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View Structure Prediction Details

Protein: TOP3
Organism: Saccharomyces cerevisiae
Length: 656 amino acids
Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076



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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 TOP3.

Description E-value Query
Range
Subject
Range
TOP3_YEAST - DNA topoisomerase 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOP3 PE=1 SV=1
TOP3 - DNA Topoisomerase III, conserved protein that functions in a complex with Sgs1p and Rmi1p to relax s...
0.0 [1..656] [1..656]
TOP1_VIBCH - DNA topoisomerase 1 OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=topA...
gi|229343427, gi... - gi|229518738|ref|ZP_04408181.1| DNA topoisomerase I [Vibrio cholerae RC9], gi|229343427|gb|EEO08402....
gi|229607737, gi... - gi|229607737|ref|YP_002878385.1| DNA topoisomerase I [Vibrio cholerae MJ-1236], gi|229370392|gb|ACQ6...
gi|116189994, gi... - gi|75831063|ref|ZP_00760331.1| COG0550: Topoisomerase IA [Vibrio cholerae MO10], gi|254848847|ref|ZP...
gi|229511599, gi... - gi|229511599|ref|ZP_04401078.1| DNA topoisomerase I [Vibrio cholerae B33], gi|229351564|gb|EEO16505....
TOP1_VIBCH - DNA topoisomerase 1 OS=Vibrio cholerae GN=topA PE=3 SV=1
0.0 [2..643] [3..590]
gi|107102561 - gi|107102561|ref|ZP_01366479.1| hypothetical protein PaerPA_01003625 [Pseudomonas aeruginosa PACS2]
gi|218771013, gi... - gi|218890790|ref|YP_002439654.1| DNA topoisomerase I [Pseudomonas aeruginosa LESB58], gi|218771013|e...
gi|46163975, gi|... - gi|46163975|ref|ZP_00136359.2| COG0550: Topoisomerase IA [Pseudomonas aeruginosa UCBPP-PA14], gi|116...
TOP1_PSEAE - DNA topoisomerase 1 OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) ...
TOP1_PSEAE - DNA topoisomerase 1 OS=Pseudomonas aeruginosa GN=topA PE=3 SV=1
gi|126195092, gi... - gi|84326258|ref|ZP_00974286.1| COG0550: Topoisomerase IA [Pseudomonas aeruginosa 2192], gi|254241714...
gi|194546969, gi... - gi|84320177|ref|ZP_00968561.1| COG0550: Topoisomerase IA [Pseudomonas aeruginosa C3719], gi|25423598...
0.0 [2..645] [3..590]
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.....
0.0 [2..644] [3..584]
gi|194424000, gi... - gi|83587411|ref|ZP_00926039.1| COG0550: Topoisomerase IA [Escherichia coli 101-1], gi|194437017|ref|...
EG11013 - DNA topoisomerase I, omega subunit / Topoisomerase I; omega protein
TOP1_ECOLI - DNA topoisomerase 1 (EC 5.99.1.2) (DNA topoisomerase I) (Omega-protein) (Relaxing enzyme) (Untwistin...
gi|253973255, gi... - gi|254161354|ref|YP_003044462.1| DNA topoisomerase I [Escherichia coli B str. REL606], gi|253973255|...
gi|218360595, gi... - gi|218553827|ref|YP_002386740.1| DNA topoisomerase I [Escherichia coli IAI1], gi|218360595|emb|CAQ98...
gi|253324773, gi... - gi|254288162|ref|YP_003053910.1| DNA topoisomerase I [Escherichia coli BL21(DE3)], gi|253977469|gb|A...
gi|124500579, gi... - gi|124528347|ref|ZP_01699657.1| DNA topoisomerase I [Escherichia coli B], gi|124500579|gb|EAY48050.1...
gi|218351578, gi... - gi|218694846|ref|YP_002402513.1| DNA topoisomerase I [Escherichia coli 55989], gi|218351578|emb|CAU9...
gi|242377052, gi... - gi|251784779|ref|YP_002999083.1| hypothetical protein B21_01260 [Escherichia coli BL21], gi|24237705...
gi|238860844, gi... - gi|238900507|ref|YP_002926303.1| DNA topoisomerase I, omega subunit [Escherichia coli BW2952], gi|23...
EG11013 - DNA topoisomerase I, omega subunit / Topoisomerase I; omega protein
gi|75195422, gi|... - gi|75195422|ref|ZP_00705492.1| COG0550: Topoisomerase IA [Escherichia coli HS], gi|157160779|ref|YP_...
gi|191166667, gi... - gi|75230170|ref|ZP_00716671.1| COG0550: Topoisomerase IA [Escherichia coli B7A], gi|191166667|ref|ZP...
gi|193069993, gi... - gi|75235220|ref|ZP_00719457.1| COG0550: Topoisomerase IA [Escherichia coli E110019], gi|193069993|re...
gi|1742069, gi|8... - gi|89108120|ref|AP_001900.1| DNA topoisomerase I, omega subunit [Escherichia coli str. K-12 substr. ...
gi|75515114, gi|... - gi|75515114|ref|ZP_00737318.1| COG0550: Topoisomerase IA [Escherichia coli 53638], gi|188491784|ref|...
gi|82544272, gi|... - gi|82544272|ref|YP_408219.1| DNA topoisomerase I [Shigella boydii Sb227], gi|81245683|gb|ABB66391.1|...
gi|170020362, gi... - gi|170020362|ref|YP_001725316.1| DNA topoisomerase I [Escherichia coli ATCC 8739], gi|169755290|gb|A...
gi|169888786, gi... - gi|170080951|ref|YP_001730271.1| DNA topoisomerase I, omega subunit [Escherichia coli str. K-12 subs...
gi|209911772, gi... - gi|209918513|ref|YP_002292597.1| DNA topoisomerase I [Escherichia coli SE11], gi|209911772|dbj|BAG76...
0.0 [2..644] [3..584]
gi|115347926, gi... - gi|218929315|ref|YP_002347190.1| DNA topoisomerase I [Yersinia pestis CO92], gi|16122447|ref|NP_4057...
gi|165990422, gi... - gi|166010720|ref|ZP_02231618.1| DNA topoisomerase I [Yersinia pestis biovar Antiqua str. E1979001], ...
gi|108779485, gi... - gi|108807572|ref|YP_651488.1| DNA topoisomerase I [Yersinia pestis Antiqua], gi|108779485|gb|ABG1354...
gi|165938217, gi... - gi|165938217|ref|ZP_02226776.1| DNA topoisomerase I [Yersinia pestis biovar Orientalis str. IP275], ...
gi|108811848, gi... - gi|229902151|ref|ZP_04517272.1| DNA topoisomerase I, omega subunit [Yersinia pestis Nepal516], gi|22...
gi|167049839, gi... - gi|167400986|ref|ZP_02306492.1| DNA topoisomerase I [Yersinia pestis biovar Antiqua str. UG05-0454],...
gi|166208018, gi... - gi|166210838|ref|ZP_02236873.1| DNA topoisomerase I [Yersinia pestis biovar Antiqua str. B42003004],...
gi|162419163, gi... - gi|77636197|ref|ZP_00798273.1| COG0550: Topoisomerase IA [Yersinia pestis Angola], gi|162419163|ref|...
gi|167424963, gi... - gi|167424963|ref|ZP_02316716.1| DNA topoisomerase I [Yersinia pestis biovar Mediaevalis str. K197300...
gi|167420237, gi... - gi|167420237|ref|ZP_02311990.1| DNA topoisomerase I [Yersinia pestis biovar Orientalis str. MG05-102...
gi|145598214, gi... - gi|145598214|ref|YP_001162290.1| DNA topoisomerase I [Yersinia pestis Pestoides F], gi|145209910|gb|...
gi|229894904, gi... - gi|229894904|ref|ZP_04510082.1| DNA topoisomerase I, omega subunit [Yersinia pestis Pestoides A], gi...
gi|165927366, gi... - gi|165927366|ref|ZP_02223198.1| DNA topoisomerase I [Yersinia pestis biovar Orientalis str. F1991016...
gi|229693984, gi... - gi|229897647|ref|ZP_04512803.1| DNA topoisomerase I, omega subunit [Yersinia pestis biovar Orientali...
gi|229898292, gi... - gi|229898292|ref|ZP_04513439.1| DNA topoisomerase I, omega subunit [Yersinia pestis biovar Orientali...
gi|25292772 - pir||AE0270 DNA topoisomerase (EC 5.99.1.2) [imported] - Yersinia pestis (strain CO92)
gi|45441816, gi|... - gi|45441816|ref|NP_993355.1| DNA topoisomerase I [Yersinia pestis biovar Microtus str. 91001], gi|45...
gi|21958891, gi|... - gi|22125950|ref|NP_669373.1| DNA topoisomerase I [Yersinia pestis KIM], gi|21958891|gb|AAM85624.1|AE...
gi|149292275, gi... - gi|149365862|ref|ZP_01887897.1| DNA topoisomerase I [Yersinia pestis CA88-4125], gi|149292275|gb|EDM...
0.0 [2..644] [3..590]
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...
0.0 [2..644] [3..584]
gi|1127274 - gi|1127274|pdb|1ECL| Chain , Amino Terminal 67kda Domain Of Escherichia Coli Dna Topoisomerase I (...
0.0 [2..644] [3..584]
TOP3B_MOUSE - DNA topoisomerase 3-beta-1 OS=Mus musculus GN=Top3b PE=1 SV=1
0.0 [1..648] [1..606]
TOP1_PASMU - DNA topoisomerase 1 OS=Pasteurella multocida (strain Pm70) GN=topA PE=3 SV=1
TOP1_PASMU - DNA topoisomerase 1 OS=Pasteurella multocida GN=topA PE=3 SV=1
0.0 [2..639] [3..585]

Back

Predicted Domain #1
Region A:
Residues: [1-37]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKVLCVAEKN SIAKAVSQIL GGGRSTSRDS GYMYVKN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [93-174]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IMNNNQKKIA SNIKREARNA DYLMIWTDCD REGEYIGWEI WQEAKRGNRL IQNDQVYRAV  60
   61 FSHLERQHIL NAARNPSRLD MK

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 408.9897
Match: 1ecl__
Description: DNA topoisomerase I, 67K N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
DNA topoisomerase activity 10.2798831210729 bayes_pls_golite062009
DNA topoisomerase type I activity 8.04585827786358 bayes_pls_golite062009
isomerase activity 5.61256457337998 bayes_pls_golite062009
DNA binding 5.20730175008144 bayes_pls_golite062009
nucleic acid binding 4.95671919332271 bayes_pls_golite062009
binding 4.3089127577748 bayes_pls_golite062009
catalytic activity 1.50449367975676 bayes_pls_golite062009
protein binding 0.377429709958808 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [38-92]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YDFMFSGFPF ARNGANCEVT MTSVAGHLTG IDFSHDSHGW GKCAIQELFD APLNE

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [175-253]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SVHAVGTRIE IDLRAGVTFT RLLTETLRNK LRNQATMTKD GAKHRGGNKN DSQVVSYGTC  60
   61 QFPTLGFVVD RFERIRNFV

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [526-656]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APPKPMTESE LILLMDTNGI GTDATIAEHI DKIQVRNYVR SEKVGKETYL QPTTLGVSLV  60
   61 HGFEAIGLED SFAKPFQRRE MEQDLKKICE GHASKTDVVK DIVEKYRKYW HKTNACKNTL 120
  121 LQVYDRVKAS M

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 408.9897
Match: 1ecl__
Description: DNA topoisomerase I, 67K N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3
Region A:
Residues: [254-312]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PEEFWYIQLV VENKDNGGTT TFQWDRGHLF DRLSVLTFYE TCIETAGNVA QVVDLKSKP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [464-483]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QSMTLVLDWA VERFSASGLV 

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [500-525]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TTKQLPRLEM NALVDIAKAE MKAGTT

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 408.9897
Match: 1ecl__
Description: DNA topoisomerase I, 67K N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [313-463]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TTKYRPLPLT TVELQKNCAR YLRLNAKQSL DAAEKLYQKG FISYPRTETD TFPHAMDLKS  60
   61 LVEKQAQLDQ LAAGGRTAWA SYAASLLQPE NTSNNNKFKF PRSGSHDDKA HPPIHPIVSL 120
  121 GPEANVSPVE RRVYEYVARH FLACCSEDAK G

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [484-499]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VLERNFLDVY PWARWE

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 408.9897
Match: 1ecl__
Description: DNA topoisomerase I, 67K N-terminal domain
Matching Structure (courtesy of the PDB):

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle