YRC Public Data Repository - Protein Structure Prediction

Protein:	GYRA_ECOLI
Organism:	Escherichia coli
Length:	875 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 GYRA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|2731385 - gi\|2731385\|gb\|AAB95117.1\| DNA gyrase [Serratia marcescens]	1146.0	[0..1]	[873..1]
gi\|206709494, gi... - gi\|207857691\|ref\|YP_002244342.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar E... gi\|224467770, gi... - gi\|224583243\|ref\|YP_002637041.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar P... gi\|194450393, gi... - gi\|194450393\|ref\|YP_002046326.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar H... gi\|197211911, gi... - gi\|197248208\|ref\|YP_002147228.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar ... gi\|197242233, gi... - gi\|197263978\|ref\|ZP_03164052.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar S... gi\|197093240, gi... - gi\|197361764\|ref\|YP_002141400.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar P... gi\|205349514, gi... - gi\|205349514\|gb\|EDZ36145.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar Hadar... gi\|195631306, gi... - gi\|195631306\|gb\|EDX49866.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar Newpo... gi\|168818000, gi... - gi\|205344910\|gb\|EDZ31674.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar Welte... gi\|194445296, gi... - gi\|194445296\|ref\|YP_002041533.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar ... GYRA_SALTY - DNA gyrase subunit A OS=Salmonella typhimurium GN=gyrA PE=3 SV=3 gi\|161362374, gi... - gi\|161613010\|ref\|YP_001586975.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar P... gi\|167549737, gi... - gi\|205325309\|gb\|EDZ13148.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar Saint... GYRA_SALTY - DNA gyrase subunit A OS=Salmonella typhimurium GN=gyrA PE=3 SV=3 GYRA_SALTY - DNA gyrase subunit A OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=gyrA PE=1 SV... gi\|56412831, gi\|... - gi\|56412831\|ref\|YP_149906.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Parat... gi\|205338650, gi... - gi\|205338650\|gb\|EDZ25414.1\| DNA gyrase, A subunit [Salmonella enterica subsp. enterica serovar Heide... lcl\|NC_016856.1_... - [gene=gyrA] [protein=DNA gyrase subunit A] [protein_id=YP_005238340.1] [location=complement(2425264....	1144.0	[0..1]	[868..1]
gi\|213646449 - gi\|213646449\|ref\|ZP_03376502.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Ty... gi\|16503499, gi\|... - gi\|25292862\|pir\|\|AF0790 DNA topoisomerase (ATP-hydrolysing) (EC 5.99.1.3) - Salmonella enterica subs... gi\|16761200 - gi\|16761200\|ref\|NP_456817.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Typhi...	1143.0	[0..1]	[868..1]
gi\|90581243, gi\|... - gi\|90581243\|ref\|ZP_01237041.1\| putative DNA topoisomerase (ATP-hydrolyzing) [Vibrio angustum S14], g...	1143.0	[0..1]	[875..1]
gi\|29141106, gi\|... - gi\|29141106\|ref\|NP_804448.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Typhi...	1143.0	[0..1]	[868..1]
gi\|62128478, gi\|... - gi\|62180845\|ref\|YP_217262.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Chole...	1142.0	[0..1]	[868..1]
gi\|157161714, gi... - gi\|75196273\|ref\|ZP_00706343.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	1140.0	[0..1]	[875..1]
gi\|218365917, gi... - gi\|218559148\|ref\|YP_002392061.1\| DNA gyrase subunit A [Escherichia coli S88], gi\|218365917\|emb\|CAR03... gi\|26109024, gi\|... - gi\|26248619\|ref\|NP_754659.1\| DNA gyrase subunit A [Escherichia coli CFT073], gi\|26109024\|gb\|AAN81227... gi\|218427958, gi... - gi\|218690394\|ref\|YP_002398606.1\| DNA gyrase subunit A [Escherichia coli ED1a], gi\|218427958\|emb\|CAR0... gi\|215265520, gi... - gi\|215487448\|ref\|YP_002329879.1\| DNA gyrase subunit A [Escherichia coli O127:H6 str. E2348/69], gi\|2... gi\|91073098, gi\|... - gi\|91211524\|ref\|YP_541510.1\| DNA gyrase subunit A [Escherichia coli UTI89], gi\|91073098\|gb\|ABE07979.... gi\|227835638, gi... - gi\|227887288\|ref\|ZP_04005093.1\| DNA gyrase subunit A [Escherichia coli 83972], gi\|227835638\|gb\|EEJ46... gi\|237704706, gi... - gi\|237704706\|ref\|ZP_04535187.1\| subunit A [Escherichia sp. 3_2_53FAA], gi\|226901072\|gb\|EEH87331.1\| s... gi\|115513549, gi... - gi\|117624425\|ref\|YP_853338.1\| DNA gyrase subunit A [Escherichia coli APEC O1], gi\|115513549\|gb\|ABJ01...	1139.0	[0..1]	[875..1]
gi\|254593522, gi... - gi\|254794122\|ref\|YP_003078959.1\| DNA gyrase (type II topoisomerase), subunit A [Escherichia coli O15... gi\|25292834, gi\|... - pir\|\|B91018 DNA gyrase subunit A [imported] - Escherichia coli (strain O157:H7, substrain RIMD 05099... gi\|13362583, gi\|... - gi\|15832368\|ref\|NP_311141.1\| DNA gyrase subunit A [Escherichia coli O157:H7], gi\|13362583\|dbj\|BAB365... gi\|208738993, gi... - gi\|208818870\|ref\|ZP_03259190.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4042], gi\|208... gi\|209157353, gi... - gi\|209395953\|ref\|YP_002271637.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4115], gi\|20... gi\|217326866, gi... - gi\|217326866\|ref\|ZP_03442949.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. TW14588], gi\|21... gi\|218705761, gi... - gi\|218705761\|ref\|YP_002413280.1\| DNA gyrase subunit A [Escherichia coli UMN026], gi\|218432858\|emb\|CA... gi\|189378991, gi... - gi\|189378991\|gb\|EDU97407.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC508], gi\|16879839... gi\|195935604 - gi\|195935604\|ref\|ZP_03080986.1\| DNA gyrase subunit A [Escherichia coli O157:H7 str. EC4024] gi\|208729386, gi... - gi\|208809585\|ref\|ZP_03251922.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4206], gi\|208... gi\|13362583, gi\|... - gi\|15832368\|ref\|NP_311141.1\| DNA gyrase subunit A [Escherichia coli O157:H7 str. Sakai], gi\|13362583... gi\|208814055, gi... - gi\|208814055\|ref\|ZP_03255384.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4045], gi\|208... gi\|168767849, gi... - gi\|189362953\|gb\|EDU81372.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4486], gi\|1687678... gi\|187771122, gi... - gi\|187771122\|gb\|EDU34966.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4196], gi\|1687730... gi\|189002080, gi... - gi\|189002080\|gb\|EDU71066.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4076], gi\|1687800... gi\|189372927, gi... - gi\|189372927\|gb\|EDU91343.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC869], gi\|16878713... gi\|188016049, gi... - gi\|188016049\|gb\|EDU54171.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4113], gi\|1687496... gi\|189357583, gi... - gi\|189357583\|gb\|EDU76002.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4401], gi\|1687549... gi\|168761339, gi... - gi\|189368282\|gb\|EDU86698.1\| DNA gyrase, A subunit [Escherichia coli O157:H7 str. EC4501], gi\|1687613...	1139.0	[0..1]	[875..1]
gi\|251785593, gi... - gi\|251785593\|ref\|YP_002999897.1\| hypothetical protein B21_02116 [Escherichia coli BL21], gi\|24237786... gi\|253974143, gi... - gi\|254162242\|ref\|YP_003045350.1\| DNA gyrase subunit A [Escherichia coli B str. REL606], gi\|253974143... gi\|253772846, gi... - gi\|254289003\|ref\|YP_003054751.1\| DNA gyrase subunit A [Escherichia coli BL21(DE3)], gi\|253978310\|gb\|... gi\|188490375, gi... - gi\|75512707\|ref\|ZP_00735209.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|83588217, gi\|... - gi\|83588217\|ref\|ZP_00926842.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	1139.0	[0..1]	[875..1]

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Predicted Domain #1

Region A:
Residues: [1-528]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN  60
   61 KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM 120
  121 RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT 180
  181 NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV 240
  241 YIRARAEVEV DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG 300
  301 MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI IAAFVRHRRE 360
  361 VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA PTPAEAKTAL VANPWQLGNV 420
  421 AAMLERAGDD AARPEWLEPE FGVRDGLYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE 480
  481 LLDQIAELLR ILGSADRLME VIREELELVR EQFGDKRRTE ITANSADI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1ab4A
Description:	59KDA FRAGMENT OF GYRASE A FROM E. COLI
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA topoisomerase activity	16.1862836613251	bayes_pls_golite062009
DNA topoisomerase (ATP-hydrolyzing) activity	15.3845248199845	bayes_pls_golite062009
isomerase activity	11.5598219279347	bayes_pls_golite062009
DNA binding	4.42972615310468	bayes_pls_golite062009
nucleic acid binding	4.21774496265744	bayes_pls_golite062009
binding	3.95084202265591	bayes_pls_golite062009
catalytic activity	1.83123392049501	bayes_pls_golite062009
DNA-dependent ATPase activity	1.17291817800492	bayes_pls_golite062009
protein binding	0.0229806746449869	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [529-875]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NLEDLITQED VVVTLSHQGY VKYQPLSEYE AQRRGGKGKS AARIKEEDFI DRLLVANTHD  60
   61 HILCFSSRGR VYSMKVYQLP EATRGARGRP IVNLLPLEQD ERITAILPVT EFEEGVKVFM 120
  121 ATANGTVKKT VLTEFNRLRT AGKVAIKLVD GDELIGVDLT SGEDEVMLFS AEGKVVRFKE 180
  181 SSVRAMGCNT TGVRGIRLGE GDKVVSLIVP RGDGAILTAT QNGYGKRTAV AEYPTKSRAT 240
  241 KGVISIKVTE RNGLVVGAVQ VDDCDQIMMI TDAGTLVRTR VSEISIVGRN TQGVILIRTA 300
  301 EDENVVGLQR VAEPVDEEDL DTIDGSAAEG DDEIAPEVDV DDEPEEE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	108.0
Match:	1zi0A
Description:	A Superhelical Spiral in Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias
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: