YRC Public Data Repository - Protein Structure Prediction

Protein:	HFQ_YERPA
Organism:	Yersinia pestis Antiqua
Length:	101 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_YERPA.

Description	E-value	Query Range	Subject Range
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...	8.0E-41	[1..101]	[1..101]
gi\|238714287, gi... - gi\|77957806\|ref\|ZP_00821853.1\| COG1923: Uncharacterized host factor I protein [Yersinia bercovieri A...	9.0E-41	[1..101]	[1..101]
HFQ_SODGM - RNA-binding protein Hfq OS=Sodalis glossinidius (strain morsitans) GN=hfq PE=3 SV=1	1.0E-37	[1..101]	[1..101]
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	2.0E-37	[1..101]	[1..102]
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	4.0E-37	[1..101]	[1..102]
HFQ_ECOLC - RNA-binding protein Hfq OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=hfq PE=3 SV=1 EG10438 - global sRNA chaperone; HF-I, host factor for RNA phage Q beta replication / Global regulator of sRNA... HFQ_ESCF3 - RNA-binding protein Hfq OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73) GN=h... gi\|217321789, gi... - gi\|217325568\|ref\|ZP_03441652.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. TW14588], gi\|217321... gi\|85676923, gi\|... - gi\|89110892\|ref\|AP_004672.1\| HF-I, host factor for RNA phage Q beta replication [Escherichia coli st... HFQ_ECO45 - RNA-binding protein Hfq OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=hfq PE=3 SV=1 HFQ_SHIBS - RNA-binding protein Hfq OS=Shigella boydii serotype 4 (strain Sb227) GN=hfq PE=3 SV=1 HFQ_ECOUT - RNA-binding protein Hfq OS=Escherichia coli (strain UTI89 / UPEC) GN=hfq PE=3 SV=1 HFQ_ECO8A - RNA-binding protein Hfq OS=Escherichia coli O8 (strain IAI1) GN=hfq PE=3 SV=1 HFQ_ECO55 - RNA-binding protein Hfq OS=Escherichia coli (strain 55989 / EAEC) GN=hfq PE=3 SV=1 HFQ_ECO81 - RNA-binding protein Hfq OS=Escherichia coli O81 (strain ED1a) GN=hfq PE=3 SV=1 HFQ_ECOK1 - RNA-binding protein Hfq OS=Escherichia coli O1:K1 / APEC GN=hfq PE=3 SV=1 gi\|227836358, gi... - gi\|227886785\|ref\|ZP_04004590.1\| host factor I [Escherichia coli 83972], gi\|227836358\|gb\|EEJ46824.1\| ... gi\|124528231, gi... - gi\|124528231\|ref\|ZP_01699555.1\| RNA chaperone Hfq [Escherichia coli B], gi\|124500673\|gb\|EAY48143.1\| ... HFQ_ECO7I - RNA-binding protein Hfq OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=hfq PE=3 SV=1 gi\|237703839, gi... - gi\|237703839\|ref\|ZP_04534320.1\| host factor I for bacteriophage Q beta replication [Escherichia sp. ... gi\|191174520, gi... - gi\|75236175\|ref\|ZP_00720297.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli F11]... gi\|126143548 - gi\|126143548\|dbj\|BAF47288.1\| Hfq protein [Shigella sonnei] gi\|195935962 - gi\|195935962\|ref\|ZP_03081344.1\| RNA-binding protein Hfq [Escherichia coli O157:H7 str. EC4024] HFQ_ECOBW - RNA-binding protein Hfq OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=hfq PE=3 SV=1 gi\|75234279, gi\|... - gi\|75234279\|ref\|ZP_00718667.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli E110... gi\|194434571, gi... - gi\|194434571\|ref\|ZP_03066828.1\| RNA chaperone Hfq [Shigella dysenteriae 1012], gi\|194417156\|gb\|EDX33... gi\|251787421, gi... - gi\|251787421\|ref\|YP_003001725.1\| hypothetical protein B21_04001 [Escherichia coli BL21], gi\|24237969... gi\|75231235, gi\|... - gi\|75231235\|ref\|ZP_00717642.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli B7A]... gi\|208735780, gi... - gi\|208814503\|ref\|ZP_03255832.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4045], gi\|2087357... gi\|253326247, gi... - gi\|254290851\|ref\|YP_003056599.1\| RNA-binding protein Hfq [Escherichia coli BL21(DE3)], gi\|253980158\|... gi\|194426632, gi... - gi\|75212279\|ref\|ZP_00712319.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli B171... gi\|208726606, gi... - gi\|208806805\|ref\|ZP_03249142.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4206], gi\|2087266... gi\|226840292, gi... - gi\|254037186\|ref\|ZP_04871263.1\| hfq protein [Escherichia sp. 1_1_43], gi\|226840292\|gb\|EEH72294.1\| hf... HFQ_SHISS - RNA-binding protein Hfq OS=Shigella sonnei (strain Ss046) GN=hfq PE=3 SV=1 gi\|15834402, gi\|... - gi\|15834402\|ref\|NP_313175.1\| RNA-binding protein Hfq [Escherichia coli O157:H7 str. Sakai], gi\|13364... HFQ_ECO5E - RNA-binding protein Hfq OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=hfq PE=3 SV=1 gi\|254164101, gi... - gi\|254164101\|ref\|YP_003047209.1\| RNA-binding protein Hfq [Escherichia coli B str. REL606], gi\|253976... HFQ_ECOL6 - Protein hfq OS=Escherichia coli O6 GN=hfq PE=3 SV=2 HFQ_ECOL5 - RNA-binding protein Hfq OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=hfq PE=3 SV=1 gi\|208739508, gi... - gi\|208819385\|ref\|ZP_03259705.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4042], gi\|2087395... gi\|254595591, gi... - gi\|254796191\|ref\|YP_003081028.1\| host factor I for bacteriophage Q beta replication, a growth-relate... gi\|75515411, gi\|... - gi\|75515411\|ref\|ZP_00737568.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli 5363... HFQ_SHIF8 - RNA-binding protein Hfq OS=Shigella flexneri serotype 5b (strain 8401) GN=hfq PE=3 SV=1 HFQ_ECO27 - RNA-binding protein Hfq OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=hfq PE=3 SV=1 gi\|192926336, gi... - gi\|75255899\|ref\|ZP_00727631.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli E22]... HFQ_ECOSE - RNA-binding protein Hfq OS=Escherichia coli (strain SE11) GN=hfq PE=3 SV=1 HFQ_SHIFL - RNA-binding protein Hfq OS=Shigella flexneri GN=hfq PE=3 SV=2 HFQ_ECOLI - Protein hfq (Host factor-I protein) (HF-I) (HF-1) - Escherichia coli gi\|24115527, gi\|... - gi\|24115527\|ref\|NP_710037.1\| RNA-binding protein Hfq [Shigella flexneri 2a str. 301], gi\|24054855\|gb... HFQ_ECOL6 - RNA-binding protein Hfq OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=hfq PE=3 S... gi\|30043808, gi\|... - gi\|30065544\|ref\|NP_839715.1\| RNA-binding protein Hfq [Shigella flexneri 2a str. 2457T], gi\|30043808\|... HFQ_ECOHS - RNA-binding protein Hfq OS=Escherichia coli O9:H4 (strain HS) GN=hfq PE=3 SV=1 HFQ_ECO57 - RNA-binding protein Hfq OS=Escherichia coli O157:H7 GN=hfq PE=3 SV=2 HFQ_ECO24 - RNA-binding protein Hfq OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=hfq PE=3 SV=1 EG10438 - global sRNA chaperone; HF-I, host factor for RNA phage Q beta replication / Global regulator of sRNA... gi\|194421514, gi... - gi\|83585090\|ref\|ZP_00923743.1\| COG1923: Uncharacterized host factor I protein [Escherichia coli 101-... gi\|12519157, gi\|... - gi\|15804761\|ref\|NP_290802.1\| RNA-binding protein Hfq [Escherichia coli O157:H7 EDL933], gi\|12519157\|... sp\|B7UQI1\|HFQ_ECO27 - Protein hfq OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=hfq PE=3 SV=1 gi\|168766449, gi... - gi\|189363952\|gb\|EDU82371.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4486], gi\|168766449\|r... gi\|168760411, gi... - gi\|189368893\|gb\|EDU87309.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4501], gi\|168760411\|r... gi\|168780602, gi... - gi\|189001835\|gb\|EDU70821.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4076], gi\|168780602\|r... gi\|168774117, gi... - gi\|187770223\|gb\|EDU34067.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4196], gi\|168774117\|r... gi\|189376091, gi... - gi\|189376091\|gb\|EDU94507.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC508], gi\|168801825\|re... gi\|168784807, gi... - gi\|189374845\|gb\|EDU93261.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC869], gi\|168784807\|re... HFQ_ECOSM - RNA-binding protein Hfq OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=hfq PE=3 SV=1 HFQ_ECODH - RNA-binding protein Hfq OS=Escherichia coli (strain K12 / DH10B) GN=hfq PE=3 SV=1 gi\|189357810, gi... - gi\|189357810\|gb\|EDU76229.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4401], gi\|168754741\|r... gi\|168751478, gi... - gi\|188014498\|gb\|EDU52620.1\| RNA chaperone Hfq [Escherichia coli O157:H7 str. EC4113], gi\|168751478\|r...	1.0E-36	[1..101]	[1..102]
gi\|1305418 - gi\|1305418\|gb\|AAA99108.1\| host factor I gi\|1305418\|gb\|AA... - host factor I	2.0E-36	[1..101]	[1..102]
HFQ_SHIDS - RNA-binding protein Hfq OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=hfq PE=3 SV=1	2.0E-36	[1..101]	[1..102]
HFQ_SHIB3 - RNA-binding protein Hfq OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=hfq PE=3 SV=1	2.0E-36	[1..101]	[1..102]
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	3.0E-36	[1..101]	[1..102]

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Predicted Domain #1

Region A:
Residues: [1-101]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQVESFD QFVILLKNTV SQMVYKHAIS  60
   61 TVVPSRPVSH HSNTPSGSTN NYHGSNPSAP QQPQQDSDDA E

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	34.30103
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: