YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|89109379, gi\|...
Organism:	Escherichia coli str. K-12 substr. W3110
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|89109379, gi|....

Description	E-value	Query Range	Subject Range
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...	181.0	[0..1]	[191..1]
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...	180.0	[0..1]	[191..1]
gi\|30749943, gi\|... - gi\|30749945\|pdb\|1OR7\|B Chain B, Crystal Structure Of Escherichia Coli Sigmae With The Cytoplasmic Do...	180.0	[0..1]	[191..4]
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]	179.0	[0..1]	[191..1]
gi\|75237408, gi\|... - gi\|75237408\|ref\|ZP_00721443.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	179.0	[0..1]	[189..1]
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...	179.0	[0..1]	[189..1]
gi\|194432064, gi... - gi\|83570809\|ref\|ZP_00922252.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	178.0	[0..1]	[191..1]
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\|...	178.0	[0..1]	[191..12]
gi\|91227859, gi\|... - gi\|91227859\|ref\|ZP_01262032.1\| RNA polymerase sigma-70 factor [Vibrio alginolyticus 12G01], gi\|91188... gi\|116183469, gi... - gi\|75854013\|ref\|ZP_00761739.1\| COG1595: DNA-directed RNA polymerase specialized sigma subunit, sigma...	178.0	[0..1]	[191..1]
gi\|213974352 - gi\|213974352\|ref\|ZP_03401611.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|214000661 - gi\|214000661\|ref\|ZP_03411396.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|224469021, gi... - gi\|224584494\|ref\|YP_002638292.1\| RNA polymerase sigma-70 factor [Salmonella enterica subsp. enterica... gi\|213052327 - gi\|213052327\|ref\|ZP_03345205.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|213420277 - gi\|213420277\|ref\|ZP_03353343.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|213425270 - gi\|213425270\|ref\|ZP_03358020.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|213646348 - gi\|213646348\|ref\|ZP_03376401.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|199605728, gi... - gi\|200388630\|ref\|ZP_03215242.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica s... gi\|204321401, gi... - gi\|204929682\|ref\|ZP_03220756.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica s... gi\|205353683, gi... - gi\|205353683\|ref\|YP_002227484.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteri... gi\|207857994, gi... - gi\|207857994\|ref\|YP_002244645.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteri... gi\|197250418, gi... - gi\|197250418\|ref\|YP_002147545.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica ... gi\|197242179, gi... - gi\|197263924\|ref\|ZP_03163998.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica s... gi\|197361472, gi... - gi\|197361472\|ref\|YP_002141108.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteri... gi\|198244605, gi... - gi\|198244605\|ref\|YP_002216654.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica ... RPOE_SALTY - RNA polymerase sigma-E factor OS=Salmonella typhimurium GN=rpoE PE=3 SV=1 gi\|62128848, gi\|... - gi\|62181215\|ref\|YP_217632.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enterica s... RPOE_SALTI - ECF RNA polymerase sigma-E factor OS=Salmonella typhi GN=rpoE PE=3 SV=1 gi\|194402303, gi... - gi\|194443640\|ref\|YP_002041906.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica ... RPOE_SALTY - ECF RNA polymerase sigma-E factor OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN... gi\|194407603, gi... - gi\|194449299\|ref\|YP_002046649.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteri... gi\|194455573, gi... - gi\|194469209\|ref\|ZP_03075193.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica s... RPOE_SALTY - RNA polymerase sigma-E factor OS=Salmonella typhimurium GN=rpoE PE=3 SV=1 RPOE_SALTI - RNA polymerase sigma-E factor OS=Salmonella typhi GN=rpoE PE=3 SV=1 gi\|194709594, gi... - gi\|194734092\|ref\|YP_002115651.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica ... gi\|168245098, gi... - gi\|205336126\|gb\|EDZ22890.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|205349418, gi... - gi\|205349418\|gb\|EDZ36049.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|29136429, gi\|... - gi\|29140804\|ref\|NP_804146.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enterica s... gi\|195628867, gi... - gi\|195628867\|gb\|EDX48281.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... RPOE_SALT1 - ECF RNA polymerase sigma-E factor OS=Salmonella typhimurium (strain 14028s / SGSC 2262) GN=rpoE PE=2... gi\|16761499 - gi\|16761499\|ref\|NP_457116.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enterica s... gi\|205340543, gi... - gi\|205340543\|gb\|EDZ27307.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|56412537, gi\|... - gi\|56412537\|ref\|YP_149612.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enterica s... gi\|205321938, gi... - gi\|205321938\|gb\|EDZ09777.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|167994852, gi... - gi\|205327354\|gb\|EDZ14118.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|168232167, gi... - gi\|205333581\|gb\|EDZ20345.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|238912705 - gi\|238912705\|ref\|ZP_04656542.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteric... gi\|197288862, gi... - gi\|197288862\|gb\|EDY28235.1\| RNA polymerase sigma-E factor [Salmonella enterica subsp. enterica serov... gi\|161362006, gi... - gi\|161612642\|ref\|YP_001586607.1\| RNA polymerase sigma factor RpoE [Salmonella enterica subsp. enteri...	177.0	[0..1]	[191..1]

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Predicted Domain #1

Region A:
Residues: [1-191]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEQLTDQVL VERVQKGDQK AFNLLVVRYQ HKVASLVSRY VPSGDVPDVV QEAFIKAYRA  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:	45.522879
Match:	1or7A
Description:	SigmaE factor (RpoE)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription initiation factor activity	5.78609205758337	bayes_pls_golite062009
sigma factor activity	5.64833683794078	bayes_pls_golite062009
transcription regulator activity	3.74356768143558	bayes_pls_golite062009
binding	1.07192234179226	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: