YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29141106, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	878 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 gi|29141106, gi|....

Description	E-value	Query Range	Subject Range
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....	0.0	[1..868]	[1..868]
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...	0.0	[1..868]	[1..868]
gi\|2731385 - gi\|2731385\|gb\|AAB95117.1\| DNA gyrase [Serratia marcescens]	0.0	[1..878]	[1..877]
gi\|62128478, gi\|... - gi\|62180845\|ref\|YP_217262.1\| DNA gyrase subunit A [Salmonella enterica subsp. enterica serovar Chole...	0.0	[1..868]	[1..868]
gi\|238788613, gi... - gi\|77975439\|ref\|ZP_00830974.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[1..878]	[1..881]
gi\|77956426, gi\|... - gi\|77956426\|ref\|ZP_00820526.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[1..863]	[1..865]
gi\|90581243, gi\|... - gi\|90581243\|ref\|ZP_01237041.1\| putative DNA topoisomerase (ATP-hydrolyzing) [Vibrio angustum S14], g...	0.0	[1..874]	[1..886]
gi\|238725695, gi... - gi\|77976959\|ref\|ZP_00832423.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[1..864]	[1..865]
gi\|238797460, gi... - gi\|77960358\|ref\|ZP_00824233.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[1..849]	[1..849]
gi\|77636493, gi\|... - gi\|77636493\|ref\|ZP_00798567.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	0.0	[1..850]	[1..850]

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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 AHGLMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT 180
  181 NIPPHNLTEV INGCLAYIDN EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV 240
  241 YIRARAEVEA DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKDKRVEGIS ALRDESDKDG 300
  301 MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI ISAFVRHRRE 360
  361 VVTRRTIFEL RKARDRAHIL EALAIALANI DPIIELIRRA PTPAEAKAAL ISRPWDLGNV 420
  421 AAMLERAGDD AARPEWLEPE FGVRDGQYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE 480
  481 LLEQIAELLH ILGSADRLME VIREEMELIR DQFGDERRTE 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: [529-878]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIEDLISQEN VVVTLSHQGY VKYQPLTDYE AQRRGGKGKS AARIKEEDFI DRLLVANTHD  60
   61 TILCFSSRGR LYWMKVYQLP EASRGARGRP IVNLLPLEAN ERITAILPVR EYEEGVNVFM 120
  121 ATASGTVKKT ALTEFSRPRS AGIIAVNLND GDELIGVDLT SGSDEVMLFS AAGKVVRFKE 180
  181 DAVRAMGRTA TGVRGIKLAG DDKVVSLIIP RGEGAILTVT QNGYGKRTAA DEYPTKSRAT 240
  241 QGVISIKVTE RNGSVVGAVQ VDDCDQIMMI TDAGTLVRTR VSEISVVGRN TQGVILIRTA 300
  301 EDENVVGLQR VAEPVDDEEL DAIDGSVTEG DEDIAPEAES DDDVADDADE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
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: