YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29137692, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
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|29137692, 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..865]	[1..865]
gi\|187733938, gi... - gi\|75179082\|ref\|ZP_00699100.1\| COG0550: Topoisomerase IA [Shigella boydii BS512], gi\|187733938\|ref\|Y...	0.0	[1..865]	[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..865]	[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..865]	[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..865]	[15..879]
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...	0.0	[1..865]	[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..865]	[1..865]
gi\|62180281, gi\|... - gi\|62180281\|ref\|YP_216698.1\| DNA topoisomerase I [Salmonella enterica subsp. enterica serovar Choler...	0.0	[1..865]	[1..865]
gi\|190908714, gi... - gi\|75242073\|ref\|ZP_00725867.1\| COG0550: Topoisomerase IA [Escherichia coli F11], gi\|191170982\|ref\|ZP...	0.0	[1..865]	[1..865]
gi\|157081451, gi... - gi\|75190358\|ref\|ZP_00703625.1\| COG0550: Topoisomerase IA [Escherichia coli E24377A], gi\|157159421\|re...	0.0	[1..865]	[1..865]

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Predicted Domain #1

Region A:
Residues: [1-589]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK  60
   61 KDERGALVNR MGVDPWHNWD AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA 120
  121 WHLREVIGGD DARYSRVVFN EITKNAIRQA FEQPGELNIN RVNAQQARRF MDRVVGYMVS 180
  181 PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EIDANTTTPS GEALPLQVTH 240
  241 QNDKPFRPVN REQTLAAVSL LEKARYSVLE REDKPTSSKP GAPFITSTLQ QAASTRLGFG 300
  301 VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIG DNFGKKYLPD NPNQYASKEN 360
  361 SQEAHEAIRP SDVAVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAQYDS TTLTVGAGEF 420
  421 RLKARGRILR FDGWTKVMPA LRKGDEDRTL PAVNKGDALT LLELTPAQHF TKPPARFSEA 480
  481 SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY 540
  541 DFTAQMEDSL DQVANHQAEW KAVLDNFFSD FTQQLDKAEK DPEEGGMRP

[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: [590-667]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NQMVLTSIDC PTCGRKMGIR TASTGVFLGC SGYALSPKER CKTTINLVPE NEVLNVLEGD  60
   61 DAETNALRAK RRCQKCGT

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.8
Match:	2gaiA
Description:	No description for 2gaiA was found.

Predicted Domain #3

Region A:
Residues: [668-735]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AMDSYLIDPK RKLHVCGNNP TCDGYEIEEG EFRIKGYDGP IVECEKCGSE MHLKMGRFGK  60
   61 YMACTNDE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11.045757
Match:	2yt9A
Description:	No description for 2yt9A was found.

Predicted Domain #4

Region A:
Residues: [736-865]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CKNTRKILRN GEVAPPKEDP VPLPELPCEK SDAYFVLRDG AAGIFLAANT FPKSRETRAP  60
   61 LVEELYRFRD RLPEKLRYLA DAPQQDPEGN KTVVRFSRKT KQQYVAAEKD GKATGWSAFF 120
  121 VDGKWVEGKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.154902
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: