YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229896408, gi...
Organism:	Yersinia pestis Pestoides A
Length:	356 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|229896408, gi....

Description	E-value	Query Range	Subject Range
gi\|66270756 - gi\|66270756\|gb\|AAY43691.1\| RecA/GFP fusion protein [Cloning vector pSJS1472]	0.0	[1..356]	[1..353]
RECA_YERPS - Protein RecA OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=recA PE=3 SV=1 RECA_YERP3 - Protein RecA OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=recA PE=3 SV=1 RECA_YERPB - Protein RecA OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) GN=recA PE=3 SV=1 RECA_YERPS - Protein RecA OS=Yersinia pseudotuberculosis GN=recA PE=3 SV=1	0.0	[1..356]	[1..356]
RECA_PROMH - Protein RecA OS=Proteus mirabilis (strain HI4320) GN=recA PE=3 SV=1 RECA_PROMI - Protein RecA OS=Proteus mirabilis GN=recA PE=3 SV=2	0.0	[1..354]	[1..355]
gi\|480992, gi\|406794 - pir\|\|S37586 recombination protein recA - Yersinia pestis, gi\|406794\|emb\|CAA53084.1\| RecA protein [Ye...	0.0	[1..356]	[1..356]
RECA_SALTI - Protein recA OS=Salmonella typhi GN=recA PE=3 SV=2 RECA_SALTY - Protein RecA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=recA PE=1 SV=2 gi\|29143089, gi\|... - gi\|29143089\|ref\|NP_806431.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str. T... RECA_SALCH - Protein RecA OS=Salmonella choleraesuis (strain SC-B67) GN=recA PE=3 SV=3 RECA_SALTY - Protein recA OS=Salmonella typhimurium GN=recA PE=3 SV=2 RECA_SALCH - Protein recA OS=Salmonella choleraesuis GN=recA PE=3 SV=3 RECA_SALTI - Protein RecA OS=Salmonella typhi GN=recA PE=3 SV=2 gi\|16761605 - gi\|16761605\|ref\|NP_457222.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str. C... gi\|168464049, gi... - gi\|195633723\|gb\|EDX52137.1\| protein RecA [Salmonella enterica subsp. enterica serovar Newport str. S... gi\|168820488, gi... - gi\|205342838\|gb\|EDZ29602.1\| protein RecA [Salmonella enterica subsp. enterica serovar Weltevreden st... RECA_SALNS - Protein RecA OS=Salmonella newport (strain SL254) GN=recA PE=3 SV=1 RECA_SALHS - Protein RecA OS=Salmonella heidelberg (strain SL476) GN=recA PE=3 SV=1 gi\|238909595 - gi\|238909595\|ref\|ZP_04653432.1\| recombinase A [Salmonella enterica subsp. enterica serovar Tennessee... gi\|205327960, gi... - gi\|205327960\|gb\|EDZ14724.1\| protein RecA [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- s... gi\|168235857, gi... - gi\|197290652\|gb\|EDY30006.1\| protein RecA [Salmonella enterica subsp. enterica serovar Schwarzengrund... gi\|205335992, gi... - gi\|205335992\|gb\|EDZ22756.1\| protein RecA [Salmonella enterica subsp. enterica serovar Heidelberg str... gi\|168262060, gi... - gi\|205349184\|gb\|EDZ35815.1\| protein RecA [Salmonella enterica subsp. enterica serovar Hadar str. RI_... lcl\|NC_016856.1_... - [gene=recA] [protein=recombinase A] [protein_id=YP_005238927.1] [location=complement(2995089..299615... gi\|213648097 - gi\|213648097\|ref\|ZP_03378150.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|214000004 - gi\|214000004\|ref\|ZP_03410739.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALPC - Protein RecA OS=Salmonella paratyphi C (strain RKS4594) GN=recA PE=3 SV=1 gi\|213028317 - gi\|213028317\|ref\|ZP_03342764.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|109453384, gi... - gi\|109453400\|gb\|ABG34180.1\| RecA [Salmonella enterica subsp. enterica], gi\|109453398\|gb\|ABG34179.1\| ... gi\|213051937 - gi\|213051937\|ref\|ZP_03344815.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|213426123 - gi\|213426123\|ref\|ZP_03358873.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALPB - Protein RecA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=recA PE=3 SV=1 gi\|213579899 - gi\|213579899\|ref\|ZP_03361725.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALTY - Protein RecA OS=Salmonella typhimurium GN=recA PE=3 SV=2 RECA_SALPB - Protein recA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=recA PE=3 SV=1 gi\|199603797, gi... - gi\|200386699\|ref\|ZP_03213311.1\| protein RecA [Salmonella enterica subsp. enterica serovar Virchow st... RECA_SALCH - Protein RecA OS=Salmonella choleraesuis GN=recA PE=3 SV=3 gi\|204928070, gi... - gi\|204928070\|ref\|ZP_03219270.1\| protein RecA [Salmonella enterica subsp. enterica serovar Javiana st... RECA_SALG2 - Protein RecA OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=recA PE=3 SV=1 RECA_SALEP - Protein RecA OS=Salmonella enteritidis PT4 (strain P125109) GN=recA PE=3 SV=1 RECA_SALSV - Protein RecA OS=Salmonella schwarzengrund (strain CVM19633) GN=recA PE=3 SV=1 RECA_SALA4 - Protein RecA OS=Salmonella agona (strain SL483) GN=recA PE=3 SV=1 gi\|197241862, gi... - gi\|197263607\|ref\|ZP_03163681.1\| protein RecA [Salmonella enterica subsp. enterica serovar Saintpaul ... RECA_SALDC - Protein RecA OS=Salmonella dublin (strain CT_02021853) GN=recA PE=3 SV=1	0.0	[1..356]	[1..353]
gi\|55670292, gi\|... - gi\|58177454\|pdb\|1XMV\|A Chain A, "e. Coli Reca In Complex With Mgadp", gi\|58177451\|pdb\|1XMS\|A Chain A...	0.0	[1..356]	[4..356]
gi\|238798515, gi... - gi\|77961322\|ref\|ZP_00825162.1\| COG0468: RecA/RadA recombinase [Yersinia mollaretii ATCC 43969], gi\|2...	0.0	[1..356]	[1..354]
RECA_SALPK - Protein RecA OS=Salmonella paratyphi A (strain AKU_12601) GN=recA PE=3 SV=1 RECA_SALPA - Protein RecA OS=Salmonella paratyphi A GN=recA PE=3 SV=3 RECA_SALPA - Protein RecA OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=recA PE=3 SV=3	0.0	[1..356]	[1..353]
gi\|77958683, gi\|... - gi\|77958683\|ref\|ZP_00822712.1\| COG0468: RecA/RadA recombinase [Yersinia bercovieri ATCC 43970], gi\|2...	0.0	[1..356]	[1..354]
RECA_SHIFL - Protein RecA OS=Shigella flexneri GN=recA PE=3 SV=2 gi\|83585642, gi\|... - gi\|83585642\|ref\|ZP_00924285.1\| COG0468: RecA/RadA recombinase [Escherichia coli 101-1], gi\|194439005... RECA_ECOL6 - Protein RecA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=recA PE=3 SV=2 RECA_SHIB3 - Protein RecA OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=recA PE=3 SV=1 gi\|30064059, gi\|... - gi\|30064059\|ref\|NP_838230.1\| recombinase A [Shigella flexneri 2a str. 2457T], gi\|30042315\|gb\|AAP1804... RECA_ECO57 - Protein RecA OS=Escherichia coli O157:H7 GN=recA PE=3 SV=2 gi\|83569945, gi\|... - gi\|83569945\|ref\|ZP_00921393.1\| COG0468: RecA/RadA recombinase [Shigella dysenteriae 1012], gi\|194432... EG10823 - DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding pro... gi\|75210898, gi\|... - gi\|75210898\|ref\|ZP_00711022.1\| COG0468: RecA/RadA recombinase [Escherichia coli B171], gi\|194427861\|... gi\|75229774, gi\|... - gi\|75229774\|ref\|ZP_00716304.1\| COG0468: RecA/RadA recombinase [Escherichia coli B7A], gi\|191167104\|r... RECA_ECO24 - Protein RecA OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=recA PE=3 SV=1 RECA_ECOHS - Protein RecA OS=Escherichia coli O9:H4 (strain HS) GN=recA PE=3 SV=1 RECA_ECO8A - Protein RecA OS=Escherichia coli O8 (strain IAI1) GN=recA PE=3 SV=1 RECA_ESCF3 - Protein RecA OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73) GN=recA PE=3 SV... RECA_ECO81 - Protein RecA OS=Escherichia coli O81 (strain ED1a) GN=recA PE=3 SV=1 RECA_ECO45 - Protein RecA OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=recA PE=3 SV=1 RECA_ECO7I - Protein RecA OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=recA PE=3 SV=1 RECA_ECO55 - Protein RecA OS=Escherichia coli (strain 55989 / EAEC) GN=recA PE=3 SV=1 RECA_ECOLU - Protein RecA OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=recA PE=3 SV=1 RECA_ECOLI - Protein recA (Recombinase A) - Escherichia coli gi\|188015763, gi... - gi\|188015763\|gb\|EDU53885.1\| protein RecA [Escherichia coli O157:H7 str. EC4113], gi\|168749979\|ref\|ZP... gi\|208727717, gi... - gi\|208807916\|ref\|ZP_03250253.1\| protein RecA [Escherichia coli O157:H7 str. EC4206], gi\|208727717\|gb... gi\|195938448 - gi\|195938448\|ref\|ZP_03083830.1\| recombinase A [Escherichia coli O157:H7 str. EC4024] gi\|208820218, gi... - gi\|208820218\|ref\|ZP_03260538.1\| protein RecA [Escherichia coli O157:H7 str. EC4042], gi\|208740341\|gb... gi\|208811896, gi... - gi\|208811896\|ref\|ZP_03253225.1\| protein RecA [Escherichia coli O157:H7 str. EC4045], gi\|208733173\|gb... RECA_ECOSE - Protein RecA OS=Escherichia coli (strain SE11) GN=recA PE=3 SV=1 RECA_ECO5E - Protein RecA OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=recA PE=3 SV=1 gi\|217319758, gi... - gi\|217327391\|ref\|ZP_03443474.1\| protein RecA [Escherichia coli O157:H7 str. TW14588], gi\|217319758\|g... RECA_ECO27 - Protein RecA OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=recA PE=3 SV=1 gi\|189366842, gi... - gi\|189366842\|gb\|EDU85258.1\| protein RecA [Escherichia coli O157:H7 str. EC4501], gi\|168762905\|ref\|ZP... gi\|189357312, gi... - gi\|189357312\|gb\|EDU75731.1\| protein RecA [Escherichia coli O157:H7 str. EC4401], gi\|168755441\|ref\|ZP... gi\|187769610, gi... - gi\|187769610\|gb\|EDU33454.1\| protein RecA [Escherichia coli O157:H7 str. EC4196], gi\|168774772\|ref\|ZP... gi\|189362165, gi... - gi\|189362165\|gb\|EDU80584.1\| protein RecA [Escherichia coli O157:H7 str. EC4486], gi\|168768787\|ref\|ZP... gi\|168787951, gi... - gi\|189372187\|gb\|EDU90603.1\| protein RecA [Escherichia coli O157:H7 str. EC869], gi\|168787951\|ref\|ZP_... gi\|168778678, gi... - gi\|189003321\|gb\|EDU72307.1\| protein RecA [Escherichia coli O157:H7 str. EC4076], gi\|168778678\|ref\|ZP... RECA_ECOSM - Protein RecA OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=recA PE=3 SV=1 gi\|189377451, gi... - gi\|189377451\|gb\|EDU95867.1\| protein RecA [Escherichia coli O157:H7 str. EC508], gi\|168800223\|ref\|ZP_... gi\|124528065, gi... - gi\|124528065\|ref\|ZP_01699418.1\| recA protein [Escherichia coli B], gi\|124500957\|gb\|EAY48425.1\| recA ... gi\|242378256, gi... - gi\|251785983\|ref\|YP_003000287.1\| hypothetical protein B21_02514 [Escherichia coli BL21], gi\|24237825... gi\|254289391, gi... - gi\|254289391\|ref\|YP_003055139.1\| recombinase A [Escherichia coli BL21(DE3)], gi\|253978698\|gb\|ACT4436... gi\|253974531, gi... - gi\|254162630\|ref\|YP_003045738.1\| recombinase A [Escherichia coli B str. REL606], gi\|253974531\|gb\|ACT... gi\|254594041, gi... - gi\|254794641\|ref\|YP_003079478.1\| DNA strand exchange and recombination protein with protease and nuc... EG10823 - DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding pro... RECA_ECOUT - Protein RecA OS=Escherichia coli (strain UTI89 / UPEC) GN=recA PE=3 SV=1 gi\|13363027, gi\|... - gi\|15832810\|ref\|NP_311583.1\| recombinase A [Escherichia coli O157:H7 str. Sakai], gi\|13363027\|dbj\|BA... RECA_ECOL5 - Protein RecA OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=recA PE=3 SV=1 RECA_SHIF8 - Protein RecA OS=Shigella flexneri serotype 5b (strain 8401) GN=recA PE=3 SV=1 gi\|85675524, gi\|... - gi\|89109486\|ref\|AP_003266.1\| DNA strand exchange and recombination protein with protease and nucleas... gi\|56480164, gi\|... - gi\|56480164\|ref\|NP_708507.2\| recombinase A [Shigella flexneri 2a str. 301], gi\|56383715\|gb\|AAN44214.... gi\|192927309, gi... - gi\|75256899\|ref\|ZP_00728475.1\| COG0468: RecA/RadA recombinase [Escherichia coli E22], gi\|193065012\|r... sp\|B7UHB7\|RECA_ECO27 - Protein RecA OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=recA PE=3 SV=1 gi\|75512391, gi\|... - gi\|75512391\|ref\|ZP_00734943.1\| COG0468: RecA/RadA recombinase [Escherichia coli 53638], gi\|188495073... gi\|192957051, gi... - gi\|75235708\|ref\|ZP_00719882.1\| COG0468: RecA/RadA recombinase [Escherichia coli E110019], gi\|1930696... gi\|75241642, gi\|... - gi\|75241642\|ref\|ZP_00725479.1\| COG0468: RecA/RadA recombinase [Escherichia coli F11], gi\|191171319\|r... RECA_SHIDS - Protein RecA OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=recA PE=3 SV=1 RECA_SHIBS - Protein RecA OS=Shigella boydii serotype 4 (strain Sb227) GN=recA PE=3 SV=1 RECA_SHISS - Protein RecA OS=Shigella sonnei (strain Ss046) GN=recA PE=3 SV=1 RECA_ECOL6 - Protein RecA OS=Escherichia coli O6 GN=recA PE=3 SV=2 RECA_ECOLC - Protein RecA OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=recA PE=3 SV=1 RECA_ECOBW - Protein RecA OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=recA PE=3 SV=1	0.0	[1..356]	[1..353]

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Predicted Domain #1

Region A:
Residues: [1-356]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAIDENKQKA LAAALGQIEK QFGKGSIMRL GEDRSMDVET ISTGSLSLDI ALGAGGLPMG  60
   61 RIVEIYGPES SGKTTLTLQV IAAAQREGKT CAFIDAEHAL DPIYAKKLGV DIDNLLCSQP 120
  121 DTGEQALEIC DALTRSGAVD VIIVDSVAAL TPKAEIEGEI GDSHMGLAAR MMSQAMRKLA 180
  181 GNLKNANTLL IFINQIRMKI GVMFGNPETT TGGNALKFYA SVRLDIRRIG AVKDGDVVVG 240
  241 SETRVKVVKN KIAAPFKQAE FQILYGEGIN INGELVDLGV KHKLIEKAGA WYSYNGDKIG 300
  301 QGKANASNYL KENPAIAAEL DKKLREMLLN GGNGEQPVAA ATAEFADGAD ETNEEF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	104.0
Match:	1u94A
Description:	Crystal Structure of E. Coli RecA in a Compressed Helical Filament Form 2
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleoside-triphosphatase activity	1.5002869400376	bayes_pls_golite062009
pyrophosphatase activity	1.49611313354225	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.47468810672455	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.47371190790284	bayes_pls_golite062009
binding	1.41264401383678	bayes_pls_golite062009
hydrolase activity	1.29419296935491	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
ATPase activity	0.844502974582959	bayes_pls_golite062009
DNA-dependent ATPase activity	0.510757066819002	bayes_pls_golite062009
helicase activity	0.51056840156051	bayes_pls_golite062009
purine nucleotide binding	0.360529478474946	bayes_pls_golite062009
nucleotide binding	0.354857598792381	bayes_pls_golite062009
purine ribonucleotide binding	0.35235724478784	bayes_pls_golite062009
ribonucleotide binding	0.352298062690593	bayes_pls_golite062009
protein binding	0.231495635179652	bayes_pls_golite062009
nucleic acid binding	0.216266069700019	bayes_pls_golite062009
DNA helicase activity	0.148854929640752	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: