 2 11 0.000000 NE
+Rv1144 - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 9 10 1 2 0.000000 NE
+Rv1145 mmpL13a PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL13A 6 10 1 2 0.000000 NE
+Rv1146 mmpL13b PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL13B 16 21 2 46 0.000000 NE
+Rv1147 - hypothetical protein Rv1147 4 9 3 186 0.000000 NE
+Rv1148c - hypothetical protein Rv1148c 7 10 2 424 0.084500 U
+Rv1149 - POSSIBLE TRANSPOSASE 1 2 1 2 -1.000000 S
+Rv1151c - NAD-dependent deacetylase 7 9 1 2 0.000000 NE
+Rv1152 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 4 5 1 2 0.000000 NE
+Rv1153c omt PROBABLE O-METHYLTRANSFERASE OMT 13 18 3 68 0.000000 NE
+Rv1154c - hypothetical protein Rv1154c 13 14 1 2 0.000000 NE
+Rv1155 - hypothetical protein Rv1155 9 10 1 2 0.000000 NE
+Rv1156 - hypothetical protein Rv1156 9 12 2 13 0.000000 NE
+Rv1157c - CONSERVED HYPOTHETICAL ALA-, PRO-RICH PROTEIN 4 8 2 73 0.000000 NE
+Rv1158c - CONSERVED HYPOTHETICAL ALA-, PRO-RICH PROTEIN 4 10 4 137 0.000000 NE
+Rv1159 pimE mannosyltransferase 4 25 9 478 0.983400 U
+Rv1159A phhB pterin-4-alpha-carbinolamine dehydratase 4 11 3 42 0.000000 NE
+Rv1160 mutT2 PROBABLE MUTATOR PROTEIN MUTT (7,8-dihydro-8-oxoguanine-triphosphatase) (8-OXO-DGTPASE) 4 4 0 0 0.000000 NE
+Rv1161 narG PROBABLE RESPIRATORY NITRATE REDUCTASE (ALPHA CHAIN) NARG 41 66 6 293 0.049500 U
+Rv1162 narH PROBABLE RESPIRATORY NITRATE REDUCTASE (BETA CHAIN) NARH 30 34 1 2 0.000000 NE
+Rv1163 narJ PROBABLE RESPIRATORY NITRATE REDUCTASE (DELTA CHAIN) NARJ 11 13 1 2 0.000000 NE
+Rv1164 narI PROBABLE RESPIRATORY NITRATE REDUCTASE (GAMMA CHAIN) NARI 13 18 1 2 0.000000 NE
+Rv1165 typA POSSIBLE GTP-BINDING TRANSLATION ELONGATION FACTOR TYPA (TYROSINE PHOSPHORYLATED PROTEIN A) (GTP-BINDING PROTEIN) 12 15 2 51 0.000000 NE
+Rv1166 lpqW PROBABLE CONSERVED LIPOPROTEIN LPQW 0 22 22 1652 1.000000 E
+Rv1167c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 4 9 2 41 0.000000 NE
+Rv1168c PPE17 PPE FAMILY PROTEIN 11 14 2 43 0.000000 NE
+Rv1169c PE11 PE FAMILY PROTEIN 3 3 0 0 -1.000000 S
+Rv1170 mshB N-Acetyl-1-D-myo-Inosityl-2-Amino-2-Deoxy-alpha- D-Glucopyranoside Deacetylase mshB (GlcNAc-Ins deacetylase) 3 11 6 244 0.023100 NE
+Rv1171 - hypothetical protein Rv1171 4 5 1 2 0.000000 NE
+Rv1172c PE12 PE FAMILY PROTEIN 11 15 1 2 0.000000 NE
+Rv1173 fbiC FO synthase 10 38 12 792 0.998600 E
+Rv1174c TB8.4 LOW MOLECULAR WEIGHT T-CELL ANTIGEN TB8.4 7 7 0 0 0.000000 NE
+Rv1175c fadH PROBABLE NADPH DEPENDENT 2,4-DIENOYL-COA REDUCTASE FADH (2,4-dienoyl coenzyme A reductase) (4-enoyl-CoA reductase) 17 23 2 23 0.000000 NE
+Rv1176c - hypothetical protein Rv1176c 10 13 2 30 0.000000 NE
+Rv1177 fdxC PROBABLE FERREDOXIN FDXC 0 6 6 125 -1.000000 S
+Rv1178 - N-succinyldiaminopimelate aminotransferase 14 20 3 65 0.000000 NE
+Rv1179c - hypothetical protein Rv1179c 30 37 2 16 0.000000 NE
+Rv1180 pks3 PROBABLE POLYKETIDE BETA-KETOACYL SYNTHASE PKS3 11 23 4 216 0.000000 NE
+Rv1181 pks4 PROBABLE POLYKETIDE BETA-KETOACYL SYNTHASE PKS4 41 63 7 188 0.000000 NE
+Rv1182 papA3 PROBABLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA3 23 38 2 68 0.000000 NE
+Rv1183 mmpL10 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL10 25 50 8 208 0.000100 NE
+Rv1184c - POSSIBLE EXPORTED PROTEIN 15 21 2 159 0.000000 NE
+Rv1185c fadD21 acyl-CoA synthetase 21 28 2 19 0.000000 NE
+Rv1186c - hypothetical protein Rv1186c 10 18 2 74 0.000000 NE
+Rv1187 rocA PROBABLE PYRROLINE-5-CARBOXYLATE DEHYDROGENASE ROCA 4 22 9 449 0.986700 U
+Rv1188 - PROBABLE PROLINE DEHYDROGENASE 8 22 7 331 0.904700 U
+Rv1189 sigI RNA polymerase sigma factor SigI 4 6 2 303 0.067200 U
+Rv1190 - hypothetical protein Rv1190 7 9 2 79 0.000000 NE
+Rv1191 - hypothetical protein Rv1191 5 8 2 151 0.000000 NE
+Rv1192 - hypothetical protein Rv1192 9 13 1 2 0.000000 NE
+Rv1193 fadD36 acyl-CoA synthetase 9 18 4 321 0.148600 U
+Rv1194c - hypothetical protein Rv1194c 11 16 3 96 0.000000 NE
+Rv1195 PE13 PE FAMILY PROTEIN 5 5 0 0 0.000000 NE
+Rv1196 PPE18 PPE FAMILY PROTEIN 3 3 0 0 0.000000 NE
+Rv1197 esxK ESAT-6 LIKE PROTEIN ESXK (ESAT-6 LIKE PROTEIN 3) 0 0 0 0 -1.000000 S
+Rv1198 esxL PUTATIVE ESAT-6 LIKE PROTEIN ESXL (ESAT-6 LIKE PROTEIN 4) 0 0 0 0 -1.000000 S
+Rv1199c - POSSIBLE TRANSPOSASE 0 2 2 44 -1.000000 S
+Rv1200 - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 20 24 1 2 0.000000 NE
+Rv1201c - PROBABLE TRANSFERASE 0 10 10 576 0.999500 E
+Rv1202 dapE dipeptidase 0 15 15 798 1.000000 E
+Rv1203c - hypothetical protein Rv1203c 2 6 4 265 0.228500 U
+Rv1204c - hypothetical protein Rv1204c 16 16 0 0 0.000000 NE
+Rv1205 - hypothetical protein Rv1205 10 12 1 2 0.000000 NE
+Rv1206 fadD6 acyl-CoA synthetase 21 29 3 64 0.000000 NE
+Rv1207 folP2 PROBABLE DIHYDROPTEROATE SYNTHASE 2 FOLP2 (DHPS 2) (Dihydropteroate pyrophosphorylase 2) 5 10 2 8 0.000000 NE
+Rv1208 - hypothetical protein Rv1208 0 12 12 837 1.000000 E
+Rv1209 - hypothetical protein Rv1209 3 4 1 2 0.000000 NE
+Rv1210 tagA PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE I TAGA (TAG I) (3-methyladenine-DNA glycosylase I, constitutive) (DNA-3-methyladenine glycosidase I ) 9 11 2 19 0.000000 NE
+Rv1211 - hypothetical protein Rv1211 0 2 2 31 -1.000000 S
+Rv1212c - PUTATIVE GLYCOSYL TRANSFERASE 19 27 3 54 0.000000 NE
+Rv1213 glgC glucose-1-phosphate adenylyltransferase 17 27 3 47 0.000000 NE
+Rv1214c PE14 PE FAMILY PROTEIN 4 5 1 2 -1.000000 S
+Rv1215c - hypothetical protein Rv1215c 13 23 6 281 0.121100 U
+Rv1216c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 12 15 2 11 0.000000 NE
+Rv1217c - PROBABLE TETRONASIN-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER 9 18 3 155 0.000000 NE
+Rv1218c - PROBABLE TETRONASIN-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 4 6 1 2 0.000000 NE
+Rv1219c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 8 10 2 12 0.000000 NE
+Rv1220c - PROBABLE METHYLTRANSFERASE 6 10 3 147 0.000000 NE
+Rv1221 sigE RNA polymerase sigma factor SigE 3 16 13 431 1.000000 E
+Rv1222 - hypothetical protein Rv1222 1 2 1 2 -1.000000 S
+Rv1223 htrA PROBABLE SERINE PROTEASE HTRA (DEGP PROTEIN) 0 17 17 1270 1.000000 E
+Rv1224 tatB sec-independent translocase 0 5 5 220 0.994700 E
+Rv1225c - hypothetical protein Rv1225c 5 6 1 2 0.000000 NE
+Rv1226c - PROBABLE TRANSMEMBRANE PROTEIN 11 15 2 84 0.000000 NE
+Rv1227c - PROBABLE TRANSMEMBRANE PROTEIN 5 6 1 2 0.000000 NE
+Rv1228 lpqX PROBABLE LIPOPROTEIN LPQX 7 8 1 2 0.000000 NE
+Rv1229c mrp PROBABLE MRP-RELATED PROTEIN MRP 0 14 14 1032 1.000000 E
+Rv1230c - POSSIBLE MEMBRANE PROTEIN 15 20 2 76 0.000000 NE
+Rv1231c - PROBABLE MEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv1232c - hypothetical protein Rv1232c 5 8 2 152 0.000000 NE
+Rv1233c - hypothetical protein Rv1233c 12 18 2 17 0.000000 NE
+Rv1234 - PROBABLE TRANSMEMBRANE PROTEIN 5 8 2 54 0.000000 NE
+Rv1235 lpqY PROBABLE SUGAR-BINDING LIPOPROTEIN LPQY 16 28 4 194 0.000000 NE
+Rv1236 sugA PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER SUGA 10 18 2 23 0.000000 NE
+Rv1237 sugB PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER SUGB 4 11 4 252 0.005100 NE
+Rv1238 sugC PROBABLE SUGAR-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER SUGC 9 24 9 463 0.984000 U
+Rv1239c corA POSSIBLE MAGNESIUM AND COBALT TRANSPORT TRANSMEMBRANE PROTEIN CORA 16 23 2 52 0.000000 NE
+Rv1240 mdh malate dehydrogenase 0 3 3 767 0.692600 U
+Rv1241 - hypothetical protein Rv1241 1 1 0 0 -1.000000 S
+Rv1242 - hypothetical protein Rv1242 8 9 1 2 0.000000 NE
+Rv1243c PE_PGRS23 PE-PGRS FAMILY PROTEIN 12 15 1 2 0.000000 NE
+Rv1244 lpqZ PROBABLE LIPOPROTEIN LPQZ 6 8 1 2 0.000000 NE
+Rv1245c - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 10 13 2 11 0.000000 NE
+Rv1246c - hypothetical protein Rv1246c 6 7 1 2 0.000000 NE
+Rv1247c - hypothetical protein Rv1247c 3 4 1 2 -1.000000 S
+Rv1248c kgd alpha-ketoglutarate decarboxylase 0 41 41 3175 1.000000 E
+Rv1249c - POSSIBLE MEMBRANE PROTEIN 8 11 1 2 0.000000 NE
+Rv1250 - PROBABLE DRUG-TRANSPORT INTEGRAL MEMBRANE PROTEIN 21 26 2 26 0.000000 NE
+Rv1251c - hypothetical protein Rv1251c 33 53 3 71 0.000000 NE
+Rv1252c lprE PROBABLE LIPOPROTEIN LPRE 7 7 0 0 0.000000 NE
+Rv1253 deaD PROBABLE COLD-SHOCK DEAD-BOX PROTEIN A HOMOLOG DEAD (ATP-dependent RNA helicase deaD homolog) 18 32 5 184 0.000000 NE
+Rv1254 - PROBABLE ACYLTRANSFERASE 1 26 25 911 1.000000 E
+Rv1255c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 5 8 2 17 0.000000 NE
+Rv1256c cyp130 PROBA BLE CYTOCHROME P450 130 CYP130 11 14 1 2 0.000000 NE
+Rv1257c - PROBABLE OXIDOREDUCTASE 9 15 3 307 0.049000 U
+Rv1258c - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 15 21 3 152 0.000000 NE
+Rv1259 - hypothetical protein Rv1259 7 11 2 28 0.000000 NE
+Rv1260 - hypothetical protein Rv1260 11 24 6 226 0.001100 NE
+Rv1261c - hypothetical protein Rv1261c 6 10 2 47 0.000000 NE
+Rv1262c - HYPOTHETICAL HIT-LIKE PROTEIN 4 4 0 0 0.000000 NE
+Rv1263 amiB2 amidase 11 21 3 64 0.000000 NE
+Rv1264 - ADENYLYL CYCLASE (ATP PYROPHOSPHATE-LYASE) (ADENYLATE CYCLASE) 9 13 2 157 0.000000 NE
+Rv1265 - hypothetical protein Rv1265 4 11 3 87 0.000000 NE
+Rv1266c pknH PROBABLE TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE H PKNH (PROTEIN KINASE H) (STPK H) 23 26 1 2 0.000000 NE
+Rv1267c embR PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN EMBR 15 19 2 32 0.000000 NE
+Rv1268c - hypothetical protein Rv1268c 9 11 1 2 0.000000 NE
+Rv1269c - CONSERVED PROBABLE SECRETED PROTEIN 5 7 1 2 0.000000 NE
+Rv1270c lprA POSSIBLE LIPOPROTEIN LPRA 9 10 1 2 0.000000 NE
+Rv1271c - CONSERVED HYPOTHETICAL SECRETED PROTEIN 3 5 1 2 0.000000 NE
+Rv1272c - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 11 28 6 171 0.000000 NE
+Rv1273c - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 10 29 6 510 0.558200 U
+Rv1274 lprB POSSIBLE LIPOPROTEIN LPRB 0 3 3 137 -1.000000 S
+Rv1275 lprC POSSIBLE LIPOPROTEIN LPRC 0 6 6 404 0.980100 U
+Rv1276c - hypothetical protein Rv1276c 2 6 4 145 0.000000 NE
+Rv1277 - hypothetical protein Rv1277 16 19 2 33 0.000000 NE
+Rv1278 - hypothetical protein Rv1278 9 24 8 558 0.913500 U
+Rv1279 - PROBABLE DEHYDROGENASE FAD flavoprotein GMC oxidoreductase 18 25 5 71 0.000000 NE
+Rv1280c oppA PROBABLE PERIPLASMIC OLIGOPEPTIDE-BINDING LIPOPROTEIN OPPA 17 25 2 92 0.000000 NE
+Rv1281c oppD PROBABLE OLIGOPEPTIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER OPPD 16 25 2 32 0.000000 NE
+Rv1282c oppC PROBABLE OLIGOPEPTIDE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER OPPC 11 15 2 33 0.000000 NE
+Rv1283c oppB PROBABLE OLIGOPEPTIDE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER OPPB 10 17 5 179 0.000000 NE
+Rv1284 - hypothetical protein Rv1284 2 4 1 2 0.000000 NE
+Rv1285 cysD sulfate adenylyltransferase subunit 2 0 9 9 736 0.998100 E
+Rv1286 cysN bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein 2 27 23 1277 1.000000 E
+Rv1287 - hypothetical protein Rv1287 5 10 2 41 0.000000 NE
+Rv1288 - hypothetical protein Rv1288 25 30 4 84 0.000000 NE
+Rv1289 - hypothetical protein Rv1289 7 10 1 2 0.000000 NE
+Rv1290A - hypothetical protein Rv1290A 4 7 2 84 0.000000 NE
+Rv1290c - hypothetical protein Rv1290c 28 32 1 2 0.000000 NE
+Rv1291c - CONSERVED HYPOTHETICAL SECRETED PROTEIN 2 2 0 0 -1.000000 S
+Rv1292 argS arginyl-tRNA synthetase 0 33 33 1379 1.000000 E
+Rv1293 lysA PROBABLE DIAMINOPIMELATE DECARBOXYLASE LYSA (DAP DECARBOXYLASE) 0 24 24 1155 1.000000 E
+Rv1294 thrA homoserine dehydrogenase 0 20 20 840 1.000000 E
+Rv1295 thrC threonine synthase 0 17 17 878 1.000000 E
+Rv1296 thrB homoserine kinase 0 14 14 781 1.000000 E
+Rv1297 rho transcription termination factor Rho 1 17 16 1510 1.000000 E
+Rv1298 rpmE 50S ribosomal protein L31 0 6 6 170 0.997100 E
+Rv1299 prfA peptide chain release factor 1 0 14 14 584 1.000000 E
+Rv1300 hemK PROBABLE HEMK PROTEIN HOMOLOG HEMK 0 14 14 752 1.000000 E
+Rv1301 - hypothetical protein Rv1301 0 10 10 560 0.998800 E
+Rv1302 rfe PROBABLE UNDECAPAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE RFE (UDP-GlcNAc TRANSFERASE) 0 16 16 1036 1.000000 E
+Rv1303 - hypothetical protein Rv1303 1 4 3 73 0.000100 NE
+Rv1304 atpB F0F1 ATP synthase subunit A 0 10 10 648 0.999300 E
+Rv1305 atpE F0F1 ATP synthase subunit C 0 6 6 158 0.997400 E
+Rv1306 atpF F0F1 ATP synthase subunit B 0 3 3 140 -1.000000 S
+Rv1307 atpH PROBABLE ATP SYNTHASE DELTA CHAIN ATPH 0 15 15 1158 1.000000 E
+Rv1308 atpA F0F1 ATP synthase subunit alpha 0 21 21 1318 1.000000 E
+Rv1309 atpG F0F1 ATP synthase subunit gamma 0 16 16 593 1.000000 E
+Rv1310 atpD F0F1 ATP synthase subunit beta 0 18 18 1020 1.000000 E
+Rv1311 atpC F0F1 ATP synthase subunit epsilon 0 1 1 2 -1.000000 S
+Rv1312 - CONSERVED HYPOTHETICAL SECRETED PROTEIN 1 8 4 122 0.000000 NE
+Rv1313c - POSSIBLE TRANSPOSASE 0 2 2 610 -1.000000 S
+Rv1314c - hypothetical protein Rv1314c 8 12 2 45 0.000000 NE
+Rv1315 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase 0 13 13 1007 1.000000 E
+Rv1316c ogt PROBABLE METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE OGT (6-O-methylguanine-DNA methyltransferase) (O-6-methylguanine-DNA-alkyltransferase) 4 7 3 152 0.000000 NE
+Rv1317c alkA PROBABLE ADA REGULATORY PROTEIN ALKA (Regulatory protein of adaptative response) (Methylated-DNA--protein-cysteine methyltransferase) (O-6-methylguanine-DNA alkyltransferase) (O-6-methylguanine-DNA methyltransferase) (3-methyladenine DNA glycosylase II) 10 10 0 0 0.000000 NE
+Rv1318c - POSSIBLE ADENYLATE CYCLASE (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) 15 17 1 2 0.000000 NE
+Rv1319c - POSSIBLE ADENYLATE CYCLASE (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) 24 28 1 2 0.000000 NE
+Rv1320c - POSSIBLE ADENYLATE CYCLASE (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) 22 27 2 41 0.000000 NE
+Rv1321 - hypothetical protein Rv1321 7 9 1 2 0.000000 NE
+Rv1322 - hypothetical protein Rv1322 4 5 1 2 -1.000000 S
+Rv1322A - hypothetical protein Rv1322A 5 6 1 2 0.000000 NE
+Rv1323 fadA4 acetyl-CoA acetyltransferase 10 12 2 167 0.000000 NE
+Rv1324 - POSSIBLE THIOREDOXIN 0 5 5 346 0.976300 U
+Rv1325c PE_PGRS24 PE-PGRS FAMILY PROTEIN 5 8 3 338 0.129900 U
+Rv1326c glgB glycogen branching enzyme 0 41 41 1958 1.000000 E
+Rv1327c glgE PROBABLE GLUCANASE GLGE 0 35 35 1802 1.000000 E
+Rv1328 glgP PROBABLE GLYCOGEN PHOSPHORYLASE GLGP 21 40 4 91 0.000000 NE
+Rv1329c dinG PROBABLE ATP-DEPENDENT HELICASE DING 11 23 4 171 0.000000 NE
+Rv1330c - nicotinate phosphoribosyltransferase 17 23 2 12 0.000000 NE
+Rv1331 clpS ATP-dependent Clp protease adaptor protein ClpS 4 5 1 2 0.000000 NE
+Rv1332 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 6 2 5 0.000000 NE
+Rv1333 - PROBABLE HYDROLASE 6 10 2 134 0.000000 NE
+Rv1334 - hypothetical protein Rv1334 10 10 0 0 0.000000 NE
+Rv1335 - 9.5 KDA CULTURE FILTRATE ANTIGEN CFP10A 4 4 0 0 -1.000000 S
+Rv1336 cysM PROBABLE CYSTEINE SYNTHASE B CYSM (CSASE B) (O-acetylserine sulfhydrylase B) (O-acetylserine (Thiol)-lyase B) 13 16 1 2 0.000000 NE
+Rv1337 - PROBABLE INTEGRAL MEMBRANE PROTEIN 10 12 1 2 0.000000 NE
+Rv1338 murI glutamate racemase 0 16 16 640 1.000000 E
+Rv1339 - hypothetical protein Rv1339 0 16 16 666 1.000000 E
+Rv1340 rph ribonuclease PH 4 13 5 188 0.000200 NE
+Rv1341 - putative deoxyribonucleotide triphosphate pyrophosphatase 4 5 1 2 0.000000 NE
+Rv1342c - hypothetical protein Rv1342c 0 5 5 134 -1.000000 S
+Rv1343c lprD PROBABLE CONSERVED LIPOPROTEIN LPRD 0 11 11 207 1.000000 E
+Rv1344 - acyl carrier protein 6 7 1 2 0.000000 NE
+Rv1345 fadD33 acyl-CoA synthetase 16 23 2 15 0.000000 NE
+Rv1346 fadE14 POSSIBLE ACYL-CoA DEHYDROGENASE FADE14 6 13 3 150 0.000000 NE
+Rv1347c - hypothetical protein Rv1347c 0 13 13 395 1.000000 E
+Rv1348 - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 2 37 16 1210 1.000000 E
+Rv1349 - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 0 17 17 1265 1.000000 E
+Rv1350 fabG 3-ketoacyl-(acyl-carrier-protein) reductase 5 12 4 123 0.000000 NE
+Rv1351 - hypothetical protein Rv1351 6 10 1 2 0.000000 NE
+Rv1352 - hypothetical protein Rv1352 4 5 1 2 0.000000 NE
+Rv1353c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 7 12 2 8 0.000000 NE
+Rv1354c - hypothetical protein Rv1354c 23 40 3 58 0.000000 NE
+Rv1355c moeY hypothetical protein Rv1355c 14 36 9 434 0.948400 U
+Rv1356c - hypothetical protein Rv1356c 12 25 3 58 0.000000 NE
+Rv1357c - hypothetical protein Rv1357c 11 12 1 2 0.000000 NE
+Rv1358 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 39 66 6 95 0.000000 NE
+Rv1359 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 11 17 2 16 0.000000 NE
+Rv1360 - PROBABLE OXIDOREDUCTASE 11 12 1 2 0.000000 NE
+Rv1361c PPE19 PPE FAMILY PROTEIN 3 6 3 685 0.387100 U
+Rv1362c - POSSIBLE MEMBRANE PROTEIN 11 13 1 2 0.000000 NE
+Rv1363c - POSSIBLE MEMBRANE PROTEIN 5 6 1 2 0.000000 NE
+Rv1364c - hypothetical protein Rv1364c 14 31 4 202 0.000000 NE
+Rv1365c rsfA ANTI-ANTI-SIGMA FACTOR RSFA (ANTI-SIGMA FACTOR ANTAGONIST) (REGULATOR OF SIGMA F A) 5 5 0 0 0.000000 NE
+Rv1366 - hypothetical protein Rv1366 13 17 2 34 0.000000 NE
+Rv1367c - hypothetical protein Rv1367c 11 13 1 2 0.000000 NE
+Rv1368 lprF PROBABLE CONSERVED LIPOPROTEIN LPRF 6 7 1 2 0.000000 NE
+Rv1369c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv1370c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv1371 - PROBABLE CONSERVED MEMBRANE PROTEIN 11 28 7 145 0.000000 NE
+Rv1372 - hypothetical protein Rv1372 6 18 4 146 0.000000 NE
+Rv1373 - GLYCOLIPID SULFOTRANSFERASE 16 17 1 2 0.000000 NE
+Rv1374c - hypothetical protein Rv1374c 11 12 1 2 0.000000 NE
+Rv1375 - hypothetical protein Rv1375 17 20 1 2 0.000000 NE
+Rv1376 - hypothetical protein Rv1376 13 14 1 2 0.000000 NE
+Rv1377c - PUTATIVE TRANSFERASE 10 10 0 0 0.000000 NE
+Rv1378c - hypothetical protein Rv1378c 13 19 2 4 0.000000 NE
+Rv1379 pyrR pyrimidine regulatory protein PyrR 1 7 6 270 0.679300 U
+Rv1380 pyrB aspartate carbamoyltransferase catalytic subunit 0 12 12 597 1.000000 E
+Rv1381 pyrC dihydroorotase 0 9 9 960 0.999200 E
+Rv1382 - PROBABLE EXPORT OR MEMBRANE PROTEIN 0 6 6 284 0.997000 E
+Rv1383 carA carbamoyl phosphate synthase small subunit 0 10 10 935 0.999700 E
+Rv1384 carB carbamoyl phosphate synthase large subunit 0 42 42 2966 1.000000 E
+Rv1385 pyrF orotidine 5'-phosphate decarboxylase 0 5 5 263 0.994200 E
+Rv1386 PE15 PE FAMILY PROTEIN 5 5 0 0 0.000000 NE
+Rv1387 PPE20 PPE FAMILY PROTEIN 22 24 1 2 0.000000 NE
+Rv1388 mihF PUTATIVE INTEGRATION HOST FACTOR MIHF 2 5 2 33 -1.000000 S
+Rv1389 gmk guanylate kinase 0 6 6 387 0.986000 U
+Rv1390 rpoZ DNA-directed RNA polymerase subunit omega 0 6 6 149 -1.000000 S
+Rv1391 dfp bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 0 15 15 1102 1.000000 E
+Rv1392 metK S-adenosylmethionine synthetase 0 17 17 1033 1.000000 E
+Rv1393c - PROBABLE MONOXYGENASE 19 24 2 56 0.000000 NE
+Rv1394c cyp132 PROBABLE CYTOCHROME P450 132 CYP132 14 18 1 2 0.000000 NE
+Rv1395 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 8 13 2 46 0.000000 NE
+Rv1396c PE_PGRS25 PE-PGRS FAMILY PROTEIN 9 12 2 59 0.000000 NE
+Rv1397c - hypothetical protein Rv1397c 3 6 1 2 -1.000000 S
+Rv1398c - hypothetical protein Rv1398c 3 3 0 0 -1.000000 S
+Rv1399c lipH PROBABLE LIPASE LIPH 12 14 1 2 0.000000 NE
+Rv1400c lipI PROBABLE LIPASE LIPH 3 15 9 592 0.995700 E
+Rv1401 - POSSIBLE MEMBRANE PROTEIN 1 5 2 25 0.000000 NE
+Rv1402 priA primosome assembly protein PriA 0 22 22 1311 1.000000 E
+Rv1403c - PUTATIVE METHYLTRANSFERASE 9 13 2 32 0.000000 NE
+Rv1404 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 0 5 5 191 0.993000 E
+Rv1405c - PUTATIVE METHYLTRANSFERASE 9 10 1 2 0.000000 NE
+Rv1406 fmt methionyl-tRNA formyltransferase 0 9 9 462 0.998600 E
+Rv1407 fmu PROBABLE FMU PROTEIN (SUN PROTEIN) 13 19 2 30 0.000000 NE
+Rv1408 rpe ribulose-phosphate 3-epimerase 0 11 11 620 0.999700 E
+Rv1409 ribG PROBABLE BIFUNCTIONAL riboflavin biosynthesis protein RIBG : Diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino) uracil reductase (HTP reductase) 0 12 12 850 1.000000 E
+Rv1410c - AMINOGLYCOSIDES/TETRACYCLINE-TRANSPORT INTEGRAL MEMBRANE PROTEIN 14 27 4 214 0.000100 NE
+Rv1411c lprG PROBABLE CONSERVED LIPOPROTEIN LPRG 5 8 2 59 0.000000 NE
+Rv1412 ribC riboflavin synthase subunit alpha 0 6 6 483 0.972200 U
+Rv1413 - hypothetical protein Rv1413 4 4 0 0 0.000000 NE
+Rv1414 - hypothetical protein Rv1414 1 3 2 57 0.000000 NE
+Rv1415 ribA2 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein 0 14 14 1025 1.000000 E
+Rv1416 ribH riboflavin synthase subunit beta 0 4 4 120 -1.000000 S
+Rv1417 - POSSIBLE CONSERVED MEMBRANE PROTEIN 1 8 5 264 0.249400 U
+Rv1418 lprH PROBABLE LIPOPROTEIN LPRH 9 13 2 24 0.000000 NE
+Rv1419 - hypothetical protein Rv1419 3 3 0 0 0.000000 NE
+Rv1420 uvrC excinuclease ABC subunit C 6 25 13 788 0.999800 E
+Rv1421 - hypothetical protein Rv1421 6 19 3 32 0.000000 NE
+Rv1422 - hypothetical protein Rv1422 3 9 6 655 0.940500 U
+Rv1423 whiA PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIA 0 9 9 758 0.998800 E
+Rv1424c - POSSIBLE MEMBRANE PROTEIN 9 17 4 240 0.000700 NE
+Rv1425 - hypothetical protein Rv1425 11 17 2 11 0.000000 NE
+Rv1426c lipO PROBABLE ESTERASE LIPO 11 26 4 65 0.000000 NE
+Rv1427c fadD12 acyl-CoA synthetase 10 16 3 426 0.072700 U
+Rv1428c - hypothetical protein Rv1428c 11 16 1 2 0.000000 NE
+Rv1429 - hypothetical protein Rv1429 13 21 3 33 0.000000 NE
+Rv1430 PE16 PE FAMILY PROTEIN 25 36 3 81 0.000000 NE
+Rv1431 - hypothetical protein Rv1431 15 25 4 180 0.000000 NE
+Rv1432 - PROBABLE DEHYDROGENASE 6 15 5 224 0.000300 NE
+Rv1433 - POSSIBLE CONSERVED EXPORTED PROTEIN 13 16 2 12 0.000000 NE
+Rv1434 - hypothetical protein Rv1434 1 1 0 0 -1.000000 S
+Rv1435c - Probable conserved Proline, Glycine, Valine-rich secreted protein 7 15 4 53 0.000000 NE
+Rv1436 gap glyceraldehyde-3-phosphate dehydrogenase 0 12 12 902 1.000000 E
+Rv1437 pgk phosphoglycerate kinase 0 14 14 1065 1.000000 E
+Rv1438 tpiA triosephosphate isomerase 0 14 14 593 1.000000 E
+Rv1439c - hypothetical protein Rv1439c 6 7 1 2 0.000000 NE
+Rv1440 secG preprotein translocase subunit SecG 0 4 4 123 -1.000000 S
+Rv1441c PE_PGRS26 PE-PGRS FAMILY PROTEIN 10 17 2 27 0.000000 NE
+Rv1442 bisC PROBABLE BIOTIN SULFOXIDE REDUCTASE BISC (BDS reductase) (BSO reductase) 28 35 2 151 0.000000 NE
+Rv1443c - hypothetical protein Rv1443c 0 1 1 2 -1.000000 S
+Rv1444c - hypothetical protein Rv1444c 2 3 1 2 0.000000 NE
+Rv1445c devB 6-phosphogluconolactonase 3 7 2 52 0.000000 NE
+Rv1446c opcA PUTATIVE OXPP CYCLE PROTEIN OPCA 3 13 5 281 0.177600 U
+Rv1447c zwf2 glucose-6-phosphate 1-dehydrogenase 10 15 2 94 0.000000 NE
+Rv1448c tal transaldolase 3 11 4 105 0.000000 NE
+Rv1449c tkt transketolase 0 20 20 1724 1.000000 E
+Rv1450c PE_PGRS27 PE-PGRS FAMILY PROTEIN 5 24 7 929 0.899900 U
+Rv1451 ctaB protoheme IX farnesyltransferase 0 15 15 797 1.000000 E
+Rv1452c PE_PGRS28 PE-PGRS FAMILY PROTEIN 7 11 3 548 0.084100 U
+Rv1453 - POSSIBLE TRANSCRIPTIONAL ACTIVATOR PROTEIN 10 10 0 0 0.000000 NE
+Rv1454c qor PROBABLE QUINONE REDUCTASE QOR (NADPH:quinone reductase) (Zeta-crystallin homolog protein) 11 15 1 2 0.000000 NE
+Rv1455 - hypothetical protein Rv1455 11 12 1 2 0.000000 NE
+Rv1456c - PROBABLE UNIDENTIFIED ANTIBIOTIC-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER 0 14 14 775 1.000000 E
+Rv1457c - PROBABLE UNIDENTIFIED ANTIBIOTIC-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER 0 8 8 614 0.996100 E
+Rv1458c - PROBABLE UNIDENTIFIED ANTIBIOTIC-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 2 13 6 503 0.868300 U
+Rv1459c - POSSIBLE CONSERVED INTEGRAL MEMBRANE PROTEIN 3 23 11 679 0.998700 E
+Rv1460 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 7 4 350 0.563900 U
+Rv1461 - hypothetical protein Rv1461 0 56 56 2093 1.000000 E
+Rv1462 - hypothetical protein Rv1462 0 14 14 943 1.000000 E
+Rv1463 - PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER 0 10 10 581 0.999500 E
+Rv1464 csd PROBABLE CYSTEINE DESULFURASE CSD 0 15 15 1088 1.000000 E
+Rv1465 - POSSIBLE NITROGEN FIXATION RELATED PROTEIN 1 7 6 326 0.975300 U
+Rv1466 - hypothetical protein Rv1466 0 1 1 2 -1.000000 S
+Rv1467c fadE15 PROBABLE ACYL-CoA DEHYDROGENASE FADE15 17 25 1 2 0.000000 NE
+Rv1468c PE_PGRS29 PE-PGRS FAMILY PROTEIN 6 9 2 12 0.000000 NE
+Rv1469 ctpD PROBABLE CATION TRANSPORTER P-TYPE ATPASE D CTPD 11 18 2 10 0.000000 NE
+Rv1470 trxA PROBABLE THIOREDOXIN TRXA 5 5 0 0 0.000000 NE
+Rv1471 trxB1 PROBABLE THIOREDOXIN TRXB1 2 2 0 0 -1.000000 S
+Rv1472 echA12 enoyl-CoA hydratase 11 14 1 2 0.000000 NE
+Rv1473 - PROBABLE MACROLIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 12 22 3 20 0.000000 NE
+Rv1473A - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 4 2 19 -1.000000 S
+Rv1474c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 4 8 1 2 0.000000 NE
+Rv1475c acn aconitate hydratase 0 47 47 2459 1.000000 E
+Rv1476 - POSSIBLE MEMBRANE PROTEIN 0 5 5 269 0.994800 E
+Rv1477 - HYPOTHETICAL INVASION PROTEIN 0 21 21 1216 1.000000 E
+Rv1478 - HYPOTHETICAL INVASION PROTEIN 5 7 1 2 0.000000 NE
+Rv1479 moxR1 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN MOXR1 0 13 13 828 1.000000 E
+Rv1480 - hypothetical protein Rv1480 1 6 5 747 0.918100 U
+Rv1481 - PROBABLE MEMBRANE PROTEIN 0 11 11 838 0.999700 E
+Rv1482c - hypothetical protein Rv1482c 9 14 2 36 0.000000 NE
+Rv1483 fabG1 3-OXOACYL- 0 12 12 654 1.000000 E
+Rv1484 inhA enoyl-(acyl carrier protein) reductase 0 7 7 498 0.990400 E
+Rv1485 hemH ferrochelatase 0 24 24 829 1.000000 E
+Rv1486c - hypothetical protein Rv1486c 7 7 0 0 0.000000 NE
+Rv1487 - hypothetical protein Rv1487 1 3 2 91 0.000000 NE
+Rv1488 - POSSIBLE EXPORTED CONSERVED PROTEIN 12 14 1 2 0.000000 NE
+Rv1489 - hypothetical protein Rv1489 6 6 0 0 0.000000 NE
+Rv1489A - hypothetical protein Rv1489A 4 4 0 0 -1.000000 S
+Rv1490 - PROBABLE MEMBRANE PROTEIN 11 37 9 193 0.000800 NE
+Rv1491c - hypothetical protein Rv1491c 11 14 1 2 0.000000 NE
+Rv1492 mutA PROBABLE METHYLMALONYL-CoA MUTASE SMALL SUBUNIT MUTA (MCM) 9 13 2 39 0.000000 NE
+Rv1493 mutB methylmalonyl-CoA mutase 17 28 3 110 0.000000 NE
+Rv1494 - hypothetical protein Rv1494 5 8 3 97 0.000100 NE
+Rv1495 - hypothetical protein Rv1495 5 5 0 0 0.000000 NE
+Rv1496 - arginine/ornithine transport system ATPase 3 3 0 0 0.000000 NE
+Rv1497 lipL PROBABLE ESTERASE LIPL 11 14 3 31 0.000000 NE
+Rv1498A - hypothetical protein Rv1498A 3 3 0 0 0.000000 NE
+Rv1498c - PROBABLE METHYLTRANSFERASE 13 16 2 19 0.000000 NE
+Rv1499 - hypothetical protein Rv1499 3 4 1 2 0.000000 NE
+Rv1500 - PROBABLE GLYCOSYLTRANSFERASE 10 32 9 179 0.000500 NE
+Rv1501 - hypothetical protein Rv1501 12 30 9 191 0.000900 NE
+Rv1502 - hypothetical protein Rv1502 8 32 12 373 0.999400 E
+Rv1503c - hypothetical protein Rv1503c 12 18 3 54 0.000000 NE
+Rv1504c - hypothetical protein Rv1504c 10 12 1 2 0.000000 NE
+Rv1505c - hypothetical protein Rv1505c 7 25 16 322 1.000000 E
+Rv1506c - hypothetical protein Rv1506c 9 19 4 151 0.000000 NE
+Rv1507A - hypothetical protein Rv1507A 6 16 4 62 0.000000 NE
+Rv1507c - hypothetical protein Rv1507c 3 26 18 430 1.000000 E
+Rv1508A - hypothetical protein Rv1508A 7 13 4 151 0.000000 NE
+Rv1508c - Probable membrane protein 30 40 2 13 0.000000 NE
+Rv1509 - hypothetical protein Rv1509 3 16 11 336 0.998900 E
+Rv1510 - conserved probable membrane protein 21 22 1 2 0.000000 NE
+Rv1511 gmdA GDP-D-mannose dehydratase gmdA (GDP-mannose 4,6 dehydratase) (GMD) 17 19 2 95 0.000000 NE
+Rv1512 epiA probable nucleotide-sugar epimerase epiA 0 11 11 785 0.999800 E
+Rv1513 - hypothetical protein Rv1513 2 7 4 222 0.000400 NE
+Rv1514c - hypothetical protein Rv1514c 8 17 3 142 0.000000 NE
+Rv1515c - hypothetical protein Rv1515c 11 16 1 2 0.000000 NE
+Rv1516c - probable sugar transferase 7 11 1 2 0.000000 NE
+Rv1517 - hypothetical protein Rv1517 6 13 5 96 0.000000 NE
+Rv1518 - hypothetical protein Rv1518 7 11 2 16 0.000000 NE
+Rv1519 - hypothetical protein Rv1519 2 3 1 2 0.000000 NE
+Rv1520 - probable sugar transferase 18 20 1 2 0.000000 NE
+Rv1521 fadD25 acyl-CoA synthetase 22 35 3 18 0.000000 NE
+Rv1522c mmpL12 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL12 24 46 12 202 0.010600 NE
+Rv1523 - Probable methyltransferase 11 15 2 59 0.000000 NE
+Rv1524 - Probable glycosyltransferase 8 12 2 247 0.000100 NE
+Rv1525 wbbL2 POSSIBLE RHAMNOSYL TRANSFERASE WBBL2 3 20 9 338 0.990700 E
+Rv1526c - Probable glycosyltransferase 9 18 4 192 0.000000 NE
+Rv1527c pks5 Probable polyketide synthase pks5 59 86 3 82 0.000000 NE
+Rv1528c papA4 PROBABLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA4 7 7 0 0 0.000000 NE
+Rv1529 fadD24 acyl-CoA synthetase 16 33 6 117 0.000000 NE
+Rv1530 adh Probable alcohol dehydrogenase adh 10 22 4 419 0.210600 U
+Rv1531 - hypothetical protein Rv1531 3 8 3 44 0.000000 NE
+Rv1532c - hypothetical protein Rv1532c 3 4 1 2 0.000000 NE
+Rv1533 - hypothetical protein Rv1533 6 10 2 329 0.072200 U
+Rv1534 - Probable transcriptional regulator 13 16 2 11 0.000000 NE
+Rv1535 - hypothetical protein Rv1535 4 4 0 0 0.000000 NE
+Rv1536 ileS isoleucyl-tRNA synthetase 0 72 72 2755 1.000000 E
+Rv1537 dinX DNA polymerase IV 9 13 2 25 0.000000 NE
+Rv1538c ansA Probable L-aparaginase ansA 0 14 14 868 1.000000 E
+Rv1539 lspA lipoprotein signal peptidase 1 8 7 398 0.986900 U
+Rv1540 - CONSERVED HYPOTHETICAL PROTEIN MEMBER OF yabO/yceC/yfiI FAMILY 0 12 12 648 1.000000 E
+Rv1541c lprI Possible lipoprotein lprI 8 9 1 2 0.000000 NE
+Rv1542c glbN Probable hemoglobin glbN 7 7 0 0 0.000000 NE
+Rv1543 - POSSIBLE FATTY ACYL-CoA REDUCTASE 9 14 2 15 0.000000 NE
+Rv1544 - Possible ketoacyl reductase 8 11 1 2 0.000000 NE
+Rv1545 - hypothetical protein Rv1545 2 3 1 2 -1.000000 S
+Rv1546 - hypothetical protein Rv1546 3 3 0 0 0.000000 NE
+Rv1547 dnaE DNA polymerase III subunit alpha 0 45 45 2981 1.000000 E
+Rv1548c PPE21 PPE FAMILY PROTEIN 14 41 6 205 0.000000 NE
+Rv1549 fadD11.1 POSSIBLE FATTY-ACID-CoA LIGASE FADD11.1 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 7 9 1 2 0.000000 NE
+Rv1550 fadD11 PROBABLE FATTY-ACID-CoA LIGASE FADD11 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 20 25 3 76 0.000000 NE
+Rv1551 plsB1 glycerol-3-phosphate acyltransferase 17 29 6 61 0.000000 NE
+Rv1552 frdA fumarate reductase flavoprotein subunit 21 34 4 130 0.000000 NE
+Rv1553 frdB PROBABLE FUMARATE REDUCTASE 11 13 2 20 0.000000 NE
+Rv1554 frdC PROBABLE FUMARATE REDUCTASE 6 9 2 31 0.000000 NE
+Rv1555 frdD fumarate reductase subunit D 3 3 0 0 0.000000 NE
+Rv1556 - Possible regulatory protein 10 12 1 2 0.000000 NE
+Rv1557 mmpL6 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL6 12 19 3 144 0.000000 NE
+Rv1558 - hypothetical protein Rv1558 7 8 1 2 0.000000 NE
+Rv1559 ilvA threonine dehydratase 0 23 23 1109 1.000000 E
+Rv1560 - hypothetical protein Rv1560 1 2 1 2 -1.000000 S
+Rv1561 - hypothetical protein Rv1561 6 9 3 76 0.000000 NE
+Rv1562c treZ Maltooligosyltrehalose trehalohydrolase TreZ 11 30 8 446 0.916800 U
+Rv1563c treY Maltooligosyltrehalose synthase TreY 8 31 8 461 0.876700 U
+Rv1564c treX Probable Maltooligosyltrehalose synthase TreX 19 42 10 548 0.982300 U
+Rv1565c - hypothetical protein Rv1565c 3 41 13 897 0.999500 E
+Rv1566c - Possible inv protein 6 10 1 2 0.000000 NE
+Rv1567c - Probable hypothetical membrane protein 5 8 2 9 0.000000 NE
+Rv1568 bioA adenosylmethionine--8-amino-7-oxononanoate transaminase 0 15 15 1165 1.000000 E
+Rv1569 bioF1 8-amino-7-oxononanoate synthase 1 7 3 393 0.209300 U
+Rv1570 bioD dithiobiotin synthetase 0 2 2 370 -1.000000 S
+Rv1571 - hypothetical protein Rv1571 0 2 2 52 -1.000000 S
+Rv1572c - hypothetical protein Rv1572c 0 1 1 2 -1.000000 S
+Rv1573 - Probable phiRV1 phage protein 0 1 1 2 -1.000000 S
+Rv1574 - Probable phiRV1 phage related protein 0 1 1 2 -1.000000 S
+Rv1575 - Probable phiRV1 phage protein 4 10 5 45 0.000000 NE
+Rv1576c - Probable phiRV1 phage protein 0 7 7 963 0.994200 E
+Rv1577c - Probable phiRv1 phage protein 2 7 4 72 0.000000 NE
+Rv1578c - Probable phiRv1 phage protein 1 4 3 150 0.181600 U
+Rv1579c - Probable phiRv1 phage protein 2 4 2 37 -1.000000 S
+Rv1580c - Probable phiRv1 phage protein 4 5 1 2 0.000000 NE
+Rv1581c - Probable phiRv1 phage protein 6 6 0 0 0.000000 NE
+Rv1582c - Probable phiRv1 phage protein 8 29 12 464 0.998700 E
+Rv1583c - Probable phiRv1 phage protein 3 3 0 0 -1.000000 S
+Rv1584c - Possible phiRv1 phage protein 2 3 1 2 -1.000000 S
+Rv1585c - Possible phage phiRv1 protein 0 8 8 362 0.998300 E
+Rv1586c - Probable phiRv1 integrase 14 20 5 186 0.000000 NE
+Rv1587c - Partial REP13E12 repeat protein 4 6 2 7 0.000000 NE
+Rv1588c - Partial REP13E12 repeat protein 0 2 2 182 -1.000000 S
+Rv1589 bioB biotin synthase 0 9 9 817 0.999000 E
+Rv1590 - hypothetical protein Rv1590 0 3 3 31 -1.000000 S
+Rv1591 - PROBABLE TRANSMEMBRANE PROTEIN 8 8 0 0 0.000000 NE
+Rv1592c - hypothetical protein Rv1592c 19 24 2 86 0.000000 NE
+Rv1593c - hypothetical protein Rv1593c 6 11 2 4 0.000000 NE
+Rv1594 nadA quinolinate synthetase 0 10 10 876 0.999600 E
+Rv1595 nadB L-aspartate oxidase 0 23 23 1337 1.000000 E
+Rv1596 nadC nicotinate-nucleotide pyrophosphorylase 0 12 12 725 1.000000 E
+Rv1597 - hypothetical protein Rv1597 10 12 2 29 0.000000 NE
+Rv1598c - hypothetical protein Rv1598c 6 8 1 2 0.000000 NE
+Rv1599 hisD histidinol dehydrogenase 0 14 14 1108 1.000000 E
+Rv1600 hisC1 histidinol-phosphate aminotransferase 0 24 24 969 1.000000 E
+Rv1601 hisB imidazoleglycerol-phosphate dehydratase 0 14 14 507 1.000000 E
+Rv1602 hisH imidazole glycerol phosphate synthase subunit HisH 0 7 7 427 0.991500 E
+Rv1603 hisA 1-(5-phosphoribosyl)-5- 0 8 8 599 0.994500 E
+Rv1604 impA PROBABLE INOSITOL-MONOPHOSPHATASE IMPA (IMP) 4 11 4 162 0.000000 NE
+Rv1605 hisF imidazole glycerol phosphate synthase subunit HisF 0 6 6 605 0.975000 U
+Rv1606 hisI phosphoribosyl-AMP cyclohydrolase 0 7 7 257 0.998700 E
+Rv1607 chaA Probable ionic transporter integral membrane protein chaA 8 9 1 2 0.000000 NE
+Rv1608c bcpB Probable peroxidoxin BcpB 5 6 1 2 0.000000 NE
+Rv1609 trpE anthranilate synthase component I 0 25 25 1337 1.000000 E
+Rv1610 - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 5 5 405 0.954400 U
+Rv1611 trpC indole-3-glycerol-phosphate synthase 0 11 11 639 0.999800 E
+Rv1612 trpB tryptophan synthase subunit beta 0 18 18 1041 1.000000 E
+Rv1613 trpA tryptophan synthase subunit alpha 0 16 16 667 1.000000 E
+Rv1614 lgt prolipoprotein diacylglyceryl transferase 2 23 20 737 1.000000 E
+Rv1615 - Probable hypothetical membrane protein 6 8 1 2 0.000000 NE
+Rv1616 - hypothetical protein Rv1616 7 10 2 74 0.000000 NE
+Rv1617 pykA pyruvate kinase 0 13 13 1196 1.000000 E
+Rv1618 tesB1 Probable acyl-CoA thioesterase II tesB1 12 15 1 2 0.000000 NE
+Rv1619 - hypothetical protein Rv1619 9 23 7 310 0.745300 U
+Rv1620c cydC PROBABLE 'COMPONENT LINKED WITH THE ASSEMBLY OF CYTOCHROME' TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER CYDC 1 18 13 964 1.000000 E
+Rv1621c cydD PROBABLE 'COMPONENT LINKED WITH THE ASSEMBLY OF CYTOCHROME' TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER CYDD 1 20 13 893 1.000000 E
+Rv1622c cydB Probable integral membrane cytochrome D ubiquinol oxidase (subunit II) cydB (Cytochrome BD-I oxidase subunit II) 2 20 7 378 0.894400 U
+Rv1623c cydA Probable integral membrane cytochrome D ubiquinol oxidase (subunit I) cydA (Cytochrome BD-I oxidase subunit I) 3 18 9 522 0.985900 U
+Rv1624c - Probable conserved membrane protein 4 5 1 2 0.000000 NE
+Rv1625c cya MEMBRANE-ANCHORED ADENYLYL CYCLASE CYA (ATP PYROPHOSPHATE-LYASE) (ADENYLATE CYCLASE) 24 29 3 62 0.000000 NE
+Rv1626 - Probable two-component system transcriptional regulator 5 5 0 0 0.000000 NE
+Rv1627c - lipid-transfer protein 9 17 7 313 0.879000 U
+Rv1628c - hypothetical protein Rv1628c 3 7 3 35 0.000000 NE
+Rv1629 polA DNA polymerase I 0 38 38 2249 1.000000 E
+Rv1630 rpsA 30S ribosomal protein S1 0 14 14 1281 1.000000 E
+Rv1631 coaE dephospho-CoA kinase/unknown domain fusion protein 0 11 11 810 0.999900 E
+Rv1632c - hypothetical protein Rv1632c 10 10 0 0 0.000000 NE
+Rv1633 uvrB excinuclease ABC subunit B 24 38 4 138 0.000000 NE
+Rv1634 - Possible drug efflux membrane protein 26 28 1 2 0.000000 NE
+Rv1635c - Probable conserved transmembrane protein 24 29 1 2 0.000000 NE
+Rv1636 TB15.3 IRON-REGULATED CONSERVED HYPOTHETICAL PROTEIN TB15.3 0 7 7 359 0.996300 E
+Rv1637c - hypothetical protein Rv1637c 10 10 0 0 0.000000 NE
+Rv1638 uvrA excinuclease ABC subunit A 21 37 3 59 0.000000 NE
+Rv1638A - hypothetical protein Rv1638A 2 5 3 59 0.000900 NE
+Rv1639c - hypothetical protein Rv1639c 8 13 3 146 0.000000 NE
+Rv1640c lysS lysyl-tRNA synthetase 34 59 6 574 0.246100 U
+Rv1641 infC translation initiation factor IF-3 1 11 10 403 0.999100 E
+Rv1642 rpmI 50S ribosomal protein L35 0 1 1 2 -1.000000 S
+Rv1643 rplT 50S ribosomal protein L20 0 7 7 169 0.998700 E
+Rv1644 tsnR Possible 23S rRNA methyltransferase tsnR 10 10 0 0 0.000000 NE
+Rv1645c - hypothetical protein Rv1645c 21 23 1 2 0.000000 NE
+Rv1646 PE17 PE FAMILY PROTEIN 13 15 2 14 0.000000 NE
+Rv1647 - hypothetical protein Rv1647 7 9 1 2 0.000000 NE
+Rv1648 - Probable transmembrane protein 11 12 1 2 0.000000 NE
+Rv1649 pheS phenylalanyl-tRNA synthetase subunit alpha 0 13 13 844 0.999900 E
+Rv1650 pheT phenylalanyl-tRNA synthetase subunit beta 0 33 33 2150 1.000000 E
+Rv1651c PE_PGRS30 PE-PGRS FAMILY PROTEIN 32 44 3 107 0.000000 NE
+Rv1652 argC N-acetyl-gamma-glutamyl-phosphate reductase 0 15 15 782 1.000000 E
+Rv1653 argJ bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein 0 3 3 973 0.806000 U
+Rv1654 argB acetylglutamate kinase 0 4 4 554 0.832900 U
+Rv1655 argD acetylornithine aminotransferase 0 10 10 1010 0.999700 E
+Rv1656 argF ornithine carbamoyltransferase 0 5 5 509 0.930100 U
+Rv1657 argR arginine repressor 2 3 1 2 -1.000000 S
+Rv1658 argG argininosuccinate synthase 0 16 16 1036 1.000000 E
+Rv1659 argH argininosuccinate lyase 0 8 8 1051 0.998300 E
+Rv1660 pks10 Possible chalcone synthase pks10 9 9 0 0 0.000000 NE
+Rv1661 pks7 Probable polyketide synthase pks7 17 73 12 656 0.992100 E
+Rv1662 pks8 Probable polyketide synthase pks8 10 62 17 1441 1.000000 E
+Rv1663 pks17 Probable polyketide synthase pks17 5 17 11 790 0.999300 E
+Rv1664 pks9 Probable polyketide synthase pks9 19 42 6 311 0.191500 U
+Rv1665 pks11 Possible chalcone synthase pks11 6 10 1 2 0.000000 NE
+Rv1666c cyp139 Probable cytochrome P450 139 CYP139 15 18 1 2 0.000000 NE
+Rv1667c - PROBABLE SECOND PART OF MACROLIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 7 9 1 2 0.000000 NE
+Rv1668c - PROBABLE FIRST PART OF MACROLIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 7 12 1 2 0.000000 NE
+Rv1669 - hypothetical protein Rv1669 4 7 2 40 0.000000 NE
+Rv1670 - hypothetical protein Rv1670 8 10 1 2 0.000000 NE
+Rv1671 - PROBABLE MEMBRANE PROTEIN 5 13 5 117 0.000000 NE
+Rv1672c - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 11 20 4 217 0.000000 NE
+Rv1673c - hypothetical protein Rv1673c 8 13 3 83 0.000000 NE
+Rv1674c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 6 9 2 12 0.000000 NE
+Rv1675c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 7 10 3 146 0.000000 NE
+Rv1676 - hypothetical protein Rv1676 3 8 5 254 0.051700 U
+Rv1677 dsbF PROBABLE CONSERVED LIPOPROTEIN DSBF 5 11 3 48 0.000000 NE
+Rv1678 - PROBABLE INTEGRAL MEMBRANE PROTEIN 5 10 4 333 0.450600 U
+Rv1679 fadE16 POSSIBLE ACYL-CoA DEHYDROGENASE FADE16 3 8 2 36 0.000000 NE
+Rv1680 - hypothetical protein Rv1680 7 14 3 62 0.000000 NE
+Rv1681 moeX POSSIBLE MOLYBDOPTERIN BIOSYNTHESIS PROTEIN MOEX 10 12 1 2 0.000000 NE
+Rv1682 - Probable coiled-coil structural protein 6 13 2 53 0.000000 NE
+Rv1683 - acyl-CoA synthetase 7 37 10 937 0.996600 E
+Rv1684 - hypothetical protein Rv1684 0 4 4 43 -1.000000 S
+Rv1685c - hypothetical protein Rv1685c 0 7 7 528 0.990100 E
+Rv1686c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER 3 12 5 165 0.000000 NE
+Rv1687c - PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER 6 10 2 62 0.000000 NE
+Rv1688 mpg 3-methyladenine DNA glycosylase 7 8 1 2 0.000000 NE
+Rv1689 tyrS tyrosyl-tRNA synthetase 0 17 17 1069 1.000000 E
+Rv1690 lprJ PROBABLE LIPOPROTEIN LPRJ 4 6 1 2 0.000000 NE
+Rv1691 - hypothetical protein Rv1691 5 9 2 30 0.000000 NE
+Rv1692 - PROBABLE PHOSPHATASE 8 10 1 2 0.000000 NE
+Rv1693 - hypothetical protein Rv1693 1 1 0 0 -1.000000 S
+Rv1694 tlyA CYTOTOXIN|HAEMOLYSIN HOMOLOGUE TLYA 4 8 3 234 0.000800 NE
+Rv1695 ppnK inorganic polyphosphate/ATP-NAD kinase 0 7 7 719 0.987900 U
+Rv1696 recN PROBABLE DNA REPAIR PROTEIN RECN (RECOMBINATION PROTEIN N) 9 18 5 504 0.404800 U
+Rv1697 - hypothetical protein Rv1697 0 15 15 1024 1.000000 E
+Rv1698 - hypothetical protein Rv1698 3 12 5 144 0.000000 NE
+Rv1699 pyrG CTP synthetase 0 34 34 1552 1.000000 E
+Rv1700 - hypothetical protein Rv1700 1 10 5 385 0.822700 U
+Rv1701 xerD site-specific tyrosine recombinase XerD 8 13 3 52 0.000000 NE
+Rv1702c - hypothetical protein Rv1702c 16 20 2 10 0.000000 NE
+Rv1703c - Probable catechol-o-methyltransferase 9 11 1 2 0.000000 NE
+Rv1704c cycA PROBABLE D-SERINE/ALANINE/GLYCINE TRANSPORTER PROTEIN CYCA 14 18 2 197 0.000000 NE
+Rv1705c PPE22 PPE FAMILY PROTEIN 16 23 3 77 0.000000 NE
+Rv1706A - hypothetical protein Rv1706A 0 2 2 122 -1.000000 S
+Rv1706c PPE23 PPE FAMILY PROTEIN 14 18 2 252 0.000400 NE
+Rv1707 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 14 19 3 36 0.000000 NE
+Rv1708 - PUTATIVE INITIATION INHIBITOR PROTEIN 1 16 15 629 0.999900 E
+Rv1709 - hypothetical protein Rv1709 8 11 1 2 0.000000 NE
+Rv1710 - hypothetical protein Rv1710 8 13 2 80 0.000000 NE
+Rv1711 - hypothetical protein Rv1711 0 9 9 518 0.999000 E
+Rv1712 cmk cytidylate kinase 1 11 9 442 0.997700 E
+Rv1713 engA GTP-binding protein EngA 0 11 11 1195 1.000000 E
+Rv1714 - Probable oxidoreductase 3 6 2 165 0.000000 NE
+Rv1715 fadB3 PROBABLE 3-HYDROXYBUTYRYL-CoA DEHYDROGENASE FADB3 (BETA-HYDROXYBUTYRYL-CoA DEHYDROGENASE) (BHBD) 4 9 2 14 0.000000 NE
+Rv1716 - hypothetical protein Rv1716 7 11 2 10 0.000000 NE
+Rv1717 - hypothetical protein Rv1717 4 4 0 0 0.000000 NE
+Rv1718 - hypothetical protein Rv1718 6 7 1 2 0.000000 NE
+Rv1719 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 6 2 51 0.000000 NE
+Rv1720c - hypothetical protein Rv1720c 6 9 2 28 0.000000 NE
+Rv1721c - hypothetical protein Rv1721c 1 2 1 2 -1.000000 S
+Rv1722 - biotin carboxylase-like protein 19 22 1 2 0.000000 NE
+Rv1723 - PROBABLE HYDROLASE 13 16 1 2 0.000000 NE
+Rv1724c - hypothetical protein Rv1724c 8 11 2 18 0.000000 NE
+Rv1725c - hypothetical protein Rv1725c 7 9 2 61 0.000000 NE
+Rv1726 - PROBABLE OXIDOREDUCTASE 12 15 2 20 0.000000 NE
+Rv1727 - hypothetical protein Rv1727 4 4 0 0 0.000000 NE
+Rv1728c - hypothetical protein Rv1728c 9 17 2 45 0.000000 NE
+Rv1729c - hypothetical protein Rv1729c 8 21 2 26 0.000000 NE
+Rv1730c - POSSIBLE PENICILLIN-BINDING PROTEIN 11 29 7 220 0.000600 NE
+Rv1731 gabD2 succinic semialdehyde dehydrogenase 17 23 1 2 0.000000 NE
+Rv1732c - hypothetical protein Rv1732c 7 8 1 2 0.000000 NE
+Rv1733c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 5 1 2 0.000000 NE
+Rv1734c - hypothetical protein Rv1734c 2 2 0 0 -1.000000 S
+Rv1735c - HYPOTHETICAL MEMBRANE PROTEIN 4 6 1 2 0.000000 NE
+Rv1736c narX PROBABLE NITRATE REDUCTASE NARX 30 37 1 2 0.000000 NE
+Rv1737c narK2 POSSIBLE NITRATE/NITRITE TRANSPORTER NARK2 12 13 1 2 0.000000 NE
+Rv1738 - hypothetical protein Rv1738 2 2 0 0 -1.000000 S
+Rv1739c - PROBABLE SULPHATE-TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER 26 36 3 52 0.000000 NE
+Rv1740 - hypothetical protein Rv1740 2 4 2 44 -1.000000 S
+Rv1741 - hypothetical protein Rv1741 5 6 1 2 0.000000 NE
+Rv1742 - hypothetical protein Rv1742 11 13 1 2 0.000000 NE
+Rv1743 pknE PROBABLE TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE E PKNE (PROTEIN KINASE E) (STPK E) 20 29 2 8 0.000000 NE
+Rv1744c - PROBABLE MEMBRANE PROTEIN 3 5 1 2 -1.000000 S
+Rv1745c idi isopentenyl-diphosphate delta-isomerase 7 11 4 130 0.000000 NE
+Rv1746 pknF ANCHORED-MEMBRANE SERINE/THREONINE-PROTEIN KINASE PKNF (PROTEIN KINASE F) (STPK F) 12 13 1 2 0.000000 NE
+Rv1747 - PROBABLE CONSERVED TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 21 29 1 2 0.000000 NE
+Rv1748 - hypothetical protein Rv1748 9 12 2 33 0.000000 NE
+Rv1749c - POSSIBLE INTEGRAL MEMBRANE PROTEIN 13 16 1 2 0.000000 NE
+Rv1750c fadD1 acyl-CoA synthetase 23 36 4 52 0.000000 NE
+Rv1751 - hypothetical protein Rv1751 10 19 4 219 0.000000 NE
+Rv1752 - hypothetical protein Rv1752 3 4 1 2 0.000000 NE
+Rv1753c PPE24 PPE FAMILY PROTEIN 16 61 12 179 0.000500 NE
+Rv1754c - hypothetical protein Rv1754c 21 33 5 114 0.000000 NE
+Rv1755c plcD PROBABLE PHOSPHOLIPASE C 4 (FRAGMENT) PLCD 3 15 5 119 0.000000 NE
+Rv1756c - PUTATIVE TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv1757c - PUTATIVE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv1758 cut1 PROBABLE CUTINASE CUT1 8 11 2 9 0.000000 NE
+Rv1759c wag22 PE-PGRS FAMILY PROTEIN 12 23 4 320 0.059900 U
+Rv1760 - hypothetical protein Rv1760 18 26 4 230 0.000300 NE
+Rv1761c - hypothetical protein Rv1761c 3 4 1 2 0.000000 NE
+Rv1762c - hypothetical protein Rv1762c 7 9 2 139 0.000000 NE
+Rv1763 - PUTATIVE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv1764 - PUTATIVE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv1765A - PUTATIVE TRANSPOSASE (FRAGMENT) 3 3 0 0 -1.000000 S
+Rv1765c - hypothetical protein Rv1765c 1 1 0 0 -1.000000 S
+Rv1766 - hypothetical protein Rv1766 2 3 1 2 0.000000 NE
+Rv1767 - hypothetical protein Rv1767 5 7 1 2 0.000000 NE
+Rv1768 PE_PGRS31 PE-PGRS FAMILY PROTEIN 16 17 1 2 0.000000 NE
+Rv1769 - hypothetical protein Rv1769 15 20 2 54 0.000000 NE
+Rv1770 - hypothetical protein Rv1770 13 16 2 195 0.000000 NE
+Rv1771 - PROBABLE OXIDOREDUCTASE 17 22 1 2 0.000000 NE
+Rv1772 - hypothetical protein Rv1772 2 4 1 2 0.000000 NE
+Rv1773c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 5 10 5 260 0.049000 U
+Rv1774 - PROBABLE OXIDOREDUCTASE 20 27 1 2 0.000000 NE
+Rv1775 - hypothetical protein Rv1775 9 12 1 2 0.000000 NE
+Rv1776c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 6 11 2 33 0.000000 NE
+Rv1777 cyp144 Probable cytochrome p450 144 CYP144 13 23 2 47 0.000000 NE
+Rv1778c - hypothetical protein Rv1778c 3 5 1 2 0.000000 NE
+Rv1779c - HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN 6 12 4 394 0.213700 U
+Rv1780 - hypothetical protein Rv1780 7 9 2 74 0.000000 NE
+Rv1781c malQ PROBABLE 4-ALPHA-GLUCANOTRANSFERASE MALQ (Amylomaltase) (Disproportionating enzyme) (D-enzyme) 20 25 1 2 0.000000 NE
+Rv1782 - PROBABLE CONSERVED MEMBRANE PROTEIN 4 16 10 672 0.996500 E
+Rv1783 - PROBABLE CONSERVED MEMBRANE PROTEIN 1 15 14 623 1.000000 E
+Rv1784 - hypothetical protein Rv1784 6 38 11 356 0.991300 E
+Rv1785c cyp143 PROBABLE CYTOCHROME P450 143 CYP143 10 16 2 30 0.000000 NE
+Rv1786 - PROBABLE FERREDOXIN 1 1 0 0 -1.000000 S
+Rv1787 PPE25 PPE FAMILY PROTEIN 3 7 2 15 0.000000 NE
+Rv1788 PE18 PE FAMILY PROTEIN 4 4 0 0 -1.000000 S
+Rv1789 PPE26 PPE FAMILY PROTEIN 14 18 2 40 0.000000 NE
+Rv1790 PPE27 PPE FAMILY PROTEIN 3 5 2 15 0.000000 NE
+Rv1791 PE19 PE FAMILY PROTEIN 2 6 3 65 0.000000 NE
+Rv1793 esxN PUTATIVE ESAT-6 LIKE PROTEIN ESXN (ESAT-6 LIKE PROTEIN 5) 0 0 0 0 -1.000000 S
+Rv1794 - hypothetical protein Rv1794 7 18 3 34 0.000000 NE
+Rv1795 - hypothetical protein Rv1795 5 18 8 416 0.946900 U
+Rv1796 mycP5 PROBABLE PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP5 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-5) 13 29 4 172 0.000000 NE
+Rv1797 - hypothetical protein Rv1797 2 15 8 561 0.983300 U
+Rv1798 - hypothetical protein Rv1798 16 30 3 25 0.000000 NE
+Rv1799 lppT PROBABLE LIPOPROTEIN LPPT 1 2 1 2 -1.000000 S
+Rv1800 PPE28 PPE FAMILY PROTEIN 28 39 2 76 0.000000 NE
+Rv1801 PPE29 PPE FAMILY PROTEIN 16 21 2 23 0.000000 NE
+Rv1802 PPE30 PPE FAMILY PROTEIN 15 18 1 2 0.000000 NE
+Rv1803c PE_PGRS32 PE-PGRS FAMILY PROTEIN 19 31 4 90 0.000000 NE
+Rv1804c - hypothetical protein Rv1804c 5 9 3 132 0.000000 NE
+Rv1805c - hypothetical protein Rv1805c 2 5 3 94 0.000000 NE
+Rv1806 PE20 PE FAMILY PROTEIN 2 5 1 2 0.000000 NE
+Rv1807 PPE31 PPE FAMILY PROTEIN 9 17 3 136 0.000000 NE
+Rv1808 PPE32 PPE FAMILY PROTEIN 22 25 1 2 0.000000 NE
+Rv1809 PPE33 PPE FAMILY PROTEIN 10 20 4 268 0.006400 NE
+Rv1810 - hypothetical protein Rv1810 8 11 1 2 0.000000 NE
+Rv1811 mgtC POSSIBLE Mg2+ TRANSPORT P-TYPE ATPASE C MGTC 14 15 1 2 0.000000 NE
+Rv1812c - PROBABLE DEHYDROGENASE 17 22 1 2 0.000000 NE
+Rv1813c - hypothetical protein Rv1813c 8 9 1 2 0.000000 NE
+Rv1814 erg3 MEMBRANE-BOUND C-5 STEROL DESATURASE ERG3 (STEROL-C5-DESATURASE) 18 21 1 2 0.000000 NE
+Rv1815 - hypothetical protein Rv1815 6 7 1 2 0.000000 NE
+Rv1816 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 8 15 2 18 0.000000 NE
+Rv1817 - hypothetical protein Rv1817 22 26 1 2 0.000000 NE
+Rv1818c PE_PGRS33 PE-PGRS FAMILY PROTEIN 6 11 3 449 0.153700 U
+Rv1819c - PROBABLE DRUGS-TRANSPORT TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSPORTER 25 29 2 18 0.000000 NE
+Rv1820 ilvG hypothetical protein Rv1820 14 16 1 2 0.000000 NE
+Rv1821 secA2 preprotein translocase subunit SecA 12 36 12 754 0.999300 E
+Rv1822 pgsA2 PROBABLE CDP-DIACYLGLYCEROL--GLYCEROL-3-PHOSPHATE 3-PHOSPHATIDYLTRANSFERASE PGSA2 (PGP SYNTHASE) (PHOSPHATIDYLGLYCEROPHOSPHATE SYNTHASE) (3-PHOSPHATIDYL-1'-GLYCEROL-3'PHOSPHATE SYNTHASE) 1 17 16 480 1.000000 E
+Rv1823 - hypothetical protein Rv1823 10 14 1 2 0.000000 NE
+Rv1824 - hypothetical protein Rv1824 4 4 0 0 -1.000000 S
+Rv1825 - hypothetical protein Rv1825 8 9 1 2 0.000000 NE
+Rv1826 gcvH glycine cleavage system protein H 0 8 8 356 0.998900 E
+Rv1827 cfp17 CONSERVED HYPOTHETICAL PROTEIN CFP17 0 6 6 304 0.996400 E
+Rv1828 - hypothetical protein Rv1828 0 13 13 629 1.000000 E
+Rv1829 - hypothetical protein Rv1829 7 9 1 2 0.000000 NE
+Rv1830 - hypothetical protein Rv1830 0 10 10 464 0.999600 E
+Rv1831 - hypothetical protein Rv1831 4 5 1 2 -1.000000 S
+Rv1832 gcvB glycine dehydrogenase 0 50 50 2270 1.000000 E
+Rv1833c - haloalkane dehalogenase 10 13 1 2 0.000000 NE
+Rv1834 - Probable hydrolase 8 10 1 2 0.000000 NE
+Rv1835c - hypothetical protein Rv1835c 30 34 2 20 0.000000 NE
+Rv1836c - hypothetical protein Rv1836c 3 37 13 610 0.999700 E
+Rv1837c glcB malate synthase G 0 22 22 1828 1.000000 E
+Rv1838c - hypothetical protein Rv1838c 9 10 1 2 0.000000 NE
+Rv1839c - hypothetical protein Rv1839c 1 1 0 0 -1.000000 S
+Rv1840c PE_PGRS34 PE-PGRS FAMILY PROTEIN 7 15 6 455 0.740700 U
+Rv1841c - hypothetical protein Rv1841c 10 13 3 128 0.000000 NE
+Rv1842c - hypothetical protein Rv1842c 11 15 2 9 0.000000 NE
+Rv1843c guaB1 inositol-5-monophosphate dehydrogenase 17 20 2 59 0.000000 NE
+Rv1844c gnd1 6-phosphogluconate dehydrogenase 13 14 1 2 0.000000 NE
+Rv1845c - hypothetical protein Rv1845c 1 13 9 402 0.992900 E
+Rv1846c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 3 0 0 0.000000 NE
+Rv1847 - hypothetical protein Rv1847 3 5 1 2 -1.000000 S
+Rv1848 ureA urease subunit gamma 2 2 0 0 -1.000000 S
+Rv1849 ureB urease subunit beta 2 6 4 238 0.701800 U
+Rv1850 ureC urease subunit alpha 6 11 2 62 0.000000 NE
+Rv1851 ureF Urease accessory protein uref 1 2 1 2 -1.000000 S
+Rv1852 ureG Urease accessory protein ureG 2 4 1 2 0.000000 NE
+Rv1853 ureD Probable urease accessory protein ureD 3 5 1 2 0.000000 NE
+Rv1854c ndh PROBABLE NADH DEHYDROGENASE NDH 0 17 17 1191 1.000000 E
+Rv1855c - POSSIBLE OXIDOREDUCTASE 10 11 1 2 0.000000 NE
+Rv1856c - short chain dehydrogenase 3 4 1 2 0.000000 NE
+Rv1857 modA PROBABLE MOLYBDATE-BINDING LIPOPROTEIN MODA 4 5 1 2 0.000000 NE
+Rv1858 modB PROBABLE MOLBDENUM-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER MODB 15 17 1 2 0.000000 NE
+Rv1859 modC PROBABLE MOLYBDENUM-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER MODC 12 16 1 2 0.000000 NE
+Rv1860 apa ALANINE AND PROLINE RICH SECRETED PROTEIN APA (FIBRONECTIN ATTACHMENT PROTEIN) (Immunogenic protein MPT32) (Antigen MPT-32) (45-kDa glycoprotein) (45/47 kDa antigen) 11 14 1 2 0.000000 NE
+Rv1861 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 3 7 4 141 0.561000 U
+Rv1862 adhA Probable alcohol dehydrogenase adhA 13 15 1 2 0.000000 NE
+Rv1863c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 8 10 1 2 0.000000 NE
+Rv1864c - hypothetical protein Rv1864c 8 9 1 2 0.000000 NE
+Rv1865c - short chain dehydrogenase 10 12 1 2 0.000000 NE
+Rv1866 - hypothetical protein Rv1866 14 32 6 87 0.000000 NE
+Rv1867 - acetyl-CoA acetyltransferase 12 18 2 22 0.000000 NE
+Rv1868 - hypothetical protein Rv1868 19 27 3 221 0.000000 NE
+Rv1869c - Probable reductase 19 23 2 14 0.000000 NE
+Rv1870c - hypothetical protein Rv1870c 8 10 1 2 0.000000 NE
+Rv1871c - hypothetical protein Rv1871c 7 8 1 2 0.000000 NE
+Rv1872c lldD2 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2 8 13 2 90 0.000000 NE
+Rv1873 - hypothetical protein Rv1873 9 9 0 0 0.000000 NE
+Rv1874 - hypothetical protein Rv1874 10 11 1 2 0.000000 NE
+Rv1875 - hypothetical protein Rv1875 4 4 0 0 0.000000 NE
+Rv1876 bfrA PROBABLE BACTERIOFERRITIN BFRA 9 10 1 2 0.000000 NE
+Rv1877 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 27 30 1 2 0.000000 NE
+Rv1878 glnA3 PROBABLE GLUTAMINE SYNTHETASE GLNA3 (GLUTAMINE SYNTHASE) (GS-I) 17 26 2 11 0.000000 NE
+Rv1879 - hypothetical protein Rv1879 13 17 2 34 0.000000 NE
+Rv1880c cyp140 Probable cytochrome p450 140 CYP140 11 15 2 51 0.000000 NE
+Rv1881c lppE POSSIBLE CONSERVED LIPOPROTEIN LPPE 7 8 1 2 0.000000 NE
+Rv1882c - short chain dehydrogenase 13 14 1 2 0.000000 NE
+Rv1883c - hypothetical protein Rv1883c 6 6 0 0 0.000000 NE
+Rv1884c rpfC PROBABLE RESUSCITATION-PROMOTING FACTOR RPFC 4 5 1 2 0.000000 NE
+Rv1885c - chorismate mutase 6 9 1 2 0.000000 NE
+Rv1886c fbpB SECRETED ANTIGEN 85-B FBPB (85B) (ANTIGEN 85 COMPLEX B) (MYCOLYL TRANSFERASE 85B) (FIBRONECTIN-BINDING PROTEIN B) (EXTRACELLULAR ALPHA-ANTIGEN) 18 23 2 43 0.000000 NE
+Rv1887 - hypothetical protein Rv1887 13 19 4 37 0.000000 NE
+Rv1888A - hypothetical protein Rv1888A 0 0 0 0 -1.000000 S
+Rv1888c - POSSIBLE TRANSMEMBRANE PROTEIN 9 13 1 2 0.000000 NE
+Rv1889c - hypothetical protein Rv1889c 1 3 2 168 0.017800 NE
+Rv1890c - hypothetical protein Rv1890c 6 8 1 2 0.000000 NE
+Rv1891 - hypothetical protein Rv1891 7 8 1 2 0.000000 NE
+Rv1892 - PROBABLE MEMBRANE PROTEIN 4 7 3 34 0.000000 NE
+Rv1893 - hypothetical protein Rv1893 0 0 0 0 -1.000000 S
+Rv1894c - hypothetical protein Rv1894c 10 11 1 2 0.000000 NE
+Rv1895 - POSSIBLE DEHYDROGENASE 13 17 1 2 0.000000 NE
+Rv1896c - hypothetical protein Rv1896c 11 21 5 110 0.000000 NE
+Rv1897c - D-tyrosyl-tRNA deacylase 3 4 1 2 0.000000 NE
+Rv1898 - hypothetical protein Rv1898 2 3 1 2 -1.000000 S
+Rv1899c lppD POSSIBLE LIPOPROTEIN LPPD 10 10 0 0 0.000000 NE
+Rv1900c lipJ PROBABLE LIGNIN PEROXIDASE LIPJ 15 19 1 2 0.000000 NE
+Rv1901 cinA competence damage-inducible protein A 15 17 1 2 0.000000 NE
+Rv1902c nanT PROBABLE SIALIC ACID-TRANSPORT INTEGRAL MEMBRANE PROTEIN NANT 20 30 4 125 0.000000 NE
+Rv1903 - PROBABLE CONSERVED MEMBRANE PROTEIN 5 5 0 0 0.000000 NE
+Rv1904 - hypothetical protein Rv1904 9 10 1 2 0.000000 NE
+Rv1905c aao PROBABLE D-AMINO ACID OXIDASE AAO 16 17 1 2 0.000000 NE
+Rv1906c - hypothetical protein Rv1906c 6 9 2 26 0.000000 NE
+Rv1907c - hypothetical protein Rv1907c 6 10 1 2 0.000000 NE
+Rv1908c katG CATALASE-PEROXIDASE-PEROXYNITRITASE T KATG 0 34 34 1894 1.000000 E
+Rv1909c furA FERRIC UPTAKE REGULATION PROTEIN FURA (FUR) 3 9 4 224 0.002300 NE
+Rv1910c - PROBABLE EXPORTED PROTEIN 9 12 1 2 0.000000 NE
+Rv1911c lppC PROBABLE LIPOPROTEIN LPPC 5 7 1 2 0.000000 NE
+Rv1912c fadB5 POSSIBLE OXIDOREDUCTASE FADB5 10 13 1 2 0.000000 NE
+Rv1913 - hypothetical protein Rv1913 4 10 2 52 0.000000 NE
+Rv1914c - hypothetical protein Rv1914c 3 5 1 2 0.000000 NE
+Rv1915 aceAa PROBABLE ISOCITRATE LYASE aceAa 17 21 2 237 0.000100 NE
+Rv1916 aceAb isocitrate lyase 12 16 2 27 0.000000 NE
+Rv1917c PPE34 PPE FAMILY PROTEIN 38 98 15 353 0.998700 E
+Rv1918c PPE35 PPE FAMILY PROTEIN 25 71 25 476 1.000000 E
+Rv1919c - hypothetical protein Rv1919c 6 7 1 2 0.000000 NE
+Rv1920 - PROBABLE MEMBRANE PROTEIN 8 11 2 59 0.000000 NE
+Rv1921c lppF PROBABLE CONSERVED LIPOPROTEIN LPPF 17 20 1 2 0.000000 NE
+Rv1922 - PROBABLE CONSERVED LIPOPROTEIN 14 19 1 2 0.000000 NE
+Rv1923 lipD PROBABLE LIPASE LIPD 25 28 1 2 0.000000 NE
+Rv1924c - hypothetical protein Rv1924c 8 9 1 2 0.000000 NE
+Rv1925 fadD31 acyl-CoA synthetase 25 34 1 2 0.000000 NE
+Rv1926c mpt63 IMMUNOGENIC PROTEIN MPT63 (ANTIGEN MPT63/MPB63) (16 kDa IMMUNOPROTECTIVE EXTRACELLULAR PROTEIN) 6 8 1 2 0.000000 NE
+Rv1927 - hypothetical protein Rv1927 13 16 1 2 0.000000 NE
+Rv1928c - short chain dehydrogenase 12 17 1 2 0.000000 NE
+Rv1929c - hypothetical protein Rv1929c 6 9 1 2 0.000000 NE
+Rv1930c - hypothetical protein Rv1930c 3 4 1 2 0.000000 NE
+Rv1931c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 1 2 1 2 -1.000000 S
+Rv1932 tpx thiol peroxidase 5 7 1 2 0.000000 NE
+Rv1933c fadE18 PROBABLE ACYL-CoA DEHYDROGENASE FADE18 7 9 1 2 0.000000 NE
+Rv1934c fadE17 PROBABLE ACYL-CoA DEHYDROGENASE FADE17 9 11 2 11 0.000000 NE
+Rv1935c echA13 enoyl-CoA hydratase 9 10 1 2 0.000000 NE
+Rv1936 - POSSIBLE MONOOXYGENASE 14 15 1 2 0.000000 NE
+Rv1937 - POSSIBLE OXYGENASE 26 44 4 170 0.000000 NE
+Rv1938 ephB PROBABLE EPOXIDE HYDROLASE EPHB (EPOXIDE HYDRATASE) 9 16 3 50 0.000000 NE
+Rv1939 - PROBABLE OXIDOREDUCTASE 1 5 3 185 0.000000 NE
+Rv1940 ribA1 Probable Riboflavin biosynthesis protein ribA1 (GTP cyclohydrolase II) 5 8 3 419 0.208400 U
+Rv1941 - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 2 3 1 2 -1.000000 S
+Rv1942c - hypothetical protein Rv1942c 1 2 1 2 -1.000000 S
+Rv1943c - hypothetical protein Rv1943c 3 10 7 215 0.147900 U
+Rv1944c - hypothetical protein Rv1944c 6 7 1 2 0.000000 NE
+Rv1945 - hypothetical protein Rv1945 4 10 3 259 0.002400 NE
+Rv1946c lppG POSSIBLE LIPOPROTEIN 5 7 2 37 0.000000 NE
+Rv1947 - hypothetical protein Rv1947 3 3 0 0 -1.000000 S
+Rv1948c - hypothetical protein Rv1948c 9 14 2 6 0.000000 NE
+Rv1949c - hypothetical protein Rv1949c 11 17 2 17 0.000000 NE
+Rv1950c - hypothetical protein Rv1950c 5 5 0 0 -1.000000 S
+Rv1951c - hypothetical protein Rv1951c 3 5 1 2 0.000000 NE
+Rv1952 - hypothetical protein Rv1952 2 2 0 0 -1.000000 S
+Rv1953 - hypothetical protein Rv1953 4 9 3 9 0.000000 NE
+Rv1954c - hypothetical protein Rv1954c 7 7 0 0 0.000000 NE
+Rv1955 - hypothetical protein Rv1955 8 9 1 2 0.000000 NE
+Rv1956 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 5 8 2 4 0.000000 NE
+Rv1957 - hypothetical protein Rv1957 9 13 1 2 0.000000 NE
+Rv1958c - hypothetical protein Rv1958c 6 11 3 202 0.000000 NE
+Rv1959c - hypothetical protein Rv1959c 3 5 2 63 0.001000 NE
+Rv1960c - hypothetical protein Rv1960c 2 3 1 2 0.000000 NE
+Rv1961 - hypothetical protein Rv1961 8 8 0 0 0.000000 NE
+Rv1962c - hypothetical protein Rv1962c 10 13 1 2 0.000000 NE
+Rv1963c mce3R PROBABLE TRANSCRIPTIONAL REPRESSOR (PROBABLY TETR-FAMILY) MCE3R 7 16 6 303 0.616600 U
+Rv1964 yrbE3A CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE3A 5 6 1 2 0.000000 NE
+Rv1965 yrbE3B CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE3B 9 13 2 24 0.000000 NE
+Rv1966 mce3A MCE-FAMILY PROTEIN MCE3A 10 15 2 20 0.000000 NE
+Rv1967 mce3B MCE-FAMILY PROTEIN MCE3B 10 12 1 2 0.000000 NE
+Rv1968 mce3C MCE-FAMILY PROTEIN MCE3C 4 12 3 86 0.000000 NE
+Rv1969 mce3D MCE-FAMILY PROTEIN MCE3D 10 13 2 29 0.000000 NE
+Rv1970 lprM POSSIBLE MCE-FAMILY LIPOPROTEIN LPRM (MCE-FAMILY LIPOPROTEIN MCE3E) 3 7 2 12 0.000000 NE
+Rv1971 mce3F MCE-FAMILY PROTEIN MCE3F 17 18 1 2 0.000000 NE
+Rv1972 - PROBABLE CONSERVED MCE ASSOCIATED MEMBRANE PROTEIN 4 4 0 0 0.000000 NE
+Rv1973 - POSSIBLE CONSERVED MCE ASSOCIATED MEMBRANE PROTEIN 2 3 1 2 0.000000 NE
+Rv1974 - PROBABLE CONSERVED MEMBRANE PROTEIN 8 8 0 0 0.000000 NE
+Rv1975 - hypothetical protein Rv1975 8 12 2 48 0.000000 NE
+Rv1976c - hypothetical protein Rv1976c 2 3 1 2 0.000000 NE
+Rv1977 - hypothetical protein Rv1977 12 12 0 0 0.000000 NE
+Rv1978 - hypothetical protein Rv1978 12 13 1 2 0.000000 NE
+Rv1979c - POSSIBLE CONSERVED PERMEASE 25 33 2 15 0.000000 NE
+Rv1980c mpt64 IMMUNOGENIC PROTEIN MPT64 (ANTIGEN MPT64/MPB64) 16 19 1 2 0.000000 NE
+Rv1981c nrdF ribonucleotide-diphosphate reductase subunit beta 18 23 2 35 0.000000 NE
+Rv1982c - hypothetical protein Rv1982c 3 4 1 2 0.000000 NE
+Rv1983 PE_PGRS35 PE-PGRS FAMILY PROTEIN 21 29 2 37 0.000000 NE
+Rv1984c cfp21 PROBABLE CUTINASE PRECURSOR CFP21 12 13 1 2 0.000000 NE
+Rv1985c - chromosome replication initiation inhibitor protein 11 13 2 107 0.000000 NE
+Rv1986 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 7 8 1 2 0.000000 NE
+Rv1987 - POSSIBLE CHITINASE 5 7 2 100 0.000000 NE
+Rv1988 - PROBABLE METHYLTRANSFERASE 5 6 1 2 0.000000 NE
+Rv1989c - hypothetical protein Rv1989c 10 10 0 0 0.000000 NE
+Rv1990A - POSSIBLE DEHYDROGENASE (FRAGMENT) 3 4 1 2 0.000000 NE
+Rv1990c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 0 5 5 230 0.993800 E
+Rv1991c - hypothetical protein Rv1991c 4 4 0 0 -1.000000 S
+Rv1992c ctpG PROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE G CTPG 26 31 2 51 0.000000 NE
+Rv1993c - hypothetical protein Rv1993c 3 4 1 2 -1.000000 S
+Rv1994c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 1 6 3 87 0.000300 NE
+Rv1995 - hypothetical protein Rv1995 6 7 1 2 0.000000 NE
+Rv1996 - hypothetical protein Rv1996 9 12 2 21 0.000000 NE
+Rv1997 ctpF PROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE A CTPF 17 23 3 267 0.001400 NE
+Rv1998c - hypothetical protein Rv1998c 10 17 4 207 0.000100 NE
+Rv1999c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 17 23 2 74 0.000000 NE
+Rv2000 - hypothetical protein Rv2000 26 32 2 25 0.000000 NE
+Rv2001 - hypothetical protein Rv2001 8 13 3 69 0.000000 NE
+Rv2002 fabG3 POSSIBLE 20-BETA-HYDROXYSTEROID DEHYDROGENASE FABG3 (Cortisone reductase) ((R)-20-hydroxysteroid dehydrogenase) 5 9 2 26 0.000000 NE
+Rv2003c - hypothetical protein Rv2003c 7 12 2 28 0.000000 NE
+Rv2004c - hypothetical protein Rv2004c 13 24 4 112 0.000000 NE
+Rv2005c - hypothetical protein Rv2005c 6 10 2 145 0.000000 NE
+Rv2006 otsB1 PROBABLE TREHALOSE-6-PHOSPHATE PHOSPHATASE OTSB1 (TREHALOSE-PHOSPHATASE) (TPP) 33 78 17 722 1.000000 E
+Rv2007c fdxA PROBABLE FERREDOXIN FDXA 6 7 1 2 0.000000 NE
+Rv2008c - hypothetical protein Rv2008c 16 27 6 113 0.000000 NE
+Rv2009 - hypothetical protein Rv2009 1 2 1 2 -1.000000 S
+Rv2010 - hypothetical protein Rv2010 6 7 1 2 0.000000 NE
+Rv2011c - hypothetical protein Rv2011c 5 6 1 2 0.000000 NE
+Rv2012 - hypothetical protein Rv2012 7 10 2 22 0.000000 NE
+Rv2013 - POSSIBLE TRANSPOSASE 0 2 2 350 -1.000000 S
+Rv2014 - POSSIBLE TRANSPOSASE 3 4 1 2 0.000000 NE
+Rv2015c - hypothetical protein Rv2015c 2 3 1 2 -1.000000 S
+Rv2016 - hypothetical protein Rv2016 5 7 1 2 0.000000 NE
+Rv2017 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 0 12 12 878 1.000000 E
+Rv2018 - hypothetical protein Rv2018 1 14 7 252 0.134700 U
+Rv2019 - hypothetical protein Rv2019 6 6 0 0 0.000000 NE
+Rv2020c - hypothetical protein Rv2020c 4 4 0 0 0.000000 NE
+Rv2021c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 5 2 139 0.000500 NE
+Rv2022c - hypothetical protein Rv2022c 11 13 2 18 0.000000 NE
+Rv2023c - hypothetical protein Rv2023c 2 2 0 0 -1.000000 S
+Rv2024c - hypothetical protein Rv2024c 10 12 1 2 0.000000 NE
+Rv2025c - POSSIBLE CONSERVED MEMBRANE PROTEIN 7 10 2 107 0.000000 NE
+Rv2026c - hypothetical protein Rv2026c 3 9 3 176 0.000000 NE
+Rv2027c - Probable histidine kinase response regulator 13 14 1 2 0.000000 NE
+Rv2028c - hypothetical protein Rv2028c 7 11 3 192 0.000000 NE
+Rv2029c pfkB Probable phosphofructokinase PfkB (PHOSPHOHEXOKINASE) 8 9 1 2 0.000000 NE
+Rv2030c - hypothetical protein Rv2030c 21 32 2 31 0.000000 NE
+Rv2031c hspX HEAT SHOCK PROTEIN HSPX (ALPHA-CRSTALLIN HOMOLOG) (14 kDa ANTIGEN) (HSP16.3) 7 8 1 2 0.000000 NE
+Rv2032 acg Conserved hypothetical protein Acg 10 17 3 96 0.000000 NE
+Rv2033c - hypothetical protein Rv2033c 7 10 1 2 0.000000 NE
+Rv2034 - Probable ArsR-type repressor protein 1 2 1 2 -1.000000 S
+Rv2035 - hypothetical protein Rv2035 9 12 2 22 0.000000 NE
+Rv2036 - hypothetical protein Rv2036 4 7 2 166 0.000000 NE
+Rv2037c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 9 16 5 206 0.000100 NE
+Rv2038c - Probable sugar-transport ATP-binding protein ABC transporter 4 16 5 241 0.003200 NE
+Rv2039c - Probable sugar-transport integral membrane protein ABC transporter 7 14 4 130 0.000000 NE
+Rv2040c - Probable sugar-transport integral membrane protein ABC transporter 8 16 4 60 0.000000 NE
+Rv2041c - Probable sugar-binding lipoprotein 15 21 2 28 0.000000 NE
+Rv2042c - hypothetical protein Rv2042c 6 14 5 91 0.000000 NE
+Rv2043c pncA PYRAZINAMIDASE/NICOTINAMIDAS PNCA (PZase) 8 11 2 40 0.000000 NE
+Rv2044c - hypothetical protein Rv2044c 5 7 1 2 0.000000 NE
+Rv2045c lipT Probable carboxylesterase LipT 14 27 4 89 0.000000 NE
+Rv2046 lppI Probable lipoprotein lppI 9 10 1 2 0.000000 NE
+Rv2047c - hypothetical protein Rv2047c 4 30 12 680 0.998900 E
+Rv2048c pks12 Probable polyketide synthase pks12 14 111 20 1666 1.000000 E
+Rv2049c - hypothetical protein Rv2049c 1 1 0 0 -1.000000 S
+Rv2050 - hypothetical protein Rv2050 0 5 5 250 0.993200 E
+Rv2051c ppm1 Polyprenol-monophosphomannose synthase Ppm1 11 32 18 1049 1.000000 E
+Rv2052c - hypothetical protein Rv2052c 17 19 1 2 0.000000 NE
+Rv2053c fxsA FxsA 2 3 1 2 -1.000000 S
+Rv2054 - hypothetical protein Rv2054 14 15 1 2 0.000000 NE
+Rv2055c rpsR 30S ribosomal protein S18 1 3 1 2 0.000000 NE
+Rv2056c rpsN 30S ribosomal protein S14 3 3 0 0 -1.000000 S
+Rv2057c rpmG 50S ribosomal protein L33 3 4 1 2 -1.000000 S
+Rv2058c rpmB 50S ribosomal protein L28 4 5 1 2 -1.000000 S
+Rv2059 - hypothetical protein Rv2059 15 17 1 2 0.000000 NE
+Rv2060 - Possible conserved integral membrane protein 2 3 1 2 0.000000 NE
+Rv2061c - hypothetical protein Rv2061c 3 5 2 23 0.000000 NE
+Rv2062c cobN cobaltochelatase 27 46 7 775 0.718000 U
+Rv2063 - hypothetical protein Rv2063 1 2 1 2 -1.000000 S
+Rv2064 cobG Possible cobalamin biosynthesis protein CobG 2 8 6 386 0.917800 U
+Rv2065 cobH precorrin-8X methylmutase 4 5 1 2 0.000000 NE
+Rv2066 cobI Probable bifunctional protein, CobI-CobJ fusion protein: S-adenosyl-L-methionine-precorrin-2 methyl transferase + precorrin-3 methylase 15 20 2 11 0.000000 NE
+Rv2067c - hypothetical protein Rv2067c 15 31 7 242 0.016000 NE
+Rv2068c blaC CLASS A BETA-LACTAMASE BLAC 12 13 1 2 0.000000 NE
+Rv2069 sigC RNA polymerase sigma factor SigC 6 8 1 2 0.000000 NE
+Rv2070c cobK cobalt-precorrin-6x reductase 7 15 3 60 0.000000 NE
+Rv2071c cobM Probable precorrin-4 C11-methyltransferase CobM 9 13 2 21 0.000000 NE
+Rv2072c cobL Probable precorrin-6y methyltransferase CobL 12 13 1 2 0.000000 NE
+Rv2073c - Probable shortchain dehydrogenase 8 8 0 0 0.000000 NE
+Rv2074 - hypothetical protein Rv2074 4 5 1 2 0.000000 NE
+Rv2075c - Possible hypothetical exported or envelope protein 22 23 1 2 0.000000 NE
+Rv2076c - hypothetical protein Rv2076c 4 5 1 2 0.000000 NE
+Rv2077A - hypothetical protein Rv2077A 4 7 3 62 0.000000 NE
+Rv2077c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 15 18 1 2 0.000000 NE
+Rv2078 - hypothetical protein Rv2078 1 3 2 73 0.000000 NE
+Rv2079 - hypothetical protein Rv2079 15 31 5 184 0.000000 NE
+Rv2080 lppJ Possible lipoprotein lppJ 9 10 1 2 0.000000 NE
+Rv2081c - POSSIBLE TRANSMEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv2082 - hypothetical protein Rv2082 21 34 5 428 0.190300 U
+Rv2083 - hypothetical protein Rv2083 4 4 0 0 0.000000 NE
+Rv2084 - hypothetical protein Rv2084 17 25 2 182 0.000000 NE
+Rv2085 - hypothetical protein Rv2085 0 3 3 79 -1.000000 S
+Rv2086 - hypothetical protein Rv2086 7 10 1 2 0.000000 NE
+Rv2087 - hypothetical protein Rv2087 1 4 2 91 0.000800 NE
+Rv2088 pknJ PROBABLE TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE J PKNJ (PROTEIN KINASE J) (STPK J) 9 23 5 164 0.000000 NE
+Rv2089c pepE Probable dipeptidase PepE 10 19 5 258 0.012100 NE
+Rv2090 - Probable 5'-3' exonuclease 13 15 1 2 0.000000 NE
+Rv2091c - Probable membrane protein 15 18 2 14 0.000000 NE
+Rv2092c helY PROBABLE ATP-DEPENDENT DNA HELICASE HELY 29 36 2 101 0.000000 NE
+Rv2093c tatC Probable Sec-independent protein translocase transmembrane protein tatC 0 11 11 680 0.999800 E
+Rv2094c tatA twin argininte translocase protein A 0 2 2 50 -1.000000 S
+Rv2095c - hypothetical protein Rv2095c 12 14 2 131 0.000000 NE
+Rv2096c - hypothetical protein Rv2096c 9 13 1 2 0.000000 NE
+Rv2097c - hypothetical protein Rv2097c 0 20 20 1167 1.000000 E
+Rv2100 - hypothetical protein Rv2100 13 18 3 25 0.000000 NE
+Rv2101 helZ PROBABLE HELICASE HELZ 20 27 2 19 0.000000 NE
+Rv2102 - hypothetical protein Rv2102 9 11 2 83 0.000000 NE
+Rv2103c - hypothetical protein Rv2103c 4 5 1 2 0.000000 NE
+Rv2104c - hypothetical protein Rv2104c 1 1 0 0 -1.000000 S
+Rv2105 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2106 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2107 PE22 PE FAMILY PROTEIN 6 9 1 2 0.000000 NE
+Rv2108 PPE36 PPE FAMILY PROTEIN 15 19 3 90 0.000000 NE
+Rv2109c prcA proteasome (alpha subunit) PrcA 0 17 17 643 1.000000 E
+Rv2110c prcB proteasome (beta subunit) PrcB 0 16 16 628 1.000000 E
+Rv2111c - hypothetical protein Rv2111c 0 1 1 2 -1.000000 S
+Rv2112c - hypothetical protein Rv2112c 3 29 21 980 1.000000 E
+Rv2113 - Probable integral membrane protein 9 11 2 68 0.000000 NE
+Rv2114 - hypothetical protein Rv2114 11 12 1 2 0.000000 NE
+Rv2115c - Probable ATPase 1 23 13 678 0.999600 E
+Rv2116 lppK Probable conserved lipoprotein lppK 4 5 1 2 0.000000 NE
+Rv2117 - hypothetical protein Rv2117 2 2 0 0 -1.000000 S
+Rv2118c - POSSIBLE RNA METHYLTRANSFERASE 10 12 2 126 0.000000 NE
+Rv2119 - hypothetical protein Rv2119 14 18 1 2 0.000000 NE
+Rv2120c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 3 7 4 137 0.000000 NE
+Rv2121c hisG ATP phosphoribosyltransferase 0 9 9 578 0.997800 E
+Rv2122c hisE phosphoribosyl-ATP pyrophosphatase 0 2 2 93 -1.000000 S
+Rv2123 PPE37 PPE FAMILY PROTEIN 11 20 5 267 0.017900 NE
+Rv2124c metH Probable 5-methyltetrahydrofolate--homocystein methyltransferase MetH (Methionine synthase, vitamin-B12 dependent isozyme) (MS) 25 38 3 185 0.000000 NE
+Rv2125 - hypothetical protein Rv2125 8 9 1 2 0.000000 NE
+Rv2126c PE_PGRS37 PE-PGRS FAMILY PROTEIN 3 5 1 2 0.000000 NE
+Rv2127 ansP1 Probable L-asparagine permease ansP1 18 24 2 34 0.000000 NE
+Rv2128 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 6 2 19 -1.000000 S
+Rv2129c - short chain dehydrogenase 6 11 2 104 0.000000 NE
+Rv2130c cysS cysteinyl-tRNA synthetase 0 22 22 1109 1.000000 E
+Rv2131c cysQ POSSIBLE MONOPHOSPHATASE CYSQ 0 9 9 570 0.998300 E
+Rv2132 - hypothetical protein Rv2132 2 2 0 0 -1.000000 S
+Rv2133c - hypothetical protein Rv2133c 9 9 0 0 0.000000 NE
+Rv2134c - hypothetical protein Rv2134c 5 7 1 2 0.000000 NE
+Rv2135c - hypothetical protein Rv2135c 1 4 2 60 0.000000 NE
+Rv2136c uppP undecaprenyl pyrophosphate phosphatase 7 12 2 143 0.000000 NE
+Rv2137c - hypothetical protein Rv2137c 5 6 1 2 0.000000 NE
+Rv2138 lppL Probable conserved lipoprotein LppL 1 18 9 542 0.991500 E
+Rv2139 pyrD dihydroorotate dehydrogenase 2 0 12 12 733 0.999900 E
+Rv2140c TB18.6 hypothetical protein Rv2140c 7 9 1 2 0.000000 NE
+Rv2141c - hypothetical protein Rv2141c 14 18 1 2 0.000000 NE
+Rv2142c - hypothetical protein Rv2142c 10 13 1 2 0.000000 NE
+Rv2143 - hypothetical protein Rv2143 13 13 0 0 0.000000 NE
+Rv2144c - Probable transmembrane protein 3 4 1 2 0.000000 NE
+Rv2145c wag31 CONSERVED HYPOTHETICAL PROTEIN WAG31 0 10 10 636 0.999500 E
+Rv2146c - Possible conserved transmembrane protein 1 1 0 0 -1.000000 S
+Rv2147c - hypothetical protein Rv2147c 0 15 15 429 1.000000 E
+Rv2148c - hypothetical protein Rv2148c 1 5 3 114 0.000000 NE
+Rv2149c yfiH conserved hypothetical protein YfiH 3 5 1 2 0.000000 NE
+Rv2150c ftsZ cell division protein FtsZ 0 6 6 610 0.970400 U
+Rv2151c ftsQ POSSIBLE CELL DIVISION PROTEIN FTSQ 0 6 6 632 0.968800 U
+Rv2152c murC UDP-N-acetylmuramate--L-alanine ligase 0 14 14 1124 1.000000 E
+Rv2153c murG N-acetylglucosaminyl transferase 0 14 14 820 1.000000 E
+Rv2154c ftsW FtsW-like protein FtsW 1 15 14 1102 1.000000 E
+Rv2155c murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 0 18 18 1099 1.000000 E
+Rv2156c mraY phospho-N-acetylmuramoyl-pentapeptide-transferase 0 9 9 588 0.998000 E
+Rv2157c murF Probable UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate- D-alanyl-D-alanyl ligase MurF 0 9 9 1220 0.999900 E
+Rv2158c murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase 0 10 10 891 0.999700 E
+Rv2159c - hypothetical protein Rv2159c 5 5 0 0 0.000000 NE
+Rv2160A - hypothetical protein Rv2160A 0 4 4 434 0.872100 U
+Rv2160c - hypothetical protein Rv2160c 0 2 2 39 -1.000000 S
+Rv2161c - hypothetical protein Rv2161c 7 8 1 2 0.000000 NE
+Rv2162c PE_PGRS38 PE-PGRS FAMILY PROTEIN 9 13 1 2 0.000000 NE
+Rv2163c pbpB Probable penicillin-binding membrane protein pbpB 0 29 29 1546 1.000000 E
+Rv2164c - PROBABLE CONSERVED PROLINE RICH MEMBRANE PROTEIN 0 10 10 808 0.999600 E
+Rv2165c mraW S-adenosyl-methyltransferase MraW 0 18 18 878 1.000000 E
+Rv2166c - hypothetical protein Rv2166c 0 7 7 242 0.999200 E
+Rv2167c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2168c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2169c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 5 5 316 0.989000 U
+Rv2170 - hypothetical protein Rv2170 7 12 2 90 0.000000 NE
+Rv2171 lppM Probable conserved lipoprotein lppM 6 8 1 2 0.000000 NE
+Rv2172c - hypothetical protein Rv2172c 0 16 16 731 1.000000 E
+Rv2173 idsA2 PROBABLE GERANYLGERANYL PYROPHOSPHATE SYNTHETASE IDSA2 (GGPPSASE) (GGPP SYNTHETASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE) 9 17 2 53 0.000000 NE
+Rv2174 - Possible conserved integral membrane protein 0 22 22 1344 1.000000 E
+Rv2175c - conserved hypothetical regulatory protein 4 5 1 2 0.000000 NE
+Rv2176 pknL PROBABLE TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE L PKNL (PROTEIN KINASE L) (STPK L) 12 21 2 20 0.000000 NE
+Rv2177c - POSSIBLE TRANSPOSASE 3 4 1 2 -1.000000 S
+Rv2178c aroG Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG (DAHP synthetase, phenylalanine-repressible) 0 15 15 1014 1.000000 E
+Rv2179c - hypothetical protein Rv2179c 1 5 4 191 0.949700 U
+Rv2180c - Probable conserved integral membrane protein 9 11 1 2 0.000000 NE
+Rv2181 - Probable conserved integral membrane protein 15 19 1 2 0.000000 NE
+Rv2182c - 1-acylglycerol-3-phosphate O-acyltransferase 0 18 18 603 1.000000 E
+Rv2183c - hypothetical protein Rv2183c 3 4 1 2 0.000000 NE
+Rv2184c - hypothetical protein Rv2184c 11 16 1 2 0.000000 NE
+Rv2185c TB16.3 hypothetical protein Rv2185c 8 13 1 2 0.000000 NE
+Rv2186c - hypothetical protein Rv2186c 0 8 8 321 0.999100 E
+Rv2187 fadD15 Probable long-chain-fatty-acid-CoA ligase fadD15 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 25 31 1 2 0.000000 NE
+Rv2188c - hypothetical protein Rv2188c 0 16 16 931 1.000000 E
+Rv2189c - hypothetical protein Rv2189c 4 10 2 166 0.000000 NE
+Rv2190c - hypothetical protein Rv2190c 7 16 6 398 0.771800 U
+Rv2191 - hypothetical protein Rv2191 16 25 2 4 0.000000 NE
+Rv2192c trpD anthranilate phosphoribosyltransferase 0 7 7 703 0.988400 U
+Rv2193 ctaE PROBABLE CYTOCHROME C OXIDASE (SUBUNIT III) CTAE 0 14 14 463 1.000000 E
+Rv2194 qcrC Probable Ubiquinol-cytochrome C reductase QcrC(cytochrome C subunit) 0 11 11 647 0.999800 E
+Rv2195 qcrA Probable Rieske iron-sulfur protein QcrA 0 21 21 1147 1.000000 E
+Rv2196 qcrB Probable Ubiquinol-cytochrome C reductase QcrB (cytochrome B subunit) 1 29 27 1284 1.000000 E
+Rv2197c - Probable conserved transmembrane protein 8 10 1 2 0.000000 NE
+Rv2198c mmpS3 PROBABLE CONSERVED MEMBRANE PROTEIN MMPS3 1 14 11 506 0.999700 E
+Rv2199c - Possible conserved integral membrane protein 2 7 5 202 0.002300 NE
+Rv2200c ctaC PROBABLE TRANSMEMBRANE CYTOCHROME C OXIDASE (SUBUNIT II) CTAC 0 18 18 780 1.000000 E
+Rv2201 asnB Probable asparagine synthetase AsnB 0 27 27 1562 1.000000 E
+Rv2202c cbhK Probable carbohydrate kinase CbhK 0 17 17 826 1.000000 E
+Rv2203 - POSSIBLE CONSERVED MEMBRANE PROTEIN 10 12 1 2 0.000000 NE
+Rv2204c - hypothetical protein Rv2204c 0 4 4 130 -1.000000 S
+Rv2205c - hypothetical protein Rv2205c 8 9 1 2 0.000000 NE
+Rv2206 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 9 2 10 0.000000 NE
+Rv2207 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 3 8 2 20 0.000000 NE
+Rv2208 cobS cobalamin synthase 7 9 1 2 0.000000 NE
+Rv2209 - Probable conserved integral membrane protein 18 23 2 34 0.000000 NE
+Rv2210c ilvE branched-chain amino acid aminotransferase 0 21 21 943 1.000000 E
+Rv2211c gcvT glycine cleavage system aminomethyltransferase T 0 17 17 694 1.000000 E
+Rv2212 - hypothetical protein Rv2212 7 9 1 2 0.000000 NE
+Rv2213 pepB leucyl aminopeptidase 6 12 4 221 0.000200 NE
+Rv2214c ephD short chain dehydrogenase 21 26 2 113 0.000000 NE
+Rv2215 dlaT dihydrolipoamide acetyltransferase 0 13 13 1032 1.000000 E
+Rv2216 - hypothetical protein Rv2216 4 11 3 104 0.000000 NE
+Rv2217 lipB lipoyltransferase 1 9 8 514 0.994400 E
+Rv2218 lipA lipoyl synthase 0 11 11 764 0.999800 E
+Rv2219 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 7 7 640 0.990100 E
+Rv2219A - PROBABLE CONSERVED MEMBRANE PROTEIN 1 2 1 2 -1.000000 S
+Rv2220 glnA1 GLUTAMINE SYNTHETASE GLNA1 (GLUTAMINE SYNTHASE) (GS-I) 0 25 25 1038 1.000000 E
+Rv2221c glnE GLUTAMATE-AMMONIA-LIGASE ADENYLYLTRANSFERASE GLNE (Glutamine-synthetase adenylyltransferase) 0 35 35 2248 1.000000 E
+Rv2222c glnA2 PROBABLE GLUTAMINE SYNTHETASE GLNA2 (GLUTAMINE SYNTHASE) (GS-II) 9 15 1 2 0.000000 NE
+Rv2223c - Probable exported protease 24 27 1 2 0.000000 NE
+Rv2224c - Probable exported protease 22 26 2 13 0.000000 NE
+Rv2225 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase 0 11 11 718 0.999900 E
+Rv2226 - hypothetical protein Rv2226 19 24 1 2 0.000000 NE
+Rv2227 - hypothetical protein Rv2227 8 18 3 56 0.000000 NE
+Rv2228c - hypothetical protein Rv2228c 0 16 16 941 1.000000 E
+Rv2229c - hypothetical protein Rv2229c 0 4 4 471 0.854800 U
+Rv2230c - hypothetical protein Rv2230c 5 15 5 95 0.000000 NE
+Rv2231c cobC hypothetical protein Rv2231c 5 15 5 336 0.501300 U
+Rv2232 - hypothetical protein Rv2232 6 10 2 246 0.000400 NE
+Rv2234 ptpA PHOSPHOTYROSINE PROTEIN PHOSPHATASE PTPA (PROTEIN-TYROSINE-PHOSPHATASE) (PTPase) (LMW PHOSPHATASE) 3 7 3 123 0.000000 NE
+Rv2235 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 14 14 641 1.000000 E
+Rv2236c cobD cobalamin biosynthesis protein 5 10 4 325 0.445600 U
+Rv2237 - hypothetical protein Rv2237 12 17 2 8 0.000000 NE
+Rv2238c ahpE Probable peroxiredoxin AhpE 1 4 2 126 0.000000 NE
+Rv2239c - hypothetical protein Rv2239c 4 4 0 0 0.000000 NE
+Rv2240c - hypothetical protein Rv2240c 6 11 2 31 0.000000 NE
+Rv2241 aceE pyruvate dehydrogenase subunit E1 0 53 53 2379 1.000000 E
+Rv2242 - hypothetical protein Rv2242 0 15 15 1034 1.000000 E
+Rv2243 fabD acyl-carrier-protein S-malonyltransferase 0 5 5 714 0.926700 U
+Rv2244 acpP acyl carrier protein 0 6 6 195 0.997500 E
+Rv2245 kasA 3-oxoacyl-(acyl carrier protein) synthase II 0 14 14 1021 1.000000 E
+Rv2246 kasB 3-oxoacyl-(acyl carrier protein) synthase II 0 14 14 1170 1.000000 E
+Rv2247 accD6 ACETYL/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD6 0 13 13 1111 1.000000 E
+Rv2248 - hypothetical protein Rv2248 4 11 5 259 0.047400 U
+Rv2249c glpD1 PROBABLE GLYCEROL-3-PHOSPHATE DEHYDROGENASE GLPD1 10 18 2 136 0.000000 NE
+Rv2250A - POSSIBLE FLAVOPROTEIN 1 3 2 109 0.000000 NE
+Rv2250c - Possible transcriptional regulatory protein 7 9 1 2 0.000000 NE
+Rv2251 - POSSIBLE FLAVOPROTEIN 4 8 1 2 0.000000 NE
+Rv2252 - diacylglycerol kinase 7 17 4 225 0.000300 NE
+Rv2253 - Possible secreted unknown protein 10 12 1 2 0.000000 NE
+Rv2254c - Probable integral membrane protein 2 5 2 114 0.000300 NE
+Rv2255c - hypothetical protein Rv2255c 1 1 0 0 -1.000000 S
+Rv2256c - hypothetical protein Rv2256c 0 6 6 413 0.982000 U
+Rv2257c - hypothetical protein Rv2257c 5 7 1 2 0.000000 NE
+Rv2258c - Possible transcriptional regulatory protein 11 13 1 2 0.000000 NE
+Rv2259 adhE2 Probable zinc-dependent alcohol dehydrogenase AdhE2 4 13 5 470 0.652200 U
+Rv2260 - hypothetical protein Rv2260 2 5 2 23 0.000000 NE
+Rv2261c - hypothetical protein Rv2261c 4 4 0 0 0.000000 NE
+Rv2262c - hypothetical protein Rv2262c 9 14 4 188 0.000100 NE
+Rv2263 - short chain dehydrogenase 9 12 2 67 0.000000 NE
+Rv2264c - conserved hypothetical proline rich protein 18 26 3 82 0.000000 NE
+Rv2265 - Possible conserved integral membrane protein 13 14 1 2 0.000000 NE
+Rv2266 cyp124 Probable cytochrome P450 124 CYP124 14 16 1 2 0.000000 NE
+Rv2267c - hypothetical protein Rv2267c 18 35 6 193 0.000100 NE
+Rv2268c cyp128 PROBABLE CYTOCHROME P450 128 CYP128 8 25 6 274 0.078900 U
+Rv2269c - hypothetical protein Rv2269c 4 11 2 11 0.000000 NE
+Rv2270 lppN PROBABLE LIPOPROTEIN LPPN 8 10 1 2 0.000000 NE
+Rv2271 - hypothetical protein Rv2271 5 5 0 0 0.000000 NE
+Rv2272 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 3 4 1 2 0.000000 NE
+Rv2273 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 5 1 2 -1.000000 S
+Rv2274c - hypothetical protein Rv2274c 4 7 2 99 0.000000 NE
+Rv2275 - hypothetical protein Rv2275 6 17 4 104 0.000000 NE
+Rv2276 cyp121 CYTOCHROME P450 121 CYP121 7 17 5 222 0.000400 NE
+Rv2277c - Possible glycerolphosphodiesterase 4 11 5 204 0.000200 NE
+Rv2278 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2279 - PROBABLE TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv2280 - Probable dehydrogenase 10 17 2 54 0.000000 NE
+Rv2281 pitB Putative phosphate-transport permease PitB 12 23 6 468 0.616600 U
+Rv2282c - Probable transcription regulator (lysR family) 7 11 2 8 0.000000 NE
+Rv2283 - hypothetical protein Rv2283 1 2 1 2 -1.000000 S
+Rv2284 lipM Probable esterase LipM 16 26 3 100 0.000000 NE
+Rv2285 - hypothetical protein Rv2285 15 20 2 60 0.000000 NE
+Rv2286c - hypothetical protein Rv2286c 6 9 2 93 0.000000 NE
+Rv2287 yjcE Probable conserved integral membrane transport protein YjcE 11 17 3 193 0.000000 NE
+Rv2288 - hypothetical protein Rv2288 3 4 1 2 -1.000000 S
+Rv2289 cdh CDP-diacylglycerol pyrophosphatase 15 21 2 8 0.000000 NE
+Rv2290 lppO Probable conserved lipoprotein lppO 8 11 2 21 0.000000 NE
+Rv2291 sseB Probable thiosulfate sulfurtransferase SseB 10 16 5 176 0.000000 NE
+Rv2292c - hypothetical protein Rv2292c 2 2 0 0 -1.000000 S
+Rv2293c - hypothetical protein Rv2293c 12 12 0 0 0.000000 NE
+Rv2294 - Probable aminotransferase 16 18 1 2 0.000000 NE
+Rv2295 - hypothetical protein Rv2295 8 10 2 33 0.000000 NE
+Rv2296 - haloalkane dehalogenase 13 15 1 2 0.000000 NE
+Rv2297 - hypothetical protein Rv2297 3 8 3 169 0.000000 NE
+Rv2298 - hypothetical protein Rv2298 14 16 2 86 0.000000 NE
+Rv2299c htpG heat shock protein 90 19 24 2 23 0.000000 NE
+Rv2300c - hypothetical protein Rv2300c 11 14 2 155 0.000000 NE
+Rv2301 cut2 PROBABLE CUTINASE CUT2 7 9 1 2 0.000000 NE
+Rv2302 - hypothetical protein Rv2302 4 4 0 0 -1.000000 S
+Rv2303c - PROBABLE ANTIBIOTIC-RESISTANCE PROTEIN 9 16 2 15 0.000000 NE
+Rv2304c - hypothetical protein Rv2304c 1 1 0 0 -1.000000 S
+Rv2305 - hypothetical protein Rv2305 6 8 1 2 0.000000 NE
+Rv2306A - POSSIBLE CONSERVED MEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv2306B - POSSIBLE CONSERVED MEMBRANE PROTEIN 2 5 2 61 0.000000 NE
+Rv2307A - HYPOTHETICAL GLYCINE RICH PROTEIN 2 3 1 2 -1.000000 S
+Rv2307B - HYPOTHETICAL GLYCINE RICH PROTEIN 7 20 6 31 0.000000 NE
+Rv2307D - hypothetical protein Rv2307D 4 5 1 2 -1.000000 S
+Rv2307c - hypothetical protein Rv2307c 15 18 1 2 0.000000 NE
+Rv2308 - hypothetical protein Rv2308 13 16 1 2 0.000000 NE
+Rv2309A - hypothetical protein Rv2309A 10 12 2 17 0.000000 NE
+Rv2309c - POSSIBLE INTEGRASE (FRAGMENT) 5 7 2 61 0.000000 NE
+Rv2310 - POSSIBLE EXCISIONASE 2 3 1 2 -1.000000 S
+Rv2311 - hypothetical protein Rv2311 7 7 0 0 0.000000 NE
+Rv2312 - hypothetical protein Rv2312 3 3 0 0 0.000000 NE
+Rv2313c - hypothetical protein Rv2313c 7 9 1 2 0.000000 NE
+Rv2314c - hypothetical protein Rv2314c 7 13 3 233 0.000300 NE
+Rv2315c - hypothetical protein Rv2315c 14 31 5 131 0.000000 NE
+Rv2316 uspA PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER USPA 5 10 3 99 0.000000 NE
+Rv2317 uspB PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER USPB 1 12 9 493 0.997800 E
+Rv2318 uspC PROBABLE PERIPLASMIC SUGAR-BINDING LIPOPROTEIN USPC 11 30 10 336 0.989100 U
+Rv2319c - hypothetical protein Rv2319c 7 14 3 37 0.000000 NE
+Rv2320c rocE PROBABLE CATIONIC AMINO ACID TRANSPORT INTEGRAL MEMBRANE PROTEIN ROCE 20 27 3 49 0.000000 NE
+Rv2321c rocD2 PROBABLE ORNITHINE AMINOTRANSFERASE (C-terminus part) ROCD2 (ORNITHINE--OXO-ACID AMINOTRANSFERASE) 3 8 2 9 0.000000 NE
+Rv2322c rocD1 PROBABLE ORNITHINE AMINOTRANSFERASE (N-terminus part) ROCD1 (ORNITHINE--OXO-ACID AMINOTRANSFERASE) 2 8 3 39 0.000000 NE
+Rv2323c - hypothetical protein Rv2323c 14 20 2 13 0.000000 NE
+Rv2324 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ASNC-FAMILY) 1 2 1 2 -1.000000 S
+Rv2325c - hypothetical protein Rv2325c 3 7 4 325 0.684600 U
+Rv2326c - POSSIBLE TRANSMEMBRANE ATP-BINDING PROTEIN ABC TRANSORTER 18 22 1 2 0.000000 NE
+Rv2327 - hypothetical protein Rv2327 3 5 1 2 0.000000 NE
+Rv2328 PE23 PE FAMILY PROTEIN 11 12 1 2 0.000000 NE
+Rv2329c narK1 PROBABLE NITRITE EXTRUSION PROTEIN 1 NARK1 (NITRITE FACILITATOR 1) 23 27 1 2 0.000000 NE
+Rv2330c lppP PROBABLE LIPOPROTEIN LPPP 4 6 2 35 0.000000 NE
+Rv2331 - hypothetical protein Rv2331 4 5 1 2 0.000000 NE
+Rv2331A - hypothetical protein Rv2331A 3 4 1 2 0.000000 NE
+Rv2332 mez PROBABLE 19 26 2 85 0.000000 NE
+Rv2333c - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 14 17 2 208 0.000000 NE
+Rv2334 cysK1 PROBABLE CYSTEINE SYNTHASE A CYSK1 (O-ACETYLSERINE SULFHYDRYLASE A) (O-ACETYLSERINE (THIOL)-LYASE A) (CSASE A) 4 13 4 148 0.000000 NE
+Rv2335 cysE PROBABLE SERINE ACETYLTRANSFERASE CYSE (SAT) 2 5 2 27 0.000000 NE
+Rv2336 - hypothetical protein Rv2336 9 28 6 144 0.000000 NE
+Rv2337c - hypothetical protein Rv2337c 4 6 2 155 0.000000 NE
+Rv2338c moeW hypothetical protein Rv2338c 10 34 7 215 0.000900 NE
+Rv2339 mmpL9 PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL9 23 79 21 587 1.000000 E
+Rv2340c PE_PGRS39 PE-PGRS FAMILY PROTEIN 12 13 1 2 0.000000 NE
+Rv2341 lppQ PROBABLE CONSERVED LIPOPROTEIN LPPQ 3 3 0 0 -1.000000 S
+Rv2342 - hypothetical protein Rv2342 2 3 1 2 -1.000000 S
+Rv2343c dnaG DNA primase 0 20 20 1513 1.000000 E
+Rv2344c dgt deoxyguanosinetriphosphate triphosphohydrolase-like protein 15 24 2 63 0.000000 NE
+Rv2345 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 26 28 1 2 0.000000 NE
+Rv2346c esxO PUTATIVE ESAT-6 LIKE PROTEIN ESXO (ESAT-6 LIKE PROTEIN 6) 0 0 0 0 -1.000000 S
+Rv2347c esxP PUTATIVE ESAT-6 LIKE PROTEIN ESXP (ESAT-6 LIKE PROTEIN 7) 1 1 0 0 -1.000000 S
+Rv2348c - hypothetical protein Rv2348c 2 2 0 0 -1.000000 S
+Rv2349c plcC PROBABLE PHOSPHOLIPASE C 3 PLCC 22 25 1 2 0.000000 NE
+Rv2350c plcB PROBABLE MEMBRANE-ASSOCIATED PHOSPHOLIPASE C 2 PLCB 18 20 1 2 0.000000 NE
+Rv2351c plcA PROBABLE MEMBRANE-ASSOCIATED PHOSPHOLIPASE C 1 PLCA (MTP40 ANTIGEN) 18 23 2 42 0.000000 NE
+Rv2352c PPE38 PPE FAMILY PROTEIN 15 15 0 0 0.000000 NE
+Rv2353c PPE39 PPE FAMILY PROTEIN 7 22 6 259 0.038900 U
+Rv2354 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2355 - PROBABLE TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv2356c PPE40 PPE FAMILY PROTEIN 13 26 9 518 0.978800 U
+Rv2357c glyS glycyl-tRNA synthetase 0 28 28 1168 1.000000 E
+Rv2358 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARSR-FAMILY) 0 4 4 277 0.987300 U
+Rv2359 furB PROBABLE FERRIC UPTAKE REGULATION PROTEIN FURB 1 5 3 141 0.000100 NE
+Rv2360c - hypothetical protein Rv2360c 4 5 1 2 0.000000 NE
+Rv2361c - LONG (C50) CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHASE (Z-DECAPRENYL DIPHOSPHATE SYNTHASE) 0 15 15 755 1.000000 E
+Rv2362c recO DNA repair protein RecO 3 8 2 93 0.000000 NE
+Rv2363 amiA2 amidase 7 17 4 105 0.000000 NE
+Rv2364c era GTP-binding protein Era 0 15 15 681 1.000000 E
+Rv2365c - hypothetical protein Rv2365c 2 2 0 0 -1.000000 S
+Rv2366c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 10 19 3 40 0.000000 NE
+Rv2367c - hypothetical protein Rv2367c 1 7 6 434 0.970100 U
+Rv2368c phoH1 PROBABLE PHOH-LIKE PROTEIN PHOH1 (PHOSPHATE STARVATION-INDUCIBLE PROTEIN PSIH) 15 17 1 2 0.000000 NE
+Rv2369c - hypothetical protein Rv2369c 3 3 0 0 -1.000000 S
+Rv2370c - hypothetical protein Rv2370c 12 17 2 9 0.000000 NE
+Rv2371 PE_PGRS40 PE-PGRS FAMILY PROTEIN 0 1 1 2 -1.000000 S
+Rv2372c - hypothetical protein Rv2372c 3 4 1 2 0.000000 NE
+Rv2373c dnaJ2 PROBABLE CHAPERONE PROTEIN DNAJ2 0 8 8 781 0.997000 E
+Rv2374c hrcA heat-inducible transcription repressor 4 21 10 552 0.996000 E
+Rv2375 - hypothetical protein Rv2375 8 8 0 0 0.000000 NE
+Rv2376c cfp2 LOW MOLECULAR WEIGHT ANTIGEN CFP2 (LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 2) (CFP-2) 2 2 0 0 -1.000000 S
+Rv2377c mbtH PUTATIVE CONSERVED PROTEIN MBTH 0 2 2 60 -1.000000 S
+Rv2378c mbtG LYSINE-N-OXYGENASE MBTG (L-LYSINE 6-MONOOXYGENASE) (LYSINE N6-HYDROXYLASE) 5 8 2 59 0.000000 NE
+Rv2379c mbtF PEPTIDE SYNTHETASE MBTF (PEPTIDE SYNTHASE) 14 59 18 1315 1.000000 E
+Rv2380c mbtE PEPTIDE SYNTHETASE MBTE (PEPTIDE SYNTHASE) 32 72 8 662 0.693400 U
+Rv2381c mbtD POLYKETIDE SYNTHETASE MBTD (POLYKETIDE SYNTHASE) 6 40 12 466 0.996700 E
+Rv2382c mbtC POLYKETIDE SYNTHETASE MBTC (POLYKETIDE SYNTHASE) 6 16 4 175 0.000000 NE
+Rv2383c mbtB PHENYLOXAZOLINE SYNTHASE MBTB (PHENYLOXAZOLINE SYNTHETASE) 25 47 3 22 0.000000 NE
+Rv2384 mbtA BIFUNCTIONAL ENZYME MBTA: SALICYL-AMP LIGASE (SAL-AMP LIGASE) + SALICYL-S-ArCP SYNTHETASE 8 20 4 103 0.000000 NE
+Rv2385 mbtJ PUTATIVE ACETYL HYDROLASE MBTJ 14 18 1 2 0.000000 NE
+Rv2386c mbtI salicylate synthase MbtI 4 16 11 961 0.999700 E
+Rv2387 - hypothetical protein Rv2387 21 23 1 2 0.000000 NE
+Rv2388c hemN coproporphyrinogen III oxidase 14 19 3 95 0.000000 NE
+Rv2389c rpfD PROBABLE RESUSCITATION-PROMOTING FACTOR RPFD 5 7 2 10 0.000000 NE
+Rv2390c - hypothetical protein Rv2390c 4 5 1 2 0.000000 NE
+Rv2391 nirA PROBABLE FERREDOXIN-DEPENDENT NITRITE REDUCTASE NIRA 0 19 19 1436 1.000000 E
+Rv2392 cysH phosphoadenosine phosphosulfate reductase 0 12 12 473 1.000000 E
+Rv2393 - hypothetical protein Rv2393 0 6 6 537 0.973100 U
+Rv2394 ggtB PROBABLE GAMMA-GLUTAMYLTRANSPEPTIDASE PRECURSOR GGTB (GAMMA-GLUTAMYLTRANSFERASE) (GLUTAMYL TRANSPEPTIDASE) 24 30 2 24 0.000000 NE
+Rv2395 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 24 33 3 87 0.000000 NE
+Rv2396 PE_PGRS41 PE-PGRS FAMILY PROTEIN 7 12 4 185 0.000000 NE
+Rv2397c cysA1 PROBABLE SULFATE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER CYSA1 0 12 12 886 0.999800 E
+Rv2398c cysW PROBABLE SULFATE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER CYSW 0 16 16 671 1.000000 E
+Rv2399c cysT PROBABLE SULFATE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER CYST 0 10 10 715 0.999400 E
+Rv2400c subI PROBABLE SULFATE-BINDING LIPOPROTEIN SUBI 0 17 17 826 1.000000 E
+Rv2401 - hypothetical protein Rv2401 1 3 1 2 0.000000 NE
+Rv2401A - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 1 1 2 -1.000000 S
+Rv2402 - hypothetical protein Rv2402 22 26 2 88 0.000000 NE
+Rv2403c lppR PROBABLE CONSERVED LIPOPROTEIN LPPR 4 7 2 99 0.000000 NE
+Rv2404c lepA GTP-binding protein LepA 21 27 2 143 0.000000 NE
+Rv2405 - hypothetical protein Rv2405 6 8 1 2 0.000000 NE
+Rv2406c - hypothetical protein Rv2406c 6 7 1 2 0.000000 NE
+Rv2407 - ribonuclease Z 4 9 1 2 0.000000 NE
+Rv2408 PE24 POSSIBLE PE FAMILY-RELATED PROTEIN 12 13 1 2 0.000000 NE
+Rv2409c - hypothetical protein Rv2409c 16 18 1 2 0.000000 NE
+Rv2410c - hypothetical protein Rv2410c 3 9 3 206 0.000000 NE
+Rv2411c - hypothetical protein Rv2411c 20 22 1 2 0.000000 NE
+Rv2412 rpsT 30S ribosomal protein S20 0 1 1 2 -1.000000 S
+Rv2413c - hypothetical protein Rv2413c 0 13 13 810 1.000000 E
+Rv2414c - hypothetical protein Rv2414c 4 9 3 290 0.034600 NE
+Rv2415c - hypothetical protein Rv2415c 9 14 3 59 0.000000 NE
+Rv2416c eis hypothetical protein Rv2416c 10 26 4 141 0.000000 NE
+Rv2417c - hypothetical protein Rv2417c 4 10 4 108 0.000000 NE
+Rv2418c - hypothetical protein Rv2418c 3 20 9 286 0.963700 U
+Rv2419c - PROBABLE PHOSPHOGLYCERATE MUTASE (PHOSPHOGLYCEROMUTASE) 4 7 2 97 0.000000 NE
+Rv2420c - hypothetical protein Rv2420c 1 4 2 51 0.000300 NE
+Rv2421c nadD nicotinic acid mononucleotide adenyltransferase 0 12 12 487 0.999800 E
+Rv2422 - hypothetical protein Rv2422 4 4 0 0 0.000000 NE
+Rv2423 - hypothetical protein Rv2423 15 17 1 2 0.000000 NE
+Rv2424c - PROBABLE TRANSPOSASE 3 4 1 2 0.000000 NE
+Rv2425c - hypothetical protein Rv2425c 14 16 1 2 0.000000 NE
+Rv2426c - hypothetical protein Rv2426c 9 10 1 2 0.000000 NE
+Rv2427c proA gamma-glutamyl phosphate reductase 9 15 1 2 0.000000 NE
+Rv2428 ahpC ALKYL HYDROPEROXIDE REDUCTASE C PROTEIN AHPC (ALKYL HYDROPEROXIDASE C) 2 8 3 224 0.000500 NE
+Rv2429 ahpD ALKYL HYDROPEROXIDE REDUCTASE D PROTEIN AHPD (ALKYL HYDROPEROXIDASE D) 8 10 1 2 0.000000 NE
+Rv2430c PPE41 PPE FAMILY PROTEIN 7 8 1 2 0.000000 NE
+Rv2431c PE25 PE FAMILY PROTEIN 4 5 1 2 0.000000 NE
+Rv2432c - hypothetical protein Rv2432c 3 7 2 26 0.000000 NE
+Rv2433c - hypothetical protein Rv2433c 2 6 3 42 -1.000000 S
+Rv2434c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 10 23 6 236 0.002200 NE
+Rv2435c - PROBABLE CYCLASE (ADENYLYL-OR GUANYLYL-)(ADENYLATE-OR GUANYLATE-) 22 50 7 111 0.000000 NE
+Rv2436 rbsK RIBOKINASE RBSK 4 11 6 175 0.000000 NE
+Rv2437 - hypothetical protein Rv2437 4 9 3 38 0.000000 NE
+Rv2438A - hypothetical protein Rv2438A 1 5 4 153 0.043000 U
+Rv2438c nadE NAD synthetase 0 35 35 1723 1.000000 E
+Rv2439c proB gamma-glutamyl kinase 0 11 11 982 0.999900 E
+Rv2440c obgE GTPase ObgE 0 11 11 969 0.999900 E
+Rv2441c rpmA 50S ribosomal protein L27 0 4 4 158 0.985900 U
+Rv2442c rplU 50S ribosomal protein L21 0 3 3 212 0.962500 U
+Rv2443 dctA PROBABLE C4-DICARBOXYLATE-TRANSPORT TRANSMEMBRANE PROTEIN DCTA 18 19 1 2 0.000000 NE
+Rv2444c rne POSSIBLE RIBONUCLEASE E RNE 1 28 27 1758 1.000000 E
+Rv2445c ndk nucleoside diphosphate kinase 0 3 3 180 0.963800 U
+Rv2446c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 5 6 1 2 0.000000 NE
+Rv2447c folC PROBABLE FOLYLPOLYGLUTAMATE SYNTHASE PROTEIN FOLC (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS) 0 13 13 1221 1.000000 E
+Rv2448c valS valyl-tRNA synthetase 0 24 24 1969 1.000000 E
+Rv2449c - hypothetical protein Rv2449c 19 23 2 38 0.000000 NE
+Rv2450c rpfE PROBABLE RESUSCITATION-PROMOTING FACTOR RPFE 5 7 1 2 0.000000 NE
+Rv2451 - HYPOTHETICAL PROLINE AND SERINE RICH PROTEIN 5 8 2 25 0.000000 NE
+Rv2452c - hypothetical protein Rv2452c 3 7 2 5 -1.000000 S
+Rv2453c mobA molybdopterin-guanine dinucleotide biosynthesis protein A 4 5 1 2 0.000000 NE
+Rv2454c - 2-oxoglutarate ferredoxin oxidoreductase subunit beta 0 15 15 855 1.000000 E
+Rv2455c - PROBABLE OXIDOREDUCTASE (ALPHA SUBUNIT) 0 37 37 1734 1.000000 E
+Rv2456c - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 17 20 1 2 0.000000 NE
+Rv2457c clpX ATP-dependent protease ATP-binding subunit 0 17 17 1058 1.000000 E
+Rv2458 mmuM homocysteine methyltransferase 14 17 1 2 0.000000 NE
+Rv2459 - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 16 20 1 2 0.000000 NE
+Rv2460c clpP2 ATP-dependent Clp protease proteolytic subunit 0 9 9 551 0.997700 E
+Rv2461c clpP ATP-dependent Clp protease proteolytic subunit 0 10 10 507 0.999400 E
+Rv2462c tig trigger factor 14 18 2 23 0.000000 NE
+Rv2463 lipP PROBABLE ESTERASE/LIPASE LIPP 13 17 1 2 0.000000 NE
+Rv2464c - POSSIBLE DNA GLYCOSYLASE 7 10 3 200 0.000000 NE
+Rv2465c - ribose-5-phosphate isomerase B 0 6 6 401 0.985000 U
+Rv2466c - hypothetical protein Rv2466c 7 9 1 2 0.000000 NE
+Rv2467 pepN PROBABLE AMINOPEPTIDASE N PEPN (LYSYL AMINOPEPTIDASE) (LYS-AP) (ALANINE AMINOPEPTIDASE) 28 35 2 26 0.000000 NE
+Rv2468c - hypothetical protein Rv2468c 5 5 0 0 0.000000 NE
+Rv2469c - hypothetical protein Rv2469c 6 8 1 2 0.000000 NE
+Rv2470 glbO POSSIBLE GLOBIN (OXYGEN-BINDING PROTEIN) GLBO 2 8 4 80 0.000000 NE
+Rv2471 aglA PROBABLE ALPHA-GLUCOSIDASE AGLA (MALTASE) (GLUCOINVERTASE) (GLUCOSIDOSUCRASE) (MALTASE-GLUCOAMYLASE) (LYSOSOMAL ALPHA-GLUCOSIDASE) (ACID MALTASE) 12 16 2 9 0.000000 NE
+Rv2472 - hypothetical protein Rv2472 6 8 2 30 0.000000 NE
+Rv2473 - POSSIBLE ALANINE AND PROLINE RICH MEMBRANE PROTEIN 13 15 1 2 0.000000 NE
+Rv2474c - hypothetical protein Rv2474c 4 13 5 46 0.000000 NE
+Rv2475c - hypothetical protein Rv2475c 5 8 2 79 0.000000 NE
+Rv2476c gdh PROBABLE NAD-DEPENDENT GLUTAMATE DEHYDROGENASE GDH (NAD-GDH) (NAD-DEPENDENT GLUTAMIC DEHYDROGENASE) 2 56 36 2530 1.000000 E
+Rv2477c - putative ABC transporter ATP-binding protein 0 23 23 1245 1.000000 E
+Rv2478c - hypothetical protein Rv2478c 5 5 0 0 0.000000 NE
+Rv2479c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2480c - POSSIBLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2481c - hypothetical protein Rv2481c 1 2 1 2 -1.000000 S
+Rv2482c plsB2 glycerol-3-phosphate acyltransferase 21 38 4 177 0.000000 NE
+Rv2483c plsC POSSIBLE TRANSMEMBRANE PHOSPHOLIPID BIOSYNTHESIS BIFUNCTIONNAL ENZYME PLSC: PUTATIVE L-3-PHOSPHOSERINE PHOSPHATASE (O-PHOSPHOSERINE PHOSPHOHYDROLASE) (PSP) (PSPASE) + 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (1-AGP ACYLTRANSFERASE) (1-AGPAT) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE) (LPAAT) 11 23 4 215 0.000000 NE
+Rv2484c - hypothetical protein Rv2484c 17 20 1 2 0.000000 NE
+Rv2485c lipQ PROBABLE CARBOXYLESTERASE LIPQ 16 19 2 82 0.000000 NE
+Rv2486 echA14 enoyl-CoA hydratase 8 9 1 2 0.000000 NE
+Rv2487c PE_PGRS42 PE-PGRS FAMILY PROTEIN 12 21 4 392 0.105200 U
+Rv2488c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (LUXR-FAMILY) 30 38 4 102 0.000000 NE
+Rv2489c - HYPOTHETICAL ALANINE RICH PROTEIN 4 4 0 0 0.000000 NE
+Rv2490c PE_PGRS43 PE-PGRS FAMILY PROTEIN 29 45 3 44 0.000000 NE
+Rv2491 - hypothetical protein Rv2491 2 14 9 169 0.001600 NE
+Rv2492 - hypothetical protein Rv2492 7 26 8 167 0.000200 NE
+Rv2493 - hypothetical protein Rv2493 0 0 0 0 -1.000000 S
+Rv2494 - hypothetical protein Rv2494 4 5 1 2 0.000000 NE
+Rv2495c pdhC branched-chain alpha-keto acid dehydrogenase subunit E2 5 14 4 314 0.311600 U
+Rv2496c pdhB PROBABLE PYRUVATE DEHYDROGENASE E1 COMPONENT (BETA SUBUNIT) PDHB (PYRUVATE DECARBOXYLASE) (PYRUVATE DEHYDROGENASE) (PYRUVIC DEHYDROGENASE) 4 23 9 308 0.975100 U
+Rv2497c pdhA PROBABLE PYRUVATE DEHYDROGENASE E1 COMPONENT (ALPHA SUBUNIT) PDHA (PYRUVATE DECARBOXYLASE) (PYRUVATE DEHYDROGENASE) (PYRUVIC DEHYDROGENASE) 9 22 4 95 0.000000 NE
+Rv2498c citE PROBABLE CITRATE (PRO-3S)-LYASE (BETA SUBUNIT) CITE (CITRASE) (CITRATASE) (CITRITASE) (CITRIDESMOLASE) (CITRASE ALDOLASE) 6 9 2 111 0.000000 NE
+Rv2499c - POSSIBLE OXIDASE REGULATORY-RELATED PROTEIN 3 5 1 2 0.000000 NE
+Rv2500c fadE19 POSSIBLE ACYL-CoA DEHYDROGENASE FADE19 (MMGC) 3 23 11 479 0.998600 E
+Rv2501c accA1 PROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA1: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) 7 21 5 333 0.264700 U
+Rv2502c accD1 PROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD1 14 25 3 192 0.000000 NE
+Rv2503c scoB PROBABLE SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE (BETA SUBUNIT) SCOB (3-OXO-ACID:COA TRANSFERASE) (OXCT B) (SUCCINYL CoA:3-OXOACID CoA-TRANSFERASE) 2 7 4 200 0.000000 NE
+Rv2504c scoA PROBABLE SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE (ALPHA SUBUNIT) SCOA (3-OXO ACID:CoA TRANSFERASE) (OXCT A) (SUCCINYL-COA:3-OXOACID-COENZYME A TRANSFERASE) 8 12 3 108 0.000000 NE
+Rv2505c fadD35 acyl-CoA synthetase 19 32 2 20 0.000000 NE
+Rv2506 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 7 7 0 0 0.000000 NE
+Rv2507 - POSSIBLE CONSERVED PROLINE RICH MEMBRANE PROTEIN 0 18 18 726 1.000000 E
+Rv2508c - PROBABLE CONSERVED INTEGRAL MEMBRANE LEUCINE AND ALANINE RICH PROTEIN 12 15 2 52 0.000000 NE
+Rv2509 - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 0 9 9 575 0.998600 E
+Rv2510c - hypothetical protein Rv2510c 10 15 3 63 0.000000 NE
+Rv2511 orn oligoribonuclease 0 8 8 483 0.996100 E
+Rv2512c - IS1081 transposase 0 2 2 44 -1.000000 S
+Rv2513 - hypothetical protein Rv2513 7 8 1 2 0.000000 NE
+Rv2514c - hypothetical protein Rv2514c 3 5 2 26 -1.000000 S
+Rv2515c - hypothetical protein Rv2515c 13 20 5 129 0.000000 NE
+Rv2516c - hypothetical protein Rv2516c 1 13 6 369 0.879600 U
+Rv2517c - hypothetical protein Rv2517c 5 7 1 2 -1.000000 S
+Rv2518c lppS PROBABLE CONSERVED LIPOPROTEIN LPPS 2 18 9 504 0.992000 E
+Rv2519 PE26 PE FAMILY PROTEIN 22 30 3 39 0.000000 NE
+Rv2520c - POSSIBLE CONSERVED MEMBRANE PROTEIN 0 1 1 2 -1.000000 S
+Rv2521 bcp PROBABLE BACTERIOFERRITIN COMIGRATORY PROTEIN BCP 8 9 1 2 0.000000 NE
+Rv2522c - hypothetical protein Rv2522c 10 17 2 18 0.000000 NE
+Rv2523c acpS 4'-phosphopantetheinyl transferase 0 4 4 113 -1.000000 S
+Rv2524c fas PROBABLE FATTY ACID SYNTHASE FAS (FATTY ACID SYNTHETASE) 0 61 61 7559 1.000000 E
+Rv2525c - hypothetical protein Rv2525c 11 12 1 2 0.000000 NE
+Rv2526 - hypothetical protein Rv2526 0 0 0 0 -1.000000 S
+Rv2527 - hypothetical protein Rv2527 5 9 1 2 0.000000 NE
+Rv2528c mrr PROBABLE RESTRICTION SYSTEM PROTEIN MRR 3 8 3 221 0.000100 NE
+Rv2529 - hypothetical protein Rv2529 10 16 5 152 0.000000 NE
+Rv2530A - hypothetical protein Rv2530A 2 4 2 40 -1.000000 S
+Rv2530c - hypothetical protein Rv2530c 1 3 2 159 0.040200 U
+Rv2531c - PROBABLE AMINO ACID DECARBOXYLASE 28 47 4 95 0.000000 NE
+Rv2532c - hypothetical protein Rv2532c 4 5 1 2 0.000000 NE
+Rv2533c nusB transcription antitermination protein NusB 0 4 4 250 0.985500 U
+Rv2534c efp elongation factor P 0 9 9 476 0.998600 E
+Rv2535c pepQ PROBABLE CYTOPLASMIC PEPTIDASE PEPQ 5 19 5 88 0.000000 NE
+Rv2536 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 6 8 1 2 0.000000 NE
+Rv2537c aroD 3-dehydroquinate dehydratase 0 6 6 347 0.991900 E
+Rv2538c aroB 3-dehydroquinate synthase 0 6 6 852 0.980800 U
+Rv2539c aroK shikimate kinase 0 5 5 308 0.990800 E
+Rv2540c aroF chorismate synthase 0 9 9 716 0.998500 E
+Rv2541 - HYPOTHETICAL ALANINE RICH PROTEIN 1 3 2 45 0.000000 NE
+Rv2542 - hypothetical protein Rv2542 10 11 1 2 0.000000 NE
+Rv2543 lppA PROBABLE CONSERVED LIPOPROTEIN LPPA 7 14 4 49 0.000000 NE
+Rv2544 lppB PROBABLE CONSERVED LIPOPROTEIN LPPB 5 14 4 83 0.000000 NE
+Rv2545 - hypothetical protein Rv2545 7 10 2 9 -1.000000 S
+Rv2546 - hypothetical protein Rv2546 7 9 1 2 0.000000 NE
+Rv2547 - hypothetical protein Rv2547 2 2 0 0 -1.000000 S
+Rv2548 - hypothetical protein Rv2548 2 4 2 22 0.000000 NE
+Rv2549c - hypothetical protein Rv2549c 4 4 0 0 -1.000000 S
+Rv2550c - hypothetical protein Rv2550c 2 5 2 4 0.000000 NE
+Rv2551c - hypothetical protein Rv2551c 1 2 1 2 -1.000000 S
+Rv2552c aroE shikimate 5-dehydrogenase 0 5 5 681 0.930000 U
+Rv2553c - PROBABLE CONSERVED MEMBRANE PROTEIN 0 17 17 972 1.000000 E
+Rv2554c - Holliday junction resolvase-like protein 0 4 4 370 0.922500 U
+Rv2555c alaS alanyl-tRNA synthetase 0 39 39 2351 1.000000 E
+Rv2556c - hypothetical protein Rv2556c 4 5 1 2 -1.000000 S
+Rv2557 - hypothetical protein Rv2557 9 9 0 0 0.000000 NE
+Rv2558 - hypothetical protein Rv2558 3 4 1 2 0.000000 NE
+Rv2559c - recombination factor protein RarA 12 14 2 77 0.000000 NE
+Rv2560 - PROBABLE PROLINE AND GLYCINE RICH TRANSMEMBRANE PROTEIN 18 24 2 28 0.000000 NE
+Rv2561 - hypothetical protein Rv2561 3 3 0 0 0.000000 NE
+Rv2562 - hypothetical protein Rv2562 7 8 1 2 0.000000 NE
+Rv2563 - PROBABLE GLUTAMINE-TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER 6 8 1 2 0.000000 NE
+Rv2564 glnQ PROBABLE GLUTAMINE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER GLNQ 10 12 1 2 0.000000 NE
+Rv2565 - hypothetical protein Rv2565 15 22 2 273 0.002400 NE
+Rv2566 - LONG CONSERVED HYPOTHETICAL PROTEIN 34 42 2 22 0.000000 NE
+Rv2567 - CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN 11 34 10 648 0.989400 U
+Rv2568c - hypothetical protein Rv2568c 9 17 4 255 0.006100 NE
+Rv2569c - hypothetical protein Rv2569c 13 22 3 60 0.000000 NE
+Rv2570 - hypothetical protein Rv2570 2 3 1 2 0.000000 NE
+Rv2571c - PROBABLE TRANSMEMBRANE ALANINE AND VALINE AND LEUCINE RICH PROTEIN 5 6 1 2 0.000000 NE
+Rv2572c aspS aspartyl-tRNA synthetase 0 19 19 1281 1.000000 E
+Rv2573 - 2-dehydropantoate 2-reductase 3 3 0 0 -1.000000 S
+Rv2574 - hypothetical protein Rv2574 4 6 1 2 0.000000 NE
+Rv2575 - POSSIBLE CONSERVED MEMBRANE GLYCINE RICH PROTEIN 12 17 3 42 0.000000 NE
+Rv2576c - POSSIBLE CONSERVED MEMBRANE PROTEIN 8 10 1 2 0.000000 NE
+Rv2577 - hypothetical protein Rv2577 24 36 3 121 0.000000 NE
+Rv2578c - hypothetical protein Rv2578c 13 16 1 2 0.000000 NE
+Rv2579 dhaA haloalkane dehalogenase 9 11 2 216 0.000000 NE
+Rv2580c hisS histidyl-tRNA synthetase 0 15 15 1035 1.000000 E
+Rv2581c - POSIBLE GLYOXALASE II (HYDROXYACYLGLUTATHIONE HYDROLASE) (GLX II) 1 7 4 234 0.003600 NE
+Rv2582 ppiB PROBABLE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PPIB (CYCLOPHILIN) (PPIASE) (ROTAMASE) (PEPTIDYLPROLYL ISOMERASE) 0 17 17 691 1.000000 E
+Rv2583c relA PROBABLE GTP PYROPHOSPHOKINASE RELA (ATP:GTP 3'-PYROPHOSPHOTRANSFERASE) (PPGPP SYNTHETASE I) ((P)PPGPP SYNTHETASE) (GTP DIPHOSPHOKINASE) 5 33 15 1076 0.999900 E
+Rv2584c apt adenine phosphoribosyltransferase 7 10 2 32 0.000000 NE
+Rv2585c - POSSIBLE CONSERVED LIPOPROTEIN 16 24 2 39 0.000000 NE
+Rv2586c secF preprotein translocase subunit SecF 2 17 15 898 1.000000 E
+Rv2587c secD preprotein translocase subunit SecD 0 21 21 1265 1.000000 E
+Rv2588c yajC preprotein translocase subunit YajC 2 2 0 0 -1.000000 S
+Rv2589 gabT 4-aminobutyrate aminotransferase 18 22 2 22 0.000000 NE
+Rv2590 fadD9 PROBABLE FATTY-ACID-CoA LIGASE FADD9 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 46 55 1 2 0.000000 NE
+Rv2591 PE_PGRS44 PE-PGRS FAMILY PROTEIN 10 12 1 2 0.000000 NE
+Rv2592c ruvB Holliday junction DNA helicase B 0 8 8 846 0.997400 E
+Rv2593c ruvA Holliday junction DNA helicase motor protein 1 6 3 222 0.000500 NE
+Rv2594c ruvC Holliday junction resolvase 0 4 4 356 0.938200 U
+Rv2595 - hypothetical protein Rv2595 0 0 0 0 -1.000000 S
+Rv2596 - hypothetical protein Rv2596 8 8 0 0 0.000000 NE
+Rv2597 - PROBABLE MEMBRANE PROTEIN 6 6 0 0 0.000000 NE
+Rv2598 - hypothetical protein Rv2598 2 4 2 174 0.000000 NE
+Rv2599 - PROBABLE CONSERVED MEMBRANE PROTEIN 11 12 1 2 0.000000 NE
+Rv2600 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 7 9 2 25 0.000000 NE
+Rv2601 speE spermidine synthase 22 24 1 2 0.000000 NE
+Rv2601A - hypothetical protein Rv2601A 1 2 1 2 -1.000000 S
+Rv2602 - hypothetical protein Rv2602 7 7 0 0 0.000000 NE
+Rv2603c - hypothetical protein Rv2603c 0 7 7 528 0.989200 U
+Rv2604c - hypothetical protein Rv2604c 0 4 4 165 0.983000 U
+Rv2605c tesB2 PROBABLE ACYL-CoA THIOESTERASE II TESB2 (TEII) 5 9 4 134 0.000000 NE
+Rv2606c - pyridoxine biosynthesis protein 0 10 10 588 0.999600 E
+Rv2607 pdxH pyridoxamine 5'-phosphate oxidase 9 12 2 75 0.000000 NE
+Rv2608 PPE42 PPE FAMILY PROTEIN 24 30 2 145 0.000000 NE
+Rv2609c - PROBABLE CONSERVED MEMBRANE PROTEIN 6 13 6 404 0.817600 U
+Rv2610c pimA ALPHA-MANNOSYLTRANSFERASE PIMA 0 14 14 988 1.000000 E
+Rv2611c - lipid A biosynthesis lauroyl acyltransferase 0 13 13 707 1.000000 E
+Rv2612c pgsA1 PROBABLE PI SYNTHASE PGSA1 (PHOSPHATIDYLINOSITOL SYNTHASE) (CDP-DIACYLGLYCEROL--INOSITOL3-PHOSPHATIDYLTRANSFERASE) 0 3 3 354 0.848000 U
+Rv2613c - hypothetical protein Rv2613c 2 9 5 66 0.000000 NE
+Rv2614A - hypothetical protein Rv2614A 4 6 2 43 0.000000 NE
+Rv2614c thrS threonyl-tRNA synthetase 0 27 27 1672 1.000000 E
+Rv2615c PE_PGRS45 PE-PGRS FAMILY PROTEIN 3 10 3 142 0.000000 NE
+Rv2616 - hypothetical protein Rv2616 3 4 1 2 0.000000 NE
+Rv2617c - PROBABLE TRANSMEMBRANE PROTEIN 8 8 0 0 0.000000 NE
+Rv2618 - hypothetical protein Rv2618 9 10 1 2 0.000000 NE
+Rv2619c - hypothetical protein Rv2619c 1 2 1 2 -1.000000 S
+Rv2620c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 4 0 0 0.000000 NE
+Rv2621c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 4 1 2 0.000000 NE
+Rv2622 - POSSIBLE METHYLTRANSFERASE (METHYLASE) 5 8 2 54 0.000000 NE
+Rv2623 TB31.7 hypothetical protein Rv2623 4 7 2 27 0.000000 NE
+Rv2624c - hypothetical protein Rv2624c 8 11 2 21 0.000000 NE
+Rv2625c - PROBABLE CONSERVED TRANSMEMBRANE ALANINE AND LEUCINE RICH PROTEIN 10 18 3 207 0.000000 NE
+Rv2626c - hypothetical protein Rv2626c 3 6 2 12 0.000000 NE
+Rv2627c - hypothetical protein Rv2627c 10 21 5 252 0.004800 NE
+Rv2628 - hypothetical protein Rv2628 7 8 1 2 0.000000 NE
+Rv2629 - hypothetical protein Rv2629 17 21 2 41 0.000000 NE
+Rv2630 - hypothetical protein Rv2630 7 9 2 47 0.000000 NE
+Rv2631 - hypothetical protein Rv2631 17 20 1 2 0.000000 NE
+Rv2632c - hypothetical protein Rv2632c 3 3 0 0 -1.000000 S
+Rv2633c - hypothetical protein Rv2633c 7 10 2 75 0.000000 NE
+Rv2634c PE_PGRS46 PE-PGRS FAMILY PROTEIN 17 32 3 146 0.000000 NE
+Rv2635 - hypothetical protein Rv2635 3 6 2 32 -1.000000 S
+Rv2636 - hypothetical protein Rv2636 9 14 2 11 0.000000 NE
+Rv2637 dedA POSSIBLE TRANSMEMBRANE PROTEIN DEDA 7 9 2 40 0.000000 NE
+Rv2638 - hypothetical protein Rv2638 3 4 1 2 0.000000 NE
+Rv2639c - hypothetical protein Rv2639c 6 7 1 2 0.000000 NE
+Rv2640c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARSR-FAMILY) 4 4 0 0 0.000000 NE
+Rv2641 cadI CADMIUM INDUCIBLE PROTEIN CADI 6 6 0 0 0.000000 NE
+Rv2642 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARSR-FAMILY) 3 3 0 0 0.000000 NE
+Rv2643 arsC PROBABLE ARSENIC-TRANSPORT INTEGRAL MEMBRANE PROTEIN ARSC 25 30 1 2 0.000000 NE
+Rv2644c - hypothetical protein Rv2644c 2 6 2 39 0.000000 NE
+Rv2645 - hypothetical protein Rv2645 4 4 0 0 0.000000 NE
+Rv2646 - PROBABLE INTEGRASE 16 19 2 86 0.000000 NE
+Rv2647 - hypothetical protein Rv2647 4 6 2 50 0.000200 NE
+Rv2648 - PROBABLE TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS6110 0 0 0 0 -1.000000 S
+Rv2649 - PROBABLE TRANSPOSASE FOR INSERTION SEQUENCE ELEMENT IS6110 0 1 1 2 -1.000000 S
+Rv2650c - POSSIBLE phiRv2 PROPHAGE PROTEIN 1 8 7 584 0.980100 U
+Rv2651c - POSSIBLE phiRv2 PROPHAGE PROTEASE 2 5 3 291 0.267700 U
+Rv2652c - PROBABLE phiRv2 PROPHAGE PROTEIN 2 7 3 159 0.000000 NE
+Rv2653c - POSSIBLE phiRv2 PROPHAGE PROTEIN 0 4 4 273 0.984600 U
+Rv2654c - POSSIBLE phiRv2 PROPHAGE PROTEIN 0 0 0 0 -1.000000 S
+Rv2655c - POSSIBLE phiRv2 PROPHAGE PROTEIN 15 19 1 2 0.000000 NE
+Rv2656c - POSSIBLE phiRv2 PROPHAGE PROTEIN 5 5 0 0 0.000000 NE
+Rv2657c - PROBABLE phiRv2 PROPHAGE PROTEIN 4 5 1 2 -1.000000 S
+Rv2658c - POSSIBLE PROPHAGE PROTEIN 9 10 1 2 0.000000 NE
+Rv2659c - PROBABLE phiRv2 PROPHAGE INTEGRASE 16 20 1 2 0.000000 NE
+Rv2660c - hypothetical protein Rv2660c 1 3 1 2 0.000000 NE
+Rv2661c - hypothetical protein Rv2661c 2 2 0 0 -1.000000 S
+Rv2662 - hypothetical protein Rv2662 3 4 1 2 -1.000000 S
+Rv2663 - hypothetical protein Rv2663 8 9 1 2 0.000000 NE
+Rv2664 - hypothetical protein Rv2664 0 0 0 0 -1.000000 S
+Rv2665 - HYPOTHETICAL ARGININE RICH PROTEIN 1 4 3 126 0.617300 U
+Rv2666 - truncated IS1081 transposase 0 2 2 44 -1.000000 S
+Rv2667 clpC2 POSSIBLE ATP-DEPENDENT PROTEASE ATP-BINDING SUBUNIT CLPC2 4 5 1 2 0.000000 NE
+Rv2668 - POSSIBLE EXPORTED ALANINE AND VALINE RICH PROTEIN 5 8 1 2 0.000000 NE
+Rv2669 - hypothetical protein Rv2669 3 7 2 75 0.000000 NE
+Rv2670c - hypothetical protein Rv2670c 8 16 4 92 0.000000 NE
+Rv2671 ribD hypothetical protein Rv2671 4 10 5 475 0.800800 U
+Rv2672 - POSSIBLE SECRETED PROTEASE 11 16 2 14 0.000000 NE
+Rv2673 - POSSIBLE CONSERVED INTEGRAL MEMBRANE PROTEIN 0 26 26 1057 1.000000 E
+Rv2674 - hypothetical protein Rv2674 5 6 1 2 0.000000 NE
+Rv2675c - hypothetical protein Rv2675c 14 14 0 0 0.000000 NE
+Rv2676c - hypothetical protein Rv2676c 0 12 12 583 0.999900 E
+Rv2677c hemY protoporphyrinogen oxidase 0 11 11 1149 1.000000 E
+Rv2678c hemE uroporphyrinogen decarboxylase 0 13 13 877 0.999800 E
+Rv2679 echA15 enoyl-CoA hydratase 3 4 1 2 0.000000 NE
+Rv2680 - hypothetical protein Rv2680 4 10 4 36 0.000000 NE
+Rv2681 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 15 19 2 215 0.000000 NE
+Rv2682c dxs1 1-deoxy-D-xylulose-5-phosphate synthase 0 22 22 1609 1.000000 E
+Rv2683 - hypothetical protein Rv2683 7 10 1 2 0.000000 NE
+Rv2684 arsA PROBABLE ARSENIC-TRANSPORT INTEGRAL MEMBRANE PROTEIN ARSA 12 17 2 45 0.000000 NE
+Rv2685 arsB1 PROBABLE ARSENIC-TRANSPORT INTEGRAL MEMBRANE PROTEIN ARSB1 7 9 1 2 0.000000 NE
+Rv2686c - PROBABLE ANTIBIOTIC-TRANSPORT INTEGRAL MEMBRANE LEUCINE AND ALANINE AND VALINE RICH PROTEIN ABC TRANSPORTER 8 12 2 23 0.000000 NE
+Rv2687c - PROBABLE ANTIBIOTIC-TRANSPORT INTEGRAL MEMBRANE LEUCINE AND VALINE RICH PROTEIN ABC TRANSPORTER 4 11 5 345 0.736500 U
+Rv2688c - PROBABLE ANTIBIOTIC-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER 7 11 1 2 0.000000 NE
+Rv2689c - CONSERVED HYPOTHETICAL ALANINE AND VALINE AND GLYCINE RICH PROTEIN 15 21 2 56 0.000000 NE
+Rv2690c - PROBABLE CONSERVED INTEGRAL MEMBRANE ALANINE AND VALINE AND LEUCINE RICH PROTEIN 1 31 24 1247 1.000000 E
+Rv2691 ceoB TRK SYSTEM POTASSIUM UPTAKE PROTEIN CEOB 7 14 2 13 0.000000 NE
+Rv2692 ceoC TRK SYSTEM POTASSIUM UPTAKE PROTEIN CEOC 2 2 0 0 -1.000000 S
+Rv2693c - PROBABLE CONSERVED INTEGRAL MEMBRANE ALANINE AND LEUCINE RICH PROTEIN 6 10 2 149 0.000000 NE
+Rv2694c - hypothetical protein Rv2694c 3 6 3 125 0.000100 NE
+Rv2695 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 8 10 1 2 0.000000 NE
+Rv2696c - CONSERVED HYPOTHETICAL ALANINE AND GLYCINE AND VALINE RICH PROTEIN 3 9 4 135 0.000000 NE
+Rv2697c dut deoxyuridine 5'-triphosphate nucleotidohydrolase 0 5 5 258 0.993900 E
+Rv2698 - PROBABLE CONSERVED ALANINE RICH TRANSMEMBRANE PROTEIN 0 12 12 395 1.000000 E
+Rv2699c - hypothetical protein Rv2699c 0 2 2 163 -1.000000 S
+Rv2700 - POSSIBLE CONSERVED SECRETED ALANINE RICH PROTEIN 2 7 4 350 0.809000 U
+Rv2701c suhB POSSIBLE EXTRAGENIC SUPPRESSOR PROTEIN SUHB 5 9 3 121 0.000000 NE
+Rv2702 ppgK POLYPHOSPHATE GLUCOKINASE PPGK (POLYPHOSPHATE-GLUCOSE PHOSPHOTRANSFERASE) 7 13 5 162 0.000000 NE
+Rv2703 sigA RNA polymerase sigma factor RpoD 0 18 18 1365 1.000000 E
+Rv2704 - hypothetical protein Rv2704 5 10 4 151 0.000000 NE
+Rv2705c - hypothetical protein Rv2705c 9 9 0 0 0.000000 NE
+Rv2706c - hypothetical protein Rv2706c 2 2 0 0 -1.000000 S
+Rv2707 - PROBABLE CONSERVED TRANSMEMBRANE ALANINE AND LEUCINE RICH PROTEIN 22 28 1 2 0.000000 NE
+Rv2708c - hypothetical protein Rv2708c 5 6 1 2 0.000000 NE
+Rv2709 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 7 9 1 2 0.000000 NE
+Rv2710 sigB RNA polymerase sigma factor SigB 9 12 1 2 0.000000 NE
+Rv2711 ideR IRON-DEPENDENT REPRESSOR AND ACTIVATOR IDER 0 5 5 540 0.927500 U
+Rv2712c - hypothetical protein Rv2712c 8 13 3 115 0.000000 NE
+Rv2713 sthA soluble pyridine nucleotide transhydrogenase 21 21 0 0 0.000000 NE
+Rv2714 - CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN 12 15 1 2 0.000000 NE
+Rv2715 - POSSIBLE HYDROLASE 11 16 2 19 0.000000 NE
+Rv2716 - hypothetical protein Rv2716 7 10 1 2 0.000000 NE
+Rv2717c - hypothetical protein Rv2717c 8 10 2 29 0.000000 NE
+Rv2718c - hypothetical protein Rv2718c 5 7 2 164 0.000400 NE
+Rv2719c - POSSIBLE CONSERVED MEMBRANE PROTEIN 4 4 0 0 0.000000 NE
+Rv2720 lexA LexA repressor 0 8 8 269 0.999600 E
+Rv2721c - POSSIBLE CONSERVED TRANSMEMBRANE ALANINE AND GLYCINE RICH PROTEIN 16 23 2 22 0.000000 NE
+Rv2722 - hypothetical protein Rv2722 4 6 2 81 0.002800 NE
+Rv2723 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 19 27 2 51 0.000000 NE
+Rv2724c fadE20 PROBABLE ACYL-CoA DEHYDROGENASE FADE20 19 23 1 2 0.000000 NE
+Rv2725c hflX PROBABLE GTP-BINDING PROTEIN HFLX 14 17 2 77 0.000000 NE
+Rv2726c dapF diaminopimelate epimerase 0 10 10 635 0.998400 E
+Rv2727c miaA tRNA delta(2)-isopentenylpyrophosphate transferase 0 12 12 692 0.999800 E
+Rv2728c - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 9 10 1 2 0.000000 NE
+Rv2729c - PROBABLE CONSERVED INTEGRAL MEMBRANE ALANINE VALINE AND LEUCINE RICH PROTEIN 9 11 1 2 0.000000 NE
+Rv2730 - hypothetical protein Rv2730 11 11 0 0 0.000000 NE
+Rv2731 - CONSERVED HYPOTHETICAL ALANINE AND ARGININE RICH PROTEIN 8 8 0 0 0.000000 NE
+Rv2732c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 3 6 2 114 0.000000 NE
+Rv2733c - CONSERVED HYPOTHETICAL ALANINE, ARGININE-RICH PROTEIN 12 16 1 2 0.000000 NE
+Rv2734 - hypothetical protein Rv2734 9 21 7 188 0.000100 NE
+Rv2735c - hypothetical protein Rv2735c 17 28 7 239 0.012100 NE
+Rv2736c recX recombination regulator RecX 4 6 1 2 0.000000 NE
+Rv2737A - CONSERVED HYPOTHETICAL CYSTEINE RICH PROTEIN (FRAGMENT) 1 3 1 2 -1.000000 S
+Rv2737c recA recombinase A 17 28 3 169 0.000000 NE
+Rv2738c - hypothetical protein Rv2738c 1 3 1 2 -1.000000 S
+Rv2739c - POSSIBLE ALANINE RICH TRANSFERASE 4 5 1 2 0.000000 NE
+Rv2740 - hypothetical protein Rv2740 5 5 0 0 0.000000 NE
+Rv2741 PE_PGRS47 PE-PGRS FAMILY PROTEIN 15 22 2 53 0.000000 NE
+Rv2742c - CONSERVED HYPOTHETICAL ARGININE RICH PROTEIN 15 15 0 0 0.000000 NE
+Rv2743c - POSSIBLE CONSERVED TRANSMEMBRANE ALANINE RICH PROTEIN 9 12 1 2 0.000000 NE
+Rv2744c 35kd_ag CONSERVED 35 KDA ALANINE RICH PROTEIN 4 5 1 2 0.000000 NE
+Rv2745c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 1 2 1 2 -1.000000 S
+Rv2746c pgsA3 PROBABLE PGP SYNTHASE PGSA3 (CDP-DIACYLGLYCEROL--GLYCEROL-3-PHOSPHATE 3-PHOSPHATIDYLTRANSFERASE) (PHOSPHATIDYLGLYCEROPHOSPHATE SYNTHASE) 0 13 13 520 1.000000 E
+Rv2747 - N-acetylglutamate synthase 0 7 7 389 0.994900 E
+Rv2748c ftsK POSSIBLE CELL DIVISION TRANSMEMBRANE PROTEIN FTSK 1 27 25 2216 1.000000 E
+Rv2749 - hypothetical protein Rv2749 2 3 1 2 -1.000000 S
+Rv2750 - 3-ketoacyl-(acyl-carrier-protein) reductase 6 12 3 217 0.000200 NE
+Rv2751 - hypothetical protein Rv2751 6 21 6 224 0.002700 NE
+Rv2752c - hypothetical protein Rv2752c 10 17 3 182 0.000000 NE
+Rv2753c dapA dihydrodipicolinate synthase 0 9 9 632 0.998300 E
+Rv2754c thyX FAD-dependent thymidylate synthase 0 9 9 437 0.999100 E
+Rv2755c hsdS.1 POSSIBLE TYPE I RESTRICTION/MODIFICATION SYSTEM SPECIFICITY DETERMINANT (FRAGMENT) HSDS.1 (S PROTEIN) 3 7 2 26 -1.000000 S
+Rv2756c hsdM POSSIBLE TYPE I RESTRICTION/MODIFICATION SYSTEM DNA METHYLASE HSDM (M PROTEIN) (DNA METHYLTRANSFERASE) 15 36 9 377 0.959300 U
+Rv2757c - hypothetical protein Rv2757c 4 7 2 63 0.000000 NE
+Rv2758c - hypothetical protein Rv2758c 1 4 2 5 -1.000000 S
+Rv2759c - hypothetical protein Rv2759c 5 8 1 2 0.000000 NE
+Rv2760c - hypothetical protein Rv2760c 1 1 0 0 -1.000000 S
+Rv2761c hsdS POSSIBLE TYPE I RESTRICTION/MODIFICATION SYSTEM SPECIFICITY DETERMINANT HSDS (S PROTEIN) 10 21 4 92 0.000000 NE
+Rv2762c - hypothetical protein Rv2762c 3 4 1 2 0.000000 NE
+Rv2763c dfrA DIHYDROFOLATE REDUCTASE DFRA (DHFR) (TETRAHYDROFOLATE DEHYDROGENASE) 0 7 7 297 0.999400 E
+Rv2764c thyA thymidylate synthase 0 20 20 708 1.000000 E
+Rv2765 - PROBABLE ALANINE RICH HYDROLASE 10 13 2 17 0.000000 NE
+Rv2766c fabG 3-ketoacyl-(acyl-carrier-protein) reductase 4 4 0 0 0.000000 NE
+Rv2767c - POSSIBLE MEMBRANE PROTEIN 9 9 0 0 0.000000 NE
+Rv2768c PPE43 PPE FAMILY PROTEIN 11 14 1 2 0.000000 NE
+Rv2769c PE27 PE FAMILY PROTEIN 14 15 1 2 0.000000 NE
+Rv2770c PPE44 PPE FAMILY PROTEIN 10 12 1 2 0.000000 NE
+Rv2771c - hypothetical protein Rv2771c 6 8 1 2 0.000000 NE
+Rv2772c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 6 9 2 164 0.000000 NE
+Rv2773c dapB dihydrodipicolinate reductase 0 9 9 549 0.998700 E
+Rv2774c - hypothetical protein Rv2774c 1 2 1 2 -1.000000 S
+Rv2775 - hypothetical protein Rv2775 7 10 2 34 0.000000 NE
+Rv2776c - PROBABLE OXIDOREDUCTASE 8 13 2 9 0.000000 NE
+Rv2777c - hypothetical protein Rv2777c 16 20 2 34 0.000000 NE
+Rv2778c - hypothetical protein Rv2778c 7 9 1 2 0.000000 NE
+Rv2779c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LRP/ASNC-FAMILY) 2 6 3 148 0.000000 NE
+Rv2780 ald SECRETED L-ALANINE DEHYDROGENASE ALD (40 KDA ANTIGEN) (TB43) 16 24 4 54 0.000000 NE
+Rv2781c - POSSIBLE ALANINE RICH OXIDOREDUCTASE 7 18 5 384 0.558300 U
+Rv2782c pepR PROBABLE ZINC PROTEASE PEPR 9 12 2 101 0.000000 NE
+Rv2783c gpsI polynucleotide phosphorylase/polyadenylase 0 18 18 1917 1.000000 E
+Rv2784c lppU PROBABLE LIPOPROTEIN LPPU 6 6 0 0 0.000000 NE
+Rv2785c rpsO 30S ribosomal protein S15 0 4 4 191 0.985400 U
+Rv2786c ribF bifunctional riboflavin kinase/FMN adenylyltransferase 0 11 11 813 0.999800 E
+Rv2787 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 19 21 1 2 0.000000 NE
+Rv2788 sirR PROBABLE TRANSCRIPTIONAL REPRESSOR SIRR 5 6 1 2 0.000000 NE
+Rv2789c fadE21 PROBABLE ACYL-CoA DEHYDROGENASE FADE21 7 14 3 319 0.087300 U
+Rv2790c ltp1 lipid-transfer protein 11 20 4 116 0.000000 NE
+Rv2791c - PROBABLE TRANSPOSASE 8 15 3 164 0.000000 NE
+Rv2792c - POSSIBLE RESOLVASE 4 6 1 2 0.000000 NE
+Rv2793c truB tRNA pseudouridine synthase B 2 8 4 292 0.261600 U
+Rv2794c - hypothetical protein Rv2794c 0 7 7 523 0.990100 E
+Rv2795c - hypothetical protein Rv2795c 7 16 3 242 0.000900 NE
+Rv2796c lppV PROBABLE CONSERVED LIPOPROTEIN LPPV 4 5 1 2 0.000000 NE
+Rv2797c - hypothetical protein Rv2797c 21 22 1 2 0.000000 NE
+Rv2798c - hypothetical protein Rv2798c 2 3 1 2 0.000000 NE
+Rv2799 - PROBABLE MEMBRANE PROTEIN 10 10 0 0 0.000000 NE
+Rv2800 - POSSIBLE HYDROLASE 14 17 1 2 0.000000 NE
+Rv2801c - hypothetical protein Rv2801c 3 4 1 2 0.000000 NE
+Rv2802c - HYPOTHETICAL ARGININE AND ALANINE RICH PROTEIN 6 8 2 65 0.000000 NE
+Rv2803 - hypothetical protein Rv2803 6 6 0 0 0.000000 NE
+Rv2804c - hypothetical protein Rv2804c 6 6 0 0 0.000000 NE
+Rv2805 - hypothetical protein Rv2805 3 3 0 0 0.000000 NE
+Rv2806 - POSSIBLE MEMBRANE PROTEIN 5 7 1 2 0.000000 NE
+Rv2807 - hypothetical protein Rv2807 6 11 3 165 0.000000 NE
+Rv2808 - hypothetical protein Rv2808 3 7 4 139 0.018000 NE
+Rv2809 - hypothetical protein Rv2809 6 7 1 2 0.000000 NE
+Rv2810c - PROBABLE TRANSPOSASE 9 12 1 2 0.000000 NE
+Rv2811 - hypothetical protein Rv2811 1 2 1 2 -1.000000 S
+Rv2812 - PROBABLE TRANSPOSASE 6 18 3 114 0.000000 NE
+Rv2813 - hypothetical protein Rv2813 3 9 4 335 0.632500 U
+Rv2814c - PROBABLE TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv2815c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv2816c - hypothetical protein Rv2816c 4 14 5 35 0.000000 NE
+Rv2817c - hypothetical protein Rv2817c 4 18 9 411 0.990900 E
+Rv2818c - hypothetical protein Rv2818c 15 22 4 124 0.000000 NE
+Rv2819c - hypothetical protein Rv2819c 5 20 7 581 0.926400 U
+Rv2820c - hypothetical protein Rv2820c 10 16 4 148 0.000000 NE
+Rv2821c - hypothetical protein Rv2821c 6 9 2 45 0.000000 NE
+Rv2822c - hypothetical protein Rv2822c 10 13 1 2 0.000000 NE
+Rv2823c - hypothetical protein Rv2823c 24 41 6 347 0.308400 U
+Rv2824c - hypothetical protein Rv2824c 13 16 1 2 0.000000 NE
+Rv2825c - hypothetical protein Rv2825c 0 2 2 165 -1.000000 S
+Rv2826c - hypothetical protein Rv2826c 7 11 2 84 0.000000 NE
+Rv2827c - hypothetical protein Rv2827c 0 13 13 751 1.000000 E
+Rv2828c - hypothetical protein Rv2828c 0 2 2 165 -1.000000 S
+Rv2829c - hypothetical protein Rv2829c 4 4 0 0 0.000000 NE
+Rv2830c - hypothetical protein Rv2830c 0 0 0 0 -1.000000 S
+Rv2831 echA16 enoyl-CoA hydratase 3 6 2 76 0.000000 NE
+Rv2832c ugpC PROBABLE Sn-GLYCEROL-3-PHOSPHATE TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER UGPC 1 7 6 665 0.957000 U
+Rv2833c ugpB PROBABLE Sn-GLYCEROL-3-PHOSPHATE-BINDING LIPOPROTEIN UGPB 5 19 5 83 0.000000 NE
+Rv2834c ugpE PROBABLE Sn-GLYCEROL-3-PHOSPHATE TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER UGPE 4 6 1 2 0.000000 NE
+Rv2835c ugpA PROBABLE Sn-GLYCEROL-3-PHOSPHATE TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER UGPA 6 14 4 39 0.000000 NE
+Rv2836c dinF POSSIBLE DNA-DAMAGE-INDUCIBLE PROTEIN F DINF 12 21 2 21 0.000000 NE
+Rv2837c - hypothetical protein Rv2837c 0 13 13 843 0.999900 E
+Rv2838c rbfA ribosome-binding factor A 1 7 6 355 0.979600 U
+Rv2839c infB translation initiation factor IF-2 0 24 24 2073 1.000000 E
+Rv2840c - hypothetical protein Rv2840c 1 5 4 155 0.928000 U
+Rv2841c nusA transcription elongation factor NusA 0 12 12 868 1.000000 E
+Rv2842c - hypothetical protein Rv2842c 1 6 3 80 0.000200 NE
+Rv2843 - PROBABLE CONSERVED TRANSMEMBRANE ALANINE RICH PROTEIN 1 6 5 190 0.991200 E
+Rv2844 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 0 4 4 195 0.982500 U
+Rv2845c proS prolyl-tRNA synthetase 0 29 29 1516 1.000000 E
+Rv2846c efpA POSSIBLE INTEGRAL MEMBRANE EFFLUX PROTEIN EFPA 0 28 28 1390 1.000000 E
+Rv2847c cysG POSSIBLE MULTIFUNCTIONAL ENZYME SIROHEME SYNTHASE CYSG: UROPORPHYRIN-III C-METHYLTRANSFERASE (UROGEN III METHYLASE) (SUMT) (UROPORPHYRINOGEN III METHYLASE) (UROM) + PRECORRIN-2 OXIDASE + FERROCHELATASE 0 14 14 968 1.000000 E
+Rv2848c cobB cobyrinic acid a,c-diamide synthase 15 22 2 48 0.000000 NE
+Rv2849c cobO cob(I)yrinic acid a,c-diamide adenosyltransferase 3 6 3 117 0.000000 NE
+Rv2850c - POSSIBLE MAGNESIUM CHELATASE 7 14 6 649 0.809000 U
+Rv2851c - hypothetical protein Rv2851c 6 8 2 56 0.000000 NE
+Rv2852c mqo malate:quinone oxidoreductase 13 19 2 34 0.000000 NE
+Rv2853 PE_PGRS48 PE-PGRS FAMILY PROTEIN 22 31 2 88 0.000000 NE
+Rv2854 - hypothetical protein Rv2854 10 17 4 199 0.000000 NE
+Rv2855 mtr mycothione/glutathione reductase 6 27 8 208 0.001000 NE
+Rv2856 nicT POSSIBLE NICKEL-TRANSPORT INTEGRAL MEMBRANE PROTEIN NICT 7 14 4 178 0.000000 NE
+Rv2857c - short chain dehydrogenase 5 11 4 225 0.000900 NE
+Rv2858c aldC PROBABLE ALDEHYDE DEHYDROGENASE ALDC 5 13 5 636 0.676200 U
+Rv2859c - POSSIBLE AMIDOTRANSFERASE 13 15 1 2 0.000000 NE
+Rv2860c glnA4 PROBABLE GLUTAMINE SYNTHETASE GLNA4 (GLUTAMINE SYNTHASE) (GS-II) 19 30 2 26 0.000000 NE
+Rv2861c mapB methionine aminopeptidase 0 11 11 665 0.999600 E
+Rv2862c - hypothetical protein Rv2862c 4 5 1 2 0.000000 NE
+Rv2863 - hypothetical protein Rv2863 3 3 0 0 0.000000 NE
+Rv2864c - POSSIBLE PENICILLIN-BINDING LIPOPROTEIN 13 18 3 226 0.000000 NE
+Rv2865 - hypothetical protein Rv2865 2 2 0 0 -1.000000 S
+Rv2866 - hypothetical protein Rv2866 2 3 1 2 -1.000000 S
+Rv2867c - hypothetical protein Rv2867c 8 11 2 151 0.000000 NE
+Rv2868c ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 0 11 11 749 0.999800 E
+Rv2869c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 1 18 16 924 1.000000 E
+Rv2870c dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1 14 13 1037 0.999900 E
+Rv2871 - hypothetical protein Rv2871 2 7 3 44 0.000000 NE
+Rv2872 - hypothetical protein Rv2872 8 10 1 2 0.000000 NE
+Rv2873 mpt83 CELL SURFACE LIPOPROTEIN MPT83 (LIPOPROTEIN P23) 9 12 1 2 0.000000 NE
+Rv2874 dipZ POSSIBLE INTEGRAL MEMBRANE C-TYPE CYTOCHROME BIOGENESIS PROTEIN DIPZ 27 42 4 237 0.000100 NE
+Rv2875 mpt70 MAJOR SECRETED IMMUNOGENIC PROTEIN MPT70 8 10 1 2 0.000000 NE
+Rv2876 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 1 1 0 0 -1.000000 S
+Rv2877c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 15 19 1 2 0.000000 NE
+Rv2878c mpt53 SOLUBLE SECRETED ANTIGEN MPT53 PRECURSOR 7 7 0 0 0.000000 NE
+Rv2879c - hypothetical protein Rv2879c 8 9 1 2 0.000000 NE
+Rv2880c - hypothetical protein Rv2880c 11 12 1 2 0.000000 NE
+Rv2881c cdsA PROBABLE INTEGRAL MEMBRANE PHOSPHATIDATE CYTIDYLYLTRANSFERASE CDSA (CDP-DIGLYCERIDE SYNTHETASE) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE) (CDP-DIACYLGLYCEROL SYNTHASE) (CDS) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE) (CDP-DAG SYNTHASE) (CDP-DG SYNTHETASE) 1 11 10 743 0.999200 E
+Rv2882c frr ribosome recycling factor 1 16 15 423 1.000000 E
+Rv2883c pyrH uridylate kinase 0 10 10 649 0.998900 E
+Rv2884 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 9 12 2 89 0.000000 NE
+Rv2885c - PROBABLE TRANSPOSASE 8 13 5 245 0.005200 NE
+Rv2886c - PROBABLE RESOLVASE 13 18 2 24 0.000000 NE
+Rv2887 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 5 7 1 2 0.000000 NE
+Rv2888c amiC amidase 25 29 1 2 0.000000 NE
+Rv2889c tsf elongation factor Ts 0 9 9 668 0.997800 E
+Rv2890c rpsB 30S ribosomal protein S2 0 7 7 529 0.988800 U
+Rv2891 - hypothetical protein Rv2891 8 12 2 92 0.000000 NE
+Rv2892c PPE45 PPE FAMILY PROTEIN 13 17 2 88 0.000000 NE
+Rv2893 - POSSIBLE OXIDOREDUCTASE 6 7 1 2 0.000000 NE
+Rv2894c xerC site-specific tyrosine recombinase XerC 4 11 3 141 0.000000 NE
+Rv2895c viuB POSSIBLE MYCOBACTIN UTILIZATION PROTEIN VIUB 9 11 1 2 0.000000 NE
+Rv2896c - hypothetical protein Rv2896c 11 17 3 67 0.000000 NE
+Rv2897c - hypothetical protein Rv2897c 4 11 7 594 0.951500 U
+Rv2898c - hypothetical protein Rv2898c 1 4 2 86 -1.000000 S
+Rv2899c fdhD formate dehydrogenase accessory protein 3 11 3 105 0.000000 NE
+Rv2900c fdhF POSSIBLE FORMATE DEHYDROGENASE H FDHF (FORMATE-HYDROGEN-LYASE-LINKED, SELENOCYSTEINE-CONTAINING POLYPEPTIDE) (FORMATE DEHYDROGENASE-H ALPHA SUBUNIT) (FDH-H) 16 27 3 159 0.000000 NE
+Rv2901c - hypothetical protein Rv2901c 7 9 2 37 0.000000 NE
+Rv2902c rnhB ribonuclease HII 6 10 2 66 0.000000 NE
+Rv2903c lepB PROBABLE SIGNAL PEPTIDASE I LEPB (SPASE I) (LEADER PEPTIDASE I). 0 12 12 577 0.999900 E
+Rv2904c rplS 50S ribosomal protein L19 0 4 4 101 -1.000000 S
+Rv2905 lppW PROBABLE CONSERVED ALANINE RICH LIPOPROTEIN LPPW 11 16 3 270 0.006800 NE
+Rv2906c trmD tRNA (guanine-N(1)-)-methyltransferase 0 9 9 502 0.998900 E
+Rv2907c rimM 16S rRNA-processing protein 0 6 6 233 0.996400 E
+Rv2908c - hypothetical protein Rv2908c 0 6 6 138 -1.000000 S
+Rv2909c rpsP 30S ribosomal protein S16 1 7 6 207 0.041300 U
+Rv2910c - hypothetical protein Rv2910c 8 10 1 2 0.000000 NE
+Rv2911 dacB2 PROBABLE D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACB2 (PENICILLIN-BINDING PROTEIN) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP) (DD-TRANSPEPTIDASE) (SERINE-TYPE D-ALA-D-ALA CARBOXYPEPTIDASE) (D-AMINO ACID HYDROLASE) 6 10 3 78 0.000000 NE
+Rv2912c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 4 8 4 159 0.000000 NE
+Rv2913c - POSSIBLE D-AMINO ACID AMINOHYDROLASE (D-AMINO ACID HYDROLASE) 15 25 5 380 0.267400 U
+Rv2914c pknI PROBABLE TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE I PKNI (PROTEIN KINASE I) (STPK I) (PHOSPHORYLASE B KINASE KINASE) (HYDROXYALKYL-PROTEIN KINASE) 20 23 1 2 0.000000 NE
+Rv2915c - hypothetical protein Rv2915c 10 12 2 331 0.062900 U
+Rv2916c ffh PROBABLE SIGNAL RECOGNITION PARTICLE PROTEIN FFH (FIFTY-FOUR HOMOLOG) (SRP PROTEIN) 0 9 9 1381 1.000000 E
+Rv2917 - CONSERVED HYPOTHETICAL ALANINE AND ARGININE RICH PROTEIN 20 23 1 2 0.000000 NE
+Rv2918c glnD PII uridylyl-transferase 16 25 3 96 0.000000 NE
+Rv2919c glnB PROBABLE NITROGEN REGULATORY PROTEIN P-II GLNB 3 5 1 2 0.000000 NE
+Rv2920c amt PROBABLE AMMONIUM-TRANSPORT INTEGRAL MEMBRANE PROTEIN AMT 10 17 2 25 0.000000 NE
+Rv2921c ftsY PROBABLE CELL DIVISION PROTEIN FTSY (SRP RECEPTOR) (SIGNAL RECOGNITION PARTICLE RECEPTOR) 0 13 13 856 1.000000 E
+Rv2922A acyP PROBABLE ACYLPHOSPHATASE ACYP (ACYLPHOSPHATE PHOSPHOHYDROLASE) 0 1 1 2 -1.000000 S
+Rv2922c smc PROBABLE CHROMOSOME PARTITION PROTEIN SMC 16 35 5 444 0.114600 U
+Rv2923c - hypothetical protein Rv2923c 3 5 2 34 0.000000 NE
+Rv2924c fpg formamidopyrimidine-DNA glycosylase 10 13 2 6 0.000000 NE
+Rv2925c rnc ribonuclease III 0 11 11 524 0.999800 E
+Rv2926c - hypothetical protein Rv2926c 1 4 3 33 0.000000 NE
+Rv2927c - hypothetical protein Rv2927c 0 10 10 580 0.999100 E
+Rv2928 tesA PROBABLE THIOESTERASE TESA 9 24 7 188 0.000300 NE
+Rv2929 - hypothetical protein Rv2929 1 4 2 37 0.000000 NE
+Rv2930 fadD26 acyl-CoA synthetase 19 33 8 200 0.000100 NE
+Rv2931 ppsA PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSA 51 69 2 52 0.000000 NE
+Rv2932 ppsB PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSB 50 64 3 94 0.000000 NE
+Rv2933 ppsC PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSC 61 79 3 158 0.000000 NE
+Rv2934 ppsD PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSD 42 56 3 60 0.000000 NE
+Rv2935 ppsE PHENOLPTHIOCEROL SYNTHESIS TYPE-I POLYKETIDE SYNTHASE PPSE 52 63 2 14 0.000000 NE
+Rv2936 drrA PROBABLE DAUNORUBICIN-DIM-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER DRRA 13 17 1 2 0.000000 NE
+Rv2937 drrB PROBABLE DAUNORUBICIN-DIM-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER DRRB 12 21 4 143 0.000000 NE
+Rv2938 drrC PROBABLE DAUNORUBICIN-DIM-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER DRRC 21 24 1 2 0.000000 NE
+Rv2939 papA5 acyltransferase PapA5 20 26 3 74 0.000000 NE
+Rv2940c mas PROBABLE MULTIFUNCTIONAL MYCOCEROSIC ACID SYNTHASE MEMBRANE-ASSOCIATED MAS 59 72 2 67 0.000000 NE
+Rv2941 fadD28 acyl-CoA synthetase 28 42 4 73 0.000000 NE
+Rv2942 mmpL7 CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN MMPL7 28 39 3 157 0.000000 NE
+Rv2943 - IS1533 transposase 9 10 1 2 0.000000 NE
+Rv2943A - POSSIBLE TRANSPOSASE 4 6 2 65 0.000000 NE
+Rv2944 - IS1533 transposase 5 10 2 65 0.000000 NE
+Rv2945c lppX PROBABLE CONSERVED LIPOPROTEIN LPPX 9 10 1 2 0.000000 NE
+Rv2946c pks1 PROBABLE POLYKETIDE SYNTHASE PKS1 34 44 2 108 0.000000 NE
+Rv2947c pks15 PROBABLE POLYKETIDE SYNTHASE PKS15 15 18 1 2 0.000000 NE
+Rv2948c fadD22 acyl-CoA synthetase 33 44 3 72 0.000000 NE
+Rv2949c - hypothetical protein Rv2949c 8 20 8 219 0.020900 NE
+Rv2950c fadD29 acyl-CoA synthetase 25 36 3 23 0.000000 NE
+Rv2951c - POSSIBLE OXIDOREDUCTASE 18 23 2 47 0.000000 NE
+Rv2952 - POSSIBLE METHYLTRANSFERASE (METHYLASE) 9 14 2 168 0.000000 NE
+Rv2953 - hypothetical protein Rv2953 13 23 5 66 0.000000 NE
+Rv2954c - hypothetical protein Rv2954c 10 13 2 34 0.000000 NE
+Rv2955c - hypothetical protein Rv2955c 15 16 1 2 0.000000 NE
+Rv2956 - hypothetical protein Rv2956 5 17 3 89 0.000000 NE
+Rv2957 - POSSIBLE GLYCOSYL TRANSFERASE 12 15 2 31 0.000000 NE
+Rv2958c - POSSIBLE GLYCOSYL TRANSFERASE 23 24 1 2 0.000000 NE
+Rv2959c - POSSIBLE METHYLTRANSFERASE (METHYLASE) 10 28 5 104 0.000000 NE
+Rv2960c - hypothetical protein Rv2960c 7 7 0 0 0.000000 NE
+Rv2961 - PROBABLE TRANSPOSASE 5 7 1 2 0.000000 NE
+Rv2962c - POSSIBLE GLYCOSYL TRANSFERASE 14 18 2 43 0.000000 NE
+Rv2963 - PROBABLE INTEGRAL MEMBRANE PROTEIN 19 24 2 25 0.000000 NE
+Rv2964 purU PROBABLE FORMYLTETRAHYDROFOLATE DEFORMYLASE PURU (FORMYL-FH(4) HYDROLASE) 12 17 2 223 0.000000 NE
+Rv2965c coaD phosphopantetheine adenylyltransferase 0 3 3 322 0.928000 U
+Rv2966c - POSSIBLE METHYLTRANSFERASE (METHYLASE) 5 7 2 79 0.000000 NE
+Rv2967c pca pyruvate carboxylase 17 59 8 184 0.000000 NE
+Rv2968c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 0 10 10 520 0.999600 E
+Rv2969c - POSSIBLE CONSERVED MEMBRANE OR SECRETED PROTEIN 0 10 10 548 0.999100 E
+Rv2970A - hypothetical protein Rv2970A 2 3 1 2 -1.000000 S
+Rv2970c lipN PROBABLE LIPASE/ESTERASE LIPN 14 16 2 37 0.000000 NE
+Rv2971 - PROBABLE OXIDOREDUCTASE 0 13 13 588 1.000000 E
+Rv2972c - POSSIBLE CONSERVED MEMBRANE OR EXPORTED PROTEIN 9 11 2 111 0.000000 NE
+Rv2973c recG PROBABLE ATP-DEPENDENT DNA HELICASE RECG 13 24 8 752 0.957700 U
+Rv2974c - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 15 19 2 17 0.000000 NE
+Rv2975c - hypothetical protein Rv2975c 1 2 1 2 -1.000000 S
+Rv2976c ung uracil-DNA glycosylase 3 8 3 86 0.000000 NE
+Rv2977c thiL thiamine monophosphate kinase 0 7 7 841 0.992100 E
+Rv2978c - PROBABLE TRANSPOSASE 4 11 5 261 0.017300 NE
+Rv2979c - PROBABLE RESOLVASE 6 7 1 2 0.000000 NE
+Rv2980 - POSSIBLE CONSERVED SECRETED PROTEIN 0 6 6 443 0.976500 U
+Rv2981c ddl D-alanyl-alanine synthetase A 0 13 13 915 1.000000 E
+Rv2982c gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 10 11 1 2 0.000000 NE
+Rv2983 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 1 5 3 251 0.010000 NE
+Rv2984 ppk polyphosphate kinase 0 30 30 1916 1.000000 E
+Rv2985 mutT1 POSSIBLE HYDROLASE MUTT1 9 15 3 133 0.000000 NE
+Rv2986c hupB PROBABLE DNA-BINDING PROTEIN HU HOMOLOG HUPB (HISTONE-LIKE PROTEIN) (HLP) (21-KDA LAMININ-2-BINDING PROTEIN) 0 8 8 492 0.997000 E
+Rv2987c leuD isopropylmalate isomerase small subunit 0 8 8 406 0.998000 E
+Rv2988c leuC isopropylmalate isomerase large subunit 0 12 12 1071 0.999900 E
+Rv2989 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 2 6 2 67 0.000000 NE
+Rv2990c - hypothetical protein Rv2990c 12 17 2 89 0.000000 NE
+Rv2991 - hypothetical protein Rv2991 3 5 1 2 0.000000 NE
+Rv2992c gltX glutamyl-tRNA synthetase 0 19 19 1201 1.000000 E
+Rv2993c - POSSIBLE 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) 2 8 2 61 0.000000 NE
+Rv2994 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 13 19 3 151 0.000000 NE
+Rv2995c leuB 3-isopropylmalate dehydrogenase 0 9 9 777 0.999000 E
+Rv2996c serA1 PROBABLE D-3-PHOSPHOGLYCERATE DEHYDROGENASE SERA1 (PGDH) 0 10 10 1034 0.999800 E
+Rv2997 - POSSIBLE ALANINE RICH DEHYDROGENASE 9 16 3 47 0.000000 NE
+Rv2998 - hypothetical protein Rv2998 5 5 0 0 0.000000 NE
+Rv2998A - hypothetical protein Rv2998A 0 1 1 2 -1.000000 S
+Rv2999 lppY PROBABLE CONSERVED LIPOPROTEIN LPPY 4 11 4 250 0.003800 NE
+Rv3000 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 5 8 1 2 0.000000 NE
+Rv3001c ilvC ketol-acid reductoisomerase 0 12 12 784 0.999900 E
+Rv3002c ilvH acetolactate synthase 3 regulatory subunit 0 4 4 84 -1.000000 S
+Rv3003c ilvB1 acetolactate synthase 1 catalytic subunit 0 15 15 1461 1.000000 E
+Rv3004 cfp6 LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 6 (CFP-6) 1 3 1 2 0.000000 NE
+Rv3005c - hypothetical protein Rv3005c 15 20 1 2 0.000000 NE
+Rv3006 lppZ PROBABLE CONSERVED LIPOPROTEIN LPPZ 0 16 16 926 1.000000 E
+Rv3007c - POSSIBLE OXIDOREDUCTASE 6 8 1 2 0.000000 NE
+Rv3008 - hypothetical protein Rv3008 14 15 1 2 0.000000 NE
+Rv3009c gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 0 17 17 887 1.000000 E
+Rv3010c pfkA 6-phosphofructokinase 5 8 2 229 0.000100 NE
+Rv3011c gatA aspartyl/glutamyl-tRNA amidotransferase subunit A 0 20 20 1272 1.000000 E
+Rv3012c gatC aspartyl/glutamyl-tRNA amidotransferase subunit C 0 0 0 0 -1.000000 S
+Rv3013 - hypothetical protein Rv3013 4 4 0 0 0.000000 NE
+Rv3014c ligA NAD-dependent DNA ligase LigA 0 10 10 1604 1.000000 E
+Rv3015c - hypothetical protein Rv3015c 6 9 2 188 0.000000 NE
+Rv3016 lpqA PROBABLE LIPOPROTEIN LPQA 9 10 1 2 0.000000 NE
+Rv3017c esxQ ESAT-6 LIKE PROTEIN ESXQ (TB12.9) (ESAT-6 LIKE PROTEIN 8) 6 8 1 2 0.000000 NE
+Rv3018A PE27A PE FAMILY PROTEIN 0 0 0 0 -1.000000 S
+Rv3018c PPE46 PPE FAMILY PROTEIN 7 21 6 74 0.000000 NE
+Rv3019c esxR SECRETED ESAT-6 LIKE PROTEIN ESXR (TB10.3) (ESAT-6 LIKE PROTEIN 9) 5 8 3 79 0.000200 NE
+Rv3020c esxS ESAT-6 LIKE PROTEIN ESXS 3 7 2 14 0.000000 NE
+Rv3021c PPE47 PPE FAMILY PROTEIN 1 17 14 225 0.997900 E
+Rv3022A PE29 PE FAMILY PROTEIN 5 6 1 2 0.000000 NE
+Rv3022c PPE48 PPE FAMILY PROTEIN 0 0 0 0 -1.000000 S
+Rv3023c - PROBABLE TRANSPOSASE 0 2 2 44 -1.000000 S
+Rv3024c trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 1 13 7 450 0.937300 U
+Rv3025c iscS PROBABLE CYSTEINE DESULFURASE ISCS (NIFS PROTEIN HOMOLOG) (NITROGENASE METALLOCLUSTERS BIOSYNTHESIS PROTEIN NIFS) 0 15 15 836 1.000000 E
+Rv3026c - hypothetical protein Rv3026c 7 10 2 35 0.000000 NE
+Rv3027c - hypothetical protein Rv3027c 11 17 2 17 0.000000 NE
+Rv3028c fixB PROBABLE ELECTRON TRANSFER FLAVOPROTEIN (ALPHA-SUBUNIT) FIXB (ALPHA-ETF) (ELECTRON TRANSFER FLAVOPROTEIN LARGE SUBUNIT) (ETFLS) 0 9 9 738 0.998200 E
+Rv3029c fixA PROBABLE ELECTRON TRANSFER FLAVOPROTEIN (BETA-SUBUNIT) FIXA (BETA-ETF) (ELECTRON TRANSFER FLAVOPROTEIN SMALL SUBUNIT) (ETFSS) 0 6 6 480 0.974500 U
+Rv3030 - hypothetical protein Rv3030 1 10 9 585 0.997400 E
+Rv3031 - hypothetical protein Rv3031 0 20 20 1325 1.000000 E
+Rv3032 - POSSIBLE TRANSFERASE 0 9 9 1084 0.999600 E
+Rv3033 - hypothetical protein Rv3033 2 3 1 2 0.000000 NE
+Rv3034c - POSSIBLE TRANSFERASE 2 12 9 488 0.996900 E
+Rv3035 - hypothetical protein Rv3035 0 15 15 837 1.000000 E
+Rv3036c TB22.2 PROBABLE CONSERVED SECRETED PROTEIN TB22.2 11 14 1 2 0.000000 NE
+Rv3037c - hypothetical protein Rv3037c 11 14 2 13 0.000000 NE
+Rv3038c - hypothetical protein Rv3038c 0 10 10 511 0.999200 E
+Rv3039c echA17 enoyl-CoA hydratase 2 10 8 505 0.990900 E
+Rv3040c - hypothetical protein Rv3040c 8 11 2 75 0.000000 NE
+Rv3041c - PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER 4 8 2 163 0.000000 NE
+Rv3042c serB2 phosphoserine phosphatase 0 11 11 945 0.999800 E
+Rv3043c ctaD PROBABLE CYTOCHROME C OXIDASE POLYPEPTIDE I CTAD (CYTOCHROME AA3 SUBUNIT 1) 0 22 22 1409 1.000000 E
+Rv3044 fecB PROBABLE FEIII-DICITRATE-BINDING PERIPLASMIC LIPOPROTEIN FECB 0 15 15 941 1.000000 E
+Rv3045 adhC PROBABLE NADP-DEPENDENT ALCOHOL DEHYDROGENASE ADHC 13 18 2 40 0.000000 NE
+Rv3046c - hypothetical protein Rv3046c 1 2 1 2 -1.000000 S
+Rv3047c - hypothetical protein Rv3047c 4 5 1 2 0.000000 NE
+Rv3048c nrdF ribonucleotide-diphosphate reductase subunit beta 0 21 21 748 1.000000 E
+Rv3049c - PROBABLE MONOOXYGENASE 25 29 2 56 0.000000 NE
+Rv3050c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ASNC-FAMILY) 3 7 3 83 0.000000 NE
+Rv3051c nrdE ribonucleotide-diphosphate reductase subunit alpha 0 50 50 1779 1.000000 E
+Rv3052c nrdI ribonucleotide reductase stimulatory protein 0 13 13 317 1.000000 E
+Rv3053c nrdH PROBABLE GLUTAREDOXIN ELECTRON TRANSPORT COMPONENT OF NRDEF (GLUTAREDOXIN-LIKE PROTEIN) NRDH 0 8 8 132 -1.000000 S
+Rv3054c - hypothetical protein Rv3054c 5 5 0 0 0.000000 NE
+Rv3055 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 5 7 2 8 0.000000 NE
+Rv3056 dinP DNA polymerase IV 15 18 1 2 0.000000 NE
+Rv3057c - short chain dehydrogenase 13 16 2 31 0.000000 NE
+Rv3058c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 6 9 2 22 0.000000 NE
+Rv3059 cyp136 PROBABLE CYTOCHROME P450 136 CYP136 20 22 1 2 0.000000 NE
+Rv3060c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) 14 24 5 288 0.098300 U
+Rv3061c fadE22 PROBABLE ACYL-CoA DEHYDROGENASE FADE22 15 21 3 31 0.000000 NE
+Rv3062 ligB ATP-dependent DNA ligase 12 18 2 34 0.000000 NE
+Rv3063 cstA PROBABLE CARBON STARVATION PROTEIN A HOMOLOG CSTA 25 29 2 153 0.000000 NE
+Rv3064c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 9 9 0 0 0.000000 NE
+Rv3065 mmr MULTIDRUGS-TRANSPORT INTEGRAL MEMBRANE PROTEIN MMR 6 6 0 0 -1.000000 S
+Rv3066 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY DEOR-FAMILY) 3 10 4 96 0.000000 NE
+Rv3067 - hypothetical protein Rv3067 5 8 2 35 0.000000 NE
+Rv3068c pgmA phosphoglucomutase 24 29 2 17 0.000000 NE
+Rv3069 ccrB camphor resistance protein CrcB 3 4 1 2 0.000000 NE
+Rv3070 ccrB camphor resistance protein CrcB 6 8 1 2 0.000000 NE
+Rv3071 - hypothetical protein Rv3071 10 13 1 2 0.000000 NE
+Rv3072c - hypothetical protein Rv3072c 8 9 1 2 0.000000 NE
+Rv3073c - hypothetical protein Rv3073c 4 4 0 0 0.000000 NE
+Rv3074 - hypothetical protein Rv3074 9 14 2 43 0.000000 NE
+Rv3075c - hypothetical protein Rv3075c 5 12 3 303 0.094800 U
+Rv3076 - hypothetical protein Rv3076 3 5 1 2 0.000000 NE
+Rv3077 - POSSIBLE HYDROLASE 26 34 3 91 0.000000 NE
+Rv3078 hab PROBABLE HYDROXYLAMINOBENZENE MUTASE HAB 4 5 1 2 0.000000 NE
+Rv3079c - hypothetical protein Rv3079c 10 15 3 151 0.000000 NE
+Rv3080c pknK PROBABLE SERINE/THREONINE-PROTEIN KINASE TRANSCRIPTIONAL REGULATORY PROTEIN PKNK (PROTEIN KINASE K) (STPK K) 18 26 2 36 0.000000 NE
+Rv3081 - hypothetical protein Rv3081 8 16 2 28 0.000000 NE
+Rv3082c virS VIRULENCE-REGULATING TRANSCRIPTIONAL REGULATOR VIRS (ARAC/XYLS FAMILY) 8 16 3 66 0.000000 NE
+Rv3083 - PROBABLE MONOOXYGENASE (HYDROXYLASE) 22 25 1 2 0.000000 NE
+Rv3084 lipR PROBABLE ACETYL-HYDROLASE/ESTERASE LIPR 8 11 1 2 0.000000 NE
+Rv3085 - PROBABLE SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE 3 4 1 2 0.000000 NE
+Rv3086 adhD PROBABLE ZINC-TYPE ALCOHOL DEHYDROGENASE ADHD (ALDEHYDE REDUCTASE) 9 9 0 0 0.000000 NE
+Rv3087 - hypothetical protein Rv3087 12 12 0 0 0.000000 NE
+Rv3088 - hypothetical protein Rv3088 10 13 1 2 0.000000 NE
+Rv3089 fadD13 PROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13 (FATTY-ACYL-CoA SYNTHETASE) 14 20 2 21 0.000000 NE
+Rv3090 - HYPOTHETICAL ALANINE AND VALINE RICH PROTEIN 6 7 1 2 0.000000 NE
+Rv3091 - hypothetical protein Rv3091 14 15 1 2 0.000000 NE
+Rv3092c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 8 9 1 2 0.000000 NE
+Rv3093c - HYPOTHETICAL OXIDOREDUCTASE 8 13 3 83 0.000000 NE
+Rv3094c - hypothetical protein Rv3094c 7 10 2 50 0.000000 NE
+Rv3095 - HYPOTHETICAL TRANSCRIPTIONAL REGULATORY PROTEIN 6 7 1 2 0.000000 NE
+Rv3096 - hypothetical protein Rv3096 13 15 1 2 0.000000 NE
+Rv3097c PE_PGRS63 PE-PGRS FAMILY PROTEIN, PROBABLY TRIACYLGLYCEROL LIPASE (ESTERASE/LIPASE) (TRIGLYCERIDE LIPASE) (TRIBUTYRASE) 20 25 1 2 0.000000 NE
+Rv3098c - hypothetical protein Rv3098c 7 8 1 2 0.000000 NE
+Rv3099c - hypothetical protein Rv3099c 3 5 2 22 0.000000 NE
+Rv3100c smpB SsrA-binding protein 0 3 3 278 0.966400 U
+Rv3101c ftsX PUTATIVE CELL DIVISION PROTEIN FTSX (SEPTATION COMPONENT-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER) 0 14 14 681 0.999900 E
+Rv3102c ftsE PUTATIVE CELL DIVISION ATP-BINDING PROTEIN FTSE (SEPTATION COMPONENT-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER) 0 6 6 428 0.979800 U
+Rv3103c - HYPOTHETICAL PROLINE-RICH PROTEIN 6 7 1 2 0.000000 NE
+Rv3104c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 5 9 2 55 0.000000 NE
+Rv3105c prfB peptide chain release factor 2 0 15 15 811 0.999900 E
+Rv3106 fprA NADPH:ADRENODOXIN OXIDOREDUCTASE FPRA (NADPH-FERREDOXIN REDUCTASE) 11 16 3 41 0.000000 NE
+Rv3107c agpS POSSIBLE ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE AGPS (ALKYL-DHAP SYNTHASE) (ALKYLGLYCERONE-PHOSPHATE SYNTHASE) 16 21 2 28 0.000000 NE
+Rv3108 - hypothetical protein Rv3108 3 6 2 43 0.000000 NE
+Rv3109 moaA1 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN A MOAA1 5 34 13 370 0.999700 E
+Rv3110 moaB1 PROBABLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB1 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) 3 9 6 102 0.000000 NE
+Rv3111 moaC molybdenum cofactor biosynthesis protein C 5 13 7 238 0.084100 U
+Rv3112 moaD1 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D MOAD1 (MOLYBDOPTERIN CONVERTING FACTOR SMALL SUBUNIT) (MOLYBDOPTERIN 0 6 6 219 0.998100 E
+Rv3113 - POSSIBLE PHOSPHATASE 1 7 4 49 0.000000 NE
+Rv3114 - hypothetical protein Rv3114 4 8 2 93 0.000000 NE
+Rv3115 - PROBABLE TRANSPOSASE 0 2 2 44 -1.000000 S
+Rv3116 moeB2 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOEB2 (MPT-SYNTHASE SULFURYLASE) (MOLYBDOPTERIN SYNTHASE SULPHURYLASE) 18 25 2 83 0.000000 NE
+Rv3117 cysA3 PROBABLE THIOSULFATE SULFURTRANSFERASE CYSA3 (RHODANESE-LIKE PROTEIN) (THIOSULFATE CYANIDE TRANSSULFURASE) (THIOSULFATE THIOTRANSFERASE) 1 1 0 0 -1.000000 S
+Rv3118 sseC1 CONSERVED HYPOTHETICAL PROTEIN SSEC1 1 1 0 0 -1.000000 S
+Rv3119 moaE1 PROBABLE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E MOAE1 (MOLYBDOPTERIN CONVERTING FACTOR LARGE SUBUNIT) (MOLYBDOPTERIN 10 10 0 0 0.000000 NE
+Rv3120 - hypothetical protein Rv3120 6 9 2 45 0.000000 NE
+Rv3121 cyp141 PROBABLE CYTOCHROME P450 141 CYP141 12 23 6 149 0.000000 NE
+Rv3122 - hypothetical protein Rv3122 4 5 1 2 0.000000 NE
+Rv3123 - hypothetical protein Rv3123 3 4 1 2 0.000000 NE
+Rv3124 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN 11 27 16 363 1.000000 E
+Rv3125c PPE49 PPE FAMILY PROTEIN 15 21 3 200 0.000000 NE
+Rv3126c - hypothetical protein Rv3126c 0 2 2 72 -1.000000 S
+Rv3127 - hypothetical protein Rv3127 5 16 5 181 0.000000 NE
+Rv3129 - hypothetical protein Rv3129 2 4 2 22 0.000000 NE
+Rv3130c - hypothetical protein Rv3130c 15 24 3 101 0.000000 NE
+Rv3131 - hypothetical protein Rv3131 6 14 3 94 0.000000 NE
+Rv3132c devS TWO COMPONENT SENSOR HISTIDINE KINASE DEVS 13 29 4 103 0.000000 NE
+Rv3133c devR TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR (PROBABLY LUXR/UHPA-FAMILY) 7 11 2 12 0.000000 NE
+Rv3134c - hypothetical protein Rv3134c 4 5 1 2 0.000000 NE
+Rv3135 PPE50 PPE FAMILY PROTEIN 7 7 0 0 0.000000 NE
+Rv3136 PPE51 PPE FAMILY PROTEIN 8 17 3 221 0.000000 NE
+Rv3137 - PROBABLE MONOPHOSPHATASE 0 7 7 389 0.994000 E
+Rv3138 pflA PROBABLE PYRUVATE FORMATE LYASE ACTIVATING PROTEIN PFLA (FORMATE ACETYLTRANSFERASE ACTIVATING ENZYME) ( 17 21 1 2 0.000000 NE
+Rv3139 fadE24 PROBABLE ACYL-CoA DEHYDROGENASE FADE24 9 20 4 181 0.000000 NE
+Rv3140 fadE23 PROBABLE ACYL-CoA DEHYDROGENASE FADE23 7 18 7 260 0.113900 U
+Rv3141 fadB4 PROBABLE NADPH QUINONE OXIDOREDUCTASE FADB4 (NADPH:QUINONE REDUCTASE) (ZETA-CRYSTALLIN) 9 13 2 41 0.000000 NE
+Rv3142c - hypothetical protein Rv3142c 8 10 1 2 0.000000 NE
+Rv3143 - PROBABLE RESPONSE REGULATOR 2 4 1 2 -1.000000 S
+Rv3144c PPE52 PPE-FAMILY PROTEIN 12 15 1 2 0.000000 NE
+Rv3145 nuoA NADH dehydrogenase subunit A 5 10 3 60 0.000000 NE
+Rv3146 nuoB NADH dehydrogenase subunit B 5 9 2 20 0.000000 NE
+Rv3147 nuoC NADH dehydrogenase subunit C 5 12 3 131 0.000000 NE
+Rv3148 nuoD NADH dehydrogenase subunit D 3 22 9 410 0.983600 U
+Rv3149 nuoE NADH dehydrogenase subunit E 5 9 2 162 0.000000 NE
+Rv3150 nuoF PROBABLE NADH DEHYDROGENASE I (CHAIN F) NUOF (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN F) 7 25 7 305 0.716700 U
+Rv3151 nuoG NADH dehydrogenase subunit G 12 29 6 489 0.499100 U
+Rv3152 nuoH NADH dehydrogenase subunit H 8 25 6 177 0.000000 NE
+Rv3153 nuoI NADH dehydrogenase subunit I 10 22 6 118 0.000000 NE
+Rv3154 nuoJ NADH dehydrogenase subunit J 8 9 1 2 0.000000 NE
+Rv3155 nuoK NADH dehydrogenase subunit K 2 5 2 131 0.000100 NE
+Rv3156 nuoL NADH dehydrogenase subunit L 14 29 5 405 0.244400 U
+Rv3157 nuoM NADH dehydrogenase subunit M 7 31 15 831 1.000000 E
+Rv3158 nuoN NADH dehydrogenase subunit N 22 30 2 37 0.000000 NE
+Rv3159c PPE53 PPE FAMILY PROTEIN 12 23 4 293 0.038400 U
+Rv3160c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 3 7 2 122 0.000000 NE
+Rv3161c - POSSIBLE DIOXYGENASE 10 19 4 132 0.000000 NE
+Rv3162c - POSSIBLE INTEGRAL MEMBRANE PROTEIN 6 6 0 0 0.000000 NE
+Rv3163c - POSSIBLE CONSERVED SECRETED PROTEIN 8 14 4 309 0.169700 U
+Rv3164c moxR3 PROBABLE METHANOL DEHYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN MOXR3 3 10 4 206 0.000100 NE
+Rv3165c - hypothetical protein Rv3165c 1 2 1 2 -1.000000 S
+Rv3166c - hypothetical protein Rv3166c 5 10 3 147 0.000000 NE
+Rv3167c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 6 9 1 2 0.000000 NE
+Rv3168 - hypothetical protein Rv3168 5 18 7 140 0.000000 NE
+Rv3169 - hypothetical protein Rv3169 9 15 2 22 0.000000 NE
+Rv3170 aofH PROBABLE FLAVIN-CONTAINING MONOAMINE OXIDASE AOFH (AMINE OXIDASE) (MAO) 8 16 7 288 0.633500 U
+Rv3171c hpx POSSIBLE NON-HEME HALOPEROXIDASE HPX 7 12 2 65 0.000000 NE
+Rv3172c - hypothetical protein Rv3172c 10 15 1 2 0.000000 NE
+Rv3173c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR/ACRR-FAMILY) 2 7 4 58 0.000000 NE
+Rv3174 - short chain dehydrogenase 5 10 2 29 0.000000 NE
+Rv3175 - amidase 13 17 2 100 0.000000 NE
+Rv3176c mesT PROBABLE EPOXIDE HYDROLASE MEST (EPOXIDE HYDRATASE) (ARENE-OXIDE HYDRATASE) 9 13 2 31 0.000000 NE
+Rv3177 - POSSIBLE PEROXIDASE (NON-HAEM PEROXIDASE) 3 7 2 38 0.000000 NE
+Rv3178 - hypothetical protein Rv3178 4 7 2 57 0.000000 NE
+Rv3179 - hypothetical protein Rv3179 13 13 0 0 0.000000 NE
+Rv3180c - HYPOTHETICAL ALANINE RICH PROTEIN 4 5 1 2 0.000000 NE
+Rv3181c - hypothetical protein Rv3181c 3 6 3 29 0.000000 NE
+Rv3182 - hypothetical protein Rv3182 1 1 0 0 -1.000000 S
+Rv3183 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 1 3 1 2 0.000000 NE
+Rv3184 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3185 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3186 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3187 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3188 - hypothetical protein Rv3188 5 6 1 2 0.000000 NE
+Rv3189 - hypothetical protein Rv3189 8 8 0 0 0.000000 NE
+Rv3190c - hypothetical protein Rv3190c 15 20 3 76 0.000000 NE
+Rv3191c - PROBABLE TRANSPOSASE 12 15 2 10 0.000000 NE
+Rv3192 - CONSERVED HYPOTHETICAL ALANINE AND PROLINE-RICH PROTEIN 3 4 1 2 -1.000000 S
+Rv3193c - hypothetical protein Rv3193c 7 79 21 704 1.000000 E
+Rv3194c - POSSIBLE CONSERVED SECRETED PROTEIN 8 12 1 2 0.000000 NE
+Rv3195 - hypothetical protein Rv3195 13 15 1 2 0.000000 NE
+Rv3196 - hypothetical protein Rv3196 8 9 1 2 0.000000 NE
+Rv3196A - hypothetical protein Rv3196A 1 1 0 0 -1.000000 S
+Rv3197 - PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER 14 18 1 2 0.000000 NE
+Rv3197A whiB7 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB7 3 3 0 0 -1.000000 S
+Rv3198A - POSSIBLE GLUTAREDOXIN PROTEIN 5 6 1 2 0.000000 NE
+Rv3198c uvrD2 PROBABLE ATP-DEPENDENT DNA HELICASE II UVRD2 2 30 28 1380 1.000000 E
+Rv3199c nudC NADH pyrophosphatase 7 7 0 0 0.000000 NE
+Rv3200c - POSSIBLE TRANSMEMBRANE CATION TRANSPORTER 7 13 2 58 0.000000 NE
+Rv3201c - PROBABLE ATP-DEPENDENT DNA HELICASE 24 38 5 420 0.112600 U
+Rv3202c - POSSIBLE ATP-DEPENDENT DNA HELICASE 18 27 6 537 0.432600 U
+Rv3203 lipV POSSIBLE LIPASE LIPV 9 12 1 2 0.000000 NE
+Rv3204 - POSSIBLE DNA-METHYLTRANSFERASE (MODIFICATION METHYLASE) 3 4 1 2 0.000000 NE
+Rv3205c - hypothetical protein Rv3205c 2 10 3 93 0.000000 NE
+Rv3206c moeB1 molybdopterin biosynthesis-like protein MoeZ 0 22 22 1058 1.000000 E
+Rv3207c - hypothetical protein Rv3207c 8 14 3 112 0.000000 NE
+Rv3208 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 0 9 9 416 0.998300 E
+Rv3208A TB9.4 hypothetical protein Rv3208A 3 4 1 2 0.000000 NE
+Rv3209 - CONSERVED HYPOTHETICAL THREONIN AND PROLINE RICH PROTEIN 7 9 1 2 0.000000 NE
+Rv3210c - hypothetical protein Rv3210c 0 10 10 511 0.999600 E
+Rv3211 rhlE PROBABLE ATP-DEPENDENT RNA HELICASE RHLE 9 21 9 422 0.981400 U
+Rv3212 - CONSERVED HYPOTHETICAL ALANINE VALINE RICH PROTEIN 0 18 18 878 1.000000 E
+Rv3213c - POSSIBLE SOJ/PARA-RELATED PROTEIN 6 8 2 78 0.000000 NE
+Rv3214 gpm2 POSSIBLE PHOSPHOGLYCERATE MUTASE GPM2 (PHOSPHOGLYCEROMUTASE) (PGAM) (BPG-DEPENDENT PGAM) 3 10 3 63 0.000000 NE
+Rv3215 entC isochorismate synthase 0 15 15 877 0.999900 E
+Rv3216 - POSSIBLE ACETYLTRANSFERASE 4 6 1 2 0.000000 NE
+Rv3217c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 3 3 0 0 0.000000 NE
+Rv3218 - hypothetical protein Rv3218 14 17 1 2 0.000000 NE
+Rv3219 whiB1 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB1 0 3 3 99 -1.000000 S
+Rv3220c - PROBABLE TWO COMPONENT SENSOR KINASE 18 19 1 2 0.000000 NE
+Rv3221A - POSSIBLE ANTI-SIGMA FACTOR 0 2 2 90 -1.000000 S
+Rv3221c TB7.3 hypothetical protein Rv3221c 0 2 2 36 -1.000000 S
+Rv3222c - hypothetical protein Rv3222c 0 7 7 424 0.989800 U
+Rv3223c sigH RNA polymerase sigma factor RpoE 9 14 2 24 0.000000 NE
+Rv3224 - short chain dehydrogenase 12 15 2 161 0.000000 NE
+Rv3224A - hypothetical protein Rv3224A 2 3 1 2 -1.000000 S
+Rv3224B - hypothetical protein Rv3224B 3 3 0 0 -1.000000 S
+Rv3225c - POSSIBLE TRANSFERASE 21 23 1 2 0.000000 NE
+Rv3226c - hypothetical protein Rv3226c 6 6 0 0 0.000000 NE
+Rv3227 aroA 3-phosphoshikimate 1-carboxyvinyltransferase 0 6 6 1048 0.989200 U
+Rv3228 - hypothetical protein Rv3228 2 7 3 216 0.000100 NE
+Rv3229c - POSSIBLE LINOLEOYL-CoA DESATURASE (DELTA(6)-DESATURASE) 2 21 10 588 0.997100 E
+Rv3230c - HYPOTHETICAL OXIDOREDUCTASE 0 14 14 846 1.000000 E
+Rv3231c - hypothetical protein Rv3231c 5 5 0 0 0.000000 NE
+Rv3232c pvdS POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN PVDS (PROBABLE RNA POLYMERASE SIGMA FACTOR) 19 20 1 2 0.000000 NE
+Rv3233c - hypothetical protein Rv3233c 12 12 0 0 0.000000 NE
+Rv3234c - hypothetical protein Rv3234c 12 16 2 10 0.000000 NE
+Rv3235 - HYPOTHETICAL ALANINE ARGININE PROLINE RICH PROTEIN 4 6 1 2 0.000000 NE
+Rv3236c - PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN 7 11 2 127 0.000000 NE
+Rv3237c - hypothetical protein Rv3237c 5 8 2 20 0.000000 NE
+Rv3238c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 15 18 2 35 0.000000 NE
+Rv3239c - PROBABLE CONSERVED TRANSMEMBRANE TRANSPORT PROTEIN 46 52 3 165 0.000000 NE
+Rv3240c secA1 preprotein translocase subunit SecA 2 44 42 2090 1.000000 E
+Rv3241c - hypothetical protein Rv3241c 10 10 0 0 0.000000 NE
+Rv3242c - hypothetical protein Rv3242c 2 4 1 2 0.000000 NE
+Rv3243c - hypothetical protein Rv3243c 3 4 1 2 0.000000 NE
+Rv3244c lpqB PROBABLE CONSERVED LIPOPROTEIN LPQB 0 18 18 1503 1.000000 E
+Rv3245c mtrB TWO COMPONENT SENSORY TRANSDUCTION HISTIDINE KINASE MTRB 0 19 19 1337 1.000000 E
+Rv3246c mtrA TWO COMPONENT SENSORY TRANSDUCTION TRANSCRIPTIONAL REGULATORY PROTEIN MTRA 0 10 10 458 0.998900 E
+Rv3247c tmk thymidylate kinase 0 9 9 495 0.998600 E
+Rv3248c sahH S-adenosyl-L-homocysteine hydrolase 0 17 17 1258 1.000000 E
+Rv3249c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 3 12 7 363 0.969500 U
+Rv3250c rubB PROBABLE RUBREDOXIN RUBB 3 3 0 0 -1.000000 S
+Rv3251c rubA PROBABLE RUBREDOXIN RUBA 4 4 0 0 0.000000 NE
+Rv3252c alkB PROBABLE TRANSMEMBRANE ALKANE 1-MONOOXYGENASE ALKB (ALKANE 1-HYDROXYLASE) (LAURIC ACID OMEGA-HYDROXYLASE) (OMEGA-HYDROXYLASE) (FATTY ACID OMEGA-HYDROXYLASE) (ALKANE HYDROXYLASE-RUBREDOXIN) 24 28 1 2 0.000000 NE
+Rv3253c - POSSIBLE CATIONIC AMINO ACID TRANSPORT INTEGRAL MEMBRANE PROTEIN 15 22 3 46 0.000000 NE
+Rv3254 - hypothetical protein Rv3254 13 17 2 36 0.000000 NE
+Rv3255c manA PROBABLE MANNOSE-6-PHOSPHATE ISOMERASE MANA (PHOSPHOMANNOSE ISOMERASE) (PHOSPHOMANNOISOMERASE) (PMI) (PHOSPHOHEXOISOMERASE) (PHOSPHOHEXOMUTASE) 0 17 17 1022 1.000000 E
+Rv3256c - hypothetical protein Rv3256c 5 8 2 92 0.000000 NE
+Rv3257c manB phosphomannomutase/phosphoglucomutase 0 20 20 1153 1.000000 E
+Rv3258c - hypothetical protein Rv3258c 0 5 5 427 0.950100 U
+Rv3259 - hypothetical protein Rv3259 2 2 0 0 -1.000000 S
+Rv3260c whiB2 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB2 0 2 2 109 -1.000000 S
+Rv3261 fbiA PROBABLE F420 BIOSYNTHESIS PROTEIN FBIA 3 13 7 327 0.952000 U
+Rv3262 fbiB F420-0--gamma-glutamyl ligase 5 12 3 236 0.000100 NE
+Rv3263 - PROBABLE DNA METHYLASE (MODIFICATION METHYLASE) (METHYLTRANSFERASE) 22 25 1 2 0.000000 NE
+Rv3264c manB D-ALPHA-D-MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE MANB (D-ALPHA-D-HEPTOSE-1-PHOSPHATE GUANYLYLTRANSFERASE) 0 15 15 931 1.000000 E
+Rv3265c wbbL1 PROBABLE dTDP-RHA:A-D-GlcNAc-DIPHOSPHORYL POLYPRENOL, A-3-L-RHAMNOSYL TRANSFERASE WBBL1 (ALPHA-L-RHAMNOSE-(1->3)-ALPHA-D-GlcNAc(1->P)-P-DECAPRENY L) 0 13 13 621 1.000000 E
+Rv3266c rmlD dTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE RMLD (dTDP-RHAMNOSE MODIFICATION PROTEIN) (dTDP-RHAMNOSE BIOSYNTHESIS PROTEIN) (dTDP-RHAMNOSE SYNTHASE) 0 15 15 733 1.000000 E
+Rv3267 - CONSERVED HYPOTHETICAL PROTEIN (CPSA-RELATED PROTEIN) 2 19 6 321 0.622700 U
+Rv3268 - hypothetical protein Rv3268 11 13 1 2 0.000000 NE
+Rv3269 - hypothetical protein Rv3269 0 4 4 120 -1.000000 S
+Rv3270 ctpC PROBABLE METAL CATION-TRANSPORTING P-TYPE ATPASE C CTPC 5 15 5 602 0.449600 U
+Rv3271c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 3 6 2 109 0.000000 NE
+Rv3272 - hypothetical protein Rv3272 14 18 2 65 0.000000 NE
+Rv3273 - PROBABLE TRANSMEMBRANE CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE) 17 27 2 63 0.000000 NE
+Rv3274c fadE25 PROBABLE ACYL-CoA DEHYDROGENASE FADE25 9 16 2 80 0.000000 NE
+Rv3275c purE phosphoribosylaminoimidazole carboxylase catalytic subunit 0 4 4 217 0.981700 U
+Rv3276c purK phosphoribosylaminoimidazole carboxylase ATPase subunit 0 8 8 981 0.997100 E
+Rv3277 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 2 13 10 487 0.998600 E
+Rv3278c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv3279c birA biotin--protein ligase 0 5 5 480 0.938200 U
+Rv3280 accD5 PROBABLE PROPIONYL-CoA CARBOXYLASE BETA CHAIN 5 ACCD5 (PCCASE) (PROPANOYL-COA:CARBON DIOXIDE LIGASE) 0 30 30 1407 1.000000 E
+Rv3281 - hypothetical protein Rv3281 0 3 3 130 -1.000000 S
+Rv3282 maf Maf-like protein 4 11 5 63 0.000000 NE
+Rv3283 sseA PROBABLE THIOSULFATE SULFURTRANSFERASE SSEA (RHODANESE) (THIOSULFATE CYANIDE TRANSSULFURASE) (THIOSULFATE THIOTRANSFERASE) 15 16 1 2 0.000000 NE
+Rv3284 - hypothetical protein Rv3284 5 5 0 0 0.000000 NE
+Rv3285 accA3 PROBABLE BIFUNCTIONAL PROTEIN ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE (ALPHA CHAIN) ACCA3: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) 0 23 23 1551 1.000000 E
+Rv3286c sigF RNA polymerase sigma factor SigF 8 9 1 2 0.000000 NE
+Rv3287c rsbW ANTI-SIGMA FACTOR RSBW (SIGMA NEGATIVE EFFECTOR) 2 2 0 0 -1.000000 S
+Rv3288c usfY PUTATIVE PROTEIN USFY 9 10 1 2 0.000000 NE
+Rv3289c - POSSIBLE TRANSMEMBRANE PROTEIN 5 6 1 2 0.000000 NE
+Rv3290c lat L-lysine aminotransferase 19 22 2 13 0.000000 NE
+Rv3291c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ASNC-FAMILY) 3 7 2 58 0.000000 NE
+Rv3292 - hypothetical protein Rv3292 13 18 2 87 0.000000 NE
+Rv3293 pcd PROBABLE PIPERIDEINE-6-CARBOXILIC ACID DEHYDROGENASE PCD (PIPERIDEINE-6-CARBOXYLATE DEHYDROGENASE) 9 13 3 99 0.000000 NE
+Rv3294c - hypothetical protein Rv3294c 16 20 1 2 0.000000 NE
+Rv3295 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 10 11 1 2 0.000000 NE
+Rv3296 lhr PROBABLE ATP-DEPENDENT HELICASE LHR (LARGE HELICASE-RELATED PROTEIN) 40 53 2 76 0.000000 NE
+Rv3297 nei PROBABLE ENDONUCLEASE VIII NEI 6 9 2 114 0.000000 NE
+Rv3298c lpqC POSSIBLE ESTERASE LIPOPROTEIN LPQC 9 10 1 2 0.000000 NE
+Rv3299c atsB PROBABLE ARYLSULFATASE ATSB (ARYL-SULFATE SULPHOHYDROLASE) (SULFATASE) 22 42 5 120 0.000000 NE
+Rv3300c - hypothetical protein Rv3300c 5 9 1 2 0.000000 NE
+Rv3301c phoY1 PROBABLE PHOSPHATE-TRANSPORT SYSTEM TRANSCRIPTIONAL REGULATORY PROTEIN PHOU HOMOLOG 1 PHOY1 4 6 1 2 0.000000 NE
+Rv3302c glpD2 PROBABLE GLYCEROL-3-PHOSPHATE DEHYDROGENASE GLPD2 0 28 28 1503 1.000000 E
+Rv3303c lpdA flavoprotein disulfide reductase 4 18 7 485 0.881200 U
+Rv3304 - hypothetical protein Rv3304 3 8 4 95 0.000000 NE
+Rv3305c amiA1 POSSIBLE N-ACYL-L-AMINO ACID AMIDOHYDROLASE AMIA1 (N-ACYL-L-AMINO ACID AMINOHYDROLASE) 9 19 6 451 0.770200 U
+Rv3306c amiB1 PROBABLE AMIDOHYDROLASE AMIB1 (AMINOHYDROLASE) 9 15 3 139 0.000000 NE
+Rv3307 deoD purine nucleoside phosphorylase 7 10 2 26 0.000000 NE
+Rv3308 pmmB PROBABLE PHOSPHOMANNOMUTASE PMMB (PHOSPHOMANNOSE MUTASE) 11 18 3 118 0.000000 NE
+Rv3309c upp uracil phosphoribosyltransferase 5 8 2 104 0.000000 NE
+Rv3310 - POSSIBLE ACID PHOSPHATASE (ACID PHOSPHOMONOESTERASE) (PHOSPHOMONOESTERASE) (GLYCEROPHOSPHATASE) 12 13 1 2 0.000000 NE
+Rv3311 - hypothetical protein Rv3311 5 14 3 359 0.096300 U
+Rv3312A - SECRETED PROTEIN ANTIGEN 4 4 0 0 -1.000000 S
+Rv3312c - hypothetical protein Rv3312c 13 17 1 2 0.000000 NE
+Rv3313c add adenosine deaminase 6 10 4 106 0.000000 NE
+Rv3314c deoA thymidine phosphorylase 8 10 1 2 0.000000 NE
+Rv3315c cdd cytidine deaminase 5 5 0 0 0.000000 NE
+Rv3316 sdhC PROBABLE SUCCINATE DEHYDROGENASE (CYTOCHROME B-556 SUBUNIT) SDHC (SUCCINIC DEHYDROGENASE) (FUMARATE REDUCTASE) (FUMARATE DEHYDROGENASE) (FUMARIC HYDROGENASE) 4 5 1 2 -1.000000 S
+Rv3317 sdhD PROBABLE SUCCINATE DEHYDROGENASE (HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT) SDHD (SUCCINIC DEHYDROGENASE) (FUMARATE REDUCTASE) (FUMARATE DEHYDROGENASE) (FUMARIC HYDROGENASE) 4 4 0 0 0.000000 NE
+Rv3318 sdhA succinate dehydrogenase flavoprotein subunit 14 28 4 67 0.000000 NE
+Rv3319 sdhB succinate dehydrogenase iron-sulfur subunit 4 8 2 11 0.000000 NE
+Rv3320c - hypothetical protein Rv3320c 3 5 2 21 0.000000 NE
+Rv3321c - hypothetical protein Rv3321c 2 3 1 2 0.000000 NE
+Rv3322c - POSSIBLE METHYLTRANSFERASE 4 7 1 2 0.000000 NE
+Rv3323c moaX PROBABLE MOAD-MOAE FUSION PROTEIN MOAX 8 13 2 13 0.000000 NE
+Rv3324c moaC molybdenum cofactor biosynthesis protein C 7 10 1 2 0.000000 NE
+Rv3325 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3326 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3327 - PROBABLE TRANSPOSASE FUSION PROTEIN 10 10 0 0 0.000000 NE
+Rv3328c sigJ RNA polymerase sigma factor SigJ 9 12 2 33 0.000000 NE
+Rv3329 - hypothetical protein Rv3329 17 20 2 47 0.000000 NE
+Rv3330 dacB1 PROBABLE PENICILLIN-BINDING PROTEIN DACB1 (D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (DD-PEPTIDASE) (DD-CARBOXYPEPTIDASE) (PBP) (DD-TRANSPEPTIDASE) (SERINE-TYPE D-ALA-D-ALA CARBOXYPEPTIDASE) (D-AMINO ACID HYDROLASE) 14 16 1 2 0.000000 NE
+Rv3331 sugI PROBABLE SUGAR-TRANSPORT INTEGRAL MEMBRANE PROTEIN SUGI 15 22 2 156 0.000000 NE
+Rv3332 nagA PROBABLE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE NAGA (GLCNAC 6-P DEACETYLASE) 3 5 1 2 0.000000 NE
+Rv3333c - HYPOTHETICAL PROLINE RICH PROTEIN 8 10 2 197 0.000000 NE
+Rv3334 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MERR-FAMILY) 7 8 1 2 0.000000 NE
+Rv3335c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 6 11 3 104 0.000000 NE
+Rv3336c trpS tryptophanyl-tRNA synthetase 0 12 12 750 1.000000 E
+Rv3337 - hypothetical protein Rv3337 6 9 2 11 0.000000 NE
+Rv3338 - hypothetical protein Rv3338 3 4 1 2 0.000000 NE
+Rv3339c icd1 isocitrate dehydrogenase 20 23 2 72 0.000000 NE
+Rv3340 metC O-acetylhomoserine aminocarboxypropyltransferase 3 15 6 452 0.756100 U
+Rv3341 metX homoserine O-acetyltransferase 0 14 14 985 1.000000 E
+Rv3342 - POSSIBLE METHYLTRANSFERASE (METHYLASE) 2 8 6 511 0.951000 U
+Rv3343c PPE54 PPE FAMILY PROTEIN 54 120 18 827 0.999800 E
+Rv3344c PE_PGRS49 PE-PGRS FAMILY PROTEIN 4 6 1 2 0.000000 NE
+Rv3345c PE_PGRS50 PE-PGRS FAMILY PROTEIN 23 45 6 461 0.227400 U
+Rv3346c - hypothetical protein Rv3346c 2 3 1 2 -1.000000 S
+Rv3347c PPE55 PPE FAMILY PROTEIN 83 111 5 64 0.000000 NE
+Rv3348 - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3349c - PROBABLE TRANSPOSASE 2 2 0 0 -1.000000 S
+Rv3350c PPE56 PPE FAMILY PROTEIN 82 118 10 231 0.002000 NE
+Rv3351c - hypothetical protein Rv3351c 13 15 1 2 0.000000 NE
+Rv3352c - POSSIBLE OXIDOREDUCTASE 2 2 0 0 -1.000000 S
+Rv3353c - hypothetical protein Rv3353c 3 3 0 0 -1.000000 S
+Rv3354 - hypothetical protein Rv3354 4 5 1 2 0.000000 NE
+Rv3355c - hypothetical protein Rv3355c 0 2 2 35 -1.000000 S
+Rv3356c folD PROBABLE BIFUNCTIONAL PROTEIN FOLD: METHYLENETETRAHYDROFOLATE DEHYDROGENASE + METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE 0 8 8 540 0.996200 E
+Rv3357 - hypothetical protein Rv3357 5 5 0 0 0.000000 NE
+Rv3358 - hypothetical protein Rv3358 2 2 0 0 -1.000000 S
+Rv3359 - POSSIBLE OXIDOREDUCTASE 14 17 1 2 0.000000 NE
+Rv3360 - hypothetical protein Rv3360 2 2 0 0 -1.000000 S
+Rv3361c - hypothetical protein Rv3361c 1 5 3 109 0.000000 NE
+Rv3362c - PROBABLE ATP/GTP-BINDING PROTEIN 2 6 4 294 0.943600 U
+Rv3363c - hypothetical protein Rv3363c 6 7 1 2 0.000000 NE
+Rv3364c - hypothetical protein Rv3364c 3 4 1 2 0.000000 NE
+Rv3365c - hypothetical protein Rv3365c 25 31 2 161 0.000000 NE
+Rv3366 spoU PROBABLE tRNA/rRNA METHYLASE SPOU (tRNA/rRNA METHYLTRANSFERASE) 3 5 1 2 0.000000 NE
+Rv3367 PE_PGRS51 PE-PGRS FAMILY PROTEIN 15 20 2 94 0.000000 NE
+Rv3368c - POSSIBLE OXIDOREDUCTASE 7 8 1 2 0.000000 NE
+Rv3369 - hypothetical protein Rv3369 5 6 1 2 0.000000 NE
+Rv3370c dnaE2 error-prone DNA polymerase 22 33 4 84 0.000000 NE
+Rv3371 - hypothetical protein Rv3371 15 23 3 33 0.000000 NE
+Rv3372 otsB2 POSSIBLE TREHALOSE 6-PHOSPHATE PHOSPHATASE OTSB2 (TREHALOSE-PHOSPHATASE) (TPP) 0 9 9 849 0.999200 E
+Rv3373 echA18 PROBABLE ENOYL-CoA HYDRATASE ECHA18 (ENOYL HYDRASE) (UNSATURATED ACYL-CoA HYDRATASE) (CROTONASE) 3 3 0 0 0.000000 NE
+Rv3374 echA18.1 PROBABLE ENOYL-CoA HYDRATASE (FRAGMENT) ECHA18.1 (ENOYL HYDRASE) (UNSATURATED ACYL-CoA HYDRATASE) (CROTONASE) 2 2 0 0 -1.000000 S
+Rv3375 amiD PROBABLE AMIDASE AMID (ACYLAMIDASE) (ACYLASE) 11 21 3 68 0.000000 NE
+Rv3376 - hypothetical protein Rv3376 8 8 0 0 0.000000 NE
+Rv3377c - POSSIBLE CYCLASE 12 50 16 302 1.000000 E
+Rv3378c - hypothetical protein Rv3378c 4 37 16 311 1.000000 E
+Rv3379c dxs2 1-deoxy-D-xylulose-5-phosphate synthase 15 26 4 153 0.000000 NE
+Rv3380c - PROBABLE TRANSPOSASE 0 1 1 2 -1.000000 S
+Rv3381c - PROBABLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3382c lytB1 PROBABLE LYTB-RELATED PROTEIN LYTB1 7 11 2 10 0.000000 NE
+Rv3383c idsB POSSIBLE POLYPRENYL SYNTHETASE IDSB (POLYPRENYL TRANSFERASE) (POLYPRENYL DIPHOSPHATE SYNTHASE) 9 17 5 170 0.000000 NE
+Rv3384c - hypothetical protein Rv3384c 1 2 1 2 -1.000000 S
+Rv3385c - hypothetical protein Rv3385c 2 3 1 2 0.000000 NE
+Rv3386 - POSSIBLE TRANSPOSASE 5 8 2 62 0.000000 NE
+Rv3387 - POSSIBLE TRANSPOSASE 3 5 2 69 0.000000 NE
+Rv3388 PE_PGRS52 PE-PGRS FAMILY PROTEIN 13 19 3 149 0.000000 NE
+Rv3389c - POSSIBLE DEHYDROGENASE 7 7 0 0 0.000000 NE
+Rv3390 lpqD PROBABLE CONSERVED LIPOPROTEIN LPQD 10 11 1 2 0.000000 NE
+Rv3391 acrA1 short chain dehydrogenase 20 30 3 226 0.000000 NE
+Rv3392c cmaA1 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1 CMAA1 (CYCLOPROPANE FATTY ACID SYNTHASE) (CFA SYNTHASE) (CYCLOPROPANE MYCOLIC ACID SYNTHASE 1) 5 12 6 587 0.914500 U
+Rv3393 iunH PROBABLE NUCLEOSIDE HYDROLASE IUNH (PURINE NUCLEOSIDASE) 6 9 3 142 0.000000 NE
+Rv3394c - hypothetical protein Rv3394c 10 11 1 2 0.000000 NE
+Rv3395A - PROBABLE MEMBRANE PROTEIN 5 8 2 76 0.000000 NE
+Rv3395c - hypothetical protein Rv3395c 3 4 1 2 0.000000 NE
+Rv3396c guaA bifunctional GMP synthase/glutamine amidotransferase protein 0 15 15 1259 1.000000 E
+Rv3397c phyA PROBABLE PHYTOENE SYNTHASE PHYA 9 17 4 148 0.000000 NE
+Rv3398c idsA1 PROBABLE MULTIFUNCTIONAL GERANYLGERANYL PYROPHOSPHATE SYNTHETASE IDSA1 (GGPP SYNTHETASE) (GGPPSASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE): DIMETHYLALLYLTRANSFERASE (PRENYLTRANSFERASE) (GERANYL-DIPHOSPHATE SYNTHASE) + GERANYLTRANSTRANSFERASE (FARNESYL-DIPHOSPHATE SYNTHASE) (FARNESYL-PYROPHOSPHATE SYNTHETASE) (FARNESYL DIPHOSPHATE SYNTHETASE) (FPP SYNTHETASE) + FARNESYLTRANSTRANSFERASE (GERANYLGERANYL-DIPHOSPHATE SYNTHASE) 3 8 4 527 0.484700 U
+Rv3399 - hypothetical protein Rv3399 9 15 4 81 0.000000 NE
+Rv3400 - PROBABLE HYDROLASE 4 11 3 273 0.021300 NE
+Rv3401 - hypothetical protein Rv3401 26 32 2 42 0.000000 NE
+Rv3402c - hypothetical protein Rv3402c 20 25 2 13 0.000000 NE
+Rv3403c - hypothetical protein Rv3403c 20 21 1 2 0.000000 NE
+Rv3404c - hypothetical protein Rv3404c 9 9 0 0 0.000000 NE
+Rv3405c - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 3 7 2 60 0.000000 NE
+Rv3406 - PROBABLE DIOXYGENASE 12 14 1 2 0.000000 NE
+Rv3407 - hypothetical protein Rv3407 2 2 0 0 -1.000000 S
+Rv3408 - hypothetical protein Rv3408 6 7 1 2 0.000000 NE
+Rv3409c choD PROBABLE CHOLESTEROL OXIDASE PRECURSOR CHOD (CHOLESTEROL-O2 OXIDOREDUCTASE) 13 19 3 371 0.055700 U
+Rv3410c guaB3 inositol-5-monophosphate dehydrogenase 0 12 12 997 1.000000 E
+Rv3411c guaB2 inositol-5-monophosphate dehydrogenase 0 11 11 1294 0.999900 E
+Rv3412 - hypothetical protein Rv3412 8 9 1 2 0.000000 NE
+Rv3413c - HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN 3 4 1 2 0.000000 NE
+Rv3414c sigD RNA polymerase sigma factor SigD 6 7 1 2 0.000000 NE
+Rv3415c - hypothetical protein Rv3415c 5 9 3 59 0.000000 NE
+Rv3416 whiB3 TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB3 4 4 0 0 0.000000 NE
+Rv3417c groEL chaperonin GroEL 7 14 2 195 0.000100 NE
+Rv3418c groES co-chaperonin GroES 0 4 4 47 -1.000000 S
+Rv3419c gcp O-sialoglycoprotein endopeptidase 4 12 3 131 0.000000 NE
+Rv3420c rimI PROBABLE RIBOSOMAL-PROTEIN-ALANINE ACETYLTRANSFERASE RIMI (ACETYLATING ENZYME FOR N-TERMINAL OF RIBOSOMAL PROTEIN S18) 6 10 2 44 0.000000 NE
+Rv3421c - hypothetical protein Rv3421c 4 11 3 225 0.000100 NE
+Rv3422c - hypothetical protein Rv3422c 1 5 3 143 0.000000 NE
+Rv3423c alr alanine racemase 0 19 19 1081 1.000000 E
+Rv3424c - hypothetical protein Rv3424c 1 2 1 2 -1.000000 S
+Rv3425 PPE57 PPE FAMILY PROTEIN 11 16 2 64 0.000000 NE
+Rv3426 PPE58 PPE FAMILY PROTEIN 5 17 6 207 0.001000 NE
+Rv3427c - POSSIBLE TRANSPOSASE 4 7 3 205 0.000200 NE
+Rv3428c - POSSIBLE TRANSPOSASE 6 15 3 205 0.000000 NE
+Rv3429 PPE59 PPE FAMILY PROTEIN 14 20 3 102 0.000000 NE
+Rv3430c - POSSIBLE TRANSPOSASE 18 20 2 55 0.000000 NE
+Rv3431c - POSSIBLE TRANSPOSASE (FRAGMENT) 6 9 2 12 0.000000 NE
+Rv3432c gadB PROBABLE GLUTAMATE DECARBOXYLASE GADB 19 21 1 2 0.000000 NE
+Rv3433c - hypothetical protein Rv3433c 2 7 3 198 0.000000 NE
+Rv3434c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 9 11 2 27 0.000000 NE
+Rv3435c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 8 12 3 177 0.000000 NE
+Rv3436c glmS D-fructose-6-phosphate amidotransferase 0 25 25 1570 1.000000 E
+Rv3437 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 6 8 1 2 0.000000 NE
+Rv3438 - hypothetical protein Rv3438 4 12 4 144 0.000000 NE
+Rv3439c - CONSERVED HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN 9 9 0 0 0.000000 NE
+Rv3440c - hypothetical protein Rv3440c 6 7 1 2 0.000000 NE
+Rv3441c mrsA PROBABLE PHOSPHO-SUGAR MUTASE / MRSA PROTEIN HOMOLOG 0 14 14 713 1.000000 E
+Rv3442c rpsI 30S ribosomal protein S9 0 6 6 312 0.995700 E
+Rv3443c rplM 50S ribosomal protein L13 0 6 6 374 0.986100 U
+Rv3444c esxT PUTATIVE ESAT-6 LIKE PROTEIN ESXT 3 3 0 0 -1.000000 S
+Rv3445c esxU ESAT-6 LIKE PROTEIN ESXU 2 3 1 2 0.000000 NE
+Rv3446c - HYPOTHETICAL ALANINE AND VALINE RICH PROTEIN 11 14 1 2 0.000000 NE
+Rv3447c - PROBABLE CONSERVED MEMBRANE PROTEIN 20 46 5 320 0.063400 U
+Rv3448 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 13 22 3 35 0.000000 NE
+Rv3449 mycP4 PROBABLE MEMBRANE-ANCHORED MYCOSIN MYCP4 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-4) 12 17 2 43 0.000000 NE
+Rv3450c - PROBABLE CONSERVED MEMBRANE PROTEIN 12 12 0 0 0.000000 NE
+Rv3451 cut3 PROBABLE CUTINASE PRECURSOR CUT3 12 15 2 28 0.000000 NE
+Rv3452 cut4 PROBABLE CUTINASE PRECURSOR CUT4 6 7 1 2 0.000000 NE
+Rv3453 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 7 9 1 2 0.000000 NE
+Rv3454 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 14 24 3 82 0.000000 NE
+Rv3455c truA tRNA pseudouridine synthase A 1 12 8 384 0.981100 U
+Rv3456c rplQ 50S ribosomal protein L17 0 6 6 255 0.997700 E
+Rv3457c rpoA DNA-directed RNA polymerase subunit alpha 0 11 11 875 0.999900 E
+Rv3458c rpsD 30S ribosomal protein S4 0 10 10 450 0.999800 E
+Rv3459c rpsK 30S ribosomal protein S11 0 2 2 350 -1.000000 S
+Rv3460c rpsM 30S ribosomal protein S13 0 8 8 259 0.999500 E
+Rv3461c rpmJ 50S ribosomal protein L36 0 2 2 63 -1.000000 S
+Rv3462c infA translation initiation factor IF-1 0 4 4 187 0.983000 U
+Rv3463 - hypothetical protein Rv3463 12 17 2 25 0.000000 NE
+Rv3464 rmlB dTDP-GLUCOSE 4,6-DEHYDRATASE RMLB 0 20 20 862 1.000000 E
+Rv3465 rmlC dTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC (dTDP-4-KETO-6-DEOXYGLUCOSE 3,5-EPIMERASE) (dTDP-L-RHAMNOSE SYNTHETASE) (THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE) 0 8 8 372 0.998500 E
+Rv3466 - hypothetical protein Rv3466 1 3 2 182 0.000000 NE
+Rv3467 - hypothetical protein Rv3467 2 2 0 0 -1.000000 S
+Rv3468c - POSSIBLE DTDP-GLUCOSE 4,6-DEHYDRATASE 8 16 4 245 0.001500 NE
+Rv3469c mhpE 4-hydroxy-2-ketovalerate aldolase 8 12 2 59 0.000000 NE
+Rv3470c ilvB2 PROBABLE ACETOLACTATE SYNTHASE (LARGE SUBUNIT) ILVB2 (AHAS) (ACETOHYDROXY-ACID SYNTHASE LARGE SUBUNIT) (ALS) 7 16 6 402 0.672100 U
+Rv3471c - hypothetical protein Rv3471c 5 6 1 2 0.000000 NE
+Rv3472 - hypothetical protein Rv3472 9 11 2 9 0.000000 NE
+Rv3473c bpoA POSSIBLE PEROXIDASE BPOA (NON-HAEM PEROXIDASE) 7 8 1 2 0.000000 NE
+Rv3474 - POSSIBLE TRANSPOSASE FOR INSERTION ELEMENT IS6110 0 0 0 0 -1.000000 S
+Rv3475 - POSSIBLE TRANSPOSASE FOR INSERTION ELEMENT IS6110 0 0 0 0 -1.000000 S
+Rv3476c kgtP PROBABLE DICARBOXYLIC ACID TRANSPORT INTEGRAL MEMBRANE PROTEIN KGTP (DICARBOXYLATE TRANSPORTER) 30 35 2 136 0.000000 NE
+Rv3477 PE31 PE FAMILY PROTEIN 4 5 1 2 0.000000 NE
+Rv3478 PPE60 PE FAMILY PROTEIN 7 12 2 36 0.000000 NE
+Rv3479 - POSSIBLE TRANSMEMBRANE PROTEIN 29 34 2 46 0.000000 NE
+Rv3480c - hypothetical protein Rv3480c 20 28 2 65 0.000000 NE
+Rv3481c - PROBABLE INTEGRAL MEMBRANE PROTEIN 7 8 1 2 0.000000 NE
+Rv3482c - PROBABLE CONSERVED MEMBRANE PROTEIN 9 10 1 2 0.000000 NE
+Rv3483c - hypothetical protein Rv3483c 9 9 0 0 0.000000 NE
+Rv3484 cpsA POSSIBLE CONSERVED PROTEIN CPSA 6 27 7 251 0.024400 NE
+Rv3485c - short chain dehydrogenase 8 10 2 21 0.000000 NE
+Rv3486 - hypothetical protein Rv3486 6 6 0 0 0.000000 NE
+Rv3487c lipF PROBABLE ESTERASE/LIPASE LIPF 12 13 1 2 0.000000 NE
+Rv3488 - hypothetical protein Rv3488 2 4 1 2 -1.000000 S
+Rv3489 - hypothetical protein Rv3489 0 2 2 49 -1.000000 S
+Rv3490 otsA PROBABLE ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE 1 29 21 881 1.000000 E
+Rv3491 - hypothetical protein Rv3491 8 10 1 2 0.000000 NE
+Rv3492c - CONSERVED HYPOTHETICAL MCE ASSOCIATED PROTEIN 5 9 2 8 0.000000 NE
+Rv3493c - CONSERVED HYPOTHETICAL MCE ASSOCIATED ALANINE AND VALINE RICH PROTEIN 5 9 2 33 0.000000 NE
+Rv3494c mce4F MCE-FAMILY PROTEIN MCE4F 15 23 2 18 0.000000 NE
+Rv3495c lprN POSSIBLE MCE-FAMILY LIPOPROTEIN LPRN (MCE-FAMILY LIPOPROTEIN MCE4E) 7 10 2 91 0.000000 NE
+Rv3496c mce4D MCE-FAMILY PROTEIN MCE4D 21 25 3 51 0.000000 NE
+Rv3497c mce4C MCE-FAMILY PROTEIN MCE4C 11 13 1 2 0.000000 NE
+Rv3498c mce4B MCE-FAMILY PROTEIN MCE4B 8 11 2 68 0.000000 NE
+Rv3499c mce4A MCE-FAMILY PROTEIN MCE4A 21 31 2 27 0.000000 NE
+Rv3500c yrbE4B CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE4B 13 18 2 71 0.000000 NE
+Rv3501c yrbE4A CONSERVED HYPOTHETICAL INTEGRAL MEMBRANE PROTEIN YRBE4A 6 8 1 2 0.000000 NE
+Rv3502c fabG 3-ketoacyl-(acyl-carrier-protein) reductase 6 10 1 2 0.000000 NE
+Rv3503c fdxD PROBABLE FERREDOXIN FDXD 2 2 0 0 -1.000000 S
+Rv3504 fadE26 PROBABLE ACYL-CoA DEHYDROGENASE FADE26 15 18 1 2 0.000000 NE
+Rv3505 fadE27 PROBABLE ACYL-CoA DEHYDROGENASE FADE27 5 12 4 231 0.000200 NE
+Rv3506 fadD17 acyl-CoA synthetase 18 23 1 2 0.000000 NE
+Rv3507 PE_PGRS53 PE-PGRS FAMILY PROTEIN 18 35 4 155 0.000000 NE
+Rv3508 PE_PGRS54 PE-PGRS FAMILY PROTEIN 5 21 10 3256 1.000000 E
+Rv3509c ilvX hypothetical protein Rv3509c 17 21 1 2 0.000000 NE
+Rv3510c - hypothetical protein Rv3510c 12 15 2 33 0.000000 NE
+Rv3511 PE_PGRS55 PE-PGRS FAMILY PROTEIN 17 21 3 209 0.000000 NE
+Rv3512 PE_PGRS56 PE-PGRS FAMILY PROTEIN 11 26 4 338 0.053800 U
+Rv3513c fadD18 PROBABLE FATTY-ACID-CoA LIGASE FADD18 (FRAGMENT) (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) 4 4 0 0 -1.000000 S
+Rv3514 PE_PGRS57 PE-PGRS FAMILY PROTEIN 1 11 8 2030 1.000000 E
+Rv3515c fadD19 acyl-CoA synthetase 17 19 1 2 0.000000 NE
+Rv3516 echA19 enoyl-CoA hydratase 3 7 1 2 0.000000 NE
+Rv3517 - hypothetical protein Rv3517 10 15 3 31 0.000000 NE
+Rv3518c cyp142 PROBABLE CYTOCHROME P450 MONOOXYGENASE 142 CYP142 3 12 4 376 0.283800 U
+Rv3519 - hypothetical protein Rv3519 8 10 1 2 0.000000 NE
+Rv3520c - POSSIBLE COENZYME F420-DEPENDENT OXIDOREDUCTASE 13 14 1 2 0.000000 NE
+Rv3521 - hypothetical protein Rv3521 11 12 1 2 0.000000 NE
+Rv3522 ltp4 lipid-transfer protein 14 17 1 2 0.000000 NE
+Rv3523 ltp3 acetyl-CoA acetyltransferase 9 14 2 114 0.000000 NE
+Rv3524 - PROBABLE CONSERVED MEMBRANE PROTEIN 14 16 1 2 0.000000 NE
+Rv3525c - POSSIBLE SIDEROPHORE-BINDING PROTEIN 6 8 1 2 0.000000 NE
+Rv3526 - POSSIBLE OXIDOREDUCTASE 14 20 2 44 0.000000 NE
+Rv3527 - hypothetical protein Rv3527 4 6 1 2 0.000000 NE
+Rv3528c - hypothetical protein Rv3528c 5 33 12 177 0.008700 NE
+Rv3529c - hypothetical protein Rv3529c 13 25 4 61 0.000000 NE
+Rv3530c - short chain dehydrogenase 6 16 4 139 0.000000 NE
+Rv3531c - hypothetical protein Rv3531c 15 22 3 19 0.000000 NE
+Rv3532 PPE61 PPE FAMILY PROTEIN 16 17 1 2 0.000000 NE
+Rv3533c PPE62 PPE FAMILY PROTEIN 8 16 4 488 0.199800 U
+Rv3534c - 4-hydroxy-2-ketovalerate aldolase 6 7 1 2 0.000000 NE
+Rv3535c - acetaldehyde dehydrogenase 8 10 1 2 0.000000 NE
+Rv3536c - PROBABLE HYDRATASE 5 8 1 2 0.000000 NE
+Rv3537 - 3-ketosteroid-delta-1-dehydrogenase 11 35 8 224 0.002200 NE
+Rv3538 - PROBABLE DEHYDROGENASE 3 11 3 72 0.000000 NE
+Rv3539 PPE63 PPE FAMILY PROTEIN 15 26 3 91 0.000000 NE
+Rv3540c ltp2 lipid-transfer protein 7 15 2 42 0.000000 NE
+Rv3541c - hypothetical protein Rv3541c 1 7 4 85 0.000000 NE
+Rv3542c - hypothetical protein Rv3542c 9 13 1 2 0.000000 NE
+Rv3543c fadE29 PROBABLE ACYL-CoA DEHYDROGENASE FADE29 6 15 3 82 0.000000 NE
+Rv3544c fadE28 PROBABLE ACYL-CoA DEHYDROGENASE FADE28 12 16 2 28 0.000000 NE
+Rv3545c cyp125 PROBABLE CYTOCHROME P450 125 CYP125 11 19 2 68 0.000000 NE
+Rv3546 fadA5 acetyl-CoA acetyltransferase 4 4 0 0 0.000000 NE
+Rv3547 - hypothetical protein Rv3547 12 12 0 0 0.000000 NE
+Rv3548c - short chain dehydrogenase 4 7 1 2 0.000000 NE
+Rv3549c - short chain dehydrogenase 5 10 2 23 0.000000 NE
+Rv3550 echA20 enoyl-CoA hydratase 4 5 1 2 0.000000 NE
+Rv3551 - POSSIBLE COA-TRANSFERASE (ALPHA SUBUNIT) 6 14 4 93 0.000000 NE
+Rv3552 - POSSIBLE COA-TRANSFERASE (BETA SUBUNIT) 4 9 2 50 0.000000 NE
+Rv3553 - POSSIBLE OXIDOREDUCTASE 5 7 2 19 0.000000 NE
+Rv3554 fdxB POSSIBLE ELECTRON TRANSFER PROTEIN FDXB 19 25 2 248 0.000100 NE
+Rv3555c - hypothetical protein Rv3555c 5 12 3 135 0.000000 NE
+Rv3556c fadA6 acetyl-CoA acetyltransferase 4 12 5 465 0.602100 U
+Rv3557c - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 10 15 2 34 0.000000 NE
+Rv3558 PPE64 PPE FAMILY PROTEIN 11 14 2 61 0.000000 NE
+Rv3559c - short chain dehydrogenase 5 6 1 2 0.000000 NE
+Rv3560c fadE30 PROBABLE ACYL-CoA DEHYDROGENASE FADE30 10 13 1 2 0.000000 NE
+Rv3561 fadD3 acyl-CoA synthetase 8 10 1 2 0.000000 NE
+Rv3562 fadE31 PROBABLE ACYL-CoA DEHYDROGENASE FADE31 4 12 4 88 0.000000 NE
+Rv3563 fadE32 PROBABLE ACYL-CoA DEHYDROGENASE FADE32 8 9 1 2 0.000000 NE
+Rv3564 fadE33 PROBABLE ACYL-CoA DEHYDROGENASE FADE33 5 10 2 54 0.000000 NE
+Rv3565 aspB aspartate aminotransferase 3 16 8 425 0.973500 U
+Rv3566A - hypothetical protein Rv3566A 1 3 1 2 -1.000000 S
+Rv3566c nat ARYLAMINE N-ACETYLTRANSFERASE NAT (ARYLAMINE ACETYLASE) 5 12 2 136 0.000000 NE
+Rv3567c - POSSIBLE OXIDOREDUCTASE 2 8 3 92 0.000000 NE
+Rv3568c bphC PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPHC (23OHBP OXYGENASE) (2,3-DIHYDROXYBIPHENYL DIOXYGENASE) (2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE) (DHBD) 10 12 1 2 0.000000 NE
+Rv3569c bphD 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD 10 13 1 2 0.000000 NE
+Rv3570c - POSSIBLE OXIDOREDUCTASE 5 16 6 183 0.000000 NE
+Rv3571 hmp POSSIBLE HEMOGLOBINE-RELATED PROTEIN HMP 8 11 1 2 0.000000 NE
+Rv3572 - hypothetical protein Rv3572 6 7 1 2 0.000000 NE
+Rv3573c fadE34 PROBABLE ACYL-CoA DEHYDROGENASE FADE34 12 20 2 33 0.000000 NE
+Rv3574 - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 9 12 1 2 0.000000 NE
+Rv3575c - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LACI-FAMILY) 13 16 1 2 0.000000 NE
+Rv3576 lppH POSSIBLE CONSERVED LIPOPROTEIN LPPH 7 10 2 4 0.000000 NE
+Rv3577 - hypothetical protein Rv3577 9 13 2 59 0.000000 NE
+Rv3578 arsB2 POSSIBLE ARSENICAL PUMP INTEGRAL MEMBRANE PROTEIN ARSB2 12 14 1 2 0.000000 NE
+Rv3579c - POSSIBLE TRNA/RRNA METHYLTRANSFERASE 0 10 10 703 0.999000 E
+Rv3580c cysS cysteinyl-tRNA synthetase 0 26 26 1179 1.000000 E
+Rv3581c ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 0 5 5 381 0.964700 U
+Rv3582c ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 0 10 10 511 0.999200 E
+Rv3583c - POSSIBLE TRANSCRIPTION FACTOR 0 7 7 291 0.998800 E
+Rv3584 lpqE POSSIBLE CONSERVED LIPOPROTEIN LPQE 3 5 2 57 0.000000 NE
+Rv3585 radA DNA repair protein RadA 14 18 2 176 0.000000 NE
+Rv3586 - hypothetical protein Rv3586 9 13 2 79 0.000000 NE
+Rv3587c - PROBABLE CONSERVED MEMBRANE PROTEIN 0 12 12 696 0.999900 E
+Rv3588c - CARBONIC ANHYDRASE (CARBONATE DEHYDRATASE) (CARBONIC DEHYDRATASE) 0 7 7 538 0.989700 U
+Rv3589 mutY PROBABLE ADENINE GLYCOSYLASE MUTY 10 14 2 40 0.000000 NE
+Rv3590c PE_PGRS58 PE-PGRS FAMILY PROTEIN 13 19 3 70 0.000000 NE
+Rv3591c - POSSIBLE HYDROLASE 9 14 2 45 0.000000 NE
+Rv3592 TB11.2 hypothetical protein Rv3592 2 2 0 0 -1.000000 S
+Rv3593 lpqF PROBABLE CONSERVED LIPOPROTEIN LPQF 0 16 16 903 1.000000 E
+Rv3594 - hypothetical protein Rv3594 10 14 1 2 0.000000 NE
+Rv3595c PE_PGRS59 PE-PGRS FAMILY PROTEIN 11 15 2 29 0.000000 NE
+Rv3596c clpC1 PROBABLE ATP-DEPENDENT PROTEASE ATP-BINDING SUBUNIT CLPC1 0 25 25 1830 1.000000 E
+Rv3597c lsr2 PROBABLE IRON-REGULATED LSR2 PROTEIN PRECURSOR 0 3 3 175 0.963800 U
+Rv3598c lysS lysyl-tRNA synthetase 0 30 30 1342 1.000000 E
+Rv3599c - HYPOTHETICAL SHORT PROTEIN 0 1 1 2 -1.000000 S
+Rv3600c - pantothenate kinase 10 13 1 2 0.000000 NE
+Rv3601c panD aspartate alpha-decarboxylase 0 8 8 333 0.999400 E
+Rv3602c panC pantoate--beta-alanine ligase 0 11 11 650 0.999700 E
+Rv3603c - CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN 0 12 12 770 1.000000 E
+Rv3604c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN RICH IN ALANINE AND ARGININE AND PROLINE 0 13 13 912 1.000000 E
+Rv3605c - PROBABLE CONSERVED SECRETED PROTEIN 5 6 1 2 0.000000 NE
+Rv3606c folK 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDI NE PYROPHOSPHOKINASE FOLK (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE) (HPPK) (6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE) (PPPK) (2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE DIPHOSPHOKINASE) (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-DIPHOSPHOKINASE) (6-HYDROXYMETHYL-7,8-DIHYDROPTERIN DIPHOSPHOKINASE) 2 6 4 190 0.000000 NE
+Rv3607c folB PROBABLE DIHYDRONEOPTERIN ALDOLASE FOLB (DHNA) 0 6 6 324 0.993500 E
+Rv3608c folP1 DIHYDROPTEROATE SYNTHASE 1 FOLP (DHPS 1) (DIHYDROPTEROATE PYROPHOSPHORYLASE 1) (DIHYDROPTEROATE DIPHOSPHORYLASE 1) 0 7 7 493 0.990700 E
+Rv3609c folE GTP cyclohydrolase I 0 12 12 497 1.000000 E
+Rv3610c ftsH MEMBRANE-BOUND PROTEASE FTSH (CELL DIVISION PROTEIN) 6 28 9 550 0.966200 U
+Rv3611 - HYPOTHETICAL ARGININE AND PROLINE RICH PROTEIN 1 2 1 2 -1.000000 S
+Rv3612c - hypothetical protein Rv3612c 3 4 1 2 0.000000 NE
+Rv3613c - hypothetical protein Rv3613c 0 0 0 0 -1.000000 S
+Rv3614c - hypothetical protein Rv3614c 6 8 2 34 0.000000 NE
+Rv3615c - hypothetical protein Rv3615c 9 10 1 2 0.000000 NE
+Rv3616c - CONSERVED HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN 12 16 2 115 0.000000 NE
+Rv3617 ephA PROBABLE EPOXIDE HYDROLASE EPHA (EPOXIDE HYDRATASE) (ARENE-OXIDE HYDRATASE) 13 16 1 2 0.000000 NE
+Rv3618 - POSSIBLE MONOOXYGENASE 16 22 2 16 0.000000 NE
+Rv3619c esxV PUTATIVE ESAT-6 LIKE PROTEIN ESXV (ESAT-6 LIKE PROTEIN 1) 0 0 0 0 -1.000000 S
+Rv3620c esxW PUTATIVE ESAT-6 LIKE PROTEIN ESXW (ESAT-6 LIKE PROTEIN 10) 0 0 0 0 -1.000000 S
+Rv3621c PPE65 PPE FAMILY PROTEIN 9 11 1 2 0.000000 NE
+Rv3622c PE32 PE FAMILY PROTEIN 4 4 0 0 -1.000000 S
+Rv3623 lpqG PROBABLE CONSERVED LIPOPROTEIN LPQG 5 6 1 2 0.000000 NE
+Rv3624c hpt hypoxanthine-guanine phosphoribosyltransferase 0 10 10 521 0.999400 E
+Rv3625c mesJ POSSIBLE CELL CYCLE PROTEIN MESJ 0 7 7 758 0.990700 E
+Rv3626c - hypothetical protein Rv3626c 8 11 1 2 0.000000 NE
+Rv3627c - hypothetical protein Rv3627c 0 13 13 1178 1.000000 E
+Rv3628 ppa inorganic pyrophosphatase 0 9 9 349 0.999600 E
+Rv3629c - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 14 16 1 2 0.000000 NE
+Rv3630 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 13 21 2 95 0.000000 NE
+Rv3631 - POSSIBLE TRANSFERASE (POSSIBLY GLYCOSYLTRANSFERASE) 2 5 2 366 0.333500 U
+Rv3632 - POSSIBLE CONSERVED MEMBRANE PROTEIN 6 7 1 2 0.000000 NE
+Rv3633 - hypothetical protein Rv3633 14 17 2 19 0.000000 NE
+Rv3634c galE1 UDP-GLUCOSE 4-EPIMERASE GALE1 (GALACTOWALDENASE) (UDP-GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHATE GALACTOSE 4-EPIMERASE) (URIDINE DIPHOSPHO-GALACTOSE 4-EPIMERASE) 0 18 18 668 1.000000 E
+Rv3635 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 24 24 1587 1.000000 E
+Rv3636 - POSSIBLE TRANSPOSASE 5 5 0 0 0.000000 NE
+Rv3637 - POSSIBLE TRANSPOSASE 4 5 1 2 0.000000 NE
+Rv3638 - transposase 8 12 1 2 0.000000 NE
+Rv3639c - hypothetical protein Rv3639c 4 8 3 98 0.000000 NE
+Rv3640c - PROBABLE TRANSPOSASE 12 14 1 2 0.000000 NE
+Rv3641c fic POSSIBLE CELL FILAMENTATION PROTEIN FIC 8 9 1 2 0.000000 NE
+Rv3642c - hypothetical protein Rv3642c 2 2 0 0 -1.000000 S
+Rv3643 - hypothetical protein Rv3643 8 8 0 0 0.000000 NE
+Rv3644c - DNA polymerase III subunit delta' 0 14 14 1024 1.000000 E
+Rv3645 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 20 20 1303 1.000000 E
+Rv3646c topA DNA topoisomerase I 0 48 48 2455 1.000000 E
+Rv3647c - hypothetical protein Rv3647c 2 8 6 326 0.951200 U
+Rv3648c cspA PROBABLE COLD SHOCK PROTEIN A CSPA 0 4 4 119 -1.000000 S
+Rv3649 - PROBABLE HELICASE 18 30 4 197 0.000000 NE
+Rv3650 PE33 PE FAMILY PROTEIN 0 2 2 42 -1.000000 S
+Rv3651 - hypothetical protein Rv3651 11 14 2 183 0.000000 NE
+Rv3652 PE_PGRS60 PE-PGRS FAMILY-RELATED PROTEIN 5 5 0 0 0.000000 NE
+Rv3653 PE_PGRS61 PE-PGRS FAMILY-RELATED PROTEIN 3 5 1 2 0.000000 NE
+Rv3654c - hypothetical protein Rv3654c 0 1 1 2 -1.000000 S
+Rv3655c - hypothetical protein Rv3655c 2 5 2 20 0.000000 NE
+Rv3656c - hypothetical protein Rv3656c 3 4 1 2 -1.000000 S
+Rv3657c - POSSIBLE CONSERVED ALANINE RICH MEMBRANE PROTEIN 5 7 1 2 0.000000 NE
+Rv3658c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 8 2 52 0.000000 NE
+Rv3659c - hypothetical protein Rv3659c 4 6 1 2 0.000000 NE
+Rv3660c - hypothetical protein Rv3660c 2 7 4 442 0.534900 U
+Rv3661 - hypothetical protein Rv3661 11 13 2 13 0.000000 NE
+Rv3662c - hypothetical protein Rv3662c 2 3 1 2 0.000000 NE
+Rv3663c dppD PROBABLE DIPEPTIDE-TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER DPPD 12 23 5 286 0.080900 U
+Rv3664c dppC PROBABLE DIPEPTIDE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER DPPC 6 14 6 318 0.838700 U
+Rv3665c dppB PROBABLE DIPEPTIDE-TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER DPPB 5 14 8 362 0.979500 U
+Rv3666c dppA PROBABLE PERIPLASMIC DIPEPTIDE-BINDING LIPOPROTEIN DPPA 6 22 7 264 0.092700 U
+Rv3667 acs acetyl-CoA synthetase 24 36 5 77 0.000000 NE
+Rv3668c - POSSIBLE PROTEASE 6 8 2 37 0.000000 NE
+Rv3669 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 1 4 3 90 0.000400 NE
+Rv3670 ephE POSSIBLE EPOXIDE HYDROLASE EPHE (EPOXIDE HYDRATASE) (ARENE-OXIDE HYDRATASE) 0 16 16 754 1.000000 E
+Rv3671c - POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE 0 12 12 846 0.999900 E
+Rv3672c - hypothetical protein Rv3672c 6 9 1 2 0.000000 NE
+Rv3673c - POSSIBLE MEMBRANE-ANCHORED THIOREDOXIN-LIKE PROTEIN (THIOL-DISULFIDE INTERCHANGE RELATED PROTEIN) 0 7 7 561 0.987600 U
+Rv3674c nth PROBABLE ENDONUCLEASE III NTH (DNA-(APURINIC OR APYRIMIDINIC SITE)LYASE) (AP LYASE) (AP ENDONUCLEASE CLASS I) (ENDODEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) (DEOXYRIBONUCLEASE (APURINIC OR APYRIMIDINIC)) 8 11 2 14 0.000000 NE
+Rv3675 - POSSIBLE MEMBRANE PROTEIN 2 5 2 47 0.000000 NE
+Rv3676 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY) 0 2 2 66 -1.000000 S
+Rv3677c - POSSIBLE HYDROLASE 7 9 1 2 0.000000 NE
+Rv3678A - hypothetical protein Rv3678A 2 2 0 0 -1.000000 S
+Rv3678c - hypothetical protein Rv3678c 4 6 2 34 0.000000 NE
+Rv3679 - PROBABLE ANION TRANSPORTER ATPASE 6 12 3 138 0.000000 NE
+Rv3680 - PROBABLE ANION TRANSPORTER ATPASE 10 19 2 23 0.000000 NE
+Rv3681c whiB4 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB4 5 7 1 2 0.000000 NE
+Rv3682 ponA2 PROBABLE BIFUNCTIONAL MEMBRANE-ASSOCIATED PENICILLIN-BINDING PROTEIN 1A/1B PONA2 19 36 4 184 0.000000 NE
+Rv3683 - hypothetical protein Rv3683 11 11 0 0 0.000000 NE
+Rv3684 - PROBABLE LYASE 10 16 2 143 0.000000 NE
+Rv3685c cyp137 PROBABLE CYTOCHROME P450 137 CYP137 10 17 2 16 0.000000 NE
+Rv3686c - hypothetical protein Rv3686c 4 5 1 2 0.000000 NE
+Rv3687c rsfB ANTI-ANTI-SIGMA FACTOR RSFB (ANTI-SIGMA FACTOR ANTAGONIST) (REGULATOR OF SIGMA F B) 4 5 1 2 0.000000 NE
+Rv3688c - hypothetical protein Rv3688c 4 5 1 2 0.000000 NE
+Rv3689 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 23 30 2 11 0.000000 NE
+Rv3690 - PROBABLE CONSERVED MEMBRANE PROTEIN 8 11 1 2 0.000000 NE
+Rv3691 - hypothetical protein Rv3691 13 15 2 42 0.000000 NE
+Rv3692 moxR2 PROBABLE METHANOL DEHYDROGENASE TRANSCRIPTIONAL REGULATORY PROTEIN MOXR2 11 15 2 18 0.000000 NE
+Rv3693 - POSSIBLE CONSERVED MEMBRANE PROTEIN 6 13 3 276 0.008600 NE
+Rv3694c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 7 15 3 97 0.000000 NE
+Rv3695 - POSSIBLE CONSERVED MEMBRANE PROTEIN 4 9 5 404 0.847000 U
+Rv3696c glpK glycerol kinase 5 26 6 88 0.000000 NE
+Rv3697c - POSSIBLE CONSERVED MEMBRANE PROTEIN 9 9 0 0 0.000000 NE
+Rv3698 - hypothetical protein Rv3698 18 32 2 12 0.000000 NE
+Rv3699 - hypothetical protein Rv3699 6 9 1 2 0.000000 NE
+Rv3700c - hypothetical protein Rv3700c 8 13 3 107 0.000000 NE
+Rv3701c - hypothetical protein Rv3701c 4 15 5 350 0.614200 U
+Rv3702c - hypothetical protein Rv3702c 3 8 4 217 0.000100 NE
+Rv3703c - hypothetical protein Rv3703c 12 17 1 2 0.000000 NE
+Rv3704c gshA GLUTAMATE--CYSTEINE LIGASE GSHA (GAMMA-GLUTAMYLCYSTEINE SYNTHETASE) (GAMMA-ECS) (GCS) (GAMMA-GLUTAMYL-L-CYSTEINE SYNTHETASE) 10 12 1 2 0.000000 NE
+Rv3705A - CONSERVED HYPOTHETICAL PROLINE RICH PROTEIN 3 4 1 2 -1.000000 S
+Rv3705c - hypothetical protein Rv3705c 7 9 1 2 0.000000 NE
+Rv3706c - CONSERVED HYPOTHETICAL PROLINE RICH PROTEIN 2 3 1 2 -1.000000 S
+Rv3707c - hypothetical protein Rv3707c 12 13 1 2 0.000000 NE
+Rv3708c asd aspartate-semialdehyde dehydrogenase 0 9 9 776 0.998500 E
+Rv3709c ask aspartate kinase 0 12 12 907 1.000000 E
+Rv3710 leuA 2-isopropylmalate synthase 0 26 26 1474 1.000000 E
+Rv3711c dnaQ DNA polymerase III subunit epsilon 12 14 1 2 0.000000 NE
+Rv3712 - POSSIBLE LIGASE 0 8 8 769 0.996700 E
+Rv3713 cobQ2 POSSIBLE COBYRIC ACID SYNTHASE COBQ2 0 9 9 521 0.998500 E
+Rv3714c - hypothetical protein Rv3714c 12 12 0 0 0.000000 NE
+Rv3715c recR recombination protein RecR 2 4 1 2 0.000000 NE
+Rv3716c - hypothetical protein Rv3716c 2 3 1 2 -1.000000 S
+Rv3717 - hypothetical protein Rv3717 6 10 1 2 0.000000 NE
+Rv3718c - hypothetical protein Rv3718c 3 5 1 2 0.000000 NE
+Rv3719 - hypothetical protein Rv3719 9 32 5 152 0.000000 NE
+Rv3720 - POSSIBLE FATTY ACID SYNTHASE 11 31 9 376 0.975100 U
+Rv3721c dnaZX DNA polymerase III subunits gamma and tau 0 23 23 1467 1.000000 E
+Rv3722c - hypothetical protein Rv3722c 0 25 25 1029 1.000000 E
+Rv3723 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 7 9 1 2 0.000000 NE
+Rv3724A cut5a PROBABLE CUTINASE PRECURSOR 2 2 0 0 -1.000000 S
+Rv3724B cut5b PROBABLE CUTINASE 12 17 2 26 0.000000 NE
+Rv3725 - POSSIBLE OXIDOREDUCTASE 11 12 1 2 0.000000 NE
+Rv3726 - POSSIBLE DEHYDROGENASE 11 15 1 2 0.000000 NE
+Rv3727 - POSSIBLE OXIDOREDUCTASE 34 37 2 85 0.000000 NE
+Rv3728 - PROBABLE CONSERVED TWO-DOMAIN MEMBRANE PROTEIN 22 28 1 2 0.000000 NE
+Rv3729 - POSSIBLE TRANSFERASE 19 23 3 84 0.000000 NE
+Rv3730c - hypothetical protein Rv3730c 15 19 3 190 0.000000 NE
+Rv3731 ligC ATP-dependent DNA ligase 13 16 1 2 0.000000 NE
+Rv3732 - hypothetical protein Rv3732 14 16 1 2 0.000000 NE
+Rv3733c - hypothetical protein Rv3733c 3 4 1 2 0.000000 NE
+Rv3734c - hypothetical protein Rv3734c 18 18 0 0 0.000000 NE
+Rv3735 - hypothetical protein Rv3735 5 5 0 0 0.000000 NE
+Rv3736 - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARAC/XYLS-FAMILY) 16 19 1 2 0.000000 NE
+Rv3737 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 9 15 2 20 0.000000 NE
+Rv3738c PPE66 PPE FAMILY PROTEIN 13 16 1 2 0.000000 NE
+Rv3739c PPE67 PPE FAMILY PROTEIN 2 4 1 2 -1.000000 S
+Rv3740c - hypothetical protein Rv3740c 16 17 1 2 0.000000 NE
+Rv3741c - POSSIBLE OXIDOREDUCTASE 6 7 1 2 0.000000 NE
+Rv3742c - POSSIBLE OXIDOREDUCTASE 4 5 1 2 -1.000000 S
+Rv3743c ctpJ PROBABLE CATION TRANSPORTER P-TYPE ATPASE CTPJ 23 29 2 9 0.000000 NE
+Rv3744 - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARSR-FAMILY) 7 7 0 0 0.000000 NE
+Rv3745c - hypothetical protein Rv3745c 1 2 1 2 -1.000000 S
+Rv3746c PE34 PROBABLE PE FAMILY PROTEIN (PE FAMILY-RELATED PROTEIN) 4 5 1 2 0.000000 NE
+Rv3747 - hypothetical protein Rv3747 2 4 2 46 0.000000 NE
+Rv3748 - hypothetical protein Rv3748 4 5 1 2 0.000000 NE
+Rv3749c - hypothetical protein Rv3749c 10 12 2 10 0.000000 NE
+Rv3750c - POSSIBLE EXCISIONASE 5 5 0 0 0.000000 NE
+Rv3751 - PROBABLE INTEGRASE (FRAGMENT) 1 1 0 0 -1.000000 S
+Rv3752c - POSSIBLE CYTIDINE/DEOXYCYTIDYLATE DEAMINASE 0 2 2 133 -1.000000 S
+Rv3753c - hypothetical protein Rv3753c 0 4 4 276 0.985800 U
+Rv3754 tyrA prephenate dehydrogenase 0 11 11 717 0.999800 E
+Rv3755c - hypothetical protein Rv3755c 9 11 2 30 0.000000 NE
+Rv3756c proZ POSSIBLE OSMOPROTECTANT (GLYCINE BETAINE/CARNITINE/CHOLINE/L-PROLINE) TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER PROZ 10 13 1 2 0.000000 NE
+Rv3757c proW POSSIBLE OSMOPROTECTANT (GLYCINE BETAINE/CARNITINE/CHOLINE/L-PROLINE) TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER PROW 8 12 3 41 0.000000 NE
+Rv3758c proV POSSIBLE OSMOPROTECTANT (GLYCINE BETAINE/CARNITINE/CHOLINE/L-PROLINE) TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER PROV 8 13 2 113 0.000000 NE
+Rv3759c proX POSSIBLE OSMOPROTECTANT (GLYCINE BETAINE/CARNITINE/CHOLINE/L-PROLINE) BINDING LIPOPROTEIN PROX 6 12 3 248 0.001500 NE
+Rv3760 - POSSIBLE CONSERVED MEMBRANE PROTEIN 3 5 2 49 0.000000 NE
+Rv3761c fadE36 POSSIBLE ACYL-CoA DEHYDROGENASE FADE36 10 15 2 27 0.000000 NE
+Rv3762c - POSSIBLE HYDROLASE 19 28 1 2 0.000000 NE
+Rv3763 lpqH 19 KDA LIPOPROTEIN ANTIGEN PRECURSOR LPQH 4 8 2 60 0.000000 NE
+Rv3764c - POSSIBLE TWO COMPONENT SENSOR KINASE 0 14 14 1270 1.000000 E
+Rv3765c - PROBABLE TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN 10 12 1 2 0.000000 NE
+Rv3766 - hypothetical protein Rv3766 10 15 3 74 0.000000 NE
+Rv3767c - hypothetical protein Rv3767c 8 14 3 60 0.000000 NE
+Rv3768 - hypothetical protein Rv3768 10 12 1 2 0.000000 NE
+Rv3769 - hypothetical protein Rv3769 1 1 0 0 -1.000000 S
+Rv3770A - PROBABLE REMNANT OF A TRANSPOSASE 1 2 1 2 -1.000000 S
+Rv3770B - PROBABLE REMNANT OF A TRANSPOSASE 1 2 1 2 -1.000000 S
+Rv3770c - HYPOTHETICAL LEUCINE RICH PROTEIN 5 6 1 2 0.000000 NE
+Rv3771c - hypothetical protein Rv3771c 0 2 2 93 -1.000000 S
+Rv3772 hisC2 putative aminotransferase 10 17 2 59 0.000000 NE
+Rv3773c - hypothetical protein Rv3773c 6 7 1 2 0.000000 NE
+Rv3774 echA21 enoyl-CoA hydratase 12 12 0 0 0.000000 NE
+Rv3775 lipE PROBABLE LIPASE LIPE 17 20 1 2 0.000000 NE
+Rv3776 - hypothetical protein Rv3776 16 20 3 292 0.020200 NE
+Rv3777 - PROBABLE OXIDOREDUCTASE 10 13 2 54 0.000000 NE
+Rv3778c - POSSIBLE AMINOTRANSFERASE 0 14 14 841 0.999900 E
+Rv3779 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN ALANINE AND LEUCINE RICH 28 40 2 27 0.000000 NE
+Rv3780 - hypothetical protein Rv3780 0 6 6 394 0.983500 U
+Rv3781 rfbE PROBABLE O-ANTIGEN/LIPOPOLYSACCHARIDE TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER RFBE 0 13 13 724 1.000000 E
+Rv3782 - POSSIBLE L-RHAMNOSYLTRANSFERASE 0 17 17 747 1.000000 E
+Rv3783 rfbD PROBABLE O-ANTIGEN/LIPOPOLYSACCHARIDE TRANSPORT INTEGRAL MEMBRANE PROTEIN ABC TRANSPORTER RFBD 0 8 8 563 0.994600 E
+Rv3784 - POSSIBLE dTDP-GLUCOSE 4,6-DEHYDRATASE 22 24 2 14 0.000000 NE
+Rv3785 - hypothetical protein Rv3785 10 12 1 2 0.000000 NE
+Rv3786c - hypothetical protein Rv3786c 17 20 1 2 0.000000 NE
+Rv3787c - hypothetical protein Rv3787c 5 6 1 2 0.000000 NE
+Rv3788 - nucleoside diphosphate kinase regulator 6 6 0 0 0.000000 NE
+Rv3789 - POSSIBLE CONSERVED INTEGRAL MEMBRANE PROTEIN 1 8 7 270 0.995500 E
+Rv3790 - PROBABLE OXIDOREDUCTASE 0 24 24 1140 1.000000 E
+Rv3791 - short chain dehydrogenase 0 11 11 623 0.999500 E
+Rv3792 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 31 31 1720 1.000000 E
+Rv3793 embC INTEGRAL MEMBRANE INDOLYLACETYLINOSITOL ARABINOSYLTRANSFERASE EMBC (ARABINOSYLINDOLYLACETYLINOSITOL SYNTHASE) 0 39 39 2774 1.000000 E
+Rv3794 embA INTEGRAL MEMBRANE INDOLYLACETYLINOSITOL ARABINOSYLTRANSFERASE EMBA (ARABINOSYLINDOLYLACETYLINOSITOL SYNTHASE) 1 50 29 1604 1.000000 E
+Rv3795 embB INTEGRAL MEMBRANE INDOLYLACETYLINOSITOL ARABINOSYLTRANSFERASE EMBB (ARABINOSYLINDOLYLACETYLINOSITOL SYNTHASE) 0 48 48 2861 1.000000 E
+Rv3796 - hypothetical protein Rv3796 18 23 1 2 0.000000 NE
+Rv3797 fadE35 PROBABLE ACYL-CoA DEHYDROGENASE FADE35 18 20 2 8 0.000000 NE
+Rv3798 - PROBABLE TRANSPOSASE 0 2 2 610 -1.000000 S
+Rv3799c accD4 PROBABLE PROPIONYL-CoA CARBOXYLASE BETA CHAIN 4 ACCD4 (PCCASE) (PROPANOYL-COA:CARBON DIOXIDE LIGASE) 0 16 16 1256 1.000000 E
+Rv3800c pks13 POLYKETIDE SYNTHASE PKS13 0 48 48 4612 1.000000 E
+Rv3801c fadD32 acyl-CoA synthetase 0 22 22 1567 1.000000 E
+Rv3802c - PROBABLE CONSERVED MEMBRANE PROTEIN 0 20 20 832 1.000000 E
+Rv3803c fbpD SECRETED MPT51/MPB51 ANTIGEN PROTEIN FBPD (MPT51/MPB51 ANTIGEN 85 COMPLEX C) (AG58C) (MYCOLYL TRANSFERASE 85C) (FIBRONECTIN-BINDING PROTEIN C) (85C) 8 14 3 129 0.000000 NE
+Rv3804c fbpA SECRETED ANTIGEN 85-A FBPA (MYCOLYL TRANSFERASE 85A) (FIBRONECTIN-BINDING PROTEIN A) (ANTIGEN 85 COMPLEX A) 1 13 8 409 0.976800 U
+Rv3805c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 0 38 38 1672 1.000000 E
+Rv3806c - phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase 0 17 17 714 1.000000 E
+Rv3807c - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 2 4 1 2 0.000000 NE
+Rv3808c glfT BIFUNCTIONAL UDP-GALACTOFURANOSYL TRANSFERASE GLFT 0 27 27 1591 1.000000 E
+Rv3809c glf UDP-GALACTOPYRANOSE MUTASE GLF (UDP-GALP MUTASE) (NAD+-FLAVIN ADENINE DINUCLEOTIDE-REQUIRING ENZYME) 0 33 33 998 1.000000 E
+Rv3810 pirG EXPORTED REPETITIVE PROTEIN PRECURSOR PIRG (CELL SURFACE PROTEIN) (EXP53) 1 13 12 636 1.000000 E
+Rv3811 - hypothetical protein Rv3811 19 25 2 92 0.000000 NE
+Rv3812 PE_PGRS62 PE-PGRS FAMILY PROTEIN 23 27 1 2 0.000000 NE
+Rv3813c - hypothetical protein Rv3813c 7 12 2 85 0.000000 NE
+Rv3814c - POSSIBLE ACYLTRANSFERASE 9 11 1 2 0.000000 NE
+Rv3815c - POSSIBLE ACYLTRANSFERASE 9 11 1 2 0.000000 NE
+Rv3816c - POSSIBLE ACYLTRANSFERASE 4 12 5 230 0.001100 NE
+Rv3817 - POSSIBLE PHOSPHOTRANSFERASE 6 8 1 2 0.000000 NE
+Rv3818 - hypothetical protein Rv3818 9 31 9 342 0.963600 U
+Rv3819 - hypothetical protein Rv3819 6 7 1 2 0.000000 NE
+Rv3820c papA2 POSSIBLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA2 22 38 6 145 0.000000 NE
+Rv3821 - PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN 10 17 2 33 0.000000 NE
+Rv3822 - hypothetical protein Rv3822 22 35 3 38 0.000000 NE
+Rv3823c mmpL8 PROBABLE CONSERVED INTEGRAL MEMBRANE TRANSPORT PROTEIN MMPL8 22 72 19 423 1.000000 E
+Rv3824c papA1 PROBABLE CONSERVED POLYKETIDE SYNTHASE ASSOCIATED PROTEIN PAPA1 22 38 5 51 0.000000 NE
+Rv3825c pks2 PROBABLE POLYKETIDE SYNTHASE PKS2 87 106 2 71 0.000000 NE
+Rv3826 fadD23 acyl-CoA synthetase 14 46 7 77 0.000000 NE
+Rv3827c - POSSIBLE TRANSPOSASE 12 18 2 17 0.000000 NE
+Rv3828c - POSSIBLE RESOLVASE 4 7 2 87 0.000000 NE
+Rv3829c - PROBABLE DEHYDROGENASE 19 26 2 11 0.000000 NE
+Rv3830c - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY TETR-FAMILY) 7 10 1 2 0.000000 NE
+Rv3831 - hypothetical protein Rv3831 10 11 1 2 0.000000 NE
+Rv3832c - hypothetical protein Rv3832c 6 8 2 95 0.000000 NE
+Rv3833 - TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY ARAC-FAMILY) 7 10 1 2 0.000000 NE
+Rv3834c serS seryl-tRNA synthetase 0 21 21 1006 1.000000 E
+Rv3835 - PROBABLE CONSERVED MEMBRANE PROTEIN 10 15 2 23 0.000000 NE
+Rv3836 - hypothetical protein Rv3836 3 5 2 22 -1.000000 S
+Rv3837c - PROBABLE PHOSPHOGLYCERATE MUTASE (PHOSPHOGLYCEROMUTASE) (PHOSPHOGLYCERATE PHOSPHOMUTASE) 7 10 2 107 0.000000 NE
+Rv3838c pheA prephenate dehydratase 0 11 11 821 0.999800 E
+Rv3839 - hypothetical protein Rv3839 12 15 2 36 0.000000 NE
+Rv3840 - POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN 10 10 0 0 0.000000 NE
+Rv3841 bfrB POSSIBLE BACTERIOFERRITIN BFRB 2 7 3 132 0.000000 NE
+Rv3842c glpQ1 PROBABLE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE GLPQ1 (GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE) 10 13 2 66 0.000000 NE
+Rv3843c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 17 6 226 0.002300 NE
+Rv3844 - POSSIBLE TRANSPOSASE 0 0 0 0 -1.000000 S
+Rv3845 - hypothetical protein Rv3845 3 5 1 2 0.000000 NE
+Rv3846 sodA SUPEROXIDE DISMUTASE 0 12 12 545 0.999900 E
+Rv3847 - hypothetical protein Rv3847 3 5 1 2 0.000000 NE
+Rv3848 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 4 8 2 122 0.000000 NE
+Rv3849 - hypothetical protein Rv3849 4 9 1 2 0.000000 NE
+Rv3850 - hypothetical protein Rv3850 3 5 2 17 0.000000 NE
+Rv3851 - POSSIBLE MEMBRANE PROTEIN 2 2 0 0 -1.000000 S
+Rv3852 hns POSSIBLE HISTONE-LIKE PROTEIN HNS 4 4 0 0 0.000000 NE
+Rv3853 menG ribonuclease activity regulator protein RraA 2 4 2 176 0.000000 NE
+Rv3854c ethA MONOOXYGENASE ETHA 24 30 1 2 0.000000 NE
+Rv3855 ethR TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR 9 10 1 2 0.000000 NE
+Rv3856c - hypothetical protein Rv3856c 4 8 3 142 0.000000 NE
+Rv3857c - POSSIBLE MEMBRANE PROTEIN 3 3 0 0 -1.000000 S
+Rv3858c gltD glutamate synthase subunit beta 0 10 10 1230 1.000000 E
+Rv3859c gltB PROBABLE FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 0 72 72 4046 1.000000 E
+Rv3860 - hypothetical protein Rv3860 9 12 1 2 0.000000 NE
+Rv3861 - hypothetical protein Rv3861 0 1 1 2 -1.000000 S
+Rv3862c whiB6 POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB6 5 6 1 2 0.000000 NE
+Rv3863 - HYPOTHETICAL ALANINE RICH PROTEIN 4 14 8 608 0.985000 U
+Rv3864 - hypothetical protein Rv3864 3 14 4 119 0.000000 NE
+Rv3865 - hypothetical protein Rv3865 6 9 2 24 0.000000 NE
+Rv3866 - hypothetical protein Rv3866 10 12 1 2 0.000000 NE
+Rv3867 - hypothetical protein Rv3867 5 6 1 2 0.000000 NE
+Rv3868 - hypothetical protein Rv3868 17 28 3 67 0.000000 NE
+Rv3869 - POSSIBLE CONSERVED MEMBRANE PROTEIN 23 27 2 125 0.000000 NE
+Rv3870 - POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN 27 36 3 157 0.000000 NE
+Rv3871 - hypothetical protein Rv3871 18 22 1 2 0.000000 NE
+Rv3872 PE35 PE FAMILY-RELATED PROTEIN 1 1 0 0 -1.000000 S
+Rv3873 PPE68 PPE FAMILY PROTEIN 8 10 1 2 0.000000 NE
+Rv3874 esxB 10 KDA CULTURE FILTRATE ANTIGEN ESXB (LHP) (CFP10) 2 5 1 2 0.000000 NE
+Rv3875 esxA 6 KDA EARLY SECRETORY ANTIGENIC TARGET ESXA (ESAT-6) 0 4 4 158 0.981100 U
+Rv3876 - CONSERVED HYPOTHETICAL PROLINE AND ALANINE RICH PROTEIN 18 19 1 2 0.000000 NE
+Rv3877 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 20 25 3 120 0.000000 NE
+Rv3878 - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 3 5 2 410 0.194200 U
+Rv3879c - HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN 20 30 3 41 0.000000 NE
+Rv3880c - hypothetical protein Rv3880c 3 4 1 2 0.000000 NE
+Rv3881c - CONSERVED HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN 13 21 2 68 0.000000 NE
+Rv3882c - POSSIBLE CONSERVED MEMBRANE PROTEIN 20 21 1 2 0.000000 NE
+Rv3883c mycP1 MEMBRANE-ANCHORED MYCOSIN MYCP1 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-1) 12 14 1 2 0.000000 NE
+Rv3884c - PROBABLE CBXX/CFQX FAMILY PROTEIN 20 31 4 121 0.000000 NE
+Rv3885c - POSSIBLE CONSERVED MEMBRANE PROTEIN 15 25 3 164 0.000000 NE
+Rv3886c mycP2 PROBABLE ALANINE AND PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP2 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-2) 17 22 1 2 0.000000 NE
+Rv3887c - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 18 26 2 23 0.000000 NE
+Rv3888c - PROBABLE CONSERVED MEMBRANE PROTEIN 11 26 9 153 0.000100 NE
+Rv3889c - hypothetical protein Rv3889c 9 15 4 203 0.000000 NE
+Rv3890c esxC ESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) 4 5 1 2 0.000000 NE
+Rv3891c esxD POSSIBLE ESAT-6 LIKE PROTEIN ESXD 3 8 3 48 0.000000 NE
+Rv3892c PPE69 PPE FAMILY PROTEIN 8 10 1 2 0.000000 NE
+Rv3893c PE36 PE FAMILY PROTEIN 2 2 0 0 -1.000000 S
+Rv3894c - POSSIBLE CONSERVED MEMBRANE PROTEIN 34 45 2 22 0.000000 NE
+Rv3895c - PROBABLE CONSERVED MEMBRANE PROTEIN 10 11 1 2 0.000000 NE
+Rv3896c - hypothetical protein Rv3896c 12 14 1 2 0.000000 NE
+Rv3897c - hypothetical protein Rv3897c 6 6 0 0 0.000000 NE
+Rv3898c - hypothetical protein Rv3898c 6 6 0 0 0.000000 NE
+Rv3899c - hypothetical protein Rv3899c 9 15 3 190 0.000000 NE
+Rv3900c - CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN 6 14 4 72 0.000000 NE
+Rv3901c - POSSIBLE MEMBRANE PROTEIN 10 14 2 11 0.000000 NE
+Rv3902c - hypothetical protein Rv3902c 0 23 23 452 1.000000 E
+Rv3903c - HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN 27 46 5 73 0.000000 NE
+Rv3904c esxE PUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) 1 2 1 2 -1.000000 S
+Rv3905c esxF PUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) 5 5 0 0 0.000000 NE
+Rv3906c - hypothetical protein Rv3906c 7 8 1 2 0.000000 NE
+Rv3907c pcnA PROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) 0 17 17 1251 1.000000 E
+Rv3908 - hypothetical protein Rv3908 4 11 5 137 0.000000 NE
+Rv3909 - hypothetical protein Rv3909 0 37 37 2038 1.000000 E
+Rv3910 - PROBABLE CONSERVED TRANSMEMBRANE PROTEIN 10 49 32 1259 1.000000 E
+Rv3911 sigM RNA polymerase sigma factor SigM 7 9 1 2 0.000000 NE
+Rv3912 - HYPOTHETICAL ALANINE RICH PROTEIN 5 9 2 43 0.000000 NE
+Rv3913 trxB2 PROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) 0 16 16 869 1.000000 E
+Rv3914 trxC THIOREDOXIN TRXC (TRX) (MPT46) 0 5 5 266 0.994000 E
+Rv3915 - PROBABLE HYDROLASE 0 23 23 1034 1.000000 E
+Rv3916c - hypothetical protein Rv3916c 1 8 4 245 0.018600 NE
+Rv3917c parB PROBABLE CHROMOSOME PARTITIONING PROTEIN PARB 0 17 17 845 1.000000 E
+Rv3918c parA PROBABLE CHROMOSOME PARTITIONING PROTEIN PARA 0 18 18 912 1.000000 E
+Rv3919c gidB glucose-inhibited division protein B 8 13 2 8 0.000000 NE
+Rv3920c - HYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN 3 3 0 0 0.000000 NE
+Rv3921c - putative inner membrane protein translocase component YidC 0 20 20 832 1.000000 E
+Rv3922c - hypothetical protein Rv3922c 3 11 7 105 0.001800 NE
+Rv3923c rnpA ribonuclease P 0 3 3 71 -1.000000 S
+Rv3924c rpmH 50S ribosomal protein L34 0 2 2 12 -1.000000 S
+Rvnr01 rrs 16S rRNA 0 58 58 1350 -1.000000 S
diff --git a/src/pytransit/data/hmm_glycerol_sites.dat b/src/pytransit/data/hmm_glycerol_sites.dat
new file mode 100644
index 0000000..315b457
--- /dev/null
+++ b/src/pytransit/data/hmm_glycerol_sites.dat
@@ -0,0 +1,73399 @@
+#HMM - Sites
+# Tn-HMM
+# Command Used: python transit.py
+#
+# Mean: 257.58
+# Median: 132.00
+# pins (obs): 0.541827
+# pins (est): 0.663906
+# Run length (r): 5
+# Self-Transition Prob:
+# ES: -3.5402e-12 GD: -3.5402e-12 NE: -3.5402e-12 GA: -3.5402e-12
+# State Emission Parameters (theta):
+# ES: 0.9900 GD: 0.2531 NE: 0.0051 GA: 0.0010
+# State Distributions:# ES: 16.64% GD: 4.05% NE: 78.04% GA: 1.27%
+60 0 1.00e+00 5.79e-14 8.77e-16 1.75e-16 ES Rv0001_(dnaA)
+72 0 1.00e+00 1.48e-14 4.54e-18 1.81e-19 ES Rv0001_(dnaA)
+102 0 1.00e+00 3.79e-15 2.35e-20 1.87e-22 ES Rv0001_(dnaA)
+188 0 1.00e+00 9.68e-16 1.22e-22 1.96e-25 ES Rv0001_(dnaA)
+246 0 1.00e+00 2.47e-16 6.38e-25 1.65e-27 ES Rv0001_(dnaA)
+333 0 1.00e+00 6.33e-17 1.06e-26 1.45e-27 ES Rv0001_(dnaA)
+360 0 1.00e+00 1.62e-17 7.30e-27 1.45e-27 ES Rv0001_(dnaA)
+426 0 1.00e+00 4.15e-18 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+448 0 1.00e+00 1.07e-18 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+471 0 1.00e+00 2.86e-19 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+483 0 1.00e+00 8.53e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+494 0 1.00e+00 3.38e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+504 0 1.00e+00 2.06e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+514 0 1.00e+00 1.73e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+525 0 1.00e+00 1.65e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+534 0 1.00e+00 1.63e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+601 0 1.00e+00 1.67e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+653 0 1.00e+00 1.82e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+670 0 1.00e+00 2.43e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+706 0 1.00e+00 4.82e-20 7.29e-27 1.45e-27 ES Rv0001_(dnaA)
+741 0 1.00e+00 1.42e-19 7.66e-27 1.45e-27 ES Rv0001_(dnaA)
+784 0 1.00e+00 5.07e-19 7.90e-26 1.45e-27 ES Rv0001_(dnaA)
+794 0 1.00e+00 1.94e-18 1.39e-23 1.45e-27 ES Rv0001_(dnaA)
+843 0 1.00e+00 7.53e-18 2.68e-21 1.45e-27 ES Rv0001_(dnaA)
+989 0 1.00e+00 2.94e-17 5.17e-19 1.46e-27 ES Rv0001_(dnaA)
+1092 0 1.00e+00 1.15e-16 9.98e-17 1.60e-26 ES Rv0001_(dnaA)
+1104 0 1.00e+00 4.50e-16 1.93e-14 1.40e-23 ES Rv0001_(dnaA)
+1267 0 1.00e+00 1.76e-15 3.72e-12 1.35e-20 ES Rv0001_(dnaA)
+1278 0 1.00e+00 6.88e-15 7.19e-10 1.30e-17 ES Rv0001_(dnaA)
+1345 0 1.00e+00 2.69e-14 1.39e-07 1.26e-14 ES Rv0001_(dnaA)
+1423 0 1.00e+00 1.05e-13 2.68e-05 1.22e-11 ES Rv0001_(dnaA)
+1522 124 3.63e-246 2.83e-26 1.00e+00 3.78e-06 NE Rv0001_(dnaA)
+1552 27 4.11e-76 4.13e-26 1.00e+00 2.53e-06 NE
+1635 215 0.00e+00 1.29e-49 1.00e+00 5.49e-06 NE
+1779 0 4.66e-13 5.16e-16 1.00e+00 2.27e-06 NE
+1782 0 4.68e-13 5.26e-16 1.00e+00 2.27e-06 NE
+1788 0 4.68e-13 5.26e-16 1.00e+00 2.27e-06 NE
+1847 0 4.68e-13 5.26e-16 1.00e+00 2.27e-06 NE
+1858 368 0.00e+00 7.79e-62 1.00e+00 1.03e-05 NE
+1921 21 4.13e-64 2.27e-14 1.00e+00 2.47e-06 NE
+2001 0 9.95e-01 4.52e-13 5.18e-03 1.17e-08 ES
+2012 0 1.00e+00 1.18e-13 2.68e-05 1.22e-11 ES
+2063 0 1.00e+00 3.01e-14 1.39e-07 1.26e-14 ES Rv0002_(dnaN)
+2104 0 1.00e+00 7.69e-15 7.19e-10 1.30e-17 ES Rv0002_(dnaN)
+2141 0 1.00e+00 1.97e-15 3.72e-12 1.35e-20 ES Rv0002_(dnaN)
+2232 0 1.00e+00 5.02e-16 1.93e-14 1.40e-23 ES Rv0002_(dnaN)
+2290 0 1.00e+00 1.28e-16 9.98e-17 1.60e-26 ES Rv0002_(dnaN)
+2315 0 1.00e+00 3.28e-17 5.17e-19 1.46e-27 ES Rv0002_(dnaN)
+2318 0 1.00e+00 8.40e-18 2.68e-21 1.45e-27 ES Rv0002_(dnaN)
+2333 0 1.00e+00 2.15e-18 1.39e-23 1.45e-27 ES Rv0002_(dnaN)
+2344 0 1.00e+00 5.51e-19 7.90e-26 1.45e-27 ES Rv0002_(dnaN)
+2363 0 1.00e+00 1.43e-19 7.66e-27 1.45e-27 ES Rv0002_(dnaN)
+2387 0 1.00e+00 3.80e-20 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2404 0 1.00e+00 1.13e-20 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2427 0 1.00e+00 4.49e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2479 0 1.00e+00 2.74e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2507 0 1.00e+00 2.30e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2537 0 1.00e+00 2.22e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2591 0 1.00e+00 2.29e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2648 0 1.00e+00 2.68e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2738 0 1.00e+00 4.24e-21 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2774 0 1.00e+00 1.04e-20 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2845 0 1.00e+00 3.43e-20 7.29e-27 1.45e-27 ES Rv0002_(dnaN)
+2920 0 1.00e+00 1.28e-19 7.66e-27 1.45e-27 ES Rv0002_(dnaN)
+3027 0 1.00e+00 4.93e-19 7.90e-26 1.45e-27 ES Rv0002_(dnaN)
+3056 0 1.00e+00 1.92e-18 1.39e-23 1.45e-27 ES Rv0002_(dnaN)
+3066 0 1.00e+00 7.52e-18 2.68e-21 1.45e-27 ES Rv0002_(dnaN)
+3070 0 1.00e+00 2.94e-17 5.17e-19 1.45e-27 ES Rv0002_(dnaN)
+3119 0 1.00e+00 1.15e-16 9.98e-17 1.48e-27 ES Rv0002_(dnaN)
+3131 0 1.00e+00 4.50e-16 1.93e-14 8.52e-27 ES Rv0002_(dnaN)
+3145 0 1.00e+00 1.76e-15 3.72e-12 2.46e-24 ES Rv0002_(dnaN)
+3222 0 1.00e+00 6.88e-15 7.19e-10 1.53e-21 ES Rv0002_(dnaN)
+3228 0 1.00e+00 2.69e-14 1.39e-07 1.31e-18 ES Rv0002_(dnaN)
+3277 0 1.00e+00 1.05e-13 2.68e-05 1.24e-15 ES
+3283 67 2.71e-132 3.54e-19 1.00e+00 3.03e-10 NE Rv0003_(recF)
+3329 107 5.88e-236 4.67e-29 1.00e+00 3.56e-10 NE Rv0003_(recF)
+3372 0 2.93e-06 1.75e-09 1.00e+00 2.29e-10 NE Rv0003_(recF)
+3379 0 2.94e-06 1.78e-09 1.00e+00 2.44e-13 NE Rv0003_(recF)
+3384 0 2.94e-06 1.78e-09 1.00e+00 1.22e-15 NE Rv0003_(recF)
+3396 0 2.94e-06 1.78e-09 1.00e+00 1.93e-16 NE Rv0003_(recF)
+3412 0 2.94e-06 1.78e-09 1.00e+00 3.85e-17 NE Rv0003_(recF)
+3425 0 2.94e-06 1.78e-09 1.00e+00 7.72e-18 NE Rv0003_(recF)
+3441 0 2.94e-06 1.78e-09 1.00e+00 1.56e-18 NE Rv0003_(recF)
+3467 56 3.90e-118 1.90e-16 1.00e+00 4.21e-19 NE Rv0003_(recF)
+3471 0 3.76e-13 1.73e-09 1.00e+00 8.46e-20 NE Rv0003_(recF)
+3513 0 3.78e-13 1.73e-09 1.00e+00 2.16e-20 NE Rv0003_(recF)
+3591 0 3.78e-13 1.73e-09 1.00e+00 9.06e-21 NE Rv0003_(recF)
+3682 0 3.78e-13 1.73e-09 1.00e+00 6.55e-21 NE Rv0003_(recF)
+3708 112 6.69e-237 1.92e-23 1.00e+00 1.04e-20 NE Rv0003_(recF)
+3728 0 5.22e-20 5.12e-20 1.00e+00 6.49e-21 NE Rv0003_(recF)
+3739 161 0.00e+00 4.51e-40 1.00e+00 1.30e-20 NE Rv0003_(recF)
+3770 13 2.88e-48 2.89e-17 1.00e+00 7.78e-21 NE Rv0003_(recF)
+3782 83 4.12e-188 1.02e-25 1.00e+00 1.48e-20 NE Rv0003_(recF)
+3796 0 1.01e-17 4.43e-07 1.00e+00 2.17e-20 NE Rv0003_(recF)
+3833 28 9.34e-74 1.47e-10 1.00e+00 7.06e-20 NE Rv0003_(recF)
+3925 13 2.75e-44 2.43e-08 1.00e+00 2.79e-19 NE Rv0003_(recF)
+3960 0 5.38e-17 1.48e-06 1.00e+00 1.21e-18 NE Rv0003_(recF)
+3967 0 5.19e-17 1.49e-06 1.00e+00 5.91e-18 NE Rv0003_(recF)
+3986 4 4.42e-25 4.72e-07 1.00e+00 2.99e-17 NE Rv0003_(recF)
+4011 6 3.61e-34 2.66e-07 1.00e+00 1.49e-16 NE Rv0003_(recF)
+4028 1 2.55e-19 1.12e-06 1.00e+00 7.13e-16 NE Rv0003_(recF)
+4094 0 3.85e-17 1.49e-06 1.00e+00 3.52e-15 NE Rv0003_(recF)
+4118 0 3.85e-17 1.49e-06 1.00e+00 1.76e-14 NE Rv0003_(recF)
+4121 110 6.75e-237 2.99e-20 1.00e+00 1.51e-13 NE Rv0003_(recF)
+4130 0 9.95e-01 9.21e-08 5.44e-03 1.74e-15 ES Rv0003_(recF)
+4158 0 1.00e+00 9.38e-08 2.90e-04 8.10e-18 ES Rv0003_(recF)
+4207 0 1.00e+00 9.39e-08 2.64e-04 4.10e-20 ES Rv0003_(recF)
+4217 0 1.00e+00 9.39e-08 2.63e-04 2.12e-22 ES Rv0003_(recF)
+4353 0 1.00e+00 9.39e-08 2.63e-04 3.40e-24 ES Rv0003_(recF)
+4664 0 1.00e+00 9.39e-08 2.63e-04 1.44e-23 ES Rv0004_(-)
+4721 0 1.00e+00 9.39e-08 2.63e-04 2.89e-21 ES Rv0004_(-)
+4789 0 1.00e+00 9.39e-08 2.63e-04 2.74e-18 ES Rv0004_(-)
+4912 0 1.00e+00 9.39e-08 2.63e-04 2.64e-15 ES Rv0004_(-)
+4961 0 1.00e+00 9.39e-08 2.64e-04 2.55e-12 ES Rv0004_(-)
+4970 0 1.00e+00 9.38e-08 2.90e-04 2.46e-09 ES Rv0004_(-)
+4989 23 2.06e-44 2.32e-08 1.00e+00 4.81e-04 NE Rv0004_(-)
+4995 116 9.06e-250 3.89e-21 9.99e-01 7.06e-04 NE Rv0004_(-)
+5066 284 0.00e+00 8.51e-55 9.99e-01 1.41e-03 NE
+5120 81 4.47e-184 6.18e-33 9.99e-01 6.11e-04 NE
+5128 40 3.95e-102 8.60e-28 9.99e-01 5.16e-04 NE Rv0005_(gyrB)
+5170 329 0.00e+00 1.32e-63 9.98e-01 1.69e-03 NE Rv0005_(gyrB)
+5230 0 9.95e-01 4.03e-13 5.17e-03 2.26e-06 ES Rv0005_(gyrB)
+5273 0 1.00e+00 1.05e-13 2.68e-05 2.34e-09 ES Rv0005_(gyrB)
+5287 0 1.00e+00 2.69e-14 1.39e-07 2.43e-12 ES Rv0005_(gyrB)
+5336 0 1.00e+00 6.88e-15 7.17e-10 2.51e-15 ES Rv0005_(gyrB)
+5364 0 1.00e+00 1.76e-15 3.71e-12 2.60e-18 ES Rv0005_(gyrB)
+5420 0 1.00e+00 4.50e-16 1.92e-14 2.70e-21 ES Rv0005_(gyrB)
+5439 0 1.00e+00 1.15e-16 9.96e-17 2.79e-24 ES Rv0005_(gyrB)
+5517 0 1.00e+00 2.94e-17 5.16e-19 4.34e-27 ES Rv0005_(gyrB)
+5547 0 1.00e+00 7.52e-18 2.67e-21 1.45e-27 ES Rv0005_(gyrB)
+5579 0 1.00e+00 1.92e-18 1.38e-23 1.45e-27 ES Rv0005_(gyrB)
+5586 0 1.00e+00 4.91e-19 7.89e-26 1.45e-27 ES Rv0005_(gyrB)
+5623 0 1.00e+00 1.26e-19 7.66e-27 1.45e-27 ES Rv0005_(gyrB)
+5631 0 1.00e+00 3.21e-20 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+5669 0 1.00e+00 8.21e-21 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+5687 0 1.00e+00 2.10e-21 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+5792 0 1.00e+00 5.38e-22 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+5977 0 1.00e+00 1.38e-22 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+5996 0 1.00e+00 3.63e-23 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6055 0 1.00e+00 1.02e-23 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6128 0 1.00e+00 3.63e-24 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6230 0 1.00e+00 2.36e-24 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6249 0 1.00e+00 3.64e-24 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6286 0 1.00e+00 1.03e-23 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6403 0 1.00e+00 3.65e-23 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6490 0 1.00e+00 1.39e-22 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6502 0 1.00e+00 5.42e-22 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6526 0 1.00e+00 2.12e-21 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6605 0 1.00e+00 8.27e-21 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6612 0 1.00e+00 3.24e-20 7.29e-27 1.45e-27 ES Rv0005_(gyrB)
+6672 0 1.00e+00 1.27e-19 7.63e-27 1.45e-27 ES Rv0005_(gyrB)
+6729 0 1.00e+00 4.95e-19 7.34e-26 1.45e-27 ES Rv0005_(gyrB)
+6793 0 1.00e+00 1.94e-18 1.28e-23 1.45e-27 ES Rv0005_(gyrB)
+6809 0 1.00e+00 7.57e-18 2.47e-21 1.55e-27 ES Rv0005_(gyrB)
+6856 0 1.00e+00 2.96e-17 4.76e-19 1.05e-25 ES Rv0005_(gyrB)
+6944 0 1.00e+00 1.16e-16 9.20e-17 1.00e-22 ES Rv0005_(gyrB)
+6983 0 1.00e+00 4.53e-16 1.78e-14 9.69e-20 ES Rv0005_(gyrB)
+7067 0 1.00e+00 1.77e-15 3.43e-12 9.36e-17 ES Rv0005_(gyrB)
+7077 0 1.00e+00 6.93e-15 6.62e-10 9.04e-14 ES Rv0005_(gyrB)
+7093 0 1.00e+00 2.71e-14 1.28e-07 8.73e-11 ES Rv0005_(gyrB)
+7225 0 1.00e+00 1.06e-13 2.47e-05 8.43e-08 ES Rv0005_(gyrB)
+7265 31 2.40e-60 1.15e-14 9.81e-01 1.90e-02 NE Rv0005_(gyrB)
+7299 155 0.00e+00 3.55e-32 9.69e-01 3.13e-02 NE
+7383 0 9.95e-01 4.03e-13 4.77e-03 8.14e-05 ES Rv0006_(gyrA)
+7392 0 1.00e+00 1.05e-13 2.47e-05 8.43e-08 ES Rv0006_(gyrA)
+7470 0 1.00e+00 2.69e-14 1.28e-07 8.73e-11 ES Rv0006_(gyrA)
+7551 0 1.00e+00 6.87e-15 6.62e-10 9.04e-14 ES Rv0006_(gyrA)
+7578 0 1.00e+00 1.76e-15 3.43e-12 9.36e-17 ES Rv0006_(gyrA)
+7620 0 1.00e+00 4.49e-16 1.78e-14 9.69e-20 ES Rv0006_(gyrA)
+7686 0 1.00e+00 1.15e-16 9.20e-17 1.00e-22 ES Rv0006_(gyrA)
+7763 0 1.00e+00 2.94e-17 4.76e-19 1.05e-25 ES Rv0006_(gyrA)
+7767 0 1.00e+00 7.51e-18 2.47e-21 1.55e-27 ES Rv0006_(gyrA)
+7798 0 1.00e+00 1.92e-18 1.28e-23 1.45e-27 ES Rv0006_(gyrA)
+7865 0 1.00e+00 4.91e-19 7.34e-26 1.45e-27 ES Rv0006_(gyrA)
+7970 0 1.00e+00 1.25e-19 7.63e-27 1.45e-27 ES Rv0006_(gyrA)
+8031 0 1.00e+00 3.21e-20 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8077 0 1.00e+00 8.20e-21 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8099 0 1.00e+00 2.10e-21 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8127 0 1.00e+00 5.37e-22 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8219 0 1.00e+00 1.38e-22 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8236 0 1.00e+00 3.57e-23 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8288 0 1.00e+00 9.61e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8295 0 1.00e+00 2.94e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8338 0 1.00e+00 1.23e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8391 0 1.00e+00 8.05e-25 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8394 0 1.00e+00 7.22e-25 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8436 0 1.00e+00 8.05e-25 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8486 0 1.00e+00 1.23e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8546 0 1.00e+00 2.94e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8786 0 1.00e+00 9.62e-24 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8858 0 1.00e+00 3.57e-23 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8874 0 1.00e+00 1.38e-22 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+8901 0 1.00e+00 5.37e-22 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+9030 0 1.00e+00 2.10e-21 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
+9045 0 1.00e+00 8.21e-21 7.29e-27 1.45e-27 ES Rv0006_(gyrA)
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+490758 420 0.00e+00 3.48e-75 1.00e+00 1.21e-14 NE
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+490771 100 4.51e-222 2.44e-35 1.00e+00 1.46e-15 NE
+490799 227 0.00e+00 3.74e-51 1.00e+00 1.14e-15 NE Rv0407_(fgd1)
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+491807 74 3.93e-170 4.25e-32 1.00e+00 1.47e-24 NE Rv0408_(pta)
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+493356 19 1.58e-54 3.63e-14 1.00e+00 5.65e-25 NE Rv0408_(pta)
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+493414 74 3.93e-170 1.59e-30 1.00e+00 7.38e-25 NE Rv0408_(pta)
+493481 0 1.95e-15 8.45e-18 1.00e+00 5.91e-25 NE Rv0408_(pta)
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+493684 0 1.96e-15 8.62e-18 1.00e+00 3.02e-24 NE Rv0408_(pta)
+493700 143 4.06e-301 1.32e-35 1.00e+00 2.39e-23 NE Rv0408_(pta)
+493758 1 7.95e-24 1.97e-21 1.00e+00 4.18e-23 NE Rv0408_(pta)
+493779 182 0.00e+00 5.70e-44 1.00e+00 3.87e-22 NE Rv0408_(pta)
+493806 1080 0.00e+00 2.29e-157 1.00e+00 4.39e-20 NE Rv0408_(pta)
+493856 440 0.00e+00 1.12e-77 1.00e+00 3.28e-21 NE Rv0408_(pta),Rv0409_(ackA)
+494185 81 4.08e-184 5.64e-33 1.00e+00 7.60e-22 NE Rv0409_(ackA)
+494246 138 5.47e-298 4.51e-40 1.00e+00 1.04e-21 NE Rv0409_(ackA)
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+494556 63 7.22e-146 3.40e-25 1.00e+00 5.50e-19 NE Rv0409_(ackA)
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+494665 0 1.01e-17 2.16e-19 1.00e+00 8.26e-18 NE Rv0409_(ackA)
+494703 285 0.00e+00 6.91e-55 1.00e+00 1.32e-16 NE Rv0409_(ackA)
+494733 14 2.89e-50 1.07e-22 1.00e+00 9.69e-17 NE Rv0409_(ackA)
+494745 0 5.25e-20 1.25e-20 1.00e+00 3.30e-16 NE Rv0409_(ackA)
+494783 14 5.64e-48 2.25e-22 1.00e+00 1.61e-15 NE Rv0409_(ackA)
+494848 172 0.00e+00 2.30e-42 1.00e+00 1.45e-14 NE Rv0409_(ackA)
+494852 51 3.70e-124 3.25e-29 1.00e+00 2.60e-14 NE Rv0409_(ackA)
+495013 247 0.00e+00 1.50e-53 1.00e+00 2.14e-13 NE
+495063 188 0.00e+00 3.84e-46 1.00e+00 3.88e-13 NE Rv0410c_(pknG)
+495111 0 9.95e-01 4.03e-13 5.18e-03 2.14e-15 ES Rv0410c_(pknG)
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+495428 0 1.00e+00 2.69e-14 1.39e-07 4.15e-20 ES Rv0410c_(pknG)
+495540 0 1.00e+00 6.88e-15 7.19e-10 2.12e-22 ES Rv0410c_(pknG)
+495569 0 1.00e+00 1.76e-15 3.72e-12 1.10e-24 ES Rv0410c_(pknG)
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+495660 0 1.00e+00 1.15e-16 9.98e-17 1.47e-27 ES Rv0410c_(pknG)
+495693 0 1.00e+00 2.94e-17 5.17e-19 1.45e-27 ES Rv0410c_(pknG)
+495797 0 1.00e+00 7.52e-18 2.68e-21 1.45e-27 ES Rv0410c_(pknG)
+495875 0 1.00e+00 1.92e-18 1.39e-23 1.45e-27 ES Rv0410c_(pknG)
+496014 0 1.00e+00 4.91e-19 7.90e-26 1.45e-27 ES Rv0410c_(pknG)
+496082 0 1.00e+00 1.26e-19 7.66e-27 1.45e-27 ES Rv0410c_(pknG)
+496218 0 1.00e+00 3.21e-20 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496227 0 1.00e+00 8.21e-21 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496256 0 1.00e+00 2.10e-21 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496269 0 1.00e+00 5.37e-22 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496329 0 1.00e+00 1.38e-22 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496395 0 1.00e+00 3.57e-23 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496401 0 1.00e+00 9.61e-24 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496424 0 1.00e+00 2.94e-24 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496494 0 1.00e+00 1.23e-24 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496518 0 1.00e+00 7.93e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496548 0 1.00e+00 6.81e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496614 0 1.00e+00 6.52e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496629 0 1.00e+00 6.45e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496818 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496863 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496892 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496911 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+496926 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+497056 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0410c_(pknG)
+497324 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497378 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497474 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497505 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497513 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497527 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497652 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497765 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+497885 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0411c_(glnH)
+498307 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv0412c_(-)
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+498914 0 1.00e+00 2.07e-22 7.29e-27 1.45e-27 ES Rv0412c_(-)
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+499057 0 1.00e+00 3.16e-21 7.29e-27 1.45e-27 ES Rv0412c_(-)
+499117 0 1.00e+00 1.24e-20 7.29e-27 1.45e-27 ES Rv0412c_(-)
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+499291 0 1.00e+00 1.13e-17 1.39e-23 1.45e-27 ES Rv0412c_(-)
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+499460 0 1.00e+00 6.77e-16 9.98e-17 3.37e-25 ES Rv0412c_(-)
+499626 0 1.00e+00 2.65e-15 1.93e-14 3.24e-22 ES
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+499700 8 2.00e-14 4.71e-11 1.00e+00 5.43e-05 NE
+499706 520 0.00e+00 6.93e-75 1.00e+00 4.46e-04 NE
+499734 48 4.65e-118 1.06e-28 1.00e+00 6.40e-05 NE Rv0413_(mutT3)
+499794 2 1.50e-25 6.34e-20 1.00e+00 5.29e-05 NE Rv0413_(mutT3)
+499806 0 5.83e-20 1.16e-19 1.00e+00 5.25e-05 NE Rv0413_(mutT3)
+500064 1736 0.00e+00 7.40e-236 9.38e-01 6.22e-02 NE Rv0413_(mutT3)
+500170 84 7.74e-190 4.46e-33 1.00e+00 7.42e-05 NE Rv0413_(mutT3)
+500303 775 0.00e+00 2.71e-119 9.99e-01 1.27e-03 NE Rv0413_(mutT3)
+500342 273 0.00e+00 1.53e-56 1.00e+00 1.61e-04 NE Rv0413_(mutT3)
+500364 299 0.00e+00 7.00e-60 1.00e+00 1.80e-04 NE Rv0413_(mutT3),Rv0414c_(thiE)
+500493 0 1.32e-01 7.05e-06 8.68e-01 4.56e-05 NE Rv0414c_(thiE)
+500539 0 1.32e-01 7.16e-06 8.68e-01 4.74e-08 NE Rv0414c_(thiE)
+500609 0 1.32e-01 7.16e-06 8.68e-01 1.74e-10 NE Rv0414c_(thiE)
+500676 0 1.32e-01 7.16e-06 8.68e-01 1.25e-10 NE Rv0414c_(thiE)
+500763 0 1.32e-01 7.16e-06 8.68e-01 1.25e-10 NE Rv0414c_(thiE)
+500788 0 1.32e-01 7.16e-06 8.68e-01 1.25e-10 NE Rv0414c_(thiE)
+500798 0 1.32e-01 7.16e-06 8.68e-01 1.25e-10 NE Rv0414c_(thiE)
+500854 0 1.32e-01 7.16e-06 8.68e-01 1.25e-10 NE Rv0414c_(thiE)
+500984 0 1.32e-01 7.16e-06 8.68e-01 5.21e-10 NE Rv0414c_(thiE)
+501029 113 2.71e-227 7.01e-20 1.00e+00 7.02e-07 NE
+501037 1 1.67e-21 6.06e-06 1.00e+00 4.43e-07 NE
+501052 0 2.00e-19 8.07e-06 1.00e+00 4.41e-07 NE
+501102 24 2.23e-67 8.28e-09 1.00e+00 4.87e-07 NE
+501161 0 9.95e-01 4.18e-08 5.18e-03 2.28e-09 ES Rv0415_(thiO)
+501347 0 1.00e+00 1.07e-08 2.68e-05 2.36e-12 ES Rv0415_(thiO)
+501545 0 1.00e+00 2.73e-09 1.39e-07 2.45e-15 ES Rv0415_(thiO)
+501752 0 1.00e+00 6.98e-10 7.19e-10 2.54e-18 ES Rv0415_(thiO)
+501801 0 1.00e+00 1.79e-10 3.72e-12 2.63e-21 ES Rv0415_(thiO)
+501853 0 1.00e+00 4.59e-11 1.93e-14 2.89e-24 ES Rv0415_(thiO)
+501898 0 1.00e+00 1.20e-11 9.98e-17 4.60e-26 ES Rv0415_(thiO)
+501929 0 1.00e+00 3.28e-12 5.17e-19 1.21e-26 ES Rv0415_(thiO)
+501950 0 1.00e+00 1.06e-12 2.68e-21 4.17e-27 ES Rv0415_(thiO)
+501963 0 1.00e+00 4.95e-13 1.39e-23 2.14e-27 ES Rv0415_(thiO)
+501988 0 1.00e+00 3.50e-13 8.00e-26 1.62e-27 ES Rv0415_(thiO)
+502106 0 1.00e+00 3.13e-13 7.89e-27 1.49e-27 ES Rv0415_(thiO)
+502259 0 1.00e+00 3.03e-13 7.35e-27 1.46e-27 ES Rv0416_(thiS)
+502288 0 1.00e+00 3.01e-13 7.30e-27 1.45e-27 ES Rv0416_(thiS)
+502328 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0416_(thiS)
+502342 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0416_(thiS)
+502386 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0417_(thiG)
+502425 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0417_(thiG)
+502454 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0417_(thiG)
+502479 0 1.00e+00 3.00e-13 7.29e-27 1.45e-27 ES Rv0417_(thiG)
+502502 0 1.00e+00 3.00e-13 7.66e-27 1.45e-27 ES Rv0417_(thiG)
+502571 0 1.00e+00 3.00e-13 7.90e-26 1.45e-27 ES Rv0417_(thiG)
+502709 0 1.00e+00 3.00e-13 1.39e-23 1.45e-27 ES Rv0417_(thiG)
+502754 0 1.00e+00 3.00e-13 2.68e-21 1.45e-27 ES Rv0417_(thiG)
+502759 0 1.00e+00 3.01e-13 5.17e-19 1.45e-27 ES Rv0417_(thiG)
+502793 0 1.00e+00 3.03e-13 9.98e-17 1.49e-27 ES Rv0417_(thiG)
+502800 0 1.00e+00 3.12e-13 1.93e-14 7.15e-27 ES Rv0417_(thiG)
+502854 0 1.00e+00 3.46e-13 3.72e-12 1.10e-24 ES Rv0417_(thiG)
+502872 0 1.00e+00 4.78e-13 7.19e-10 2.13e-22 ES Rv0417_(thiG)
+502929 0 1.00e+00 9.95e-13 1.39e-07 4.24e-20 ES Rv0417_(thiG)
+503056 0 1.00e+00 3.02e-12 2.68e-05 9.43e-18 ES Rv0417_(thiG)
+503122 16 2.09e-30 2.15e-11 1.00e+00 6.22e-13 NE Rv0417_(thiG)
+503161 0 9.94e-20 2.03e-09 1.00e+00 3.48e-13 NE
+503198 180 0.00e+00 7.68e-32 1.00e+00 6.24e-13 NE
+503211 595 0.00e+00 5.73e-97 1.00e+00 3.32e-12 NE
+503213 1088 0.00e+00 2.41e-158 1.00e+00 2.49e-11 NE
+503242 204 0.00e+00 4.71e-48 1.00e+00 6.33e-13 NE
+503273 0 6.97e-20 4.63e-21 1.00e+00 1.02e-13 NE
+503287 101 1.17e-221 1.22e-33 1.00e+00 3.51e-14 NE
+503296 0 5.33e-20 3.53e-21 1.00e+00 7.30e-15 NE
+503302 450 0.00e+00 3.28e-77 1.00e+00 1.59e-14 NE
+503360 0 5.25e-20 3.49e-21 1.00e+00 1.54e-15 NE
+503378 40 6.45e-100 3.65e-26 1.00e+00 3.76e-16 NE
+503400 38 3.27e-98 4.34e-27 1.00e+00 8.72e-17 NE
+503412 0 1.01e-17 1.74e-19 1.00e+00 1.69e-17 NE
+503483 0 1.01e-17 1.77e-19 1.00e+00 3.42e-18 NE
+503570 28 1.16e-73 5.68e-23 1.00e+00 8.10e-19 NE Rv0418_(lpqL)
+503582 174 0.00e+00 6.10e-43 1.00e+00 3.74e-19 NE Rv0418_(lpqL)
+503603 0 1.95e-15 3.50e-16 1.00e+00 6.19e-20 NE Rv0418_(lpqL)
+503677 0 1.96e-15 3.57e-16 1.00e+00 1.24e-20 NE Rv0418_(lpqL)
+503739 0 1.96e-15 3.57e-16 1.00e+00 2.49e-21 NE Rv0418_(lpqL)
+503757 26 2.23e-67 2.07e-19 1.00e+00 5.65e-22 NE Rv0418_(lpqL)
+503764 3 2.84e-28 1.47e-16 1.00e+00 1.13e-22 NE Rv0418_(lpqL)
+503886 0 5.22e-20 3.48e-16 1.00e+00 2.37e-23 NE Rv0418_(lpqL)
+503973 17 5.70e-54 2.62e-18 1.00e+00 6.33e-24 NE Rv0418_(lpqL)
+504010 390 0.00e+00 2.58e-65 1.00e+00 1.32e-23 NE Rv0418_(lpqL)
+504128 0 5.22e-20 3.46e-21 1.00e+00 1.91e-24 NE Rv0418_(lpqL)
+504131 171 0.00e+00 1.77e-42 1.00e+00 2.09e-24 NE Rv0418_(lpqL)
+504184 346 0.00e+00 5.68e-66 1.00e+00 4.42e-24 NE Rv0418_(lpqL)
+504418 0 5.22e-20 3.46e-21 1.00e+00 9.35e-25 NE Rv0418_(lpqL)
+504471 241 0.00e+00 3.40e-51 1.00e+00 1.93e-24 NE Rv0418_(lpqL)
+504516 42 3.34e-106 4.05e-28 1.00e+00 7.89e-25 NE Rv0418_(lpqL)
+504555 54 3.55e-130 1.30e-29 1.00e+00 6.64e-25 NE Rv0418_(lpqL)
+504564 74 3.93e-170 4.39e-32 1.00e+00 6.87e-25 NE Rv0418_(lpqL)
+504589 0 1.95e-15 1.06e-16 1.00e+00 4.79e-25 NE Rv0418_(lpqL)
+504632 0 1.96e-15 1.08e-16 1.00e+00 4.56e-25 NE Rv0418_(lpqL)
+504654 0 1.96e-15 1.08e-16 1.00e+00 5.01e-25 NE Rv0418_(lpqL)
+504711 5 2.00e-25 2.57e-17 1.00e+00 7.73e-25 NE Rv0418_(lpqL)
+504734 96 5.04e-214 1.11e-28 1.00e+00 2.98e-24 NE Rv0418_(lpqL)
+504834 961 0.00e+00 1.50e-142 1.00e+00 3.18e-22 NE Rv0418_(lpqL)
+504863 68 3.81e-158 2.35e-31 1.00e+00 8.10e-24 NE Rv0418_(lpqL)
+504884 37 3.25e-96 1.70e-27 1.00e+00 2.71e-24 NE Rv0418_(lpqL)
+504906 85 4.16e-192 1.79e-33 1.00e+00 2.41e-24 NE Rv0418_(lpqL)
+504921 632 0.00e+00 1.39e-101 1.00e+00 3.85e-23 NE Rv0418_(lpqL)
+505039 320 0.00e+00 9.82e-63 1.00e+00 1.10e-23 NE
+505080 61 3.68e-144 2.01e-30 1.00e+00 2.36e-24 NE
+505104 0 1.95e-15 8.45e-18 1.00e+00 7.97e-25 NE Rv0419_(lpqM)
+505174 0 1.96e-15 8.62e-18 1.00e+00 5.13e-25 NE Rv0419_(lpqM)
+505192 0 1.96e-15 8.62e-18 1.00e+00 4.74e-25 NE Rv0419_(lpqM)
+505389 117 3.55e-249 2.28e-32 1.00e+00 9.00e-25 NE Rv0419_(lpqM)
+505404 138 5.47e-298 4.51e-40 1.00e+00 1.25e-24 NE Rv0419_(lpqM)
+505455 345 0.00e+00 7.57e-66 1.00e+00 3.97e-24 NE Rv0419_(lpqM)
+505475 55 3.57e-132 9.75e-30 1.00e+00 1.23e-24 NE Rv0419_(lpqM)
+505503 268 0.00e+00 2.93e-56 1.00e+00 3.00e-24 NE Rv0419_(lpqM)
+505587 347 0.00e+00 4.27e-66 1.00e+00 4.83e-24 NE Rv0419_(lpqM)
+505664 0 5.22e-20 3.46e-21 1.00e+00 1.00e-24 NE Rv0419_(lpqM)
+505722 152 9.88e-324 4.10e-40 1.00e+00 1.49e-24 NE Rv0419_(lpqM)
+505745 289 0.00e+00 7.11e-59 1.00e+00 3.36e-24 NE Rv0419_(lpqM)
+505760 292 0.00e+00 3.01e-59 1.00e+00 3.84e-24 NE Rv0419_(lpqM)
+506100 60 3.66e-142 2.32e-30 1.00e+00 1.31e-24 NE Rv0419_(lpqM)
+506148 293 0.00e+00 2.26e-59 1.00e+00 3.28e-24 NE Rv0419_(lpqM)
+506277 173 0.00e+00 1.98e-44 1.00e+00 2.12e-24 NE Rv0419_(lpqM)
+506335 10 2.83e-42 5.57e-22 1.00e+00 1.06e-24 NE Rv0419_(lpqM)
+506413 0 5.22e-20 1.32e-20 1.00e+00 1.81e-24 NE Rv0419_(lpqM)
+506417 95 8.51e-210 1.93e-32 1.00e+00 9.72e-24 NE Rv0419_(lpqM)
+506518 2 2.77e-26 1.12e-21 1.00e+00 2.29e-23 NE Rv0419_(lpqM)
+506562 989 0.00e+00 1.41e-144 1.00e+00 6.00e-21 NE Rv0419_(lpqM),Rv0420c_(-)
+506571 0 5.22e-20 3.46e-21 1.00e+00 1.09e-22 NE Rv0419_(lpqM),Rv0420c_(-)
+506580 48 6.68e-116 3.65e-27 1.00e+00 1.67e-22 NE Rv0419_(lpqM),Rv0420c_(-)
+506681 220 0.00e+00 2.79e-50 1.00e+00 6.67e-22 NE Rv0420c_(-)
+506687 267 0.00e+00 3.90e-56 1.00e+00 1.62e-21 NE Rv0420c_(-)
+506742 149 5.78e-320 1.92e-41 1.00e+00 1.82e-21 NE Rv0420c_(-)
+506799 140 5.52e-302 2.54e-40 1.00e+00 3.92e-21 NE Rv0420c_(-)
+506808 88 4.23e-198 7.58e-34 1.00e+00 8.07e-21 NE Rv0420c_(-)
+506820 154 0.00e+00 4.59e-42 1.00e+00 3.30e-20 NE Rv0420c_(-)
+506872 141 5.55e-304 1.91e-40 1.00e+00 8.76e-20 NE Rv0420c_(-)
+507051 364 0.00e+00 3.26e-68 1.00e+00 6.14e-19 NE
+507066 1 1.02e-21 9.64e-20 1.00e+00 2.37e-19 NE
+507089 0 1.54e-19 1.32e-19 1.00e+00 7.28e-19 NE
+507098 131 3.00e-281 6.31e-36 1.00e+00 5.46e-18 NE
+507138 999 0.00e+00 2.79e-147 1.00e+00 6.31e-16 NE Rv0421c_(-)
+507159 270 0.00e+00 1.65e-56 1.00e+00 3.33e-17 NE Rv0421c_(-)
+507356 0 3.77e-13 2.13e-09 1.00e+00 1.19e-17 NE Rv0421c_(-)
+507394 0 3.79e-13 2.18e-09 1.00e+00 1.68e-17 NE Rv0421c_(-)
+507466 0 3.79e-13 2.18e-09 1.00e+00 4.10e-17 NE Rv0421c_(-)
+507592 0 3.79e-13 2.18e-09 1.00e+00 1.62e-16 NE Rv0421c_(-)
+507604 5 3.87e-23 5.19e-10 1.00e+00 7.85e-16 NE Rv0421c_(-)
+507674 0 3.80e-16 2.18e-09 1.00e+00 3.74e-15 NE Rv0421c_(-)
+507692 0 3.80e-16 2.18e-09 1.00e+00 1.86e-14 NE Rv0421c_(-)
+507702 111 6.70e-238 3.28e-23 1.00e+00 1.71e-13 NE Rv0421c_(-)
+507810 0 9.95e-01 9.74e-11 5.18e-03 1.78e-15 ES Rv0422c_(thiD)
+507832 0 1.00e+00 9.88e-11 2.68e-05 8.14e-18 ES Rv0422c_(thiD)
+507944 0 1.00e+00 9.88e-11 1.39e-07 4.11e-20 ES Rv0422c_(thiD)
+507966 0 1.00e+00 9.87e-11 7.19e-10 2.11e-22 ES Rv0422c_(thiD)
+507984 0 1.00e+00 9.87e-11 3.72e-12 1.10e-24 ES Rv0422c_(thiD)
+508100 0 1.00e+00 9.87e-11 2.00e-14 7.11e-27 ES Rv0422c_(thiD)
+508108 0 1.00e+00 9.87e-11 8.06e-16 1.47e-27 ES Rv0422c_(thiD)
+508112 0 1.00e+00 9.87e-11 7.06e-16 1.45e-27 ES Rv0422c_(thiD)
+508232 0 1.00e+00 9.87e-11 7.06e-16 1.83e-27 ES Rv0422c_(thiD)
+508402 0 1.00e+00 9.87e-11 7.06e-16 3.74e-25 ES Rv0422c_(thiD)
+508427 0 1.00e+00 9.87e-11 7.78e-16 3.60e-22 ES Rv0422c_(thiD)
+508432 0 1.00e+00 9.87e-11 1.45e-14 3.48e-19 ES Rv0422c_(thiD)
+508466 0 1.00e+00 9.87e-11 2.67e-12 3.36e-16 ES Rv0422c_(thiD)
+508486 0 1.00e+00 9.87e-11 5.16e-10 3.24e-13 ES Rv0422c_(thiD)
+508578 0 1.00e+00 9.88e-11 9.97e-08 3.13e-10 ES
+508591 0 1.00e+00 9.88e-11 1.93e-05 3.02e-07 ES Rv0423c_(thiC)
+508601 166 0.00e+00 4.86e-29 8.65e-01 1.35e-01 NE Rv0423c_(thiC)
+508706 0 9.96e-01 7.72e-13 3.72e-03 2.92e-04 ES Rv0423c_(thiC)
+508955 0 1.00e+00 4.79e-13 1.93e-05 3.02e-07 ES Rv0423c_(thiC)
+509021 0 1.00e+00 4.01e-13 9.97e-08 3.13e-10 ES Rv0423c_(thiC)
+509037 0 1.00e+00 3.81e-13 5.16e-10 3.24e-13 ES Rv0423c_(thiC)
+509087 0 1.00e+00 3.76e-13 2.67e-12 3.36e-16 ES Rv0423c_(thiC)
+509126 0 1.00e+00 3.75e-13 1.38e-14 3.48e-19 ES Rv0423c_(thiC)
+509193 0 1.00e+00 3.74e-13 7.17e-17 3.60e-22 ES Rv0423c_(thiC)
+509348 0 1.00e+00 3.74e-13 3.71e-19 3.74e-25 ES Rv0423c_(thiC)
+509361 0 1.00e+00 3.74e-13 1.92e-21 1.83e-27 ES Rv0423c_(thiC)
+509387 0 1.00e+00 3.74e-13 1.05e-23 1.45e-27 ES Rv0423c_(thiC)
+509486 0 1.00e+00 3.74e-13 6.38e-25 1.45e-27 ES Rv0423c_(thiC)
+509519 0 1.00e+00 3.74e-13 1.44e-23 1.45e-27 ES Rv0423c_(thiC)
+509561 0 1.00e+00 3.74e-13 2.68e-21 1.45e-27 ES Rv0423c_(thiC)
+509615 0 1.00e+00 3.74e-13 5.17e-19 1.45e-27 ES Rv0423c_(thiC)
+509899 0 1.00e+00 3.74e-13 9.98e-17 1.47e-27 ES Rv0423c_(thiC)
+510009 0 1.00e+00 3.75e-13 1.93e-14 7.11e-27 ES Rv0423c_(thiC)
+510056 0 1.00e+00 3.76e-13 3.72e-12 1.10e-24 ES Rv0423c_(thiC)
+510074 0 1.00e+00 3.81e-13 7.19e-10 2.12e-22 ES Rv0423c_(thiC)
+510132 0 1.00e+00 4.01e-13 1.39e-07 4.16e-20 ES Rv0423c_(thiC)
+510164 0 1.00e+00 4.79e-13 2.68e-05 8.67e-18 ES Rv0423c_(thiC)
+510237 294 0.00e+00 3.67e-47 1.00e+00 1.48e-12 NE
+510248 0 8.71e-20 5.78e-21 1.00e+00 2.06e-13 NE
+510264 75 1.28e-169 2.63e-30 1.00e+00 6.59e-14 NE
+510322 18 3.06e-58 5.25e-25 1.00e+00 1.82e-14 NE
+510333 51 3.52e-124 3.99e-29 1.00e+00 1.03e-14 NE
+510378 43 3.36e-108 3.05e-28 1.00e+00 7.74e-15 NE Rv0424c_(-)
+510430 256 0.00e+00 9.15e-55 1.00e+00 1.73e-14 NE Rv0424c_(-)
+510442 1338 0.00e+00 1.72e-189 1.00e+00 1.46e-12 NE Rv0424c_(-)
+510457 0 5.29e-20 3.51e-21 1.00e+00 5.86e-15 NE Rv0424c_(-)
+510516 483 0.00e+00 2.53e-81 1.00e+00 2.04e-14 NE Rv0424c_(-)
+510519 62 3.71e-146 1.32e-30 1.00e+00 2.82e-15 NE Rv0424c_(-)
+510580 701 0.00e+00 3.56e-110 1.00e+00 2.31e-14 NE Rv0424c_(-)
+510601 0 5.24e-20 3.48e-21 1.00e+00 1.06e-15 NE Rv0424c_(-)
+510637 100 8.76e-220 1.23e-33 1.00e+00 3.52e-16 NE Rv0424c_(-)
+510667 0 5.22e-20 3.46e-21 1.00e+00 6.80e-17 NE
+510715 207 0.00e+00 5.82e-47 1.00e+00 4.26e-17 NE Rv0425c_(ctpH)
+510786 21 3.00e-64 1.87e-25 1.00e+00 8.94e-18 NE Rv0425c_(ctpH)
+510797 199 0.00e+00 1.28e-47 1.00e+00 8.02e-18 NE Rv0425c_(ctpH)
+511238 0 5.22e-20 3.46e-21 1.00e+00 2.52e-18 NE Rv0425c_(ctpH)
+511254 1067 0.00e+00 4.79e-154 1.00e+00 1.66e-16 NE Rv0425c_(ctpH)
+511290 1 7.95e-24 1.97e-21 1.00e+00 1.97e-18 NE Rv0425c_(ctpH)
+511397 187 0.00e+00 1.36e-44 1.00e+00 1.02e-18 NE Rv0425c_(ctpH)
+511518 0 5.22e-20 3.46e-21 1.00e+00 1.76e-19 NE Rv0425c_(ctpH)
+511686 281 0.00e+00 3.55e-56 1.00e+00 1.49e-19 NE Rv0425c_(ctpH)
+511731 0 5.22e-20 3.46e-21 1.00e+00 2.11e-20 NE Rv0425c_(ctpH)
+511781 125 9.92e-270 9.44e-37 1.00e+00 7.79e-21 NE Rv0425c_(ctpH)
+511838 0 1.01e-17 1.71e-19 1.00e+00 1.38e-21 NE Rv0425c_(ctpH)
+511868 0 1.01e-17 1.74e-19 1.00e+00 2.84e-22 NE Rv0425c_(ctpH)
+511899 89 1.59e-195 1.42e-30 1.00e+00 9.26e-23 NE Rv0425c_(ctpH)
+512186 76 3.97e-174 2.37e-32 1.00e+00 2.79e-23 NE Rv0425c_(ctpH)
+512502 71 3.87e-164 9.92e-32 1.00e+00 1.07e-23 NE Rv0425c_(ctpH)
+512582 0 5.22e-20 3.46e-21 1.00e+00 5.26e-24 NE Rv0425c_(ctpH)
+512604 761 0.00e+00 6.06e-116 1.00e+00 1.87e-22 NE Rv0425c_(ctpH)
+512821 303 0.00e+00 1.29e-60 1.00e+00 2.95e-23 NE Rv0425c_(ctpH)
+513025 240 0.00e+00 8.98e-53 1.00e+00 1.76e-23 NE Rv0425c_(ctpH)
+513137 197 0.00e+00 2.03e-47 1.00e+00 1.22e-23 NE Rv0425c_(ctpH)
+513224 685 0.00e+00 3.50e-108 1.00e+00 9.43e-23 NE Rv0425c_(ctpH)
+513300 171 0.00e+00 3.51e-44 1.00e+00 1.03e-23 NE Rv0425c_(ctpH)
+513355 0 1.95e-15 8.45e-18 1.00e+00 2.07e-24 NE Rv0425c_(ctpH)
+513499 0 1.96e-15 8.62e-18 1.00e+00 7.63e-25 NE Rv0425c_(ctpH)
+513614 0 1.96e-15 8.62e-18 1.00e+00 5.06e-25 NE Rv0425c_(ctpH)
+513700 50 2.52e-115 5.02e-24 1.00e+00 5.79e-25 NE Rv0425c_(ctpH)
+513773 18 2.95e-58 5.75e-24 1.00e+00 5.05e-25 NE Rv0425c_(ctpH)
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+1054409 0 1.95e-15 1.40e-17 1.00e+00 8.34e-19 NE Rv0945_(-)
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+1054721 0 1.96e-15 1.43e-17 1.00e+00 1.93e-17 NE Rv0945_(-)
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+1055025 25 8.63e-70 5.27e-13 1.00e+00 7.32e-14 NE Rv0946c_(pgi)
+1055052 0 9.95e-01 5.38e-12 5.18e-03 1.56e-15 ES Rv0946c_(pgi)
+1055117 0 1.00e+00 4.54e-12 2.68e-05 7.92e-18 ES Rv0946c_(pgi)
+1055182 0 1.00e+00 4.31e-12 1.39e-07 4.08e-20 ES Rv0946c_(pgi)
+1055220 0 1.00e+00 4.25e-12 7.19e-10 2.11e-22 ES Rv0946c_(pgi)
+1055305 0 1.00e+00 4.24e-12 3.72e-12 1.10e-24 ES Rv0946c_(pgi)
+1055312 0 1.00e+00 4.23e-12 1.93e-14 7.11e-27 ES Rv0946c_(pgi)
+1055514 0 1.00e+00 4.23e-12 9.98e-17 1.48e-27 ES Rv0946c_(pgi)
+1055637 0 1.00e+00 4.23e-12 5.17e-19 1.45e-27 ES Rv0946c_(pgi)
+1055667 0 1.00e+00 4.23e-12 2.81e-21 1.45e-27 ES Rv0946c_(pgi)
+1055709 0 1.00e+00 4.23e-12 1.50e-22 1.45e-27 ES Rv0946c_(pgi)
+1055868 0 1.00e+00 4.23e-12 1.50e-22 1.45e-27 ES Rv0946c_(pgi)
+1056089 0 1.00e+00 4.23e-12 2.81e-21 1.45e-27 ES Rv0946c_(pgi)
+1056165 0 1.00e+00 4.23e-12 5.17e-19 1.45e-27 ES Rv0946c_(pgi)
+1056183 0 1.00e+00 4.23e-12 9.98e-17 1.48e-27 ES Rv0946c_(pgi)
+1056320 0 1.00e+00 4.23e-12 1.93e-14 7.92e-27 ES Rv0946c_(pgi)
+1056418 0 1.00e+00 4.23e-12 3.72e-12 1.88e-24 ES Rv0946c_(pgi)
+1056522 0 1.00e+00 4.24e-12 7.19e-10 9.67e-22 ES Rv0946c_(pgi)
+1056531 0 1.00e+00 4.26e-12 1.39e-07 7.70e-19 ES Rv0946c_(pgi)
+1056652 0 1.00e+00 4.34e-12 2.68e-05 7.12e-16 ES Rv0946c_(pgi)
+1056696 538 0.00e+00 9.00e-77 1.00e+00 1.20e-09 NE
+1056745 1458 0.00e+00 5.54e-204 1.00e+00 5.29e-08 NE
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+1056787 1168 0.00e+00 6.61e-165 1.00e+00 1.03e-08 NE
+1056904 35 8.17e-90 7.66e-25 1.00e+00 9.44e-11 NE
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+1057037 193 0.00e+00 3.78e-46 1.00e+00 4.30e-12 NE
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+1057411 392 0.00e+00 1.07e-71 1.00e+00 3.75e-13 NE
+1057452 1161 0.00e+00 1.88e-167 1.00e+00 8.81e-12 NE
+1057468 64 3.90e-150 7.71e-31 1.00e+00 9.60e-14 NE
+1057530 281 0.00e+00 7.13e-58 1.00e+00 2.01e-13 NE
+1057647 323 0.00e+00 4.19e-63 1.00e+00 2.29e-13 NE Rv0948c_(-)
+1057699 0 7.30e-11 2.08e-14 1.00e+00 5.90e-14 NE Rv0948c_(-)
+1057722 0 7.34e-11 2.12e-14 1.00e+00 5.72e-14 NE Rv0948c_(-)
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+1057847 0 7.34e-11 2.12e-14 1.00e+00 5.69e-14 NE Rv0948c_(-)
+1057925 47 9.30e-105 2.92e-20 1.00e+00 6.91e-14 NE Rv0948c_(-)
+1057968 0 5.22e-20 7.24e-17 1.00e+00 5.69e-14 NE
+1058035 474 0.00e+00 6.76e-76 1.00e+00 4.00e-13 NE
+1058059 0 1.01e-17 1.71e-19 1.00e+00 5.69e-14 NE
+1058065 0 1.01e-17 1.75e-19 1.00e+00 5.69e-14 NE
+1058209 251 0.00e+00 9.54e-51 1.00e+00 1.60e-13 NE
+1058245 97 4.43e-216 6.07e-28 1.00e+00 8.49e-14 NE
+1058400 0 4.84e-13 1.76e-05 1.00e+00 5.71e-14 NE Rv0949_(uvrD1)
+1058431 0 4.87e-13 1.80e-05 1.00e+00 5.74e-14 NE Rv0949_(uvrD1)
+1058548 0 4.86e-13 1.80e-05 1.00e+00 5.95e-14 NE Rv0949_(uvrD1)
+1058586 0 4.85e-13 1.80e-05 1.00e+00 6.99e-14 NE Rv0949_(uvrD1)
+1058641 25 5.44e-63 1.39e-08 1.00e+00 1.35e-13 NE Rv0949_(uvrD1)
+1058696 0 9.95e-01 9.31e-08 5.18e-03 1.85e-15 ES Rv0949_(uvrD1)
+1058710 0 1.00e+00 2.38e-08 2.68e-05 8.22e-18 ES Rv0949_(uvrD1)
+1058730 0 1.00e+00 6.09e-09 1.39e-07 4.12e-20 ES Rv0949_(uvrD1)
+1058789 0 1.00e+00 1.56e-09 7.19e-10 2.17e-22 ES Rv0949_(uvrD1)
+1058810 0 1.00e+00 3.98e-10 3.72e-12 2.52e-24 ES Rv0949_(uvrD1)
+1058833 0 1.00e+00 1.02e-10 1.93e-14 3.71e-25 ES Rv0949_(uvrD1)
+1058842 0 1.00e+00 2.60e-11 9.98e-17 9.45e-26 ES Rv0949_(uvrD1)
+1058938 0 1.00e+00 6.65e-12 5.17e-19 2.52e-26 ES Rv0949_(uvrD1)
+1058941 0 1.00e+00 1.70e-12 2.68e-21 7.53e-27 ES Rv0949_(uvrD1)
+1058977 0 1.00e+00 4.35e-13 1.39e-23 3.00e-27 ES Rv0949_(uvrD1)
+1059001 0 1.00e+00 1.11e-13 8.11e-26 1.84e-27 ES Rv0949_(uvrD1)
+1059005 0 1.00e+00 2.84e-14 8.18e-27 1.55e-27 ES Rv0949_(uvrD1)
+1059045 0 1.00e+00 7.27e-15 7.42e-27 1.47e-27 ES Rv0949_(uvrD1)
+1059094 0 1.00e+00 1.86e-15 7.32e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059145 0 1.00e+00 4.77e-16 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059181 0 1.00e+00 1.23e-16 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059231 0 1.00e+00 3.29e-17 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059295 0 1.00e+00 9.79e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059363 0 1.00e+00 3.88e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059376 0 1.00e+00 2.37e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059397 0 1.00e+00 1.99e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059450 0 1.00e+00 1.89e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059457 0 1.00e+00 1.86e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059484 0 1.00e+00 1.86e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059517 0 1.00e+00 1.86e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059557 0 1.00e+00 1.86e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059570 0 1.00e+00 1.88e-18 7.29e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059588 0 1.00e+00 1.98e-18 7.66e-27 1.45e-27 ES Rv0949_(uvrD1)
+1059622 0 1.00e+00 2.34e-18 7.90e-26 1.45e-27 ES Rv0949_(uvrD1)
+1059683 0 1.00e+00 3.77e-18 1.39e-23 1.45e-27 ES Rv0949_(uvrD1)
+1059696 0 1.00e+00 9.37e-18 2.68e-21 1.45e-27 ES Rv0949_(uvrD1)
+1059808 0 1.00e+00 3.12e-17 5.17e-19 1.45e-27 ES Rv0949_(uvrD1)
+1059875 0 1.00e+00 1.17e-16 9.98e-17 3.90e-27 ES Rv0949_(uvrD1)
+1059900 0 1.00e+00 4.52e-16 1.93e-14 2.35e-24 ES Rv0949_(uvrD1)
+1060038 0 1.00e+00 1.76e-15 3.72e-12 2.27e-21 ES Rv0949_(uvrD1)
+1060174 0 1.00e+00 6.88e-15 7.19e-10 2.19e-18 ES Rv0949_(uvrD1)
+1060207 0 1.00e+00 2.69e-14 1.39e-07 2.11e-15 ES Rv0949_(uvrD1)
+1060365 0 1.00e+00 1.05e-13 2.68e-05 2.04e-12 ES Rv0949_(uvrD1)
+1060453 239 0.00e+00 1.36e-40 1.00e+00 1.02e-06 NE Rv0949_(uvrD1)
+1060521 167 0.00e+00 1.69e-43 1.00e+00 7.56e-07 NE Rv0949_(uvrD1)
+1060607 0 6.33e-20 4.20e-21 1.00e+00 3.80e-07 NE
+1060666 549 0.00e+00 1.83e-89 1.00e+00 3.64e-06 NE Rv0950c_(-)
+1060679 1 8.51e-15 5.90e-06 1.00e+00 3.82e-07 NE Rv0950c_(-)
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+1060948 77 1.86e-166 2.08e-15 1.00e+00 5.19e-07 NE Rv0950c_(-)
+1060970 72 1.73e-161 1.15e-14 1.00e+00 5.08e-07 NE Rv0950c_(-)
+1060982 0 2.68e-11 9.80e-01 2.03e-02 7.66e-09 GD Rv0950c_(-)
+1060995 1 2.99e-13 9.99e-01 5.51e-04 4.15e-11 GD Rv0950c_(-)
+1061008 0 4.58e-12 1.00e+00 1.19e-05 1.68e-13 GD Rv0950c_(-)
+1061050 15 2.91e-40 1.00e+00 8.18e-05 7.01e-14 GD Rv0950c_(-)
+1061064 0 3.67e-13 1.00e+00 8.90e-07 2.16e-16 GD Rv0950c_(-)
+1061270 0 3.69e-13 1.00e+00 5.62e-07 8.78e-19 GD Rv0950c_(-)
+1061412 0 3.69e-13 1.00e+00 5.55e-07 3.59e-21 GD Rv0950c_(-)
+1061472 0 3.68e-13 1.00e+00 5.55e-07 1.52e-23 GD Rv0950c_(-)
+1061488 0 3.63e-13 1.00e+00 5.55e-07 8.03e-26 GD Rv0950c_(-)
+1061511 0 3.45e-13 1.00e+00 5.55e-07 7.17e-27 GD Rv0950c_(-)
+1061551 16 2.95e-43 1.00e+00 5.45e-05 2.11e-23 GD Rv0950c_(-)
+1061559 0 3.09e-21 1.00e+00 5.55e-07 6.28e-25 GD Rv0950c_(-)
+1061606 0 3.87e-21 1.00e+00 5.55e-07 1.06e-22 GD Rv0950c_(-)
+1061672 8 4.15e-36 1.00e+00 5.50e-06 2.67e-19 GD
+1061715 1 1.04e-17 1.00e+00 7.40e-07 8.72e-19 GD
+1061721 2 2.81e-18 1.00e+00 9.86e-07 2.08e-16 GD
+1061740 0 2.13e-11 1.00e+00 5.60e-07 1.61e-14 GD
+1061757 0 2.67e-11 1.00e+00 7.75e-07 3.95e-12 GD
+1061824 0 2.81e-11 1.00e+00 1.14e-05 9.76e-10 GD
+1061867 1 3.80e-13 9.99e-01 7.14e-04 3.22e-07 GD
+1061883 35 1.39e-79 2.13e-03 9.95e-01 2.56e-03 NE
+1061921 434 0.00e+00 9.80e-56 9.87e-01 1.32e-02 NE
+1061925 0 9.52e-12 1.82e-08 9.98e-01 2.24e-03 NE
+1061939 9 1.00e-29 1.40e-09 9.98e-01 2.32e-03 NE
+1061979 0 9.95e-01 9.56e-11 5.12e-03 1.15e-05 ES Rv0951_(sucC)
+1061995 0 1.00e+00 2.44e-11 2.65e-05 1.19e-08 ES Rv0951_(sucC)
+1062062 0 1.00e+00 6.25e-12 1.37e-07 1.23e-11 ES Rv0951_(sucC)
+1062144 0 1.00e+00 1.60e-12 7.11e-10 1.28e-14 ES Rv0951_(sucC)
+1062168 0 1.00e+00 4.10e-13 3.68e-12 1.32e-17 ES Rv0951_(sucC)
+1062242 0 1.00e+00 1.06e-13 1.91e-14 1.37e-20 ES Rv0951_(sucC)
+1062248 0 1.00e+00 2.83e-14 9.87e-17 1.42e-23 ES Rv0951_(sucC)
+1062261 0 1.00e+00 8.42e-15 5.11e-19 1.61e-26 ES Rv0951_(sucC)
+1062264 0 1.00e+00 3.34e-15 2.65e-21 1.47e-27 ES Rv0951_(sucC)
+1062268 0 1.00e+00 2.04e-15 1.37e-23 1.45e-27 ES Rv0951_(sucC)
+1062300 0 1.00e+00 1.71e-15 7.82e-26 1.45e-27 ES Rv0951_(sucC)
+1062346 0 1.00e+00 1.62e-15 7.65e-27 1.45e-27 ES Rv0951_(sucC)
+1062409 0 1.00e+00 1.60e-15 7.29e-27 1.45e-27 ES Rv0951_(sucC)
+1062693 0 1.00e+00 1.60e-15 7.29e-27 1.45e-27 ES Rv0951_(sucC)
+1062771 0 1.00e+00 1.59e-15 7.29e-27 1.45e-27 ES Rv0951_(sucC)
+1062818 0 1.00e+00 1.59e-15 7.29e-27 1.45e-27 ES Rv0951_(sucC)
+1063156 0 1.00e+00 1.59e-15 7.29e-27 1.45e-27 ES Rv0952_(sucD)
+1063220 0 1.00e+00 1.59e-15 7.66e-27 1.45e-27 ES Rv0952_(sucD)
+1063304 0 1.00e+00 1.59e-15 7.90e-26 1.45e-27 ES Rv0952_(sucD)
+1063494 0 1.00e+00 1.60e-15 1.39e-23 1.45e-27 ES Rv0952_(sucD)
+1063506 0 1.00e+00 1.60e-15 2.68e-21 1.45e-27 ES Rv0952_(sucD)
+1063562 0 1.00e+00 1.62e-15 5.17e-19 1.45e-27 ES Rv0952_(sucD)
+1063589 0 1.00e+00 1.71e-15 9.98e-17 1.47e-27 ES Rv0952_(sucD)
+1063656 0 1.00e+00 2.04e-15 1.93e-14 7.12e-27 ES Rv0952_(sucD)
+1063733 0 1.00e+00 3.35e-15 3.72e-12 1.11e-24 ES Rv0952_(sucD)
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+1143773 0 1.97e-15 8.66e-18 1.00e+00 5.36e-17 NE Rv1022_(lpqU)
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+1144330 0 5.56e-09 9.79e-01 2.09e-02 9.89e-15 GD Rv1022_(lpqU)
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+1144493 109 7.38e-233 4.30e-11 1.00e+00 4.49e-12 GD
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+1144572 0 2.52e-02 9.75e-01 1.93e-07 7.78e-20 GD Rv1023_(eno)
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+1146126 0 3.64e-03 9.96e-01 7.35e-07 3.18e-08 GD Rv1024_(-)
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+1148428 0 2.72e-06 3.85e-08 1.00e+00 1.87e-23 NE Rv1027c_(kdpE)
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+1453030 412 0.00e+00 3.90e-62 1.00e+00 1.13e-05 NE
+1453034 14 6.02e-50 5.75e-21 1.00e+00 2.20e-06 NE
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+1453088 0 1.25e-17 5.33e-19 1.00e+00 2.08e-06 NE
+1453169 101 2.08e-219 1.39e-31 1.00e+00 3.15e-06 NE
+1453212 0 2.86e-15 1.24e-17 1.00e+00 2.08e-06 NE Rv1297_(rho)
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+1453350 207 0.00e+00 2.09e-43 1.00e+00 4.87e-06 NE Rv1297_(rho)
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+1455187 0 1.00e+00 1.20e-08 9.96e-17 2.53e-23 ES Rv1298_(rpmE)
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+1455403 64 2.67e-126 4.66e-11 9.99e-01 5.95e-04 NE Rv1298_(rpmE)
+1455412 20 4.69e-60 1.40e-05 9.99e-01 4.97e-04 NE
+1455440 0 7.72e-04 4.32e-03 9.94e-01 4.55e-04 NE
+1455464 5 8.00e-14 1.03e-03 9.98e-01 4.66e-04 NE
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+1459537 500 0.00e+00 8.32e-85 1.00e+00 1.43e-04 NE
+1459540 37 4.75e-96 2.49e-27 1.00e+00 2.13e-05 NE
+1459550 636 0.00e+00 4.90e-102 1.00e+00 2.50e-04 NE
+1459560 737 0.00e+00 1.52e-114 1.00e+00 3.78e-04 NE
+1459571 23 6.72e-68 9.20e-25 1.00e+00 2.01e-05 NE
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+1459653 896 0.00e+00 1.33e-132 9.99e-01 7.28e-04 NE
+1459661 143 8.01e-308 1.54e-40 1.00e+00 3.29e-05 NE
+1459695 40 3.81e-102 1.72e-19 1.00e+00 2.15e-05 NE
+1459995 0 2.65e-15 2.87e-11 1.00e+00 1.83e-05 NE Rv1303_(-)
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+1460195 111 4.69e-237 4.41e-25 1.00e+00 2.88e-05 NE Rv1303_(-)
+1460309 0 9.95e-01 1.60e-06 5.18e-03 9.45e-08 ES Rv1304_(atpB)
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+1460574 0 1.00e+00 1.63e-06 1.39e-07 1.01e-13 ES Rv1304_(atpB)
+1460582 0 1.00e+00 1.63e-06 7.19e-10 1.05e-16 ES Rv1304_(atpB)
+1460634 0 1.00e+00 1.63e-06 3.76e-12 1.09e-19 ES Rv1304_(atpB)
+1460670 0 1.00e+00 1.63e-06 5.52e-14 1.13e-22 ES Rv1304_(atpB)
+1460684 0 1.00e+00 1.63e-06 3.59e-14 1.35e-25 ES Rv1304_(atpB)
+1460699 0 1.00e+00 1.63e-06 3.58e-14 1.81e-25 ES Rv1304_(atpB)
+1460862 0 1.00e+00 1.63e-06 3.58e-14 1.59e-22 ES Rv1304_(atpB)
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+1460994 7 4.74e-08 1.00e+00 1.80e-07 6.99e-10 ES Rv1304_(atpB)
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+1461010 0 1.00e+00 4.16e-07 2.04e-16 1.55e-19 ES
+1461017 0 1.00e+00 1.06e-07 1.06e-18 5.40e-22 ES
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+1461056 0 1.00e+00 6.96e-09 1.55e-22 2.49e-23 ES Rv1305_(atpE)
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+1463135 0 1.00e+00 6.43e-25 7.29e-27 1.45e-27 ES Rv1307_(atpH)
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+1464052 0 1.00e+00 4.89e-19 5.23e-26 1.45e-27 ES Rv1308_(atpA)
+1464068 0 1.00e+00 1.91e-18 8.70e-24 1.45e-27 ES Rv1308_(atpA)
+1464116 0 1.00e+00 7.48e-18 1.68e-21 1.96e-27 ES Rv1308_(atpA)
+1464134 0 1.00e+00 2.93e-17 3.24e-19 4.95e-25 ES Rv1308_(atpA)
+1464198 0 1.00e+00 1.14e-16 6.26e-17 4.77e-22 ES Rv1308_(atpA)
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+1808626 0 1.00e+00 2.55e-04 2.97e-21 3.06e-25 ES Rv1609_(trpE)
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+1809451 39 8.93e-74 3.50e-01 6.50e-01 2.66e-06 GD Rv1609_(trpE),Rv1610_(-)
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+1810173 35 4.91e-81 6.28e-01 3.72e-01 1.48e-06 GD
+1810379 0 7.45e-01 2.55e-01 6.62e-06 2.29e-11 ES Rv1611_(trpC)
+1810422 0 9.35e-01 6.53e-02 3.43e-08 2.39e-14 ES Rv1611_(trpC)
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+1810961 0 1.00e+00 1.19e-06 2.18e-20 4.26e-21 ES Rv1611_(trpC)
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+1811104 0 1.00e+00 1.99e-08 3.64e-22 7.13e-23 ES
+1811211 0 1.00e+00 5.09e-09 9.30e-23 1.82e-23 ES Rv1612_(trpB)
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+1812388 0 1.00e+00 1.11e-19 7.29e-27 1.45e-27 ES Rv1613_(trpA)
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+1813981 0 1.00e+00 1.05e-13 2.68e-05 2.12e-17 ES Rv1614_(lgt)
+1814038 838 0.00e+00 3.52e-115 1.00e+00 8.73e-11 NE Rv1614_(lgt)
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+1814620 200 0.00e+00 1.76e-45 1.00e+00 7.59e-13 NE
+1814707 214 0.00e+00 1.99e-49 1.00e+00 4.51e-13 NE
+1814731 361 0.00e+00 8.76e-68 1.00e+00 5.30e-13 NE
+1814746 76 4.45e-174 2.65e-32 1.00e+00 1.20e-13 NE
+1814755 16 3.02e-54 1.09e-24 1.00e+00 6.35e-14 NE
+1814760 142 5.62e-306 2.19e-40 1.00e+00 9.26e-14 NE
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+1814924 0 5.25e-20 3.48e-21 1.00e+00 4.93e-14 NE
+1815260 473 0.00e+00 4.42e-80 1.00e+00 3.36e-13 NE Rv1615_(-)
+1815370 0 5.23e-20 3.47e-21 1.00e+00 4.78e-14 NE Rv1615_(-)
+1815382 506 0.00e+00 3.43e-84 1.00e+00 3.80e-13 NE Rv1615_(-)
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+1816175 442 0.00e+00 4.22e-69 1.00e+00 3.09e-12 NE
+1816309 0 9.95e-01 5.96e-09 5.18e-03 3.82e-15 ES Rv1617_(pykA)
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+1820038 51 8.37e-121 1.48e-14 1.00e+00 5.91e-17 NE Rv1620c_(cydC)
+1820086 0 5.27e-13 3.00e-05 1.00e+00 1.57e-16 NE Rv1620c_(cydC)
+1820103 0 5.30e-13 3.06e-05 1.00e+00 6.99e-16 NE Rv1620c_(cydC)
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+1820415 0 5.27e-13 3.06e-05 1.00e+00 1.70e-14 NE Rv1620c_(cydC)
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+3215666 0 5.35e-01 4.53e-01 1.21e-02 8.60e-15 GD Rv2906c_(trmD)
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+3257940 0 4.00e-16 2.70e-17 4.84e-08 1.00e+00 GA Rv2933_(ppsC)
+3258064 612 0.00e+00 1.34e-94 4.05e-09 1.00e+00 GA Rv2933_(ppsC)
+3258143 0 1.99e-16 1.32e-17 5.47e-08 1.00e+00 GA Rv2933_(ppsC)
+3258253 485 0.00e+00 7.20e-79 7.56e-09 1.00e+00 GA Rv2933_(ppsC)
+3258268 1897 0.00e+00 1.95e-259 2.32e-11