YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24348771, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	878 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|24348771, gi|....

Description	E-value	Query Range	Subject Range
gi\|117612508, gi... - gi\|78685718\|ref\|ZP_00850494.1\| DNA topoisomerase I [Shewanella sp. ANA-3], gi\|78506605\|gb\|EAP20122.1...	1096.0	[0..1]	[878..17]
gi\|78691714, gi\|... - gi\|78691714\|ref\|ZP_00856314.1\| DNA topoisomerase I [Shewanella sp. MR-7], gi\|78508892\|gb\|EAP22314.1\|...	1092.0	[0..1]	[878..17]
gi\|82495974, gi\|... - gi\|82495974\|ref\|ZP_00881546.1\| DNA topoisomerase I [Shewanella sp. MR-4], gi\|82406015\|gb\|EAP46683.1\|...	1091.0	[0..1]	[878..17]
gi\|82740584, gi\|... - gi\|82740584\|ref\|ZP_00903322.1\| DNA topoisomerase I [Shewanella sp. W3-18-1], gi\|82722058\|gb\|EAP56886...	1081.0	[0..1]	[878..1]
gi\|77809197, gi\|... - gi\|77815842\|ref\|ZP_00815059.1\| DNA topoisomerase I [Shewanella putrefaciens CN-32], gi\|77809197\|gb\|E...	1081.0	[0..1]	[878..1]
gi\|160861243, gi... - gi\|160875721\|ref\|YP_001555037.1\| DNA topoisomerase I [Shewanella baltica OS195], gi\|160861243\|gb\|ABX... gi\|146863151, gi... - gi\|217973032\|ref\|YP_002357783.1\| DNA topoisomerase I [Shewanella baltica OS223], gi\|217498167\|gb\|ACK... gi\|151365626, gi... - gi\|153001008\|ref\|YP_001366689.1\| DNA topoisomerase I [Shewanella baltica OS185], gi\|151365626\|gb\|ABS...	1076.0	[0..1]	[878..1]
gi\|68520200, gi\|... - gi\|68542128\|ref\|ZP_00581864.1\| DNA topoisomerase I [Shewanella baltica OS155], gi\|68520200\|gb\|EAN437...	1074.0	[0..1]	[878..1]
gi\|91715682, gi\|... - gi\|91793680\|ref\|YP_563331.1\| DNA topoisomerase I [Shewanella denitrificans OS217], gi\|91715682\|gb\|AB...	1069.0	[0..1]	[877..17]
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...	1064.0	[0..1]	[872..1]
gi\|74312357, gi\|... - gi\|74312357\|ref\|YP_310776.1\| DNA topoisomerase I [Shigella sonnei Ss046], gi\|73855834\|gb\|AAZ88541.1\|...	1064.0	[0..1]	[872..1]

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Predicted Domain #1

Region A:
Residues: [1-604]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKSLVIVES PAKAKTINKY LGKEFIVKSS VGHIRDLPTS SISDGTEKVK SAAEVKKMSP  60
   61 EEKARYKKVK DHQALVSRMG VNPEKGWAAK YQILPGKEKV VKELQALADS ADQIYLATDL 120
  121 DREGEAIAWH LQEVIGGDPS RYQRVVFNEI TKSAIQEAFS KPASLDTNMV NAQQARRFLD 180
  181 RVVGFMVSPL LWKKVARGLS AGRVQSVAVR LVVERESEIK AFVPEEFWDV HAQLNTPSSE 240
  241 ALRMEVVKYL DSAFEPTNEQ QALAAVQALS SASFKVIARE DKATQSKPSA PFITSTLQQA 300
  301 ASTRLGFGVK KTMMMAQRLY EAGHITYMRT DSTNLSQEAL DSVREMIGKE YGAKYLPAEP 360
  361 IRYGSKEGAQ EAHEAIRPSN VKVEAAALTD MERDAQRLYE LIWRQFVSCQ MTPALYDATK 420
  421 LTVKAADYEL KATGRILRFD GWTRVQTAIK KKNEEDNTLP AVNEGDVLSL VELEPKQHFT 480
  481 KPPARYSEAS LVKELEKRGI GRPSTYATII STIQERGYVK VENRRFYAEK MGEIVSERLV 540
  541 NSFAELMSYD FTASMEQTLD DVAKGELDWK KVLDGFYADF TKQLEKAELA PEEGGMRLNQ 600
  601 MVMT

[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: [605-751]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIKCPTCGRP MGIRTGTTGV FLGCSGYELP PKERCKTTMN LTPGIEAISD SEDAETDALR  60
   61 AKHRCGICGT AMDSYLLDEK RKLHVCGNNP VCEGYEVEEG QFKIKGYEGP LIECDRCGHD 120
  121 MELKNGRFGK YFGCTNEECK NTRKLLK

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.28
Match:	2gaiA
Description:	No description for 2gaiA was found.

Predicted Domain #3

Region A:
Residues: [752-878]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NGEAAPPKED PIYLPELKCS KSDAHFVLRD GAAGIFLAAS TFPKSRETRA PLVEELVKYR  60
   61 EFLWPKYQYL ADAPIADDDG NKAVVKFSRK TKDQYVATEV DGKATGWSAH YVNGKWVSES 120
  121 SAKKAKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.0
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: