YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|45443603, gi\|...
Organism:	Yersinia pestis biovar Microtus str. 91001
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

[What does the above image mean?]

[Show Ginzu Version Information]

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|45443603, gi|....

Description	E-value	Query Range	Subject Range
gi\|153950166, gi... - gi\|77630559\|ref\|ZP_00793145.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol... gi\|169749257, gi... - gi\|170022723\|ref\|YP_001719228.1\| protease TldD [Yersinia pseudotuberculosis YPIII], gi\|169749257\|gb\|...	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\|36787347, gi\|... - gi\|37527911\|ref\|NP_931256.1\| protease TldD [Photorhabdus luminescens subsp. laumondii TTO1], gi\|3678...	0.0	[1..481]	[1..481]
gi\|238789798, gi... - gi\|77973450\|ref\|ZP_00828998.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol...	0.0	[1..481]	[1..481]
gi\|77961441, gi\|... - gi\|77961441\|ref\|ZP_00825278.1\| COG0312: Predicted Zn-dependent proteases and their inactivated homol...	0.0	[1..481]	[1..481]
gi\|50956513 - gi\|50956513\|gb\|AAT90762.1\| putative DNA gyrase modulator [Yersinia enterocolitica]	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\|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\|90311123, gi\|... - gi\|90407763\|ref\|ZP_01215941.1\| TldD protein [Psychromonas sp. CNPT3], gi\|90311123\|gb\|EAS39230.1\| Tld...	0.0	[1..480]	[1..480]
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]

Back

Predicted Domain #1

Region A:
Residues: [1-481]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLSFVSEQL LTANKLNHQD LFSVLGQLTE RRLDYADLYF QSSYHEAWVL EDSIIKDGSY  60
   61 NIDQGVGVRA VSGEKTGFAY ADQITLNALQ QSAHAARSIV RDTGNGKVHT LGEIAYQALY 120
  121 PLLDPLQSLS REDKIALLHR VDKVARAADK RVQEVSASLT GVYEQILVAA TDGTLAADVR 180
  181 PLVRLSVSVL VEDNGKRERG ACGGGGRFGY DYFLETVDGE VRADNFANEA VRMALVNLSA 240
  241 IAAPAGAMPV VLGAGWPGVL LHEAVGHGLE GDFNRRGSSV FSGQMGKLVA SELCTVVDDG 300
  301 TMQGRRGSLA IDDEGVPGQY NVLIENGILK GYMQDKLNAR LMGVAPTGNG RRESYAHLPM 360
  361 PRMTNTYMLA GQSTPEDIIA SVEYGLYAPN FGGGQVDITS GKFVFSTSEA YLIEKGKITH 420
  421 AVKGATLIGS GIEAMQQISM VGNDLALDKG VGVCGKEGQS LPVGVGQPTL KLDNLTVGGT 480
  481 A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	88.0
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: