YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|108779485, gi...
Organism:	Yersinia pestis Antiqua
Length:	871 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|108779485, gi....

Description	E-value	Query Range	Subject Range
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	[1..871]	[1..865]
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	[1..871]	[1..865]
gi\|187733938, gi... - gi\|75179082\|ref\|ZP_00699100.1\| COG0550: Topoisomerase IA [Shigella boydii BS512], gi\|187733938\|ref\|Y...	0.0	[1..871]	[1..865]
gi\|81240781, gi\|... - gi\|82776633\|ref\|YP_402982.1\| DNA topoisomerase I [Shigella dysenteriae Sd197], gi\|81240781\|gb\|ABB614...	0.0	[1..871]	[1..865]
gi\|74312357, gi\|... - gi\|74312357\|ref\|YP_310776.1\| DNA topoisomerase I [Shigella sonnei Ss046], gi\|73855834\|gb\|AAZ88541.1\|...	0.0	[1..871]	[1..865]
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...	0.0	[1..871]	[1..865]
gi\|157081451, gi... - gi\|75190358\|ref\|ZP_00703625.1\| COG0550: Topoisomerase IA [Escherichia coli E24377A], gi\|157159421\|re...	0.0	[1..871]	[1..865]
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....	0.0	[1..871]	[15..879]
gi\|190908714, gi... - gi\|75242073\|ref\|ZP_00725867.1\| COG0550: Topoisomerase IA [Escherichia coli F11], gi\|191170982\|ref\|ZP...	0.0	[1..871]	[1..865]
gi\|30062796, gi\|... - gi\|30062796\|ref\|NP_836967.1\| DNA topoisomerase I [Shigella flexneri 2a str. 2457T], gi\|30041044\|gb\|A...	0.0	[1..871]	[1..865]

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Predicted Domain #1

Region A:
Residues: [1-590]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GSASKKSANS AEEKAKKDDK  60
   61 PKKKVKKDEK VALVNRMGVD PYHGWKAQYE ILSGKEKVVA ELKALAENAD HIYLATDLDR 120
  121 EGEAIAWHLR EVIGGDDKRF SRVVFNEITK NAIQQAFNQP GELNISRVNA QQARRFMDRV 180
  181 VGYMVSPLLW KKIARGLSAG RVQSVAVRLV VEREKEIKAF VPEEYWELHA DLVAKGDIPI 240
  241 QMEVTHAHGK PFKPVNREQT HAALTLLENA RYKVLDREDK PTSSKPSAPF ITSTLQQAAS 300
  301 TRLSFGVKKT MMMAQRLYEA GHITYMRTDS TNLSQDALTM VRGYIGDNFG DKYLPATPNQ 360
  361 YSSKENSQEA HEAIRPSDVN VLAEQLKDME ADAQRLYQLI WRQFVACQMP PAKYDSTTLT 420
  421 VQAGDFQLRA KGRTLRFDGW TKVMPALRKG DEDRTLPVIE VGSDLDLQKL IPSQHFTKPP 480
  481 ARYSEASLVK ELEKRGIGRP STYASIISTI QDRGYVRVEN RRFYAEKMGE IVTDRLEENF 540
  541 RELMNYDFTA RMESGLDQVA NDQAEWKAVL DGFFAEFSEQ LEKAEKDPEE

[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	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: [591-753]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GGMRPNQMVM TSIDCPTCGR QMGIRTASTG VFLGCSGYAL PPKERCKTTI NLVPDAEILN  60
   61 ILEGDDAETN ALRARRRCQK CGTAMDSYLI DNQRKLHVCG NNPACDGYEI EAGEFRIKGY 120
  121 EGPIVECEKC GSEMHLKMGR FGKYMGCTND ECKNTRKILR SGE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.24
Match:	2gaiA
Description:	No description for 2gaiA was found.

Predicted Domain #3

Region A:
Residues: [754-871]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VAPPKEDPVP LLELPCEKSD AYFVLRDGAA GVFLAANTFP KSRETRAPLV EELVRFKDRL  60
   61 PEKLRYLADA PVVDKEGNKT LVRFSRKTKQ QYVSSEKDGK ATGWSAFYID GKWVEAKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.69897
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	5.9540205863426	bayes_pls_golite062009
nucleotidyltransferase activity	3.28799371541043	bayes_pls_golite062009
transcription regulator activity	3.10492296137226	bayes_pls_golite062009
DNA-directed RNA polymerase activity	2.95899525707851	bayes_pls_golite062009
RNA polymerase activity	2.95899525707851	bayes_pls_golite062009
binding	2.05994835507055	bayes_pls_golite062009
nucleic acid binding	1.92096402764448	bayes_pls_golite062009
DNA binding	1.82925061950188	bayes_pls_golite062009
protein binding	0.557273506579609	bayes_pls_golite062009
transcription elongation regulator activity	0.47808023373242	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.453051411850154	bayes_pls_golite062009
catalytic activity	0.434839928397784	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.240481799431949	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: