YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|197264369, gi...
Organism:	Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23
Length:	151 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|197264369, gi....

Description	E-value	Query Range	Subject Range
gi\|167423764, gi... - gi\|167423764\|ref\|ZP_02315517.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Mediaeva... gi\|166214121, gi... - gi\|166214121\|ref\|ZP_02240156.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Antiqua ... gi\|167420477, gi... - gi\|167420477\|ref\|ZP_02312230.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Oriental... gi\|165925870, gi... - gi\|165925870\|ref\|ZP_02221702.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Oriental... gi\|22124704, gi\|... - gi\|22124704\|ref\|NP_668127.1\| dnaK suppressor protein [Yersinia pestis KIM], gi\|21957518\|gb\|AAM84378.... gi\|165991085, gi... - gi\|166010178\|ref\|ZP_02231076.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Antiqua ... gi\|45440147, gi\|... - gi\|45440147\|ref\|NP_991686.1\| DnaK suppressor protein homologue [Yersinia pestis biovar Microtus str.... gi\|162352709, gi... - gi\|162419894\|ref\|YP_001605566.1\| DnaK transcriptional regulator DksA [Yersinia pestis Angola], gi\|16...	2.0E-46	[1..151]	[32..182]
gi\|50122239, gi\|... - gi\|50122239\|ref\|YP_051406.1\| DnaK transcriptional regulator DksA [Pectobacterium atrosepticum SCRI10... gi\|227327659 - gi\|227327659\|ref\|ZP_03831683.1\| DnaK transcriptional regulator DksA [Pectobacterium carotovorum subs... gi\|255055906, gi... - gi\|255055906\|ref\|ZP_05308131.1\| transcriptional regulator, TraR/DksA family [Pectobacterium wasabiae...	7.0E-43	[1..151]	[1..151]
gi\|253988291, gi... - gi\|253988291\|ref\|YP_003039647.1\| dnak suppressor protein [Photorhabdus asymbiotica], gi\|253779741\|em... gi\|36784296, gi\|... - gi\|37524871\|ref\|NP_928215.1\| DnaK transcriptional regulator DksA [Photorhabdus luminescens subsp. la...	2.0E-42	[1..151]	[1..151]
gi\|167051119, gi... - gi\|167398615\|ref\|ZP_02304139.1\| RNA polymerase-binding protein DksA [Yersinia pestis biovar Antiqua ... gi\|161511460 - gi\|161511460\|ref\|NP_991686.2\| DnaK transcriptional regulator DksA [Yersinia pestis biovar Microtus s... gi\|186697120, gi... - gi\|186894094\|ref\|YP_001871206.1\| DnaK transcriptional regulator DksA [Yersinia pseudotuberculosis PB... gi\|169752217, gi... - gi\|170025683\|ref\|YP_001722188.1\| DnaK transcriptional regulator DksA [Yersinia pseudotuberculosis YP... gi\|229901066, gi... - gi\|229901066\|ref\|ZP_04516189.1\| C4-type zinc finger protein, DksA/TraR family [Yersinia pestis Nepal... gi\|165915423, gi... - gi\|89102553\|ref\|ZP_01175178.1\| COG1734: DnaK suppressor protein [Yersinia pestis biovar Orientalis s... gi\|161484864 - gi\|161484864\|ref\|NP_668127.2\| DnaK transcriptional regulator DksA [Yersinia pestis KIM] gi\|229695401, gi... - gi\|229839035\|ref\|ZP_04459194.1\| C4-type zinc finger protein, DksA/TraR family [Yersinia pestis biova... gi\|108780802, gi... - gi\|108808889\|ref\|YP_652805.1\| DnaK transcriptional regulator DksA [Yersinia pestis Antiqua], gi\|1087... gi\|229896514, gi... - gi\|229896514\|ref\|ZP_04511682.1\| C4-type zinc finger protein, DksA/TraR family [Yersinia pestis Pesto... gi\|229687092, gi... - gi\|229899600\|ref\|ZP_04514741.1\| C4-type zinc finger protein, DksA/TraR family [Yersinia pestis biova... gi\|153997560, gi... - gi\|153997560\|ref\|ZP_02022660.1\| RNAP-binding protein modulating ppGpp and iNTP regulation [Yersinia ... gi\|238754485, gi... - gi\|238754485\|ref\|ZP_04615840.1\| DnaK suppressor protein [Yersinia ruckeri ATCC 29473], gi\|238707314\|... gi\|145600218, gi... - gi\|145600218\|ref\|YP_001164294.1\| DnaK transcriptional regulator DksA [Yersinia pestis Pestoides F], ... gi\|77979588, gi\|... - gi\|77979588\|ref\|ZP_00835005.1\| COG1734: DnaK suppressor protein [Yersinia intermedia ATCC 29909], gi... gi\|238786775, gi... - gi\|77976050\|ref\|ZP_00831583.1\| COG1734: DnaK suppressor protein [Yersinia frederiksenii ATCC 33641],... gi\|77634838 - gi\|77634838\|ref\|ZP_00796931.1\| COG1734: DnaK suppressor protein [Yersinia pestis Angola] gi\|77631712, gi\|... - gi\|77631712\|ref\|ZP_00794298.1\| COG1734: DnaK suppressor protein [Yersinia pseudotuberculosis IP 3175... gi\|51595084, gi\|... - gi\|51595084\|ref\|YP_069275.1\| DnaK transcriptional regulator DksA [Yersinia pseudotuberculosis IP 329... gi\|25332015 - pir\|\|AG0412 DnaK suppressor protein homolog [imported] - Yersinia pestis (strain CO92) Q66EF9\|Q66EF9_YERPS - DnaK suppressor protein - Yersinia pseudotuberculosis gi\|115349025, gi... - gi\|218930414\|ref\|YP_002348289.1\| DnaK transcriptional regulator DksA [Yersinia pestis CO92], gi\|1612...	3.0E-42	[1..151]	[1..151]
gi\|77957534 - gi\|77957534\|ref\|ZP_00821587.1\| COG1734: DnaK suppressor protein [Yersinia bercovieri ATCC 43970] gi\|238719027, gi... - gi\|77962799\|ref\|ZP_00826615.1\| COG1734: DnaK suppressor protein [Yersinia mollaretii ATCC 43969], gi...	5.0E-42	[1..151]	[1..151]
gi\|117622432, gi... - gi\|117622432\|ref\|YP_851345.1\| DnaK transcriptional regulator DksA [Escherichia coli APEC O1], gi\|115... gi\|226840669, gi... - gi\|254037563\|ref\|ZP_04871640.1\| dnaK suppressor protein [Escherichia sp. 1_1_43], gi\|226840669\|gb\|EE... gi\|237704304, gi... - gi\|237704304\|ref\|ZP_04534785.1\| dnaK suppressor protein [Escherichia sp. 3_2_53FAA], gi\|226902216\|gb... gi\|91209214, gi\|... - gi\|91209214\|ref\|YP_539200.1\| DnaK suppressor protein [Escherichia coli UTI89], gi\|91070788\|gb\|ABE056... gi\|24111583, gi\|... - ref\|NP_706093.1\| dnaK suppressor protein [Shigella flexneri 2a str. 301], gb\|AAN41800.1\| dnaK suppr... gi\|26106486, gi\|... - gi\|26246089\|ref\|NP_752128.1\| DnaK suppressor protein [Escherichia coli CFT073], gi\|26106486\|gb\|AAN78...	5.0E-42	[1..151]	[7..157]
gi\|208733384, gi... - gi\|208812107\|ref\|ZP_03253436.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. E... gi\|208726068, gi... - gi\|208806267\|ref\|ZP_03248604.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. E... gi\|209399928, gi... - gi\|209399928\|ref\|YP_002268754.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. ... gi\|208820380, gi... - gi\|208820380\|ref\|ZP_03260700.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. E... gi\|215485305, gi... - gi\|215485305\|ref\|YP_002327736.1\| DnaK transcriptional regulator DksA [Escherichia coli O127:H6 str. ... gi\|209910595, gi... - gi\|209917336\|ref\|YP_002291420.1\| DnaK transcriptional regulator DksA [Escherichia coli SE11], gi\|209... gi\|218355142, gi... - gi\|218547601\|ref\|YP_002381392.1\| DnaK transcriptional regulator DksA [Escherichia fergusonii ATCC 35... gi\|217320673, gi... - gi\|217324452\|ref\|ZP_03440536.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. T... gi\|189000398, gi... - gi\|189000398\|gb\|EDU69384.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC407... gi\|187767696, gi... - gi\|187767696\|gb\|EDU31540.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC419... gi\|170021501, gi... - gi\|170021501\|ref\|YP_001726455.1\| DnaK transcriptional regulator DksA [Escherichia coli ATCC 8739], g... gi\|168789253, gi... - gi\|189371126\|gb\|EDU89542.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC869... gi\|170679800, gi... - gi\|170679800\|ref\|YP_001742273.1\| RNA polymerase-binding protein DksA [Escherichia coli SMS-3-5], gi\|... gi\|170079782, gi... - gi\|170079782\|ref\|YP_001729102.1\| DNA-binding transcriptional regulator of rRNA transcription, DnaK s... gi\|195938173 - gi\|195938173\|ref\|ZP_03083555.1\| DnaK transcriptional regulator DksA [Escherichia coli O157:H7 str. E... gi\|170768586, gi... - gi\|170768586\|ref\|ZP_02903039.1\| RNA polymerase-binding protein DksA [Escherichia albertii TW07627], ... gi\|238899544, gi... - gi\|238899544\|ref\|YP_002925340.1\| DNA-binding transcriptional regulator of rRNA transcription, DnaK s... gi\|251783705, gi... - gi\|251783705\|ref\|YP_002998009.1\| hypothetical protein B21_00143 [Escherichia coli BL21], gi\|24237597... gi\|254287068, gi... - gi\|254287068\|ref\|YP_003052816.1\| DNA-binding transcriptional regulator of rRNA transcription, DnaK s... gi\|253972166, gi... - gi\|254160265\|ref\|YP_003043373.1\| DNA-binding transcriptional regulator of rRNA transcription, DnaK s... gi\|254791280, gi... - gi\|254791280\|ref\|YP_003076117.1\| dnaK suppressor protein [Escherichia coli O157:H7 str. TW14359], gi... gi\|218557088, gi... - gi\|218557088\|ref\|YP_002390001.1\| DnaK transcriptional regulator DksA [Escherichia coli S88], gi\|2183... gi\|218552726, gi... - gi\|218552726\|ref\|YP_002385639.1\| DnaK transcriptional regulator DksA [Escherichia coli IAI1], gi\|218... gi\|218350343, gi... - gi\|218693611\|ref\|YP_002401278.1\| DnaK transcriptional regulator DksA [Escherichia coli 55989], gi\|21... gi\|218425586, gi... - gi\|218688022\|ref\|YP_002396234.1\| DnaK transcriptional regulator DksA [Escherichia coli ED1a], gi\|218... gi\|218703401, gi... - gi\|218703401\|ref\|YP_002410920.1\| DnaK transcriptional regulator DksA [Escherichia coli UMN026], gi\|2... gi\|218368552, gi... - gi\|218698566\|ref\|YP_002406195.1\| DnaK transcriptional regulator DksA [Escherichia coli IAI39], gi\|21... EG10230 - transcriptional regulator of rRNA transcription; DnaK suppressor protein / RNAP-binding protein modu... gi\|188492076, gi... - gi\|75512021\|ref\|ZP_00734616.1\| COG1734: DnaK suppressor protein [Escherichia coli 53638], gi\|1884920... gi\|74310766, gi\|... - gi\|74310766\|ref\|YP_309185.1\| DnaK transcriptional regulator DksA [Shigella sonnei Ss046], gi\|7385424... gi\|75240264, gi\|... - gi\|75240264\|ref\|ZP_00724211.1\| COG1734: DnaK suppressor protein [Escherichia coli F11], gi\|191172786... DKSA_ECOL6 - RNA polymerase-binding transcription factor DksA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700... gi\|75258864, gi\|... - gi\|75258864\|ref\|ZP_00730254.1\| COG1734: DnaK suppressor protein [Escherichia coli E22], gi\|193063146... gi\|56383163, gi\|... - gi\|56479612\|ref\|NP_706093.2\| DnaK transcriptional regulator DksA [Shigella flexneri 2a str. 301], gi... gi\|188014572, gi... - gi\|188014572\|gb\|EDU52694.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC411... gi\|162138499 - gi\|162138499\|ref\|YP_539200.2\| DnaK transcriptional regulator DksA [Escherichia coli UTI89] gi\|82775537, gi\|... - gi\|82775537\|ref\|YP_401884.1\| DnaK transcriptional regulator DksA [Shigella dysenteriae Sd197], gi\|81... gi\|189360715, gi... - gi\|189360715\|gb\|EDU79134.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC448... gi\|81244156, gi\|... - gi\|82542745\|ref\|YP_406692.1\| DnaK transcriptional regulator DksA [Shigella boydii Sb227], gi\|8124415... gi\|168755757, gi... - gi\|189356989\|gb\|EDU75408.1\| RNA polymerase-binding protein DksA [Escherichia coli O157:H7 str. EC440... gi\|187430755, gi... - gi\|75176509\|ref\|ZP_00696646.1\| COG1734: DnaK suppressor protein [Shigella boydii BS512], gi\|18773376... gi\|157080239, gi... - gi\|75189242\|ref\|ZP_00702509.1\| COG1734: DnaK suppressor protein [Escherichia coli E24377A], gi\|15715... gi\|191166328, gi... - gi\|75230492\|ref\|ZP_00716973.1\| COG1734: DnaK suppressor protein [Escherichia coli B7A], gi\|191166328... gi\|193067514, gi... - gi\|75238850\|ref\|ZP_00722832.1\| COG1734: DnaK suppressor protein [Escherichia coli E110019], gi\|19306... gi\|157159611, gi... - gi\|75194357\|ref\|ZP_00704427.1\| COG1734: DnaK suppressor protein [Escherichia coli HS], gi\|157159611\|... gi\|194413677, gi... - gi\|75210470\|ref\|ZP_00710621.1\| COG1734: DnaK suppressor protein [Escherichia coli B171], gi\|19442830... gi\|15829403, gi\|... - gi\|15829403\|ref\|NP_308176.1\| DnaK transcriptional regulator DksA [Escherichia coli O157:H7 str. Saka... gi\|110341958, gi... - gi\|110640366\|ref\|YP_668094.1\| DnaK transcriptional regulator DksA [Escherichia coli 536], gi\|1103419... gi\|110613748, gi... - gi\|110804200\|ref\|YP_687720.1\| DnaK transcriptional regulator DksA [Shigella flexneri 5 str. 8401], g... gi\|124499785, gi... - gi\|124529629\|ref\|ZP_01700573.1\| transcriptional regulator, TraR/DksA family [Escherichia coli B], gi... gi\|83569726, gi\|... - gi\|83569726\|ref\|ZP_00921176.1\| COG1734: DnaK suppressor protein [Shigella dysenteriae 1012], gi\|1944... gi\|83585462, gi\|... - gi\|83585462\|ref\|ZP_00924107.1\| COG1734: DnaK suppressor protein [Escherichia coli 101-1], gi\|1944391... gi\|21239001, gi\|... - gi\|89107026\|ref\|AP_000806.1\| transcriptional regulator of rRNA transcription, DnaK suppressor protei... DKSA_ECOLI - DnaK suppressor protein - Escherichia coli DKSA_ECOL6 - DnaK suppressor protein OS=Escherichia coli O6 GN=dksA PE=3 SV=1 DKSA_SHIFL - RNA polymerase-binding transcription factor DksA OS=Shigella flexneri GN=dksA PE=3 SV=1 gi\|30061705, gi\|... - gi\|30061705\|ref\|NP_835876.1\| DnaK transcriptional regulator DksA [Shigella flexneri 2a str. 2457T], ... DKSA_ECO57 - RNA polymerase-binding transcription factor DksA OS=Escherichia coli O157:H7 GN=dksA PE=3 SV=1 EG10230 - transcriptional regulator of rRNA transcription; DnaK suppressor protein / RNAP-binding protein modu... gi\|15799829, gi\|... - gi\|15799829\|ref\|NP_285841.1\| DnaK transcriptional regulator DksA [Escherichia coli O157:H7 EDL933], ... gi\|156935337, gi... - gi\|156935337\|ref\|YP_001439253.1\| DnaK transcriptional regulator DksA [Enterobacter sakazakii ATCC BA...	6.0E-42	[1..151]	[1..151]
gi\|62178756, gi\|... - gi\|62178756\|ref\|YP_215173.1\| dnaK suppressor protein [Salmonella enterica subsp. enterica serovar Ch...	6.0E-42	[1..151]	[7..157]
gi\|85058470, gi\|... - gi\|85058470\|ref\|YP_454172.1\| DnaK transcriptional regulator DksA [Sodalis glossinidius str. 'morsita...	6.0E-42	[1..151]	[1..151]
gi\|145751 - gi\|145751\|gb\|AAA23687.1\| dnaK suppressor (dksA) [Escherichia coli]	8.0E-42	[1..151]	[1..151]

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Predicted Domain #1

Region A:
Residues: [1-151]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQEGQNRKTS SLSILAIAGV EPYQEKPGEE YMNEAQLSHF KRILEAWRNQ LRDEVDRTVT  60
   61 HMQDEAANFP DPVDRAAQEE EFSLELRNRD RERKLIKKIE KTLKKVEDED FGYCESCGVE 120
  121 IGIRRLEARP TADLCIDCKT LAEIREKQMA G

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.30103
Match:	1tjlA
Description:	Crystal structure of transcription factor DksA from E. coli
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.96944106977308	bayes_pls_golite062009
DNA binding	2.64662954118345	bayes_pls_golite062009
nucleic acid binding	2.60185057203337	bayes_pls_golite062009
binding	2.32420977112004	bayes_pls_golite062009
transcription factor activity	1.93863380769331	bayes_pls_golite062009
protein binding	1.39455913713025	bayes_pls_golite062009
sequence-specific DNA binding	0.71958532653437	bayes_pls_golite062009
transcription activator activity	0.715538962910453	bayes_pls_golite062009
ligand-dependent nuclear receptor activity	0.613774016982502	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.57454737035174	bayes_pls_golite062009
transcription factor binding	0.52161600305754	bayes_pls_golite062009
transition metal ion binding	0.300699898963653	bayes_pls_golite062009
catalytic activity	0.101795606736461	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: