YRC Public Data Repository - Protein Structure Prediction

Protein:	HFQ_ESCF3
Organism:	Escherichia fergusonii ATCC 35469
Length:	102 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 HFQ_ESCF3.

Description	E-value	Query Range	Subject Range
HFQ_SHIDS - RNA-binding protein Hfq OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=hfq PE=3 SV=1	161.0	[0..1]	[102..1]
HFQ_SHIB3 - RNA-binding protein Hfq OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=hfq PE=3 SV=1	160.0	[0..1]	[102..1]
gi\|168239733, gi... - gi\|197287607\|gb\|EDY26999.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Schwarzen... gi\|205336312, gi... - gi\|205336312\|gb\|EDZ23076.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Heidelber... gi\|168263287, gi... - gi\|205347951\|gb\|EDZ34582.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Hadar str... gi\|168464755, gi... - gi\|195632777\|gb\|EDX51231.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Newport s... gi\|205321592, gi... - gi\|205321592\|gb\|EDZ09431.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Saintpaul... gi\|205327104, gi... - gi\|205327104\|gb\|EDZ13868.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar 4,[5],12:... gi\|205334216, gi... - gi\|205334216\|gb\|EDZ20980.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Kentucky ... HFQ_SALPB - Protein hfq OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=hfq PE=3 SV=1 gi\|213052281 - gi\|213052281\|ref\|ZP_03345159.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|213423957 - gi\|213423957\|ref\|ZP_03356937.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|213428672 - gi\|213428672\|ref\|ZP_03361422.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|213583986 - gi\|213583986\|ref\|ZP_03365812.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|199605083, gi... - gi\|200387985\|ref\|ZP_03214597.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Virch... gi\|204927069, gi... - gi\|204927069\|ref\|ZP_03218271.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Javia... HFQ_SALEP - RNA-binding protein Hfq OS=Salmonella enteritidis PT4 (strain P125109) GN=hfq PE=3 SV=1 gi\|213023503 - gi\|213023503\|ref\|ZP_03337950.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... HFQ_SALA4 - RNA-binding protein Hfq OS=Salmonella agona (strain SL483) GN=hfq PE=3 SV=1 HFQ_SALPA - Protein hfq OS=Salmonella paratyphi A GN=hfq PE=3 SV=1 gi\|197261963, gi... - gi\|197261963\|ref\|ZP_03162037.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Saint... HFQ_SALPK - RNA-binding protein Hfq OS=Salmonella paratyphi A (strain AKU_12601) GN=hfq PE=3 SV=1 HFQ_SALDC - RNA-binding protein Hfq OS=Salmonella dublin (strain CT_02021853) GN=hfq PE=3 SV=1 gi\|168822512, gi... - gi\|205341071\|gb\|EDZ27835.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Weltevred... HFQ_SALNS - RNA-binding protein Hfq OS=Salmonella newport (strain SL254) GN=hfq PE=3 SV=1 gi\|194471437, gi... - gi\|194471437\|ref\|ZP_03077421.1\| RNA chaperone Hfq [Salmonella enterica subsp. enterica serovar Kentu... HFQ_SALSV - RNA-binding protein Hfq OS=Salmonella schwarzengrund (strain CVM19633) GN=hfq PE=3 SV=1 gi\|238910519 - gi\|238910519\|ref\|ZP_04654356.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... HFQ_SALPC - RNA-binding protein Hfq OS=Salmonella paratyphi C (strain RKS4594) GN=hfq PE=3 SV=1 lcl\|NC_016856.1_... - [gene=hfq] [protein=RNA-binding protein Hfq] [protein_id=YP_005240673.1] [location=4617406..4617714] gi\|213612848 - gi\|213612848\|ref\|ZP_03370674.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|213648969 - gi\|213648969\|ref\|ZP_03379022.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|213852839 - gi\|213852839\|ref\|ZP_03382371.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... gi\|214003359 - gi\|214003359\|ref\|ZP_03414094.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar... HFQ_SALPB - RNA-binding protein Hfq OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=hfq PE=3 SV=1 HFQ_SALTI - RNA-binding protein Hfq OS=Salmonella typhi GN=hfq PE=3 SV=2 HFQ_SALTI - Protein hfq OS=Salmonella typhi GN=hfq PE=3 SV=2 gi\|29140298, gi\|... - gi\|29144659\|ref\|NP_808001.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar Ty... HFQ_SALTY - RNA-binding protein Hfq OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=hfq PE=1 ... gi\|16763180 - gi\|16763180\|ref\|NP_458797.1\| RNA-binding protein Hfq [Salmonella enterica subsp. enterica serovar Ty... HFQ_SALPA - RNA-binding protein Hfq OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=hfq PE=3 SV=1 HFQ_SALTY - Protein hfq OS=Salmonella typhimurium GN=hfq PE=1 SV=2 HFQ_SALTY - Protein hfq OS=Salmonella typhimurium GN=hfq PE=1 SV=2	160.0	[0..1]	[102..1]
HFQ_SALG2 - RNA-binding protein Hfq OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=hfq PE=3 SV=1 HFQ_SALCH - Protein hfq OS=Salmonella choleraesuis GN=hfq PE=3 SV=1 HFQ_SALCH - Protein hfq OS=Salmonella choleraesuis GN=hfq PE=3 SV=1 HFQ_SALCH - RNA-binding protein Hfq OS=Salmonella choleraesuis (strain SC-B67) GN=hfq PE=3 SV=1	159.0	[0..1]	[102..1]
gi\|1305418 - gi\|1305418\|gb\|AAA99108.1\| host factor I gi\|1305418\|gb\|AA... - host factor I	156.0	[0..1]	[102..1]
HFQ_PHOLL - RNA-binding protein Hfq OS=Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 ... HFQ_PHOLL - Protein hfq OS=Photorhabdus luminescens subsp. laumondii GN=hfq PE=3 SV=1	154.0	[0..1]	[102..1]
HFQ_SODGM - RNA-binding protein Hfq OS=Sodalis glossinidius (strain morsitans) GN=hfq PE=3 SV=1	153.0	[0..1]	[102..1]
gi\|238714287, gi... - gi\|77957806\|ref\|ZP_00821853.1\| COG1923: Uncharacterized host factor I protein [Yersinia bercovieri A...	151.0	[0..1]	[102..1]
gi\|77973963, gi\|... - gi\|77973963\|ref\|ZP_00829506.1\| COG1923: Uncharacterized host factor I protein [Yersinia frederikseni... gi\|238797608, gi... - gi\|77961305\|ref\|ZP_00825146.1\| COG1923: Uncharacterized host factor I protein [Yersinia mollaretii A... HFQ_YEREN - RNA-binding protein Hfq OS=Yersinia enterocolitica GN=hfq PE=3 SV=3 gi\|238711615, gi... - gi\|238750071\|ref\|ZP_04611574.1\| hypothetical protein yrohd0001_6510 [Yersinia rohdei ATCC 43380], gi... gi\|238704281, gi... - gi\|238757519\|ref\|ZP_04618704.1\| hypothetical protein yaldo0001_30130 [Yersinia aldovae ATCC 35236], ... HFQ_YERE8 - RNA-binding protein Hfq OS=Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 80... gi\|238764692, gi... - gi\|238764692\|ref\|ZP_04625636.1\| hypothetical protein ykris0001_14900 [Yersinia kristensenii ATCC 336...	151.0	[0..1]	[102..1]
gi\|167050090, gi... - gi\|167400722\|ref\|ZP_02306231.1\| RNA chaperone Hfq [Yersinia pestis biovar Antiqua str. UG05-0454], g... gi\|238725421, gi... - gi\|77976470\|ref\|ZP_00831957.1\| COG1923: Uncharacterized host factor I protein [Yersinia intermedia A... gi\|167419106, gi... - gi\|167419106\|ref\|ZP_02310859.1\| RNA chaperone Hfq [Yersinia pestis biovar Orientalis str. MG05-1020]... HFQ_YERPG - RNA-binding protein Hfq OS=Yersinia pestis bv. Antiqua (strain Angola) GN=hfq PE=3 SV=1 gi\|167423280, gi... - gi\|167423280\|ref\|ZP_02315033.1\| RNA chaperone Hfq [Yersinia pestis biovar Mediaevalis str. K1973002]... HFQ_YERP3 - RNA-binding protein Hfq OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=hfq PE=3 S... HFQ_YERPY - RNA-binding protein Hfq OS=Yersinia pseudotuberculosis serotype O:3 (strain YPIII) GN=hfq PE=3 SV=1 HFQ_YERPB - RNA-binding protein Hfq OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) GN=hfq PE=3 SV=1 gi\|150260583, gi... - gi\|150260583\|ref\|ZP_01917311.1\| RNA chaperone Hfq [Yersinia pestis CA88-4125], gi\|149289991\|gb\|EDM40... gi\|165936451, gi... - gi\|89102919\|ref\|ZP_01175521.1\| COG1923: Uncharacterized host factor I protein [Yersinia pestis biova... HFQ_YERPA - RNA-binding protein Hfq OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=hfq PE=3 SV=1 HFQ_YERPN - RNA-binding protein Hfq OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=hfq PE=3 SV=1 gi\|165921329, gi... - gi\|165926706\|ref\|ZP_02222538.1\| RNA chaperone Hfq [Yersinia pestis biovar Orientalis str. F1991016],... gi\|229842323, gi... - gi\|229842323\|ref\|ZP_04462478.1\| RNA-binding protein Hfq [Yersinia pestis biovar Orientalis str. Indi... gi\|166011864, gi... - gi\|166011864\|ref\|ZP_02232762.1\| RNA chaperone Hfq [Yersinia pestis biovar Antiqua str. E1979001], gi... gi\|229696611, gi... - gi\|229840245\|ref\|ZP_04460404.1\| RNA-binding protein Hfq [Yersinia pestis biovar Orientalis str. PEXU... gi\|166213968, gi... - gi\|166213968\|ref\|ZP_02240003.1\| RNA chaperone Hfq [Yersinia pestis biovar Antiqua str. B42003004], g... gi\|229836633, gi... - gi\|229836633\|ref\|ZP_04456799.1\| RNA-binding protein Hfq [Yersinia pestis Pestoides A], gi\|229706317\|... gi\|21957342, gi\|... - gi\|22124544\|ref\|NP_667967.1\| RNA-binding protein Hfq [Yersinia pestis KIM], gi\|21957342\|gb\|AAM84218.... HFQ_YERPE - RNA-binding protein Hfq OS=Yersinia pestis GN=hfq PE=3 SV=3 HFQ_YERPS - RNA-binding protein Hfq OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=hfq PE=3 SV=1 gi\|45440383, gi\|... - gi\|45440383\|ref\|NP_991922.1\| RNA-binding protein Hfq [Yersinia pestis biovar Microtus str. 91001], g... gi\|15978471, gi\|... - gi\|218927576\|ref\|YP_002345451.1\| RNA-binding protein Hfq [Yersinia pestis CO92], gi\|16120708\|ref\|NP_... HFQ_YERPS - Protein hfq OS=Yersinia pseudotuberculosis GN=hfq PE=3 SV=1	151.0	[0..1]	[102..1]

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Predicted Domain #1

Region A:
Residues: [1-102]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS  60
   61 TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	33.045757
Match:	1u1sA
Description:	Hfq protein from Pseudomonas aeruginosa. Low-salt crystals
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	3.35169246976368	bayes_pls_golite062009
RNA binding	2.84369313702118	bayes_pls_golite062009
nucleic acid binding	2.17610586699691	bayes_pls_golite062009
binding	1.3000279455998	bayes_pls_golite062009
catalytic activity	0.312834499620126	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: