YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24372755, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	343 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|24372755, gi|....

Description	E-value	Query Range	Subject Range
gi\|148549873, gi... - gi\|82738217\|ref\|ZP_00901054.1\| DNA polymerase III, delta subunit [Pseudomonas putida F1], gi\|8271471...	214.0	[0..1]	[339..1]
tr\|I7C2C3\|I7C2C3... - DNA polymerase III subunit delta OS=Pseudomonas putida (strain DOT-T1E) GN=holA PE=4 SV=1 gi\|26991476, gi\|... - gi\|26991476\|ref\|NP_746901.1\| DNA polymerase III subunit delta [Pseudomonas putida KT2440], gi\|249865...	214.0	[0..1]	[339..1]
gi\|83577716, gi\|... - gi\|83594802\|ref\|YP_428554.1\| DNA polymerase III subunits gamma and tau [Rhodospirillum rubrum ATCC 1...	213.0	[0..14]	[339..71]
gi\|23016072 - gi\|23016072\|ref\|ZP_00055832.1\| COG2812: DNA polymerase III, gamma/tau subunits [Magnetospirillum mag...	212.0	[0..8]	[343..35]
gi\|67157250, gi\|... - gi\|67157250\|ref\|ZP_00418552.1\| DNA-directed DNA polymerase [Azotobacter vinelandii AvOP], gi\|6708551... gi\|67157250\|ref\|... - DNA-directed DNA polymerase [Azotobacter vinelandii AvOP]	212.0	[0..6]	[329..54]
gi\|66963325, gi\|... - gi\|66963325\|ref\|ZP_00410897.1\| DNA-directed DNA polymerase [Arthrobacter sp. FB24], gi\|66870985\|gb\|E...	212.0	[0..7]	[340..32]
gi\|71734194, gi\|... - gi\|71734194\|ref\|YP_274019.1\| DNA polymerase III subunits gamma and tau [Pseudomonas syringae pv. pha...	211.0	[0..6]	[329..26]
gi\|251837787, gi... - gi\|253572655\|ref\|ZP_04850056.1\| DNA polymerase III subunit gamma/tau [Bacteroides sp. 1_1_6], gi\|251... gi\|29347020, gi\|... - gi\|29347020\|ref\|NP_810523.1\| DNA polymerase III subunit gamma/tau [Bacteroides thetaiotaomicron VPI-...	211.0	[0..8]	[334..29]
gi\|95112743 - gi\|95112743\|emb\|CAK17471.1\| DNA polymerase III, delta subunit, probably ATP hydrolase [Pseudomonas e... gi\|104783756, gi... - gi\|95112743\|emb\|CAK17471.1\| DNA polymerase III, delta subunit, probably ATP hydrolase [Pseudomonas e...	211.0	[0..1]	[339..1]
gi\|53714518, gi\|... - gi\|53714518\|ref\|YP_100510.1\| DNA polymerase III subunit gamma/tau [Bacteroides fragilis YCH46], gi\|5...	211.0	[0..8]	[333..29]

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Predicted Domain #1

Region A:
Residues: [1-343]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRVYPDQLSR HLNPLHACYL IFGDDPWLLE TSKDQIRQAA KRQGFEERVQ LIQETGFNWG  60
   61 DLTQEWQAMS LFSSRRIIEL TLPSAKPGAD GSAALQSLLQ TPSPDVLLIL EGPKLASEQT 120
  121 NSKWFKTLDS LGIYLPCTTP EGDQFRRWLD SRIAHFKLNL QPDARAMLYS LYEGNLLAAD 180
  181 QAMQLLQLLS PSKPIGADEL SHYFEDQSRF TVFQLTDALL NNRQDSAQHM LAQLNGEGTA 240
  241 MPILLWALFK ELQLLLSLKS EQAQGSPLNS LFGKHRIWDK RKPLYQTALQ RLSLAQIEHM 300
  301 LAFASKLELN LKQLGHEDWT GLSHLCLLFD PKAHSHLAHI NLD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	44.69897
Match:	1jqjC
Description:	delta subunit; delta subunit of DNA polymerase III, N-domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed DNA polymerase activity	6.09279996112705	bayes_pls_golite062009
DNA polymerase activity	6.04865791514294	bayes_pls_golite062009
nucleotidyltransferase activity	3.99580940620614	bayes_pls_golite062009
DNA clamp loader activity	3.94645534451735	bayes_pls_golite062009
protein-DNA loading ATPase activity	3.91355858456767	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
pyrophosphatase activity	2.23646936731119	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.77451606086272	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
nucleic acid binding	1.49633029954726	bayes_pls_golite062009
catalytic activity	1.32370671504792	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2537888487362	bayes_pls_golite062009
transferase activity	1.23626141560528	bayes_pls_golite062009
binding	1.23424453635646	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
DNA binding	0.967303417236485	bayes_pls_golite062009
structure-specific DNA binding	0.782430219754236	bayes_pls_golite062009
transcription regulator activity	0.748437190903548	bayes_pls_golite062009
double-stranded DNA binding	0.6071273686445	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.248432446853676	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.217252531553173	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.215962398124297	bayes_pls_golite062009
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
3'-5' DNA helicase activity	0.0769112340058804	bayes_pls_golite062009
ATPase activity	0.0740243885501273	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: