YRC Public Data Repository - Protein Structure Prediction

Protein:	GYRB_ECOLI
Organism:	Escherichia coli
Length:	804 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 GYRB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|1546916 - gi\|1546916\|emb\|CAA69221.1\| subunit B of DNA gyrase [Salmonella typhimurium] gi\|1546916\|emb\|C... - subunit B of DNA gyrase [Salmonella typhimurium]	1172.0	[0..1]	[804..1]
gi\|218367543, gi... - gi\|218560774\|ref\|YP_002393687.1\| DNA gyrase subunit B [Escherichia coli S88], gi\|218367543\|emb\|CAR05... gi\|218429551, gi... - gi\|218691987\|ref\|YP_002400199.1\| DNA gyrase subunit B [Escherichia coli ED1a], gi\|218429551\|emb\|CAR1... gi\|110644042, gi... - gi\|110644042\|ref\|YP_671772.1\| DNA gyrase subunit B [Escherichia coli 536], gi\|110345634\|gb\|ABG71871.... gi\|227883920, gi... - gi\|227883920\|ref\|ZP_04001725.1\| DNA gyrase subunit B [Escherichia coli 83972], gi\|227839198\|gb\|EEJ49... gi\|190909423, gi... - gi\|75242511\|ref\|ZP_00726255.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|115515099, gi... - gi\|117625975\|ref\|YP_859298.1\| DNA gyrase subunit B [Escherichia coli APEC O1], gi\|115515099\|gb\|ABJ03...	1171.0	[0..1]	[804..1]
gi\|81243376, gi\|... - gi\|82779228\|ref\|YP_405577.1\| DNA gyrase subunit B [Shigella dysenteriae Sd197], gi\|81243376\|gb\|ABB64...	1171.0	[0..1]	[804..1]
gi\|26110870, gi\|... - gi\|26250440\|ref\|NP_756480.1\| DNA gyrase subunit B [Escherichia coli CFT073], gi\|26110870\|gb\|AAN83054... gi\|91213221, gi\|... - gi\|91213221\|ref\|YP_543207.1\| DNA gyrase subunit B [Escherichia coli UTI89], gi\|91074795\|gb\|ABE09676.... gi\|237703499, gi... - gi\|237703499\|ref\|ZP_04533980.1\| subunit B [Escherichia sp. 3_2_53FAA], gi\|226902763\|gb\|EEH89022.1\| s...	1171.0	[0..1]	[804..2]
gi\|187428646, gi... - gi\|75177732\|ref\|ZP_00697797.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|81247448, gi\|... - gi\|82546037\|ref\|YP_409984.1\| DNA gyrase subunit B [Shigella boydii Sb227], gi\|81247448\|gb\|ABB68156.1...	1169.0	[0..1]	[804..1]
gi\|194431109, gi... - gi\|83571498\|ref\|ZP_00922938.1\| COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	1169.0	[0..1]	[804..1]
gi\|290547 - gi\|290547\|gb\|AAA62050.1\| DNA gyrase, subunit B	1168.0	[0..1]	[804..1]
GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|224470162, gi... - gi\|224585634\|ref\|YP_002639433.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|214001463 - gi\|214001463\|ref\|ZP_03412198.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|213424954 - gi\|213424954\|ref\|ZP_03357704.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Ty... gi\|207859061, gi... - gi\|207859061\|ref\|YP_002245712.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar E... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=gyrB PE=1 SV... GYRB_SALTI - DNA gyrase subunit B OS=Salmonella typhi GN=gyrB PE=3 SV=2 lcl\|NC_016856.1_... - [gene=gyrB] [protein=DNA gyrase subunit B] [protein_id=YP_005240101.1] [location=complement(4052548.... gi\|29143978, gi\|... - gi\|29143978\|ref\|NP_807320.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|16762490 - gi\|16762490\|ref\|NP_458107.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Typhi... gi\|238913088 - gi\|238913088\|ref\|ZP_04656925.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Te... gi\|205325567, gi... - gi\|205325567\|gb\|EDZ13406.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Saint... GYRB_SALTY - DNA gyrase subunit B OS=Salmonella typhimurium GN=gyrB PE=3 SV=2 gi\|161616952, gi... - gi\|161616952\|ref\|YP_001590917.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P... gi\|197240529, gi... - gi\|197262274\|ref\|ZP_03162348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar S... gi\|194712574, gi... - gi\|194737072\|ref\|YP_002116779.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|194472695, gi... - gi\|194472695\|ref\|ZP_03078679.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar K... gi\|194449732, gi... - gi\|194449732\|ref\|YP_002047868.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar H... gi\|205354578, gi... - gi\|205354578\|ref\|YP_002228379.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar G... gi\|204322190, gi... - gi\|204928757\|ref\|ZP_03219956.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar J... gi\|199604199, gi... - gi\|200387101\|ref\|ZP_03213713.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar V... gi\|197938563, gi... - gi\|198244047\|ref\|YP_002217785.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|205338996, gi... - gi\|205338996\|gb\|EDZ25760.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Heide... gi\|197291517, gi... - gi\|197291517\|gb\|EDY30869.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Schwa... gi\|168233389, gi... - gi\|205332584\|gb\|EDZ19348.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Kentu... gi\|205329403, gi... - gi\|205329403\|gb\|EDZ16167.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar 4,[5]... gi\|194442844, gi... - gi\|194442844\|ref\|YP_002043085.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar ... gi\|168818305, gi... - gi\|205344661\|gb\|EDZ31425.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Welte... gi\|195632426, gi... - gi\|195632426\|gb\|EDX50910.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Newpo... gi\|168260381, gi... - gi\|205350152\|gb\|EDZ36783.1\| DNA gyrase, B subunit [Salmonella enterica subsp. enterica serovar Hadar...	1168.0	[0..1]	[804..1]
gi\|56129965, gi\|... - gi\|56415708\|ref\|YP_152783.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar Parat... gi\|197364636, gi... - gi\|197364636\|ref\|YP_002144273.1\| DNA gyrase subunit B [Salmonella enterica subsp. enterica serovar P...	1167.0	[0..1]	[804..1]

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Predicted Domain #1

Region A:
Residues: [1-394]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII  60
   61 VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV 120
  121 SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT 180
  181 EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI 240
  241 FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE 300
  301 GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY 360
  361 LLENPTDAKI VVGKIIDAAR AREAARRARE MTRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	166.0
Match:	1ei1A
Description:	DNA gyrase B
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA topoisomerase activity	12.6906165486321	bayes_pls_golite062009
DNA topoisomerase (ATP-hydrolyzing) activity	11.8861942287485	bayes_pls_golite062009
isomerase activity	8.13079712911425	bayes_pls_golite062009
transcription regulator activity	2.14522015372277	bayes_pls_golite062009
catalytic activity	2.10890475146569	bayes_pls_golite062009
protein kinase activity	1.84867054522487	bayes_pls_golite062009
kinase activity	1.68443268281997	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	1.64025200399404	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.60156177836014	bayes_pls_golite062009
DNA binding	1.5298919664856	bayes_pls_golite062009
structural constituent of ribosome	1.38725999901881	bayes_pls_golite062009
binding	1.38505389441989	bayes_pls_golite062009
nucleic acid binding	1.36270841743065	bayes_pls_golite062009
transferase activity	1.09369139087478	bayes_pls_golite062009
structural molecule activity	1.04534150109805	bayes_pls_golite062009
signal transducer activity	0.996368427522977	bayes_pls_golite062009
molecular transducer activity	0.996368427522977	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.86218415868631	bayes_pls_golite062009
exonuclease activity	0.76163144715311	bayes_pls_golite062009
nuclease activity	0.42266682237543	bayes_pls_golite062009
ribonuclease activity	0.0675296198098132	bayes_pls_golite062009
mismatched DNA binding	0.0671550940422005	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [395-730]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KGALDLAGLP GKLADCQERD PALSELYLVE GDSAGGSAKQ GRNRKNQAIL PLKGKILNVE  60
   61 KARFDKMLSS QEVATLITAL GCGIGRDEYN PDKLRYHSII IMTDADVDGS HIRTLLLTFF 120
  121 YRQMPEIVER GHVYIAQPPL YKVKKGKQEQ YIKDDEAMDQ YQISIALDGA TLHTNASAPA 180
  181 LAGEALEKLV SEYNATQKMI NRMERRYPKA MLKELIYQPT LTEADLSDEQ TVTRWVNALV 240
  241 SELNDKEQHG SQWKFDVHTN AEQNLFEPIV RVRTHGVDTD YPLDHEFITG GEYRRICTLG 300
  301 EKLRGLLEED AFIERGERRQ PVASFEQALD WLVKES

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	66.30103
Match:	1bgwA
Description:	TOPOISOMERASE RESIDUES 410-1202,
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 #3

Region A:
Residues: [731-804]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL MGDAVEPRRA  60
   61 FIEENALKAA NIDI

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.62
Match:	1bgwA
Description:	TOPOISOMERASE RESIDUES 410-1202,
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA topoisomerase activity	15.4936903203186	bayes_pls_golite062009
DNA topoisomerase (ATP-hydrolyzing) activity	14.6489242328866	bayes_pls_golite062009
isomerase activity	11.0996144353545	bayes_pls_golite062009
DNA binding	4.07071788473104	bayes_pls_golite062009
nucleic acid binding	3.8906242200463	bayes_pls_golite062009
binding	3.74481651990022	bayes_pls_golite062009
catalytic activity	1.68981384280236	bayes_pls_golite062009
DNA-dependent ATPase activity	0.95809415738291	bayes_pls_golite062009
protein binding	0.0435629034939063	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:

Predicted functions:

Predicted functions: