YRC Public Data Repository - Protein Structure Prediction

Protein:	NUSA_SHIFL
Organism:	Shigella flexneri
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 NUSA_SHIFL.

Description	E-value	Query Range	Subject Range
gi\|238727621, gi... - gi\|77978624\|ref\|ZP_00834051.1\| COG0195: Transcription elongation factor [Yersinia intermedia ATCC 29...	592.0	[0..1]	[495..1]
gi\|238724380, gi... - gi\|77974018\|ref\|ZP_00829561.1\| COG0195: Transcription elongation factor [Yersinia frederiksenii ATCC...	591.0	[0..1]	[495..1]
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...	591.0	[0..1]	[495..1]
gi\|166961564, gi... - gi\|167420758\|ref\|ZP_02312511.1\| transcription termination factor NusA [Yersinia pestis biovar Orient... gi\|167423617, gi... - gi\|167423617\|ref\|ZP_02315370.1\| transcription termination factor NusA [Yersinia pestis biovar Mediae... gi\|169752480, gi... - gi\|170025946\|ref\|YP_001722451.1\| transcription elongation factor NusA [Yersinia pseudotuberculosis Y... gi\|186893840, gi... - gi\|186893840\|ref\|YP_001870952.1\| transcription elongation factor NusA [Yersinia pseudotuberculosis P... gi\|77634857, gi\|... - gi\|77634857\|ref\|ZP_00796949.1\| COG0195: Transcription elongation factor [Yersinia pestis Angola], gi... gi\|117675032, gi... - gi\|77631476\|ref\|ZP_00794062.1\| COG0195: Transcription elongation factor [Yersinia pseudotuberculosis... gi\|25299783 - pir\|\|AB0425 N utilization substance protein A [imported] - Yersinia pestis (strain CO92) gi\|165925730, gi... - gi\|165925730\|ref\|ZP_02221562.1\| transcription termination factor NusA [Yersinia pestis biovar Orient... gi\|165991039, gi... - gi\|166010132\|ref\|ZP_02231030.1\| transcription termination factor NusA [Yersinia pestis biovar Antiqu... gi\|115349122, gi... - gi\|218930511\|ref\|YP_002348386.1\| transcription elongation factor NusA [Yersinia pestis CO92], gi\|161... gi\|166214620, gi... - gi\|166214620\|ref\|ZP_02240655.1\| transcription termination factor NusA [Yersinia pestis biovar Antiqu... gi\|51594831, gi\|... - gi\|51594831\|ref\|YP_069022.1\| transcription elongation factor NusA [Yersinia pseudotuberculosis IP 32... gi\|167049334, gi... - gi\|167401309\|ref\|ZP_02306809.1\| transcription termination factor NusA [Yersinia pestis biovar Antiqu... gi\|229899713, gi... - gi\|229899713\|ref\|ZP_04514854.1\| transcription termination/antitermination L factor [Yersinia pestis ... gi\|229679645, gi... - gi\|229903875\|ref\|ZP_04518988.1\| transcription termination/antitermination L factor [Yersinia pestis ... gi\|229896638, gi... - gi\|229896638\|ref\|ZP_04511805.1\| transcription termination/antitermination L factor [Yersinia pestis ... Q66F61\|Q66F61_YERPS - N utilization substance protein A - Yersinia pseudotuberculosis gi\|229695515, gi... - gi\|229839149\|ref\|ZP_04459308.1\| transcription termination/antitermination L factor [Yersinia pestis ... gi\|145600793, gi... - gi\|145600793\|ref\|YP_001164869.1\| transcription elongation factor NusA [Yersinia pestis Pestoides F],... gi\|149288911, gi... - gi\|153997274\|ref\|ZP_02022374.1\| N utilization substance protein A [Yersinia pestis CA88-4125], gi\|14... gi\|89101687, gi\|... - gi\|89101687\|ref\|ZP_01174396.1\| COG0195: Transcription elongation factor [Yersinia pestis biovar Orie... gi\|108806045, gi... - gi\|108806045\|ref\|YP_649961.1\| transcription elongation factor NusA [Yersinia pestis Antiqua], gi\|108...	589.0	[0..1]	[495..1]
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...	588.0	[0..1]	[495..7]
gi\|110345002, gi... - gi\|110643410\|ref\|YP_671140.1\| transcription elongation factor NusA [Escherichia coli 536], gi\|110345...	587.0	[0..1]	[495..1]
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...	586.0	[0..1]	[495..1]
gi\|194422298, gi... - gi\|83585810\|ref\|ZP_00924451.1\| COG0195: Transcription elongation factor [Escherichia coli 101-1], gi...	586.0	[0..1]	[495..1]
gi\|82778483, gi\|... - gi\|82778483\|ref\|YP_404832.1\| transcription elongation factor NusA [Shigella dysenteriae Sd197], gi\|8...	584.0	[0..1]	[495..1]
gi\|110616586, gi... - gi\|110807038\|ref\|YP_690558.1\| transcription elongation factor NusA [Shigella flexneri 5 str. 8401], ...	584.0	[0..1]	[495..1]

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Predicted Domain #1

Region A:
Residues: [1-361]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNKEILAVVE AVSNEKALPR EKIFEALESA LATATKKKYE QEIDVRVQID RKSGDFDTFR  60
   61 RWLVVDEVTQ PTKEITLEAA RYEDESLNLG DYVEDQIESV TFDRITTQTA KQVIVQKVRE 120
  121 AERAMVVDQF REHEGEIITG VVKKVNRDNI SLDLGNNAEA VILREDMLPR ENFRPGDRVR 180
  181 GVLYSVRPEA RGAQLFVTRS KPEMLIELFR IEVPEIGEEV IEIKAAARDP GSRAKIAVKT 240
  241 NDKRIDPVGA CVGMRGARVQ AVSTELGGER IDIVLWDDNP AQFVINAMAP ADVASIVVDE 300
  301 DKHTMDIAVE AGNLAQAIGR NGQNVRLASQ LSGWELNVMT VDDLQAKHQA EAHAAIDTFT 360
  361 K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	105.0
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	5.95012300460543	bayes_pls_golite062009
transcription regulator activity	3.08684997768441	bayes_pls_golite062009
binding	1.8883583267074	bayes_pls_golite062009
nucleic acid binding	1.20938494814687	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: [362-428]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YLDIDEDFAT VLVEEGFSTL EELAYVPMKE LLEIEGLDEP TVEALRERAK NALATIAQAQ  60
   61 EESLGDN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.39794
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: [429-495]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPADDLLNLE GVDRDLAFKL AARGVCTLED LAEQGIDDLA DIEGLTDEKA GALIMAARNI  60
   61 CWFGDEA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.09691
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: