YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|89101687, gi\|...
Organism:	Yersinia pestis biovar Orientalis str. IP275
Length:	495 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|89101687, gi|....

Description	E-value	Query Range	Subject Range
gi\|238727621, gi... - gi\|77978624\|ref\|ZP_00834051.1\| COG0195: Transcription elongation factor [Yersinia intermedia ATCC 29...	0.0	[1..495]	[1..495]
gi\|238724380, gi... - gi\|77974018\|ref\|ZP_00829561.1\| COG0195: Transcription elongation factor [Yersinia frederiksenii ATCC...	0.0	[1..495]	[1..495]
gi\|238783516, gi... - gi\|77958790\|ref\|ZP_00822818.1\| COG0195: Transcription elongation factor [Yersinia bercovieri ATCC 43... gi\|77961868, gi\|... - gi\|77961868\|ref\|ZP_00825697.1\| COG0195: Transcription elongation factor [Yersinia mollaretii ATCC 43...	0.0	[1..495]	[1..495]
gi\|21957405, gi\|... - gi\|22124601\|ref\|NP_668024.1\| transcription elongation factor NusA [Yersinia pestis KIM], gi\|21957405... gi\|45435297, gi\|... - gi\|45440440\|ref\|NP_991979.1\| transcription elongation factor NusA [Yersinia pestis biovar Microtus s...	0.0	[1..495]	[7..501]
gi\|218696876, gi... - gi\|218696876\|ref\|YP_002404543.1\| transcription elongation factor NusA [Escherichia coli 55989], gi\|2... gi\|218429025, gi... - gi\|218691461\|ref\|YP_002399673.1\| transcription elongation factor NusA [Escherichia coli ED1a], gi\|21... gi\|227887892, gi... - gi\|227887892\|ref\|ZP_04005697.1\| N utilization substance A [Escherichia coli 83972], gi\|227835288\|gb\|... NUSA_ECOL6 - Transcription elongation protein nusA OS=Escherichia coli O6 GN=nusA PE=3 SV=1 gi\|237706078, gi... - gi\|237706078\|ref\|ZP_04536559.1\| transcription termination/antitermination factor NusA [Escherichia s... gi\|238902273, gi... - gi\|238902273\|ref\|YP_002928069.1\| transcription termination/antitermination L factor [Escherichia col... gi\|74313706, gi\|... - gi\|74313706\|ref\|YP_312125.1\| transcription elongation factor NusA [Shigella sonnei Ss046], gi\|738571... gi\|242378714, gi... - gi\|251786441\|ref\|YP_003000745.1\| hypothetical protein B21_02987 [Escherichia coli BL21], gi\|24237871... gi\|89109934, gi\|... - gi\|89109934\|ref\|AP_003714.1\| transcription termination/antitermination L factor [Escherichia coli st... gi\|254289863, gi... - gi\|254289863\|ref\|YP_003055611.1\| transcription elongation factor NusA [Escherichia coli BL21(DE3)], ... gi\|193062170, gi... - gi\|75260099\|ref\|ZP_00731377.1\| COG0195: Transcription elongation factor [Escherichia coli E22], gi\|1... gi\|226839959, gi... - gi\|254038335\|ref\|ZP_04872393.1\| transcription termination/antitermination factor NusA [Escherichia s... gi\|188492867, gi... - gi\|75513384\|ref\|ZP_00735808.1\| COG0195: Transcription elongation factor [Escherichia coli 53638], gi... gi\|253975014, gi... - gi\|254163113\|ref\|YP_003046221.1\| transcription elongation factor NusA [Escherichia coli B str. REL60... gi\|15803711, gi\|... - gi\|15803711\|ref\|NP_289745.1\| transcription elongation factor NusA [Escherichia coli O157:H7 EDL933],... gi\|157162654, gi... - gi\|75197120\|ref\|ZP_00707190.1\| COG0195: Transcription elongation factor [Escherichia coli HS], gi\|15... gi\|75240806, gi\|... - gi\|75240806\|ref\|ZP_00724704.1\| COG0195: Transcription elongation factor [Escherichia coli F11], gi\|1... gi\|157155683, gi... - gi\|75187977\|ref\|ZP_00701244.1\| COG0195: Transcription elongation factor [Escherichia coli E24377A], ... NUSA_ECOLI - Transcription elongation protein nusA (N utilization substance protein A) (L factor) - Escherichia c... gi\|117625465, gi... - gi\|117625465\|ref\|YP_858788.1\| transcription elongation factor NusA [Escherichia coli APEC O1], gi\|11... gi\|124525923, gi... - gi\|124525923\|ref\|ZP_01697928.1\| NusA antitermination factor [Escherichia coli B], gi\|124502027\|gb\|EA... gi\|169753507, gi... - gi\|170018579\|ref\|YP_001723533.1\| transcription elongation factor NusA [Escherichia coli ATCC 8739], ... gi\|91074165, gi\|... - gi\|91212591\|ref\|YP_542577.1\| transcription elongation factor NusA [Escherichia coli UTI89], gi\|91074... gi\|168797770, gi... - gi\|189379809\|gb\|EDU98225.1\| transcription termination/antitermination factor NusA [Escherichia coli ... EG10665 - transcription termination /antitermination L factor / Transcription termination /antitermination L fac... gi\|13363523, gi\|... - gi\|15833304\|ref\|NP_312077.1\| transcription elongation factor NusA [Escherichia coli O157:H7 str. Sak... gi\|194418052, gi... - gi\|194433789\|ref\|ZP_03066064.1\| transcription termination/antitermination factor NusA [Shigella dyse... gi\|170082706, gi... - gi\|170082706\|ref\|YP_001732026.1\| transcription termination/antitermination L factor [Escherichia col... gi\|217319090, gi... - gi\|217326723\|ref\|ZP_03442806.1\| transcription termination/antitermination factor NusA [Escherichia c... gi\|215266559, gi... - gi\|215488487\|ref\|YP_002330918.1\| transcription elongation factor NusA [Escherichia coli O127:H6 str.... gi\|218560241, gi... - gi\|218560241\|ref\|YP_002393154.1\| transcription elongation factor NusA [Escherichia coli S88], gi\|218... gi\|218362509, gi... - gi\|218555741\|ref\|YP_002388654.1\| transcription elongation factor NusA [Escherichia coli IAI1], gi\|21... NUSA_SHIFL - Transcription termination/antitermination protein NusA OS=Shigella flexneri GN=nusA PE=3 SV=1 gi\|24053641, gi\|... - gi\|24114460\|ref\|NP_708970.1\| transcription elongation factor NusA [Shigella flexneri 2a str. 301], g... NUSA_ECOL6 - Transcription termination/antitermination protein NusA OS=Escherichia coli O6:H1 (strain CFT073 / AT... gi\|30064509, gi\|... - gi\|30064509\|ref\|NP_838680.1\| transcription elongation factor NusA [Shigella flexneri 2a str. 2457T],... NUSA_ECO57 - Transcription termination/antitermination protein NusA OS=Escherichia coli O157:H7 GN=nusA PE=3 SV=1 gi\|168786054, gi... - gi\|189374081\|gb\|EDU92497.1\| transcription termination/antitermination factor NusA [Escherichia coli ... EG10665 - transcription termination /antitermination L factor / Transcription termination /antitermination L fac... gi\|168762136, gi... - gi\|189367615\|gb\|EDU86031.1\| transcription termination/antitermination factor NusA [Escherichia coli ...	0.0	[1..495]	[1..495]
gi\|194422298, gi... - gi\|83585810\|ref\|ZP_00924451.1\| COG0195: Transcription elongation factor [Escherichia coli 101-1], gi...	0.0	[1..495]	[1..495]
gi\|170680571, gi... - gi\|170680571\|ref\|YP_001745443.1\| transcription termination/antitermination factor NusA [Escherichia ... gi\|218433888, gi... - gi\|218706791\|ref\|YP_002414310.1\| transcription elongation factor NusA [Escherichia coli UMN026], gi\|... gi\|209913905, gi... - gi\|209920646\|ref\|YP_002294730.1\| transcription elongation factor NusA [Escherichia coli SE11], gi\|20... gi\|218371926, gi... - gi\|218701940\|ref\|YP_002409569.1\| transcription elongation factor NusA [Escherichia coli IAI39], gi\|2... gi\|75239261, gi\|... - gi\|75239261\|ref\|ZP_00723232.1\| COG0195: Transcription elongation factor [Escherichia coli E110019], ... gi\|75228772, gi\|... - gi\|75228772\|ref\|ZP_00715381.1\| COG0195: Transcription elongation factor [Escherichia coli B7A], gi\|1...	0.0	[1..495]	[1..495]
gi\|110345002, gi... - gi\|110643410\|ref\|YP_671140.1\| transcription elongation factor NusA [Escherichia coli 536], gi\|110345...	0.0	[1..495]	[1..495]
gi\|82778483, gi\|... - gi\|82778483\|ref\|YP_404832.1\| transcription elongation factor NusA [Shigella dysenteriae Sd197], gi\|8...	0.0	[1..495]	[1..495]
gi\|110616586, gi... - gi\|110807038\|ref\|YP_690558.1\| transcription elongation factor NusA [Shigella flexneri 5 str. 8401], ...	0.0	[1..495]	[1..495]

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Predicted Domain #1

Region A:
Residues: [1-347]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNKEILAVVE AVSNEKSLPR EKIFEALETA LATATKKKYE QEIEVRVSID RKTGDFDTFR  60
   61 RWVAVDEVTM PTREITLDAA QFEDPSLQLG DYVEDQIESV TFDRITTQTA KQVIVQKVRE 120
  121 AERAMVVEQF RQYLGQIVTG IVKKVSRDSI ALDLGHNAEA VIGREDMLPR ENFRPGDRIR 180
  181 GVLYDVRPEA RGAQLFVSRS RSEMLVELFR IEVPEIGEEL IEIKAAARDP GSRAKIAVKT 240
  241 NDKRIDPVGA CVGMRGARVQ AVSSELGGER IDIVLWDDNP AQFVINAMAP ADVASIVVDE 300
  301 DKHTMDVAVE ASNLAQAIGR NGQNVRLAAQ LSGWELNVMT ADDLQAK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	109.0
Match:	1l2fA
Description:	Crystal structure of NusA from Thermotoga maritima: a structure-based role of the N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription termination factor activity	6.2940998830026	bayes_pls_golite062009
transcription regulator activity	3.30740271950804	bayes_pls_golite062009
binding	1.85922846397432	bayes_pls_golite062009
nucleic acid binding	1.26537887642247	bayes_pls_golite062009
structural constituent of ribosome	0.860693644487058	bayes_pls_golite062009
DNA binding	0.814370062643769	bayes_pls_golite062009
protein binding	0.731201599320953	bayes_pls_golite062009
structural molecule activity	0.570047646271216	bayes_pls_golite062009
structure-specific DNA binding	0.440010017405756	bayes_pls_golite062009
translation regulator activity	0.31332179848255	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.263197317040851	bayes_pls_golite062009
single-stranded DNA binding	0.19668406318255	bayes_pls_golite062009
catalytic activity	0.10089766806364	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [348-427]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HQAEAHAAID TFTKYLDIDE DFATVLVEEG FSSLEELAYV PMKELLEIDG LDEDTVEALR  60
   61 DRAKAALTTL ALAQEESFGD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.30103
Match:	1wclA
Description:	NMR structure of the carboxyterminal domains of Escherichia coli NusA
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [428-495]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKPADDLLNL AGLERSMAFK LAARGVCTLE DLAEQGIDDL ADIEGLSDEQ AGELIMAARN  60
   61 ICWFGDNA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.0
Match:	1wcnA
Description:	NMR structure of the carboxyterminal domains of Escherichia coli NusA
Matching Structure (courtesy of the PDB):

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: