YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOA_SHIF8
Organism:	Shigella flexneri 5 str. 8401
Length:	329 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 RPOA_SHIF8.

Description	E-value	Query Range	Subject Range
gi\|238797219, gi... - gi\|77962764\|ref\|ZP_00826581.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye...	0.0	[1..329]	[1..329]
gi\|89104531, gi\|... - gi\|89104531\|ref\|ZP_01177071.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye... gi\|149290126, gi... - gi\|150260718\|ref\|ZP_01917446.1\| DNA-directed RNA polymerase alpha chain [Yersinia pestis CA88-4125],... gi\|167055293, gi... - gi\|167425603\|ref\|ZP_02317356.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar M... gi\|169749103, gi... - gi\|170022569\|ref\|YP_001719074.1\| DNA-directed RNA polymerase subunit alpha [Yersinia pseudotuberculo... gi\|229690484, gi... - gi\|229842174\|ref\|ZP_04462329.1\| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis str... gi\|186897159, gi... - gi\|186897159\|ref\|YP_001874271.1\| DNA-directed RNA polymerase subunit alpha [Yersinia pseudotuberculo... gi\|229840092, gi... - gi\|229840092\|ref\|ZP_04460251.1\| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis str... RPOA_YERPE - DNA-directed RNA polymerase subunit alpha OS=Yersinia pestis GN=rpoA PE=3 SV=1 gi\|229836284, gi... - gi\|229836284\|ref\|ZP_04456451.1\| RNA polymerase, alpha subunit [Yersinia pestis Pestoides A], gi\|2297... gi\|45434947, gi\|... - gi\|45440092\|ref\|NP_991631.1\| DNA-directed RNA polymerase subunit alpha [Yersinia pestis biovar Micro... RPOA_YERPA - DNA-directed RNA polymerase subunit alpha OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=rpoA PE... gi\|22127885, gi\|... - gi\|22127885\|ref\|NP_671308.1\| DNA-directed RNA polymerase subunit alpha [Yersinia pestis KIM], gi\|219... RPOA_YERPN - DNA-directed RNA polymerase subunit alpha OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=rpoA P... gi\|115346051, gi... - gi\|218927440\|ref\|YP_002345315.1\| DNA-directed RNA polymerase subunit alpha [Yersinia pestis CO92], g... RPOA_YERPS - DNA-directed RNA polymerase subunit alpha OS=Yersinia pseudotuberculosis serotype I (strain IP32953)... RPOA_YERPP - DNA-directed RNA polymerase subunit alpha OS=Yersinia pestis (strain Pestoides F) GN=rpoA PE=3 SV=1 gi\|165927880, gi... - gi\|165927880\|ref\|ZP_02223712.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar O... gi\|165990525, gi... - gi\|166010435\|ref\|ZP_02231333.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar A... gi\|162353351, gi... - gi\|77633035\|ref\|ZP_00795192.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye... gi\|166213170, gi... - gi\|166213170\|ref\|ZP_02239205.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar A... RPOA_YERP3 - DNA-directed RNA polymerase subunit alpha OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31... gi\|167398622, gi... - gi\|167398622\|ref\|ZP_02304146.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar A... gi\|167419336, gi... - gi\|167419336\|ref\|ZP_02311089.1\| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar O... RPOA_YERPS - DNA-directed RNA polymerase subunit alpha OS=Yersinia pseudotuberculosis GN=rpoA PE=1 SV=1	0.0	[1..329]	[1..329]
gi\|251756736, gi... - gi\|253690158\|ref\|YP_003019348.1\| DNA-directed RNA polymerase, alpha subunit [Pectobacterium carotovo... gi\|255056843, gi... - gi\|255056843\|ref\|ZP_05309044.1\| DNA-directed RNA polymerase, alpha subunit [Pectobacterium wasabiae ... gi\|227115247 - gi\|227115247\|ref\|ZP_03828903.1\| DNA-directed RNA polymerase subunit alpha [Pectobacterium carotovoru... RPOA_ERWCT - DNA-directed RNA polymerase subunit alpha OS=Erwinia carotovora subsp. atroseptica GN=rpoA PE=3 SV=1 gi\|227328924 - gi\|227328924\|ref\|ZP_03832948.1\| DNA-directed RNA polymerase subunit alpha [Pectobacterium carotovoru... RPOA_PECAS - DNA-directed RNA polymerase subunit alpha OS=Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BA...	0.0	[1..329]	[1..329]
gi\|238792960, gi... - gi\|77978251\|ref\|ZP_00833683.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye... gi\|77957307, gi\|... - gi\|77957307\|ref\|ZP_00821366.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye... gi\|238707693, gi... - gi\|238754197\|ref\|ZP_04615555.1\| DNA-directed RNA polymerase subunit alpha [Yersinia ruckeri ATCC 294... gi\|238758785, gi... - gi\|238758785\|ref\|ZP_04619959.1\| DNA-directed RNA polymerase subunit alpha [Yersinia aldovae ATCC 352...	0.0	[1..329]	[1..329]
RPOA_SHIDS - DNA-directed RNA polymerase subunit alpha OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rpoA ...	0.0	[1..329]	[1..329]
gi\|253783114, gi... - gi\|253991664\|ref\|YP_003043020.1\| DNA-directed RNA polymerase alpha chain [Photorhabdus asymbiotica],... RPOA_PHOLL - DNA-directed RNA polymerase subunit alpha OS=Photorhabdus luminescens subsp. laumondii GN=rpoA PE=3 ... RPOA_PHOLL - DNA-directed RNA polymerase subunit alpha OS=Photorhabdus luminescens subsp. laumondii (strain DSM 1...	0.0	[1..329]	[1..329]
gi\|42799 - gi\|42799\|emb\|CAA26395.1\| unnamed protein product [Escherichia coli]	0.0	[1..329]	[1..329]
RPOA_SALCH - DNA-directed RNA polymerase subunit alpha OS=Salmonella choleraesuis GN=rpoA PE=3 SV=1 RPOA_SALCH - DNA-directed RNA polymerase subunit alpha OS=Salmonella choleraesuis GN=rpoA PE=3 SV=1 RPOA_SALCH - DNA-directed RNA polymerase subunit alpha OS=Salmonella choleraesuis (strain SC-B67) GN=rpoA PE=3 SV...	0.0	[1..329]	[1..329]
gi\|238752666, gi... - gi\|238752666\|ref\|ZP_04614137.1\| DNA-directed RNA polymerase subunit alpha [Yersinia rohdei ATCC 4338... gi\|238722914, gi... - gi\|77974965\|ref\|ZP_00830502.1\| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Ye... RPOA_YERE8 - DNA-directed RNA polymerase subunit alpha OS=Yersinia enterocolitica serotype O:8 / biotype 1B (stra...	0.0	[1..328]	[1..328]
RPOA_MANSM - DNA-directed RNA polymerase subunit alpha OS=Mannheimia succiniciproducens (strain MBEL55E) GN=rpoA ...	0.0	[1..329]	[1..329]

Back

Predicted Domain #1

Region A:
Residues: [1-237]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE  60
   61 IDGVLHEYST KEGVQEDILE ILLNLKGLAV RVQGKDEVIL TLNKSGIGPV TAADITHDGD 120
  121 VEIVKPQHVI CHLTDENASI SMRIKVQRGR GYVPASTRIH SEEDERPIGR LLVDACYSPV 180
  181 ERIAYNVEAA RVEQRTDLDK LVIEMETNGT IDPEEAIRRA ATILAEQLEA FVDLRDV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.69897
Match:	1bdfA
Description:	RNA polymerase alpha; RNA polymerase alpha subunit
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	9.7234602659063	bayes_pls_golite062009
RNA polymerase activity	9.7234602659063	bayes_pls_golite062009
nucleotidyltransferase activity	7.15121167353057	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.00321253017182	bayes_pls_golite062009
transferase activity	4.43019288788219	bayes_pls_golite062009
binding	1.71036005361152	bayes_pls_golite062009
catalytic activity	1.14991565197115	bayes_pls_golite062009
nucleic acid binding	0.912313560512218	bayes_pls_golite062009
DNA binding	0.830570793255009	bayes_pls_golite062009
protein binding	0.224464975113154	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [238-329]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RQPEVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK  60
   61 KSLTEIKDVL ASRGLSLGMR LENWPPASIA DE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1cooA
Description:	THE COOH-TERMINAL DOMAIN OF RNA POLYMERASE ALPHA SUBUNIT
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	9.80450362116562	bayes_pls_golite062009
RNA polymerase activity	9.80450362116562	bayes_pls_golite062009
nucleotidyltransferase activity	7.23643031680113	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.11216561090158	bayes_pls_golite062009
transferase activity	4.56918356543307	bayes_pls_golite062009
catalytic activity	1.48339787978627	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:

Predicted functions: