YRC Public Data Repository - Protein Structure Prediction

Protein:	DPO3B_ECOLI, DP3...
Organism:	Escherichia coli
Length:	366 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 DPO3B_ECOLI, DP3....

Description	E-value	Query Range	Subject Range
gi\|192957464, gi... - gi\|75236425\|ref\|ZP_00720521.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Escheri...	444.0	[0..1]	[366..1]
gi\|200387477, gi... - gi\|200387477\|ref\|ZP_03214089.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|194449346, gi... - gi\|194449346\|ref\|YP_002047870.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... DPO3B_SALTY - DNA polymerase III subunit beta OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=d... gi\|194444384, gi... - gi\|194444384\|ref\|YP_002043087.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|205338833, gi... - gi\|205338833\|gb\|EDZ25597.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... lcl\|NC_016856.1_... - [gene=dnaN] [protein=DNA polymerase III subunit beta] [protein_id=YP_005240104.1] [location=compleme... DPO3B_SALTY, DP3... - DNA polymerase III subunit beta OS=Salmonella typhimurium GN=dnaN PE=3 SV=3, (P26464) DNA polymerase... DPO3B_SALTY - DNA polymerase III subunit beta OS=Salmonella typhimurium GN=dnaN PE=3 SV=3 gi\|167992431, gi... - gi\|205329442\|gb\|EDZ16206.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se...	444.0	[0..1]	[366..1]
gi\|168464832, gi... - gi\|195632425\|gb\|EDX50909.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|238913090 - gi\|238913090\|ref\|ZP_04656927.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|205344390, gi... - gi\|205344390\|gb\|EDZ31154.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|194457777, gi... - gi\|194471413\|ref\|ZP_03077397.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|197251713, gi... - gi\|197251713\|ref\|YP_002148775.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|161616955, gi... - gi\|161616955\|ref\|YP_001590920.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|167548873, gi... - gi\|205325570\|gb\|EDZ13409.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|205332539, gi... - gi\|205332539\|gb\|EDZ19303.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|168260378, gi... - gi\|205350419\|gb\|EDZ37050.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enterica se... gi\|160866979, gi... - gi\|161505632\|ref\|YP_001572744.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. arizona... gi\|224470164, gi... - gi\|224585636\|ref\|YP_002639435.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|16504793, gi\|... - gi\|25288590\|pir\|\|AB0958 DNA polymerase III beta-chain [imported] - Salmonella enterica subsp. enteri... gi\|206710866, gi... - gi\|207859063\|ref\|YP_002245714.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|29143976, gi\|... - gi\|29143976\|ref\|NP_807318.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|213648785 - gi\|213648785\|ref\|ZP_03378838.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|213865135 - gi\|213865135\|ref\|ZP_03387254.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|214001465 - gi\|214001465\|ref\|ZP_03412200.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica... gi\|62129958, gi\|... - gi\|62182325\|ref\|YP_218742.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|197364638, gi... - gi\|197364638\|ref\|YP_002144275.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric... gi\|56415710, gi\|... - gi\|56415710\|ref\|YP_152785.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|198245644, gi... - gi\|198245644\|ref\|YP_002217787.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteri... gi\|16762488 - gi\|16762488\|ref\|NP_458105.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enterica se... gi\|204928586, gi... - gi\|204928586\|ref\|ZP_03219785.1\| DNA polymerase III, beta subunit [Salmonella enterica subsp. enteric... gi\|205274357, gi... - gi\|205354576\|ref\|YP_002228377.1\| DNA polymerase III subunit beta [Salmonella enterica subsp. enteric...	444.0	[0..1]	[366..1]
gi\|30065009, gi\|... - gi\|30065009\|ref\|NP_839180.1\| DNA polymerase III subunit beta [Shigella flexneri 2a str. 2457T], gi\|3... gi\|56480410, gi\|... - gi\|56480410\|ref\|NP_709499.2\| DNA polymerase III subunit beta [Shigella flexneri 2a str. 301], gi\|563... gi\|110807609, gi... - gi\|110807609\|ref\|YP_691129.1\| DNA polymerase III subunit beta [Shigella flexneri 5 str. 8401], gi\|11...	443.0	[0..1]	[366..1]
gi\|77958160, gi\|... - gi\|77958160\|ref\|ZP_00822198.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	438.0	[0..1]	[366..1]
gi\|238797844, gi... - gi\|77961788\|ref\|ZP_00825618.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	438.0	[0..1]	[366..1]
gi\|229839803, gi... - gi\|229839803\|ref\|ZP_04459962.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Orientalis ... gi\|229841888, gi... - gi\|229841888\|ref\|ZP_04462044.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Orientalis ... gi\|21961125, gi\|... - gi\|22127980\|ref\|NP_671403.1\| DNA polymerase III subunit beta [Yersinia pestis KIM], gi\|21961125\|gb\|A... gi\|149290377, gi... - gi\|150260969\|ref\|ZP_01917697.1\| DNA polymerase III, beta subunit protein [Yersinia pestis CA88-4125]... gi\|167049049, gi... - gi\|167401667\|ref\|ZP_02307161.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Antiqua str... gi\|229896765, gi... - gi\|229896765\|ref\|ZP_04511928.1\| DNA polymerase III, beta subunit [Yersinia pestis Pestoides A], gi\|2... gi\|25288591 - pir\|\|AF0497 DNA-directed DNA polymerase (EC 2.7.7.7) [imported] - Yersinia pestis (strain CO92) gi\|166205462, gi... - gi\|166213164\|ref\|ZP_02239199.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Antiqua str... gi\|51591508, gi\|... - gi\|51598226\|ref\|YP_072417.1\| DNA polymerase III subunit beta [Yersinia pseudotuberculosis IP 32953],... gi\|167425558, gi... - gi\|167425558\|ref\|ZP_02317311.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Mediaevalis... gi\|45438597, gi\|... - gi\|45443727\|ref\|NP_995266.1\| DNA polymerase III subunit beta [Yersinia pestis biovar Microtus str. 9... gi\|167422858, gi... - gi\|167422858\|ref\|ZP_02314611.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Orientalis ... gi\|169748798, gi... - gi\|170022264\|ref\|YP_001718769.1\| DNA polymerase III subunit beta [Yersinia pseudotuberculosis YPIII]... gi\|115349684, gi... - gi\|218931073\|ref\|YP_002348948.1\| DNA polymerase III subunit beta [Yersinia pestis CO92], gi\|16124205... Q663T3\|Q663T3_YERPS - DNA polymerase III, beta subunit protein - Yersinia pseudotuberculosis gi\|167470925 - gi\|167470925\|ref\|ZP_02335629.1\| DNA polymerase III, beta subunit [Yersinia pestis FV-1] gi\|186893346, gi... - gi\|186893346\|ref\|YP_001870458.1\| DNA polymerase III subunit beta [Yersinia pseudotuberculosis PB1/+]... gi\|117675551, gi... - gi\|77630958\|ref\|ZP_00793544.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini... gi\|89105219, gi\|... - gi\|89105219\|ref\|ZP_01177742.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini... gi\|165991478, gi... - gi\|166009556\|ref\|ZP_02230454.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Antiqua str... gi\|165926167, gi... - gi\|165926167\|ref\|ZP_02221999.1\| DNA polymerase III, beta subunit [Yersinia pestis biovar Orientalis ... gi\|108782045, gi... - gi\|108810132\|ref\|YP_654048.1\| DNA polymerase III subunit beta [Yersinia pestis Antiqua], gi\|10878204... gi\|229904653, gi... - gi\|229904653\|ref\|ZP_04519764.1\| DNA polymerase III, beta subunit [Yersinia pestis Nepal516], gi\|2296... gi\|162419235, gi... - gi\|77632970\|ref\|ZP_00795132.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	435.0	[0..1]	[366..1]
gi\|77973771, gi\|... - gi\|77973771\|ref\|ZP_00829316.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	435.0	[0..1]	[366..1]
gi\|238793144, gi... - gi\|77976617\|ref\|ZP_00832096.1\| COG0592: DNA polymerase sliding clamp subunit (PCNA homolog) [Yersini...	434.0	[0..1]	[366..1]
gi\|50123358, gi\|... - gi\|50123358\|ref\|YP_052525.1\| DNA polymerase III subunit beta [Pectobacterium atrosepticum SCRI1043],...	433.0	[0..1]	[366..1]

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Predicted Domain #1

Region A:
Residues: [1-366]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV  60
   61 QPHEPGATTV PARKFFDICR GLPEGAEIAV QLEGERMLVR SGRSRFSLST LPAADFPNLD 120
  121 DWQSEVEFTL PQATMKRLIE ATQFSMAHQD VRYYLNGMLF ETEGEELRTV ATDGHRLAVC 180
  181 SMPIGQSLPS HSVIVPRKGV IELMRMLDGG DNPLRVQIGS NNIRAHVGDF IFTSKLVDGR 240
  241 FPDYRRVLPK NPDKHLEAGC DLLKQAFARA AILSNEKFRG VRLYVSENQL KITANNPEQE 300
  301 EAEEILDVTY SGAEMEIGFN VSYVLDVLNA LKCENVRMML TDSVSSVQIE DAASQSAAYV 360
  361 VMPMRL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	125.0
Match:	1mmiA
Description:	E. COLI DNA POLYMERASE BETA SUBUNIT
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed DNA polymerase activity	10.1355867012964	bayes_pls_golite062009
DNA polymerase activity	10.0862166288891	bayes_pls_golite062009
nucleotidyltransferase activity	7.50006430161592	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	3.53479307306028	bayes_pls_golite062009
transferase activity	2.88122926655527	bayes_pls_golite062009
binding	0.65029295764999	bayes_pls_golite062009
DNA polymerase processivity factor activity	0.616404933041	bayes_pls_golite062009
catalytic activity	0.48077242755678	bayes_pls_golite062009
nucleic acid binding	0.4343174930339	bayes_pls_golite062009
DNA binding	0.129085697705275	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: