YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29142975, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	243 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|29142975, 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...	4.0E-65	[1..242]	[6..247]
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...	4.0E-65	[1..243]	[4..246]
gi\|218350409, gi... - gi\|218693677\|ref\|YP_002401344.1\| DNA polymerase III subunit epsilon [Escherichia coli 55989], gi\|218... gi\|218552790, gi... - gi\|218552790\|ref\|YP_002385703.1\| DNA polymerase III subunit epsilon [Escherichia coli IAI1], gi\|2183... gi\|209910661, gi... - gi\|209917402\|ref\|YP_002291486.1\| DNA polymerase III subunit epsilon [Escherichia coli SE11], gi\|2099... gi\|73854307, gi\|... - gi\|74310830\|ref\|YP_309249.1\| DNA polymerase III subunit epsilon [Shigella sonnei Ss046], gi\|73854307... gi\|194418956, gi... - gi\|194432694\|ref\|ZP_03064979.1\| DNA polymerase III, epsilon subunit [Shigella dysenteriae 1012], gi\|... gi\|194414304, gi... - gi\|194427534\|ref\|ZP_03060082.1\| DNA polymerase III, epsilon subunit [Escherichia coli B171], gi\|1944... gi\|192959105, gi... - gi\|193067693\|ref\|ZP_03048660.1\| DNA polymerase III, epsilon subunit [Escherichia coli E110019], gi\|1... gi\|157159676, gi... - gi\|157159676\|ref\|YP_001456994.1\| DNA polymerase III subunit epsilon [Escherichia coli HS], gi\|157065... gi\|191167032, gi... - gi\|191167032\|ref\|ZP_03028854.1\| DNA polymerase III, epsilon subunit [Escherichia coli B7A], gi\|19090... gi\|157078690, gi... - gi\|157156660\|ref\|YP_001461381.1\| DNA polymerase III subunit epsilon [Escherichia coli E24377A], gi\|1... gi\|187431096, gi... - gi\|187734104\|ref\|YP_001879012.1\| DNA polymerase III, epsilon subunit [Shigella boydii CDC 3083-94], ... gi\|82542808, gi\|... - gi\|82542808\|ref\|YP_406755.1\| DNA polymerase III subunit epsilon [Shigella boydii Sb227], gi\|81244219...	7.0E-65	[1..243]	[1..243]
gi\|75258798, gi\|... - gi\|75258798\|ref\|ZP_00730188.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75238913 - gi\|75238913\|ref\|ZP_00722895.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75229806 - gi\|75229806\|ref\|ZP_00716333.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75211233 - gi\|75211233\|ref\|ZP_00711340.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75194420 - gi\|75194420\|ref\|ZP_00704490.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75189306 - gi\|75189306\|ref\|ZP_00702573.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|75176778 - gi\|75176778\|ref\|ZP_00696894.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|83570285 - gi\|83570285\|ref\|ZP_00921731.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc...	8.0E-65	[1..243]	[4..246]
gi\|208738502, gi... - gi\|208818379\|ref\|ZP_03258699.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. E... gi\|208734611, gi... - gi\|208813334\|ref\|ZP_03254663.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. E... gi\|208729233, gi... - gi\|208809432\|ref\|ZP_03251769.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. E... gi\|189403362, gi... - gi\|189403362\|ref\|ZP_02794985.2\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. E... gi\|81239749, gi\|... - gi\|82775601\|ref\|YP_401948.1\| DNA polymerase III subunit epsilon [Shigella dysenteriae Sd197], gi\|812... gi\|209162294, gi... - gi\|209400894\|ref\|YP_002268818.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. ... gi\|168763423, gi... - gi\|189366358\|gb\|EDU84774.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC450... gi\|168757208, gi... - gi\|189355702\|gb\|EDU74121.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC440... gi\|188015573, gi... - gi\|188015573\|gb\|EDU53695.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC411... gi\|168800383, gi... - gi\|189377309\|gb\|EDU95725.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC508... gi\|168789658, gi... - gi\|189370736\|gb\|EDU89152.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC869... gi\|13359667, gi\|... - gi\|15829465\|ref\|NP_308238.1\| DNA polymerase III subunit epsilon [Escherichia coli O157:H7 str. Sakai... gi\|188999632, gi... - gi\|188999632\|gb\|EDU68618.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC407... gi\|168776181, gi... - gi\|187768434\|gb\|EDU32278.1\| DNA polymerase III, epsilon subunit [Escherichia coli O157:H7 str. EC419... gi\|254590742, gi... - gi\|254791342\|ref\|YP_003076179.1\| DNA polymerase III epsilon subunit [Escherichia coli O157:H7 str. T... gi\|13359667, gi\|... - gi\|15829465\|ref\|NP_308238.1\| DNA polymerase III subunit epsilon [Escherichia coli O157:H7], gi\|13359... gi\|209745482, gi... - pir\|\|C85506 DNA polymerase III, epsilon subunit [imported] - Escherichia coli (strain O157:H7, subst... gi\|15799891, gi\|... - gi\|15799891\|ref\|NP_285903.1\| DNA polymerase III subunit epsilon [Escherichia coli O157:H7 EDL933], g...	9.0E-65	[1..243]	[1..243]
gi\|30040009, gi\|... - gi\|30061767\|ref\|NP_835938.1\| DNA polymerase III subunit epsilon [Shigella flexneri 2a str. 2457T], g... gi\|56383177, gi\|... - gi\|56479626\|ref\|NP_706156.2\| DNA polymerase III subunit epsilon [Shigella flexneri 2a str. 301], gi\|... gi\|218547665, gi... - gi\|218547665\|ref\|YP_002381456.1\| DNA polymerase III subunit epsilon [Escherichia fergusonii ATCC 354...	9.0E-65	[1..243]	[1..243]
gi\|110804261, gi... - gi\|110804261\|ref\|YP_687782.1\| DNA polymerase III subunit epsilon [Shigella flexneri 5 str. 8401], gi...	1.0E-64	[1..243]	[4..246]
gi\|75513655 - gi\|75513655\|ref\|ZP_00736046.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|83586295 - gi\|83586295\|ref\|ZP_00924930.1\| COG0847: DNA polymerase III, epsilon subunit and related 3'-5' exonuc... gi\|169756365, gi... - gi\|170021437\|ref\|YP_001726391.1\| DNA polymerase III subunit epsilon [Escherichia coli ATCC 8739], gi... gi\|253774763, gi... - gi\|253774763\|ref\|YP_003037594.1\| DNA polymerase III, epsilon subunit [Escherichia coli BL21(DE3)], g... gi\|124500999, gi... - gi\|124527835\|ref\|ZP_01699224.1\| DNA polymerase III, epsilon subunit [Escherichia coli B], gi\|1245009...	1.0E-64	[1..243]	[4..246]
gi\|27479696 - gi\|27479696\|gb\|AAO17223.1\| DnaQ [Photorhabdus luminescens]	1.0E-64	[1..242]	[1..242]
gi\|170079846, gi... - gi\|170079846\|ref\|YP_001729166.1\| DNA polymerase III epsilon subunit [Escherichia coli str. K-12 subs... DPO3E_ECOLI, DP3... - DNA polymerase III subunit epsilon (EC 2.7.7.7) - Escherichia coli, (P03007) DNA polymerase III, eps... gi\|238899608, gi... - gi\|238899608\|ref\|YP_002925404.1\| DNA polymerase III epsilon subunit [Escherichia coli BW2952], gi\|23... EG10243 - DNA polymerase III epsilon subunit / DNA polymerase III epsilon subunit; streptomycin, azaserine res... EG10243 - DNA polymerase III epsilon subunit / DNA polymerase III epsilon subunit; streptomycin, azaserine res... gi\|4902952, gi\|8... - gi\|89107090\|ref\|AP_000870.1\| DNA polymerase III epsilon subunit [Escherichia coli str. K-12 substr. ...	1.0E-64	[1..243]	[1..243]

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Predicted Domain #1

Region A:
Residues: [1-243]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTAITRQIV LDTETTGMNQ IGAHYEGHKI IEIGAVEVIN RRLTGNNFHV YLKPDRLVDP  60
   61 EAFGVHGIAD EFLLDKPVFA DVVDEFLDYI RGAELVIHNA SFDIGFMDYE FGLLKRDIPK 120
  121 TNTFCKVTDS LALARKMFPG KRNSLDALCS RYEIDNSKRT LHGALLDAQI LAEVYLAMTG 180
  181 GQTSMTFAME GETQRQQGEA TIQRIVRQAS RLRVVFASEE ELAAHESRLD LVQKKGGSCL 240
  241 WRA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.0
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: