YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|199605728, gi...
Organism:	Salmonella enterica subsp. enterica serovar Virchow str. SL491
Length:	191 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|199605728, gi....

Description	E-value	Query Range	Subject Range
gi\|30749943, gi\|... - gi\|30749945\|pdb\|1OR7\|B Chain B, Crystal Structure Of Escherichia Coli Sigmae With The Cytoplasmic Do...	5.0E-40	[1..191]	[4..194]
gi\|27364928, gi\|... - gi\|27364928\|ref\|NP_760456.1\| RNA polymerase sigma factor RpoE [Vibrio vulnificus CMCP6], gi\|27361074... gi\|37681022, gi\|... - gi\|37681022\|ref\|NP_935631.1\| RNA polymerase sigma factor RpoE [Vibrio vulnificus YJ016], gi\|37199772...	7.0E-40	[1..191]	[1..192]
gi\|75237408, gi\|... - gi\|75237408\|ref\|ZP_00721443.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	7.0E-40	[1..189]	[1..189]
gi\|194432064, gi... - gi\|83570809\|ref\|ZP_00922252.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	8.0E-40	[1..191]	[1..191]
gi\|86146365, gi\|... - gi\|86146365\|ref\|ZP_01064689.1\| RNA polymerase sigma-70 factor [Vibrio sp. MED222], gi\|85835844\|gb\|EA... gi\|84390098, gi\|... - gi\|84390098\|ref\|ZP_00991360.1\| RNA polymerase sigma-70 factor [Vibrio splendidus 12B01], gi\|84376752...	9.0E-40	[1..191]	[1..192]
gi\|209913311, gi... - gi\|209920052\|ref\|YP_002294136.1\| RNA polymerase sigma factor RpoE [Escherichia coli SE11], gi\|209913... gi\|215265989, gi... - gi\|215487917\|ref\|YP_002330348.1\| RNA polymerase sigma factor RpoE [Escherichia coli O127:H6 str. E23... gi\|217327123, gi... - gi\|217327123\|ref\|ZP_03443206.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. TW14588... gi\|218555155, gi... - gi\|218555155\|ref\|YP_002388068.1\| RNA polymerase sigma factor RpoE [Escherichia coli IAI1], gi\|218361... gi\|218559494, gi... - gi\|218559494\|ref\|YP_002392407.1\| RNA polymerase sigma factor RpoE [Escherichia coli S88], gi\|2183662... gi\|218428253, gi... - gi\|218690689\|ref\|YP_002398901.1\| RNA polymerase sigma factor RpoE [Escherichia coli ED1a], gi\|218428... gi\|218696201, gi... - gi\|218696201\|ref\|YP_002403868.1\| RNA polymerase sigma factor RpoE [Escherichia coli 55989], gi\|21835... gi\|218701087, gi... - gi\|218701087\|ref\|YP_002408716.1\| RNA polymerase sigma factor RpoE [Escherichia coli IAI39], gi\|21837... gi\|170082182, gi... - gi\|170082182\|ref\|YP_001731502.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli str. K-... gi\|15832693, gi\|... - gi\|15832693\|ref\|NP_311466.1\| RNA polymerase sigma factor RpoE [Escherichia coli O157:H7 str. Sakai],... gi\|170519935, gi... - gi\|170682217\|ref\|YP_001744762.1\| RNA polymerase sigma-E factor [Escherichia coli SMS-3-5], gi\|170519... gi\|110344327, gi... - gi\|110642735\|ref\|YP_670465.1\| RNA polymerase sigma factor RpoE [Escherichia coli 536], gi\|110344327\|... gi\|170123762, gi... - gi\|170767428\|ref\|ZP_02901881.1\| RNA polymerase sigma-E factor [Escherichia albertii TW07627], gi\|170... gi\|110806518, gi... - gi\|110806518\|ref\|YP_690038.1\| RNA polymerase sigma factor RpoE [Shigella flexneri 5 str. 8401], gi\|1... gi\|195936720 - gi\|195936720\|ref\|ZP_03082102.1\| RNA polymerase sigma factor RpoE [Escherichia coli O157:H7 str. EC40... gi\|208727178, gi... - gi\|208807377\|ref\|ZP_03249714.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4206]... gi\|208813884, gi... - gi\|208813884\|ref\|ZP_03255213.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4045]... gi\|208742055, gi... - gi\|208821932\|ref\|ZP_03262252.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4042]... gi\|254794524, gi... - gi\|254794524\|ref\|YP_003079361.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli O157:H7... gi\|209400807, gi... - gi\|209400807\|ref\|YP_002272048.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4115... gi\|254162548, gi... - gi\|254162548\|ref\|YP_003045656.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli B str. ... gi\|253323572, gi... - gi\|254289309\|ref\|YP_003055057.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli BL21(DE... gi\|251785900, gi... - gi\|251785900\|ref\|YP_003000204.1\| hypothetical protein B21_02431 [Escherichia coli BL21], gi\|24237817... gi\|238901738, gi... - gi\|238901738\|ref\|YP_002927534.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli BW2952]... gi\|227835958, gi... - gi\|227887608\|ref\|ZP_04005413.1\| RNA polymerase sigma factor RpoE [Escherichia coli 83972], gi\|227835... gi\|218706077, gi... - gi\|218706077\|ref\|YP_002413596.1\| RNA polymerase sigma factor RpoE [Escherichia coli UMN026], gi\|2184... gi\|124499845, gi... - gi\|124529538\|ref\|ZP_01700508.1\| RNA polymerase, sigma-24 subunit, ECF subfamily [Escherichia coli B]... RPOE_ECOL6 - RNA polymerase sigma-E factor OS=Escherichia coli O6 GN=rpoE PE=3 SV=1 gi\|168748356, gi... - gi\|188017160\|gb\|EDU55282.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4113], gi... gi\|189355277, gi... - gi\|189355277\|gb\|EDU73696.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4401], gi... gi\|189362235, gi... - gi\|189362235\|gb\|EDU80654.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4486], gi... gi\|168773500, gi... - gi\|187770574\|gb\|EDU34418.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4196], gi... gi\|189003379, gi... - gi\|189003379\|gb\|EDU72365.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC4076], gi... gi\|168790373, gi... - gi\|189370138\|gb\|EDU88554.1\| RNA polymerase sigma-E factor [Escherichia coli O157:H7 str. EC869], gi\|... gi\|169754072, gi... - gi\|170019144\|ref\|YP_001724098.1\| RNA polymerase sigma factor RpoE [Escherichia coli ATCC 8739], gi\|1... RPOE_ECOL6 - ECF RNA polymerase sigma-E factor OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=... gi\|73671308\|gb\|A... - RpoE [Escherichia coli] EG11897 - RNA polymerase sigma E factor / RNA polymerase sigma E factor; role in extracytoplasmic, high temper... gi\|12516991, gi\|... - gi\|15803100\|ref\|NP_289131.1\| RNA polymerase sigma factor RpoE [Escherichia coli O157:H7 EDL933], gi\|... gi\|75513183, gi\|... - gi\|75513183\|ref\|ZP_00735625.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|74313135, gi\|... - gi\|74313135\|ref\|YP_311554.1\| RNA polymerase sigma factor RpoE [Shigella sonnei Ss046], gi\|73856612\|g... gi\|193068382, gi... - gi\|75237681\|ref\|ZP_00721697.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|75257997, gi\|... - gi\|75257997\|ref\|ZP_00729471.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|89109379, gi\|... - gi\|89109379\|ref\|AP_003159.1\| RNA polymerase, sigma 24 (sigma E) factor [Escherichia coli str. K-12 s... gi\|56480143, gi\|... - gi\|56480143\|ref\|NP_708425.2\| RNA polymerase sigma factor RpoE [Shigella flexneri 2a str. 301], gi\|56... gi\|81242147, gi\|... - gi\|82777999\|ref\|YP_404348.1\| RNA polymerase sigma factor RpoE [Shigella dysenteriae Sd197], gi\|81242... gi\|81246436, gi\|... - gi\|82545025\|ref\|YP_408972.1\| RNA polymerase sigma factor RpoE [Shigella boydii Sb227], gi\|81246436\|g... gi\|30042231, gi\|... - gi\|30063975\|ref\|NP_838146.1\| RNA polymerase sigma factor RpoE [Shigella flexneri 2a str. 2457T], gi\|... gi\|75196591, gi\|... - gi\|75196591\|ref\|ZP_00706661.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... RPOE_SHIFL - ECF RNA polymerase sigma-E factor OS=Shigella flexneri GN=rpoE PE=3 SV=1 gi\|75228852, gi\|... - gi\|75228852\|ref\|ZP_00715453.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... EG11897 - RNA polymerase sigma E factor / RNA polymerase sigma E factor; role in extracytoplasmic, high temper... gi\|194423461, gi... - gi\|83586775\|ref\|ZP_00925406.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... RPOE_ECO57 - ECF RNA polymerase sigma-E factor OS=Escherichia coli O157:H7 GN=rpoE PE=3 SV=1 gi\|157156082, gi... - gi\|75187326\|ref\|ZP_00700593.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... RPOE_ECOLI - RNA polymerase sigma-E factor (Sigma-24) - Escherichia coli	1.0E-39	[1..191]	[1..191]
gi\|226901449, gi... - gi\|237705083\|ref\|ZP_04535564.1\| RNA polymerase sigma-E factor [Escherichia sp. 3_2_53FAA], gi\|226901... gi\|987648\|dbj\|BA... - RNA polymerase sigma E [Escherichia coli] gi\|24053016, gi\|... - ref\|NP_708425.1\| RNA polymerase sigma E [Shigella flexneri 2a str. 301], gb\|AAN44132.1\| RNA polymer... gi\|987648 - gi\|987648\|dbj\|BAA10920.1\| RNA polymerase sigma E [Escherichia coli K-12] gi\|117624794, gi... - gi\|117624794\|ref\|YP_853707.1\| RNA polymerase sigma factor RpoE [Escherichia coli APEC O1], gi\|115513... gi\|26109344, gi\|... - gi\|26248938\|ref\|NP_754978.1\| RNA polymerase sigma factor RpoE [Escherichia coli CFT073], gi\|26109344... gi\|91211900, gi\|... - gi\|91211900\|ref\|YP_541886.1\| RNA polymerase sigma factor RpoE [Escherichia coli UTI89], gi\|91073474\|...	1.0E-39	[1..191]	[12..202]
gi\|153840480, gi... - gi\|153840480\|ref\|ZP_01993147.1\| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AQ3810], g... gi\|28899352, gi\|... - gi\|28899352\|ref\|NP_798957.1\| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus RIMD 2210633]... gi\|28807588 - gi\|28807588\|dbj\|BAC60841.1\| RNA polymerase sigma-E factor [Vibrio parahaemolyticus RIMD 2210633]	2.0E-39	[1..191]	[1..192]
gi\|194429260, gi... - gi\|75209497\|ref\|ZP_00709722.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	2.0E-39	[1..191]	[1..191]
gi\|11356111 - pir\|\|H82073 RNA polymerase sigma-E factor VC2467 [imported] - Vibrio cholerae (strain N16961 serogro... gi\|9657045, gi\|1... - gi\|9657045\|gb\|AAF95609.1\| RNA polymerase sigma-E factor [Vibrio cholerae O1 biovar El Tor str. N1696... gi\|121547169, gi... - gi\|121590992\|ref\|ZP_01678311.1\| RNA polymerase sigma-E factor [Vibrio cholerae 2740-80], gi\|12154716... gi\|116216118, gi... - gi\|75822887\|ref\|ZP_00752440.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|124115308, gi... - gi\|153214506\|ref\|ZP_01949415.1\| RNA polymerase sigma-E factor [Vibrio cholerae 1587], gi\|124115308\|g... gi\|121729904, gi... - gi\|75814520\|ref\|ZP_00745097.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|153222434, gi... - gi\|153222434\|ref\|ZP_01953168.1\| RNA polymerase sigma-E factor [Vibrio cholerae MAK 757], gi\|12411887... gi\|227082588, gi... - gi\|227082588\|ref\|YP_002811139.1\| RNA polymerase sigma-E factor [Vibrio cholerae M66-2], gi\|227010476... gi\|153820439, gi... - gi\|153820439\|ref\|ZP_01973106.1\| RNA polymerase sigma-E factor [Vibrio cholerae NCTC 8457], gi\|126509... gi\|254291667, gi... - gi\|254291667\|ref\|ZP_04962455.1\| RNA polymerase sigma-E factor [Vibrio cholerae AM-19226], gi\|1977510... gi\|126518781, gi... - gi\|153823693\|ref\|ZP_01976360.1\| RNA polymerase sigma-E factor [Vibrio cholerae B33], gi\|126518781\|gb... gi\|148873419, gi... - gi\|153831098\|ref\|ZP_01983765.1\| RNA polymerase sigma-E factor [Vibrio cholerae 623-39], gi\|148873419... gi\|254845297, gi... - gi\|75829328\|ref\|ZP_00758635.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|147675349, gi... - gi\|75827731\|ref\|ZP_00757166.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	5.0E-39	[1..189]	[1..190]

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Predicted Domain #1

Region A:
Residues: [1-191]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEQLTDQVL VERVQKGDQK AFNLLVVRYQ HKVASLVSRY VPSGDVPDVV QESFIKAYRA  60
   61 LDSFRGDSAF YTWLYRIAVN TAKNYLVAQG RRPPSSDVDA IEAENFESGG ALKEISNPEN 120
  121 LMLSEELRQI VFRTIESLPE DLRMAITLRE LDGLSYEEIA AIMDCPVGTV RSRIFRAREA 180
  181 IDNKVQPLIR R

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	41.39794
Match:	1or7A
Description:	SigmaE factor (RpoE)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription initiation factor activity	5.71806750193815	bayes_pls_golite062009
sigma factor activity	5.58029806879061	bayes_pls_golite062009
transcription regulator activity	3.67872017549582	bayes_pls_golite062009
binding	1.02634976114785	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: