YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|194711477, gi...
Organism:	Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633
Length:	481 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|194711477, gi....

Description	E-value	Query Range	Subject Range
gi\|62129509, gi\|... - gi\|62181876\|ref\|YP_218293.1\| protease TldD [Salmonella enterica subsp. enterica serovar Choleraesuis...	0.0	[1..481]	[35..515]
gi\|205322509, gi... - gi\|205322509\|gb\|EDZ10348.1\| protein TldD [Salmonella enterica subsp. enterica serovar Saintpaul str.... gi\|56129552, gi\|... - gi\|56415295\|ref\|YP_152370.1\| protease TldD [Salmonella enterica subsp. enterica serovar Paratyphi A ... gi\|197095702, gi... - gi\|197364225\|ref\|YP_002143862.1\| protease TldD [Salmonella enterica subsp. enterica serovar Paratyph...	0.0	[1..481]	[1..481]
gi\|89110006, gi\|... - gi\|89110006\|ref\|AP_003786.1\| predicted peptidase [Escherichia coli str. K-12 substr. W3110], gi\|8567... gi\|75188044, gi\|... - gi\|75188044\|ref\|ZP_00701311.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|157162722, gi... - gi\|75197187\|ref\|ZP_00707257.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|75209681, gi\|... - gi\|75209681\|ref\|ZP_00709893.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|75228630, gi\|... - gi\|75228630\|ref\|ZP_00715255.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|193070288, gi... - gi\|75234848\|ref\|ZP_00719139.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|75237901, gi\|... - gi\|75237901\|ref\|ZP_00721912.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|193065371, gi... - gi\|75256614\|ref\|ZP_00728244.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|188491307, gi... - gi\|75511860\|ref\|ZP_00734472.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|169753440, gi... - gi\|170018512\|ref\|YP_001723466.1\| protease TldD [Escherichia coli ATCC 8739], gi\|169753440\|gb\|ACA7613... gi\|170082775, gi... - gi\|170082775\|ref\|YP_001732095.1\| peptidase [Escherichia coli str. K-12 substr. DH10B], gi\|169890610\|... gi\|170680441, gi... - gi\|170680441\|ref\|YP_001745516.1\| protein TldD [Escherichia coli SMS-3-5], gi\|170518159\|gb\|ACB16337.1... gi\|194416866, gi... - gi\|194434890\|ref\|ZP_03067136.1\| protein TldD [Shigella dysenteriae 1012], gi\|194416866\|gb\|EDX32989.1... gi\|209920714, gi... - gi\|209920714\|ref\|YP_002294798.1\| protease TldD [Escherichia coli SE11], gi\|209913973\|dbj\|BAG79047.1\|... gi\|83585385, gi\|... - gi\|83585385\|ref\|ZP_00924031.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|215266625, gi... - gi\|215488553\|ref\|YP_002330984.1\| protease TldD [Escherichia coli O127:H6 str. E2348/69], gi\|21526662... TLDD_SHIFL - Metalloprotease TldD homolog OS=Shigella flexneri GN=tldD PE=3 SV=1 gi\|24053721, gi\|... - gi\|24114530\|ref\|NP_709040.1\| protease TldD [Shigella flexneri 2a str. 301], gi\|24053721\|gb\|AAN44747.... TLDD_ECOL6 - Metalloprotease TldD OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=tldD PE=3 SV=... gi\|227887959, gi... - gi\|227887959\|ref\|ZP_04005764.1\| possible peptidase [Escherichia coli 83972], gi\|227835355\|gb\|EEJ4582... gi\|30064576, gi\|... - gi\|30064576\|ref\|NP_838747.1\| protease TldD [Shigella flexneri 2a str. 2457T], gi\|30042835\|gb\|AAP1855... gi\|226899049, gi... - gi\|237706009\|ref\|ZP_04536490.1\| protease TldD [Escherichia sp. 3_2_53FAA], gi\|226899049\|gb\|EEH85308.... EG12826 - putative peptidase / Probable peptidase required for the maturation and secretion of the antibiotic ... gi\|238862788, gi... - gi\|238902345\|ref\|YP_002928141.1\| putative peptidase [Escherichia coli BW2952], gi\|238862788\|gb\|ACR64... gi\|251786508, gi... - gi\|251786508\|ref\|YP_003000812.1\| hypothetical protein B21_03055 [Escherichia coli BL21], gi\|24237878... gi\|254289931, gi... - gi\|254289931\|ref\|YP_003055679.1\| predicted peptidase [Escherichia coli BL21(DE3)], gi\|253979238\|gb\|A... gi\|254038404, gi... - gi\|254038404\|ref\|ZP_04872462.1\| protease TldD [Escherichia sp. 1_1_43], gi\|226840028\|gb\|EEH72049.1\| ... gi\|254163181, gi... - gi\|254163181\|ref\|YP_003046289.1\| predicted peptidase [Escherichia coli B str. REL606], gi\|253975082\|... gi\|115514652, gi... - gi\|117625528\|ref\|YP_858851.1\| protease TldD [Escherichia coli APEC O1], gi\|115514652\|gb\|ABJ02727.1\| ... gi\|124528518, gi... - gi\|124528518\|ref\|ZP_01699807.1\| peptidase U62, modulator of DNA gyrase [Escherichia coli B], gi\|1245... gi\|218362576, gi... - gi\|218555808\|ref\|YP_002388721.1\| protease TldD [Escherichia coli IAI1], gi\|218362576\|emb\|CAR00200.1\|... gi\|218691526, gi... - gi\|218691526\|ref\|YP_002399738.1\| protease TldD [Escherichia coli ED1a], gi\|218429090\|emb\|CAR10034.2\|... gi\|218696943, gi... - gi\|218696943\|ref\|YP_002404610.1\| protease TldD [Escherichia coli 55989], gi\|218353675\|emb\|CAU99917.1... gi\|218371995, gi... - gi\|218702009\|ref\|YP_002409638.1\| protease TldD [Escherichia coli IAI39], gi\|218371995\|emb\|CAR19851.1... gi\|218433955, gi... - gi\|218706858\|ref\|YP_002414377.1\| protease TldD [Escherichia coli UMN026], gi\|218433955\|emb\|CAR14872.... gi\|110616654, gi... - gi\|110807106\|ref\|YP_690626.1\| protease TldD [Shigella flexneri 5 str. 8401], gi\|110616654\|gb\|ABF0532... gi\|91074238, gi\|... - gi\|91212664\|ref\|YP_542650.1\| protease TldD [Escherichia coli UTI89], gi\|91074238\|gb\|ABE09119.1\| csrA... gi\|110643479, gi... - gi\|110643479\|ref\|YP_671209.1\| protease TldD [Escherichia coli 536], gi\|110345071\|gb\|ABG71308.1\| supp... TLDD_ECOL6 - Protein tldD OS=Escherichia coli O6 GN=tldD PE=3 SV=1 EG12826 - putative peptidase / Probable peptidase required for the maturation and secretion of the antibiotic ... TLDD_ECOLI - Protein tldD - Escherichia coli	0.0	[1..481]	[1..481]
gi\|82778552, gi\|... - gi\|82778552\|ref\|YP_404901.1\| protease TldD [Shigella dysenteriae Sd197], gi\|81242700\|gb\|ABB63410.1\| ...	0.0	[1..481]	[1..481]
gi\|73857251, gi\|... - gi\|74313774\|ref\|YP_312193.1\| protease TldD [Shigella sonnei Ss046], gi\|73857251\|gb\|AAZ89958.1\| suppr...	0.0	[1..481]	[1..481]
gi\|13363590, gi\|... - gi\|15833371\|ref\|NP_312144.1\| protease TldD [Escherichia coli O157:H7 str. Sakai], gi\|13363590\|dbj\|BA... gi\|208741377, gi... - gi\|208821254\|ref\|ZP_03261574.1\| protein TldD [Escherichia coli O157:H7 str. EC4042], gi\|208741377\|gb... gi\|209398830, gi... - gi\|209398830\|ref\|YP_002272707.1\| protein TldD [Escherichia coli O157:H7 str. EC4115], gi\|209160230\|g... gi\|217327293, gi... - gi\|217327293\|ref\|ZP_03443376.1\| protein TldD [Escherichia coli O157:H7 str. TW14588], gi\|217319660\|g... gi\|168786130, gi... - gi\|189374193\|gb\|EDU92609.1\| protein TldD [Escherichia coli O157:H7 str. EC869], gi\|168786130\|ref\|ZP_... gi\|254795187, gi... - gi\|254795187\|ref\|YP_003080024.1\| predicted peptidase [Escherichia coli O157:H7 str. TW14359], gi\|254... gi\|195939442 - gi\|195939442\|ref\|ZP_03084824.1\| protease TldD [Escherichia coli O157:H7 str. EC4024] gi\|208728915, gi... - gi\|208809114\|ref\|ZP_03251451.1\| protein TldD [Escherichia coli O157:H7 str. EC4206], gi\|208728915\|gb... gi\|208813250, gi... - gi\|208813250\|ref\|ZP_03254579.1\| protein TldD [Escherichia coli O157:H7 str. EC4045], gi\|208734527\|gb... gi\|189366121, gi... - gi\|189366121\|gb\|EDU84537.1\| protein TldD [Escherichia coli O157:H7 str. EC4501], gi\|168763781\|ref\|ZP... gi\|168769100, gi... - gi\|189361766\|gb\|EDU80185.1\| protein TldD [Escherichia coli O157:H7 str. EC4486], gi\|168769100\|ref\|ZP... gi\|187767170, gi... - gi\|187767170\|gb\|EDU31014.1\| protein TldD [Escherichia coli O157:H7 str. EC4196], gi\|168777639\|ref\|ZP... gi\|189001089, gi... - gi\|189001089\|gb\|EDU70075.1\| protein TldD [Escherichia coli O157:H7 str. EC4076], gi\|168781388\|ref\|ZP... gi\|25305200, gi\|... - pir\|\|H85988 suppresses inhibitory activity of CsrA [imported] - Escherichia coli (strain O157:H7, su... gi\|15803778, gi\|... - gi\|15803778\|ref\|NP_289812.1\| protease TldD [Escherichia coli O157:H7 EDL933], gi\|12517868\|gb\|AAG5837... gi\|188013929, gi... - gi\|188013929\|gb\|EDU52051.1\| protein TldD [Escherichia coli O157:H7 str. EC4113], gi\|168752143\|ref\|ZP... gi\|13363590, gi\|... - gi\|15833371\|ref\|NP_312144.1\| suppresses inhibitory activity of CsrA [Escherichia coli O157:H7], gi\|1... gi\|168754226, gi... - gi\|189358715\|gb\|EDU77134.1\| protein TldD [Escherichia coli O157:H7 str. EC4401], gi\|168754226\|ref\|ZP...	0.0	[1..481]	[1..481]
gi\|81246937, gi\|... - gi\|82545526\|ref\|YP_409473.1\| protease TldD [Shigella boydii Sb227], gi\|81246937\|gb\|ABB67645.1\| suppr...	0.0	[1..481]	[1..481]
gi\|36787347, gi\|... - gi\|37527911\|ref\|NP_931256.1\| protease TldD [Photorhabdus luminescens subsp. laumondii TTO1], gi\|3678...	0.0	[1..481]	[1..481]
gi\|77978742, gi\|... - gi\|77978742\|ref\|ZP_00834167.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol...	0.0	[1..481]	[1..481]
gi\|22124113, gi\|... - gi\|22124113\|ref\|NP_667536.1\| protease TldD [Yersinia pestis KIM], gi\|21956865\|gb\|AAM83787.1\|AE013619... gi\|167048601, gi... - gi\|167402015\|ref\|ZP_02307498.1\| TldD protein [Yersinia pestis biovar Antiqua str. UG05-0454], gi\|167... gi\|229687336, gi... - gi\|229899844\|ref\|ZP_04514985.1\| putative modulator of DNA gyrase [Yersinia pestis biovar Orientalis ... gi\|25305218 - pir\|\|AB0447 probable modulator of DNA gyrase tldD [imported] - Yersinia pestis (strain CO92) gi\|166204668, gi... - gi\|166214181\|ref\|ZP_02240216.1\| TldD protein [Yersinia pestis biovar Antiqua str. B42003004], gi\|166... gi\|51597849, gi\|... - gi\|51597849\|ref\|YP_072040.1\| protease TldD [Yersinia pseudotuberculosis IP 32953], gi\|51591131\|emb\|C... gi\|167425535, gi... - gi\|167425535\|ref\|ZP_02317288.1\| TldD protein [Yersinia pestis biovar Mediaevalis str. K1973002], gi\|... gi\|45443603, gi\|... - gi\|45443603\|ref\|NP_995142.1\| protease TldD [Yersinia pestis biovar Microtus str. 91001], gi\|45438473... gi\|166961543, gi... - gi\|167420737\|ref\|ZP_02312490.1\| TldD protein [Yersinia pestis biovar Orientalis str. MG05-1020], gi\|... gi\|16123815, gi\|... - gi\|218930683\|ref\|YP_002348558.1\| protease TldD [Yersinia pestis CO92], gi\|16123815\|ref\|NP_407128.1\| ... gi\|186700069, gi... - gi\|186897043\|ref\|YP_001874155.1\| protease TldD [Yersinia pseudotuberculosis PB1/+], gi\|186700069\|gb\|... gi\|162418726, gi... - gi\|77634293\|ref\|ZP_00796396.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|153997389, gi... - gi\|153997389\|ref\|ZP_02022489.1\| putative modulator of DNA gyrase [Yersinia pestis CA88-4125], gi\|149... gi\|145209291, gi... - gi\|145597595\|ref\|YP_001161671.1\| protease TldD [Yersinia pestis Pestoides F], gi\|145209291\|gb\|ABP386... gi\|165989800, gi... - gi\|166011416\|ref\|ZP_02232314.1\| TldD protein [Yersinia pestis biovar Antiqua str. E1979001], gi\|1659... gi\|165927608, gi... - gi\|165927608\|ref\|ZP_02223440.1\| TldD protein [Yersinia pestis biovar Orientalis str. F1991016], gi\|1... gi\|89105392, gi\|... - gi\|89105392\|ref\|ZP_01177912.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|108809676, gi... - gi\|108809676\|ref\|YP_653592.1\| protease TldD [Yersinia pestis Antiqua], gi\|108781589\|gb\|ABG15647.1\| m... Q665G0\|Q665G0_YERPS - Putative modulator of DNA gyrase - Yersinia pseudotuberculosis gi\|108777307, gi... - gi\|229904155\|ref\|ZP_04519266.1\| putative modulator of DNA gyrase [Yersinia pestis Nepal516], gi\|2296... gi\|229836820, gi... - gi\|229836820\|ref\|ZP_04456985.1\| putative modulator of DNA gyrase [Yersinia pestis Pestoides A], gi\|2... gi\|229695647, gi... - gi\|229839281\|ref\|ZP_04459440.1\| putative modulator of DNA gyrase [Yersinia pestis biovar Orientalis ...	0.0	[1..481]	[1..481]

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Predicted Domain #1

Region A:
Residues: [1-481]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLNLVSEQL LAANGLNHQD LFAILGQLAE RRLDYGDLYF QSSYHESWVL EDRIIKDGSY  60
   61 NIDQGVGVRA ISGEKTGFAY ADQISLLALE QSAQAARTIV RENGEGKVKT LAAVAHQPLY 120
  121 TTLDPLQSMS REEKLDILRR VDKAAREADK RVQEVNASLT GVYELILVAA TDGTLAADVR 180
  181 PLVRLSVSVQ VEEDGKRERG ASGGGGRFGY EYFLADLDGE VRADAWAKEA VRMALVNLSA 240
  241 VAAPAGTLPV VLGAGWPGVL LHEAVGHGLE GDFNRRGTSV FSGQIGEQVA SALCTVVDDG 300
  301 TMMNRRGSVA IDDEGTPGQY NVLIENGVLK GYMQDKLNAR LMGAAPTGNG RRESYAHLPM 360
  361 PRMTNTYMLA GQSTPQEIIE SVEYGIYAPN FGGGQVDITS GKFVFSTSEA YLIENGKVTT 420
  421 PVKGATLIGS GIETMQQISM VGNDLKLDNG VGVCGKEGQS LPVGVGQPTL KVDNLTVGGT 480
  481 A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.69897
Match:	1vl4A
Description:	Crystal structure of PMBA-related protein (TM0727) from Thermotoga maritima at 1.95 A resolution
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	0.844669254385544	bayes_pls_golite062009
catalytic activity	0.55839241827268	bayes_pls_golite062009
transcription repressor activity	0.0121152486203551	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: