YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229841013, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	254 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|229841013, gi....

Description	E-value	Query Range	Subject Range
gi\|238794443, gi... - gi\|77977838\|ref\|ZP_00833277.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc...	7.0E-67	[1..254]	[6..259]
gi\|77957728, gi\|... - gi\|77957728\|ref\|ZP_00821776.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc...	1.0E-65	[1..254]	[6..259]
gi\|77960261, gi\|... - gi\|77960261\|ref\|ZP_00824142.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc...	2.0E-65	[1..254]	[6..259]
gi\|238721802, gi... - gi\|77973124\|ref\|ZP_00828676.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc...	3.0E-65	[1..254]	[6..259]
gi\|27479696 - gi\|27479696\|gb\|AAO17223.1\| DnaQ [Photorhabdus luminescens]	7.0E-64	[1..246]	[1..246]
gi\|36784361, gi\|... - gi\|37524935\|ref\|NP_928279.1\| DNA polymerase III subunit epsilon [Photorhabdus luminescens subsp. lau...	5.0E-63	[1..243]	[1..243]
gi\|207855776, gi... - gi\|207855776\|ref\|YP_002242427.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. ente... gi\|205271376, gi... - gi\|205351595\|ref\|YP_002225396.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. ente... gi\|16759250 - gi\|16759250\|ref\|NP_454867.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. enterica... gi\|197095021, gi... - gi\|197363544\|ref\|YP_002143181.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. ente... DPO3E_SALTY - DNA polymerase III subunit epsilon OS=Salmonella typhimurium GN=dnaQ PE=3 SV=1 gi\|56414616, gi\|... - gi\|56414616\|ref\|YP_151691.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. enterica... lcl\|NC_016856.1_... - [gene=dnaQ] [protein=DNA polymerase III subunit epsilon] [protein_id=YP_005235932.1] [location=30410... DPO3E_SALTY - DNA polymerase III subunit epsilon OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) G... gi\|29142975, gi\|... - gi\|29142975\|ref\|NP_806317.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. enterica... DPO3E_SALTI - DNA polymerase III subunit epsilon OS=Salmonella typhi GN=dnaQ PE=3 SV=1 DP3E_SALTY, DPO3... - DNA polymerase III subunit epsilon OS=Salmonella typhimurium GN=dnaQ PE=3 SV=1, (P14566) DNA polymer... DPO3E_SALTI - DNA polymerase III subunit epsilon OS=Salmonella typhi GN=dnaQ PE=3 SV=1	1.0E-62	[1..242]	[1..242]
gi\|26106556, gi\|... - gi\|26246159\|ref\|NP_752198.1\| DNA polymerase III subunit epsilon [Escherichia coli CFT073], gi\|261065... gi\|91070857, gi\|... - gi\|91209283\|ref\|YP_539269.1\| DNA polymerase III subunit epsilon [Escherichia coli UTI89], gi\|9107085... gi\|117622497, gi... - gi\|117622497\|ref\|YP_851410.1\| DNA polymerase III subunit epsilon [Escherichia coli APEC O1], gi\|1155... gi\|227838235, gi... - gi\|227884794\|ref\|ZP_04002599.1\| DNA polymerase III subunit epsilon [Escherichia coli 83972], gi\|2278... gi\|226899002, gi... - gi\|237707792\|ref\|ZP_04538273.1\| DNA polymerase subunit III epsilon [Escherichia sp. 3_2_53FAA], gi\|2...	1.0E-62	[1..242]	[4..245]
gi\|75241725 - gi\|75241725\|ref\|ZP_00725562.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|110640430, gi... - gi\|110640430\|ref\|YP_668158.1\| DNA polymerase III subunit epsilon [Escherichia coli 536], gi\|11034202...	1.0E-62	[1..242]	[4..245]
gi\|224582105, gi... - gi\|224582105\|ref\|YP_002635903.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. ente... gi\|62126463, gi\|... - gi\|62178830\|ref\|YP_215247.1\| DNA polymerase III subunit epsilon [Salmonella enterica subsp. enterica...	2.0E-62	[1..242]	[4..245]

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Predicted Domain #1

Region A:
Residues: [1-254]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIITPTRQIV LDTETTGMNK LGVHYEGHRI IEIGAVEVIN RRLTGRNFHV YVKPDRLVDP  60
   61 EAYGVHGISD EFLADKPTFA DITPEFLDFI RGAELVIHNA AFDIGFMDYE FRMLQQDIPK 120
  121 TETFCTITDS LLMARRLFPG KRNNLDALCD RYQIDNTKRT LHGALLDAEI LAEVYLAMTG 180
  181 GQTSLTFSME GEVSQNNASE DIQRITRPAS ALKIIYATED ELANHESRLD FVMKKGGSCL 240
  241 WRMPLEAEEE TKAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.69897
Match:	1j53A
Description:	N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA polymerase activity	7.87431862983329	bayes_pls_golite062009
DNA-directed DNA polymerase activity	7.78411937387917	bayes_pls_golite062009
nucleotidyltransferase activity	5.3880945520411	bayes_pls_golite062009
exonuclease activity	2.86892175148145	bayes_pls_golite062009
nuclease activity	2.84202779131927	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	1.94077739152313	bayes_pls_golite062009
deoxyribonuclease activity	1.87431870698721	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.87430802282815	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.75713164321634	bayes_pls_golite062009
transferase activity	1.47288345517763	bayes_pls_golite062009
ribonuclease activity	1.41871623152578	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
endonuclease activity	0.935348031740788	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.782108781904855	bayes_pls_golite062009
exodeoxyribonuclease activity	0.77421125364834	bayes_pls_golite062009
3'-5' exonuclease activity	0.64268174969672	bayes_pls_golite062009
endodeoxyribonuclease activity	0.48776342704945	bayes_pls_golite062009
exoribonuclease activity	0.26279899872348	bayes_pls_golite062009
nucleic acid binding	0.251640316483416	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.18445559832317	bayes_pls_golite062009
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	0.1355017328177	bayes_pls_golite062009
binding	0.122249780594036	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: