YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|194424000, gi...
Organism:	Escherichia coli 101-1
Length:	865 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|194424000, gi....

Description	E-value	Query Range	Subject Range
gi\|168775085, gi... - gi\|187769270\|gb\|EDU33114.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4196], gi\|168775085... gi\|12515520, gi\|... - gi\|15801905\|ref\|NP_287925.1\| DNA topoisomerase I [Escherichia coli O157:H7 EDL933], gi\|12515520\|gb\|A... gi\|168771274, gi... - gi\|189359953\|gb\|EDU78372.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4486], gi\|168771274... gi\|168763576, gi... - gi\|189366286\|gb\|EDU84702.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4501], gi\|168763576... gi\|168758361, gi... - gi\|189354817\|gb\|EDU73236.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4401], gi\|168758361... gi\|208724516, gi... - gi\|208811010\|ref\|ZP_03252843.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4206], gi\|20872... gi\|195939210 - gi\|195939210\|ref\|ZP_03084592.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4024] gi\|189376271, gi... - gi\|189376271\|gb\|EDU94687.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC508], gi\|168801623\|... gi\|168783779, gi... - gi\|188998977\|gb\|EDU67963.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4076], gi\|168783779... gi\|188014773, gi... - gi\|188014773\|gb\|EDU52895.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4113], gi\|168751166... gi\|215264641, gi... - gi\|215486569\|ref\|YP_002329000.1\| DNA topoisomerase I [Escherichia coli O127:H6 str. E2348/69], gi\|21... gi\|13361311, gi\|... - gi\|15831100\|ref\|NP_309873.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. Sakai], gi\|13361311\|... gi\|209398456, gi... - gi\|209398456\|ref\|YP_002270328.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4115], gi\|2091... gi\|208741029, gi... - gi\|208820906\|ref\|ZP_03261226.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4042], gi\|20874... gi\|208815218, gi... - gi\|208815218\|ref\|ZP_03256397.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. EC4045], gi\|20873... gi\|13361311, gi\|... - gi\|15831100\|ref\|NP_309873.1\| DNA topoisomerase I [Escherichia coli O157:H7], gi\|13361311\|dbj\|BAB3526... gi\|254592262, gi... - gi\|254792862\|ref\|YP_003077699.1\| DNA topoisomerase I, omega subunit [Escherichia coli O157:H7 str. T... gi\|209771968, gi... - pir\|\|A85760 DNA topoisomerase type I, omega protein [imported] - Escherichia coli (strain O157:H7, s... gi\|217317792, gi... - gi\|217329353\|ref\|ZP_03445433.1\| DNA topoisomerase I [Escherichia coli O157:H7 str. TW14588], gi\|2173...	877.0	[0..1]	[865..1]
gi\|187733938, gi... - gi\|75179082\|ref\|ZP_00699100.1\| COG0550: Topoisomerase IA [Shigella boydii BS512], gi\|187733938\|ref\|Y...	877.0	[0..1]	[865..1]
gi\|74312357, gi\|... - gi\|74312357\|ref\|YP_310776.1\| DNA topoisomerase I [Shigella sonnei Ss046], gi\|73855834\|gb\|AAZ88541.1\|...	877.0	[0..1]	[865..1]
gi\|117623534, gi... - gi\|117623534\|ref\|YP_852447.1\| DNA topoisomerase I [Escherichia coli APEC O1], gi\|115512658\|gb\|ABJ007... gi\|237705299, gi... - gi\|237705299\|ref\|ZP_04535780.1\| DNA topoisomerase I [Escherichia sp. 3_2_53FAA], gi\|226900056\|gb\|EEH... gi\|110343099, gi... - gi\|110641507\|ref\|YP_669237.1\| DNA topoisomerase I [Escherichia coli 536], gi\|110343099\|gb\|ABG69336.1... gi\|91072140, gi\|... - gi\|91210566\|ref\|YP_540552.1\| DNA topoisomerase I [Escherichia coli UTI89], gi\|91072140\|gb\|ABE07021.1... gi\|26247605, gi\|... - gi\|26247605\|ref\|NP_753645.1\| DNA topoisomerase I [Escherichia coli CFT073], gi\|26108007\|gb\|AAN80207....	877.0	[0..1]	[865..15]
gi\|157081451, gi... - gi\|75190358\|ref\|ZP_00703625.1\| COG0550: Topoisomerase IA [Escherichia coli E24377A], gi\|157159421\|re...	877.0	[0..1]	[865..1]
gi\|193062532, gi... - gi\|75259384\|ref\|ZP_00730703.1\| COG0550: Topoisomerase IA [Escherichia coli E22], gi\|193062532\|ref\|ZP... gi\|194416043, gi... - gi\|75212711\|ref\|ZP_00712709.1\| COG0550: Topoisomerase IA [Escherichia coli B171], gi\|194425988\|ref\|Z...	877.0	[0..1]	[865..1]
gi\|81240781, gi\|... - gi\|82776633\|ref\|YP_402982.1\| DNA topoisomerase I [Shigella dysenteriae Sd197], gi\|81240781\|gb\|ABB614...	876.0	[0..1]	[865..1]
gi\|197362284, gi... - gi\|197362284\|ref\|YP_002141921.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Pa... gi\|56413360, gi\|... - gi\|56413360\|ref\|YP_150435.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Paraty...	875.0	[0..1]	[865..1]
gi\|62180281, gi\|... - gi\|62180281\|ref\|YP_216698.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Choler...	875.0	[0..1]	[865..1]
gi\|224468321, gi... - gi\|224583794\|ref\|YP_002637592.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Pa... gi\|197249078, gi... - gi\|197249078\|ref\|YP_002146312.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Ag... gi\|194468785, gi... - gi\|194468785\|ref\|ZP_03074769.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Ken... gi\|194407250, gi... - gi\|194448946\|ref\|YP_002045761.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar He... gi\|205343612, gi... - gi\|205343612\|gb\|EDZ30376.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Weltevr... gi\|213424431 - gi\|213424431\|ref\|ZP_03357244.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Typ... gi\|213162270 - gi\|213162270\|ref\|ZP_03347980.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Typ... gi\|200390968, gi... - gi\|200390968\|ref\|ZP_03217579.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Vir... gi\|197264502, gi... - gi\|197264502\|ref\|ZP_03164576.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Sai... TOP1_SALTY - DNA topoisomerase 1 OS=Salmonella typhimurium GN=topA PE=3 SV=1 gi\|167549779, gi... - gi\|205324910\|gb\|EDZ12749.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Saintpa... gi\|161613798, gi... - gi\|161613798\|ref\|YP_001587763.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Pa... gi\|238911894 - gi\|238911894\|ref\|ZP_04655731.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Ten... TOP1_SALTI - DNA topoisomerase 1 OS=Salmonella typhi GN=topA PE=3 SV=1 gi\|205351029, gi... - gi\|205351029\|gb\|EDZ37660.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Hadar s... TOP1_SALTY - DNA topoisomerase 1 OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=topA PE=3 SV=... gi\|168241291, gi... - gi\|205339604\|gb\|EDZ26368.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Heidelb... gi\|205335364, gi... - gi\|205335364\|gb\|EDZ22128.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Kentuck... TOP1_SALTI - DNA topoisomerase 1 OS=Salmonella typhi GN=topA PE=3 SV=1 gi\|167993767, gi... - gi\|205328261\|gb\|EDZ15025.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar 4,[5],1... gi\|29137692, gi\|... - gi\|29142063\|ref\|NP_805405.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Typhi ... TOP1_SALTY - DNA topoisomerase 1 OS=Salmonella typhimurium GN=topA PE=3 SV=1 gi\|16760166 - gi\|16760166\|ref\|NP_455783.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Typhi ... lcl\|NC_016856.1_... - [gene=topA] [protein=DNA topoisomerase I] [protein_id=YP_005237639.1] [location=complement(1820481.....	875.0	[0..1]	[865..1]

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Predicted Domain #1

Region A:
Residues: [1-586]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK  60
   61 KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA 120
  121 WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS 180
  181 PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH 240
  241 QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG 300
  301 VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN 360
  361 SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF 420
  421 RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA 480
  481 SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY 540
  541 DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1eclA
Description:	AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA topoisomerase activity	9.28485802237784	bayes_pls_golite062009
DNA topoisomerase type I activity	6.20416707013367	bayes_pls_golite062009
isomerase activity	5.61256457337998	bayes_pls_golite062009
nucleic acid binding	3.37048693883188	bayes_pls_golite062009
DNA binding	3.2732257752308	bayes_pls_golite062009
binding	3.07618319631815	bayes_pls_golite062009
catalytic activity	1.50449367975676	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [587-734]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRPNQMVLTS IDCPTCGRKM GIRTASTGVF LGCSGYALPP KERCKTTINL VPENEVLNVL  60
   61 EGEDAETNAL RAKRRCPKCG TAMDSYLIDP KRKLHVCGNN PTCDGYEIEE GEFRIKGYDG 120
  121 PIVECEKCGS EMHLKMGRFG KYMACTNE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.11
Match:	2gaiA
Description:	No description for 2gaiA was found.

Predicted Domain #3

Region A:
Residues: [735-865]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ECKNTRKILR NGEVAPPKED PVPLPELPCE KSDAYFVLRD GAAGVFLAAN TFPKSRETRA  60
   61 PLVEELYRFR DRLPEKLRYL ADAPQQDPEG NKTMVRFSRK TKQQYVSSEK DGKATGWSAF 120
  121 YVDGKWVEGK K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	19.0
Match:	1yuaA
Description:	C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA primase activity	3.07516234808151	bayes_pls_golite062009
nucleotidyltransferase activity	2.45202527906689	bayes_pls_golite062009
DNA-directed RNA polymerase activity	1.79551532005706	bayes_pls_golite062009
RNA polymerase activity	1.79551532005706	bayes_pls_golite062009
transcription regulator activity	0.977281907364794	bayes_pls_golite062009
binding	0.827218793613898	bayes_pls_golite062009
catalytic activity	0.434839928397784	bayes_pls_golite062009
nucleic acid binding	0.33473177315365	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0647934199260571	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: