YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24348396, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	919 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|24348396, gi|....

Description	E-value	Query Range	Subject Range
gi\|113970257, gi... - gi\|113970257\|ref\|YP_734050.1\| DNA gyrase subunit A [Shewanella sp. MR-4], gi\|113884941\|gb\|ABI38993.1...	1153.0	[0..1]	[880..27]
gi\|114047554, gi... - gi\|114047554\|ref\|YP_738104.1\| DNA gyrase subunit A [Shewanella sp. MR-7], gi\|113888996\|gb\|ABI43047.1...	1152.0	[0..1]	[880..27]
gi\|117612749, gi... - gi\|78688221\|ref\|ZP_00852935.1\| DNA gyrase, subunit A [Shewanella sp. ANA-3], gi\|78504042\|gb\|EAP17621...	1147.0	[0..1]	[880..1]
gi\|116183643, gi... - gi\|75854125\|ref\|ZP_00761839.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	1145.0	[0..1]	[870..1]
gi\|91227187, gi\|... - gi\|91227187\|ref\|ZP_01261646.1\| DNA gyrase, subunit A [Vibrio alginolyticus 12G01], gi\|91188715\|gb\|EA...	1145.0	[0..1]	[870..1]
gi\|75826650, gi\|... - gi\|75826650\|ref\|ZP_00756085.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV... gi\|227081430, gi... - gi\|227081430\|ref\|YP_002809981.1\| DNA gyrase, subunit A [Vibrio cholerae M66-2], gi\|227009318\|gb\|ACP0... gi\|229505155, gi... - gi\|229505155\|ref\|ZP_04394665.1\| DNA gyrase subunit A [Vibrio cholerae BX 330286], gi\|229357378\|gb\|EE... gi\|229345007, gi... - gi\|229518292\|ref\|ZP_04407736.1\| DNA gyrase subunit A [Vibrio cholerae RC9], gi\|229345007\|gb\|EEO09981... gi\|229339438, gi... - gi\|229525857\|ref\|ZP_04415262.1\| DNA gyrase subunit A [Vibrio cholerae bv. albensis VL426], gi\|229339... gi\|15641271, gi\|... - gi\|9655742\|gb\|AAF94417.1\| DNA gyrase, subunit A [Vibrio cholerae O1 biovar El Tor str. N16961], gi\|1... gi\|229370830, gi... - gi\|229608175\|ref\|YP_002878823.1\| DNA gyrase subunit A [Vibrio cholerae MJ-1236], gi\|229370830\|gb\|ACQ... gi\|11270988 - pir\|\|E82221 DNA gyrase, chain A VC1258 [imported] - Vibrio cholerae (strain N16961 serogroup O1) gi\|121547414, gi... - gi\|121590733\|ref\|ZP_01678064.1\| DNA gyrase, subunit A [Vibrio cholerae 2740-80], gi\|121547414\|gb\|EAX... gi\|121628470, gi... - gi\|121729795\|ref\|ZP_01682231.1\| DNA gyrase, subunit A [Vibrio cholerae V52], gi\|121628470\|gb\|EAX6096... gi\|153222492, gi... - gi\|153222492\|ref\|ZP_01953214.1\| DNA gyrase, subunit A [Vibrio cholerae MAK 757], gi\|124118829\|gb\|EAY... gi\|254844087, gi... - gi\|75829668\|ref\|ZP_00758964.1\| COG0188: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV...	1142.0	[0..1]	[865..1]
gi\|90581243, gi\|... - gi\|90581243\|ref\|ZP_01237041.1\| putative DNA topoisomerase (ATP-hydrolyzing) [Vibrio angustum S14], g...	1139.0	[0..1]	[870..1]
gi\|89074076, gi\|... - gi\|89074076\|ref\|ZP_01160577.1\| putative DNA topoisomerase (ATP-hydrolyzing) [Photobacterium sp. SKA3...	1135.0	[0..1]	[870..1]
gi\|37679431, gi\|... - gi\|37679431\|ref\|NP_934040.1\| DNA gyrase, subunit A [Vibrio vulnificus YJ016], gi\|37198175\|dbj\|BAC940...	1130.0	[0..1]	[865..1]
gi\|90412222, gi\|... - gi\|90412222\|ref\|ZP_01220228.1\| putative DNA topoisomerase (ATP-hydrolyzing) [Photobacterium profundu...	1128.0	[0..1]	[863..1]

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Predicted Domain #1

Region A:
Residues: [1-527]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTDLASSISP INIEDELKNS YLDYAMSVIV GRALPDVRDG LKPVHRRVLF AMSELKNDWN  60
   61 KPYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY TLVDGQGNFG SVDGDSAAAM 120
  121 RYTEIRMDKL AHQLLADLEK ETVDYVPNYD GTEQIPAVLP TRVPNLLING SSGIAVGMAT 180
  181 NIPPHNLTEV VKGCLALIAD PALSIEQLMD YIPGPDFPTA AIINGRKGII DAYKTGRGRA 240
  241 IMRALAEVET EENGRERIIV TEIPYQVNKA RLIEKIAELV KDKKLEGISG LRDESDKDGM 300
  301 RIVIEIKRGE VGEVVLNNLY AQTQMQCSFG INMVALTNGQ PKLFNLKEML ECFILHRREV 360
  361 VTRRTVFELR KARERAHILE ALAVALANID PIIALIKASP TPADAKVKLV EQGWALGHVQ 420
  421 GMLEKAGDDA ARPEWLEPEY GIRDGLYYLT EQQAQAILEL RLHRLTGLEH DKIIAEYEEL 480
  481 LEFIAGLLFI LRSPERLMEV IKEELEEILA EYGDARRTVI NANEIDM

[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: [528-919]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLEDLINEED VVVTLSHLGY AKYQPLSDYQ AQRRGGKGKV ATKVKDEDFV EKLLVANTHD  60
   61 TILCFSDFGK MYWLKVYQLP LASRTSRGRP IVNLLPLADG ERITAILPVR EYAEDKYIIM 120
  121 ATSNGTVKKT ALTAYSNPRA NGIIAVNLKD GDQLIGVDIT NGDDEIMLFS NEGKVVRFKE 180
  181 GEEVAVLDEN GNPVLDEEGN PQINFKGVRP MGRGATGVRG IKLEEGQRVV SLIVPKDDGA 240
  241 ILTVTENGYG KRTELSEYPS KSRATKGVVS IKVSERNGAV VGAVQVGGND EIMLISDKGT 300
  301 LVRTPANGVS IIGRNTQGVT IIRTASDEKV VGLQRIDEIQ GDEDEVELDE NGMPIAPVIA 360
  361 EGDSVQEEPL EEEDELEELD EDEELDDEQD ED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	102.0
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: