[med-svn] [hmmer2] 02/03: New upstream version 2.3.2+dfsg
Andreas Tille
tille at debian.org
Thu Apr 13 21:04:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository hmmer2.
commit 0a4a363ba8d2cbdc1adb0682eeca134e9d478234
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 13 22:32:25 2017 +0200
New upstream version 2.3.2+dfsg
---
tutorial/7LES_DROME | 157 ----------------------------------------------------
tutorial/RU1A_HUMAN | 146 ------------------------------------------------
2 files changed, 303 deletions(-)
diff --git a/tutorial/7LES_DROME b/tutorial/7LES_DROME
deleted file mode 100644
index 9bed141..0000000
--- a/tutorial/7LES_DROME
+++ /dev/null
@@ -1,157 +0,0 @@
-ID 7LES_DROME STANDARD; PRT; 2554 AA.
-AC P13368;
-DT 01-JAN-1990 (Rel. 13, Created)
-DT 01-JAN-1990 (Rel. 13, Last sequence update)
-DT 01-NOV-1997 (Rel. 35, Last annotation update)
-DE SEVENLESS PROTEIN (EC 2.7.1.112).
-GN SEV.
-OS Drosophila melanogaster (Fruit fly).
-OC Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
-OC Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
-OC Ephydroidea; Drosophilidae; Drosophila.
-RN [1]
-RP SEQUENCE FROM N.A.
-RC STRAIN=CANTON-S;
-RX MEDLINE; 88282538.
-RA BASLER K., HAFEN E.;
-RT "Control of photoreceptor cell fate by the sevenless protein requires
-RT a functional tyrosine kinase domain.";
-RL Cell 54:299-311(1988).
-RN [2]
-RP SEQUENCE FROM N.A.
-RC STRAIN=OREGON-R;
-RX MEDLINE; 88329706.
-RA BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
-RT "Nucleotide sequence and structure of the sevenless gene of
-RT Drosophila melanogaster.";
-RL Genes Dev. 2:620-634(1988).
-RN [3]
-RP IDENTIFICATION OF FN-III REPEATS.
-RX MEDLINE; 90199889.
-RA NORTON P.A., HYNES R.O., RESS D.J.G.;
-RT "Sevenless: seven found?";
-RL Cell 61:15-16(1990).
-CC -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
-CC INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
-CC LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
-CC SURFACE OF THE NEIGHBORING R8 CELL.
-CC -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
-CC PROTEIN TYROSINE PHOSPHATE.
-CC -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
-CC -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
-CC PROTEIN KINASES. SEVENLESS SUBFAMILY.
-CC -!- SIMILARITY: CONTAINS 7 FIBRONECTIN TYPE III-LIKE DOMAINS.
-CC -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
-CC NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
-CC NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
-CC --------------------------------------------------------------------------
-CC This SWISS-PROT entry is copyright. It is produced through a collaboration
-CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
-CC the European Bioinformatics Institute. There are no restrictions on its
-CC use by non-profit institutions as long as its content is in no way
-CC modified and this statement is not removed. Usage by and for commercial
-CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
-CC or send an email to license at isb-sib.ch).
-CC --------------------------------------------------------------------------
-DR EMBL; X13666; CAA31960.1; ALT_INIT.
-DR EMBL; J03158; AAA28882.1; -.
-DR PIR; A28912; TVFF7L.
-DR HSSP; P11362; 1FGI.
-DR FLYBASE; FBgn0003366; sev.
-DR PFAM; PF00041; fn3; 6.
-DR PFAM; PF00069; pkinase; 1.
-DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
-DR PROSITE; PS00109; PROTEIN_KINASE_TYR; 1.
-DR PROSITE; PS00239; RECEPTOR_TYR_KIN_II; 1.
-DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
-KW Transferase; Tyrosine-protein kinase; Transmembrane; ATP-binding;
-KW Phosphorylation; Receptor; Vision; Repeat.
-FT DOMAIN 1 2123 EXTRACELLULAR (POTENTIAL).
-FT TRANSMEM 102 122 POTENTIAL.
-FT TRANSMEM 2124 2147 POTENTIAL.
-FT DOMAIN 2148 2554 CYTOPLASMIC (POTENTIAL).
-FT DOMAIN 311 431 FIBRONECTIN TYPE-III.
-FT DOMAIN 436 528 FIBRONECTIN TYPE-III.
-FT DOMAIN 822 921 FIBRONECTIN TYPE-III.
-FT DOMAIN 1298 1392 FIBRONECTIN TYPE-III.
-FT DOMAIN 1680 1794 FIBRONECTIN TYPE-III.
-FT DOMAIN 1797 1897 FIBRONECTIN TYPE-III.
-FT DOMAIN 1898 1988 FIBRONECTIN TYPE-III.
-FT DOMAIN 2038 2046 POLY-ARG.
-FT DOMAIN 2209 2485 PROTEIN KINASE.
-FT NP_BIND 2215 2223 ATP (BY SIMILARITY).
-FT BINDING 2242 2242 ATP (BY SIMILARITY).
-FT MUTAGEN 2242 2242 K->M: INACTIVATES THE PROTEIN.
-FT MOD_RES 2380 2380 PHOSPHORYLATION (AUTO-) (BY SIMILARITY).
-FT CARBOHYD 30 30 POTENTIAL.
-FT CARBOHYD 129 129 POTENTIAL.
-FT CARBOHYD 481 481 POTENTIAL.
-FT CARBOHYD 505 505 POTENTIAL.
-FT CARBOHYD 617 617 POTENTIAL.
-FT CARBOHYD 647 647 POTENTIAL.
-FT CARBOHYD 966 966 POTENTIAL.
-FT CARBOHYD 1228 1228 POTENTIAL.
-FT CARBOHYD 1313 1313 POTENTIAL.
-FT CARBOHYD 1353 1353 POTENTIAL.
-FT CARBOHYD 1550 1550 POTENTIAL.
-FT CARBOHYD 1557 1557 POTENTIAL.
-FT CARBOHYD 1639 1639 POTENTIAL.
-FT CARBOHYD 1725 1725 POTENTIAL.
-FT CARBOHYD 1756 1756 POTENTIAL.
-FT CARBOHYD 1804 1804 POTENTIAL.
-FT CARBOHYD 1889 1889 POTENTIAL.
-FT CARBOHYD 1947 1947 POTENTIAL.
-FT CARBOHYD 2073 2073 POTENTIAL.
-FT VARIANT 392 392 M -> V.
-FT VARIANT 1668 1668 A -> V.
-FT VARIANT 1703 1703 N -> H.
-FT VARIANT 1730 1730 R -> K.
-FT VARIANT 1731 1731 G -> E.
-FT VARIANT 1741 1741 V -> M.
-FT VARIANT 2271 2271 R -> C.
-FT CONFLICT 1823 1823 E -> Q (IN REF. 2).
-SQ SEQUENCE 2554 AA; 287107 MW; 1143D891 CRC32;
- MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
- SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
- CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
- SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
- KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
- QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
- LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
- LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
- NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
- TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
- SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
- ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
- QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
- SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
- KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
- VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
- PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
- CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
- GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
- PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
- VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
- AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
- DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
- TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
- EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
- RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
- GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
- DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
- LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
- VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
- PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
- AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
- GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
- GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
- RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
- HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
- LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
- GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
- SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
- HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
- DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
- LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
- HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
-//
diff --git a/tutorial/RU1A_HUMAN b/tutorial/RU1A_HUMAN
deleted file mode 100644
index 0b4c49d..0000000
--- a/tutorial/RU1A_HUMAN
+++ /dev/null
@@ -1,146 +0,0 @@
-ID RU1A_HUMAN STANDARD; PRT; 282 AA.
-AC P09012;
-DT 01-NOV-1988 (Rel. 09, Created)
-DT 01-NOV-1988 (Rel. 09, Last sequence update)
-DT 15-JUL-1998 (Rel. 36, Last annotation update)
-DE U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A (U1 SNRNP A PROTEIN).
-GN SNRPA.
-OS Homo sapiens (Human).
-OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
-OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
-RN [1]
-RP SEQUENCE FROM N.A.
-RC TISSUE=LIVER;
-RX MEDLINE; 91340152.
-RA NELISSEN R.L.H., SILLEKENS P.T.G., BEIJER R.P.,
-RA GEURTS VAN KESSEL A.H.M., VAN VENROOIJ W.J.;
-RT "Structure, chromosomal localization and evolutionary conservation of
-RT the gene encoding human U1 snRNP-specific A protein.";
-RL Gene 102:189-196(1991).
-RN [2]
-RP SEQUENCE FROM N.A.
-RX MEDLINE; 88111575.
-RA SILLEKENS P.T.G., HABETS W.J., BEIJER R.P., VAN VENROOIJ W.J.;
-RT "cDNA cloning of the human U1 snRNA-associated A protein: extensive
-RT homology between U1 and U2 snRNP-specific proteins.";
-RL EMBO J. 6:3841-3848(1987).
-RN [3]
-RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-95.
-RX MEDLINE; 91061907.
-RA NAGAI K., OUBRIDGE C., JESSEN T.-H., LI J., EVANS P.R.;
-RT "Crystal structure of the RNA-binding domain of the U1 small nuclear
-RT ribonucleoprotein A.";
-RL Nature 348:515-520(1990).
-RN [4]
-RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS).
-RX MEDLINE; 95075454.
-RA OUBRIDGE C., ITO N., EVANS P.R., TEO C.-H., NAGAI K.;
-RT "Crystal structure at 1.92-A resolution of the RNA-binding domain of
-RT the U1A spliceosomal protein complexed with an RNA hairpin.";
-RL Nature 372:432-438(1994).
-RN [5]
-RP STRUCTURE BY NMR OF 11-94.
-RX MEDLINE; 91172834.
-RA HOFFMAN D.W., QUERY C.C., GOLDEN B.L., WHITE S.W., KEENE J.D.;
-RT "RNA-binding domain of the A protein component of the U1 small
-RT nuclear ribonucleoprotein analyzed by NMR spectroscopy is
-RT structurally similar to ribosomal proteins.";
-RL Proc. Natl. Acad. Sci. U.S.A. 88:2495-2499(1991).
-RN [6]
-RP STRUCTURE BY NMR OF 1-102.
-RX MEDLINE; 94349935.
-RA HOWE P.W.A., NAGAI K., NEUHAUS D., VARANI G.;
-RT "NMR studies of U1 snRNA recognition by the N-terminal RNP domain of
-RT the human U1A protein.";
-RL EMBO J. 13:3873-3881(1994).
-RN [7]
-RP STRUCTURE BY NMR OF 2-102.
-RX MEDLINE; 96186818.
-RA ALLAIN F.H.-T., GUBSER C.C., HOWE P.W.A., NAGAI K., NEUHAUS D.,
-RA VARANI G.;
-RT "Specificity of ribonucleoprotein interaction determined by RNA
-RT folding during complex formulation.";
-RL Nature 380:646-650(1996).
-RN [8]
-RP STRUCTURE BY NMR OF 1-117.
-RX MEDLINE; 96180024.
-RA AVIS J.M., ALLAIN F.H.-T., HOWE P.W.A., VARANI G., NAGAI K.,
-RA NEUHAUS D.;
-RT "Solution structure of the N-terminal RNP domain of U1A protein: the
-RT role of C-terminal residues in structure stability and RNA binding.";
-RL J. Mol. Biol. 257:398-411(1996).
-RN [9]
-RP STRUCTURE BY NMR OF 1-102.
-RX MEDLINE; 97459961.
-RA ALLAIN F.H.-T., HOWE P.W., NEUHAUS D., VARANI G.;
-RT "Structural basis of the RNA-binding specificity of human U1A
-RT protein.";
-RL EMBO J. 16:5764-5772(1997).
-RN [10]
-RP STRUCTURE BY NMR OF 195-282.
-RX MEDLINE; 97410326.
-RA LU J., HALL K.B.;
-RT "Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of
-RT the human U1A protein determined by NMR spectroscopy.";
-RL Biochemistry 36:10393-10405(1997).
-RN [11]
-RP MUTAGENESIS, AND DETAILED STUDIES OF RNA-BINDING.
-RX MEDLINE; 92007796.
-RA JESSEN T.-H., OUBRIDGE C., TEO C.H., PRITCHARD C., NAGAI K.;
-RT "Identification of molecular contacts between the U1 A small nuclear
-RT ribonucleoprotein and U1 RNA.";
-RL EMBO J. 10:3447-3456(1991).
-CC -!- FUNCTION: BINDS STEM LOOP II OF U1 SNRNA. IT IS THE FIRST SN-RNP
-CC TO INTERACT WITH PRE-MRNA. THIS INTERACTION IS REQUIRED FOR THE
-CC SUBSEQUENT BINDING OF U2 SN-RNP AND THE U4/U6/U5 TRI-SN-RNP.
-CC -!- SUBUNIT: BELONGS TO THE SPLICEOSOME WHERE IT IS ASSOCIATED WITH
-CC SN-RNP U1.
-CC -!- SUBCELLULAR LOCATION: NUCLEAR.
-CC -!- SIMILARITY: BELONGS TO THE U1 A/B" FAMILY.
-CC -!- SIMILARITY: CONTAINS 2 RNA RECOGNITION MOTIFS (RNP).
-CC --------------------------------------------------------------------------
-CC This SWISS-PROT entry is copyright. It is produced through a collaboration
-CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
-CC the European Bioinformatics Institute. There are no restrictions on its
-CC use by non-profit institutions as long as its content is in no way
-CC modified and this statement is not removed. Usage by and for commercial
-CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
-CC or send an email to license at isb-sib.ch).
-CC --------------------------------------------------------------------------
-DR EMBL; M60784; AAA61245.1; -.
-DR EMBL; M60779; AAA61245.1; JOINED.
-DR EMBL; M60780; AAA61245.1; JOINED.
-DR EMBL; M60781; AAA61245.1; JOINED.
-DR EMBL; M60782; AAA61245.1; JOINED.
-DR EMBL; M60783; AAA61245.1; JOINED.
-DR EMBL; X06347; CAA29653.1; -.
-DR PIR; JQ1528; JQ1528.
-DR PDB; 1NRC; 31-JAN-94.
-DR PDB; 1FHT; 11-JUL-96.
-DR PDB; 1AUD; 25-FEB-98.
-DR PDB; 1URN; 08-MAR-96.
-DR PDB; 2U1A; 26-SEP-97.
-DR PDB; 3UTR; 03-APR-96.
-DR MIM; 182285; -.
-DR PFAM; PF00076; rrm; 2.
-DR PROSITE; PS00030; RNP_1; 1.
-KW Nuclear protein; RNA-binding; Ribonucleoprotein; Repeat;
-KW Spliceosome; 3D-structure.
-FT DOMAIN 12 17 RNA-BINDING (RNP2) (BY SIMILARITY).
-FT DOMAIN 52 59 RNA-BINDING (RNP1) (BY SIMILARITY).
-FT DOMAIN 210 215 RNA-BINDING (RNP2) (BY SIMILARITY).
-FT DOMAIN 244 251 RNA-BINDING (RNP1) (BY SIMILARITY).
-FT REPEAT 1 89
-FT REPEAT 199 282
-FT MUTAGEN 11 11 T->V: ABOLISHES RNA-BINDING.
-FT MUTAGEN 13 13 Y->F: SUBSTANTIALLY REDUCES RNA-BINDING.
-FT MUTAGEN 15 15 N->V: ABOLISHES RNA-BINDING.
-FT MUTAGEN 16 16 N->V: SUBSTANTIALLY REDUCES RNA-BINDING.
-FT MUTAGEN 52 52 R->Q: ABOLISHES RNA-BINDING.
-SQ SEQUENCE 282 AA; 31279 MW; 22427816 CRC32;
- MAVPETRPNH TIYINNLNEK IKKDELKKSL YAIFSQFGQI LDILVSRSLK MRGQAFVIFK
- EVSSATNALR SMQGFPFYDK PMRIQYAKTD SDIIAKMKGT FVERDRKREK RKPKSQETPA
- TKKAVQGGGA TPVVGAVQGP VPGMPPMTQA PRIMHHMPGQ PPYMPPPGMI PPPGLAPGQI
- PPGAMPPQQL MPGQMPPAQP LSENPPNHIL FLTNLPEETN ELMLSMLFNQ FPGFKEVRLV
- PGRHDIAFVE FDNEVQAGAA RDALQGFKIT QNNAMKISFA KK
-//
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