YRC Public Data Repository - Protein Structure Prediction

Protein:	exo1
Organism:	Schizosaccharomyces pombe
Length:	571 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 exo1.

Description	E-value	Query Range	Subject Range
gi\|77960492, gi\|... - gi\|77960492\|ref\|ZP_00824361.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	413.0	[0..23]	[566..6]
gi\|238790750, gi... - gi\|77972097\|ref\|ZP_00827676.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	409.0	[0..23]	[566..6]
gi\|77630910, gi\|... - gi\|77630910\|ref\|ZP_00793496.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	409.0	[0..23]	[566..6]
gi\|162351150, gi... - gi\|77633413\|ref\|ZP_00795545.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|229836126, gi... - gi\|229836126\|ref\|ZP_04456294.1\| DNA polymerase I [Yersinia pestis Pestoides A], gi\|229706574\|gb\|EEO9... gi\|45439883, gi\|... - gi\|45439883\|ref\|NP_991422.1\| DNA polymerase I [Yersinia pestis biovar Microtus str. 91001], gi\|45434... gi\|145212822, gi... - gi\|145601126\|ref\|YP_001165202.1\| DNA polymerase I [Yersinia pestis Pestoides F], gi\|145212822\|gb\|ABP... gi\|169752936, gi... - gi\|170026402\|ref\|YP_001722907.1\| DNA polymerase I [Yersinia pseudotuberculosis YPIII], gi\|169752936\|...	408.0	[0..23]	[566..6]
gi\|149290327, gi... - gi\|150260919\|ref\|ZP_01917647.1\| DNA polymerase I [Yersinia pestis CA88-4125], gi\|149290327\|gb\|EDM404... gi\|165926116, gi... - gi\|165926116\|ref\|ZP_02221948.1\| DNA polymerase I [Yersinia pestis biovar Orientalis str. F1991016], ... gi\|165989598, gi... - gi\|166011452\|ref\|ZP_02232350.1\| DNA polymerase I [Yersinia pestis biovar Antiqua str. E1979001], gi\|... gi\|166205133, gi... - gi\|166213731\|ref\|ZP_02239766.1\| DNA polymerase I [Yersinia pestis biovar Antiqua str. B42003004], gi... gi\|25288535 - pir\|\|AB0003 DNA-directed DNA polymerase (EC 2.7.7.7) [imported] - Yersinia pestis (strain CO92) gi\|218927238, gi... - gi\|218927238\|ref\|YP_002345113.1\| DNA polymerase I [Yersinia pestis CO92], gi\|16120370\|ref\|NP_403683.... gi\|21960799, gi\|... - gi\|22127682\|ref\|NP_671105.1\| DNA polymerase I [Yersinia pestis KIM], gi\|21960799\|gb\|AAM87356.1\|AE013... gi\|229690256, gi... - gi\|229841946\|ref\|ZP_04462101.1\| DNA polymerase I [Yersinia pestis biovar Orientalis str. India 195],... gi\|167048467, gi... - gi\|167402092\|ref\|ZP_02307569.1\| DNA polymerase I [Yersinia pestis biovar Antiqua str. UG05-0454], gi... gi\|229682369, gi... - gi\|229900588\|ref\|ZP_04515713.1\| DNA polymerase I [Yersinia pestis Nepal516], gi\|229682369\|gb\|EEO7846... gi\|167418727, gi... - gi\|167418727\|ref\|ZP_02310480.1\| DNA polymerase I [Yersinia pestis biovar Orientalis str. MG05-1020],... gi\|108781429, gi... - gi\|108809516\|ref\|YP_653432.1\| DNA polymerase I [Yersinia pestis Antiqua], gi\|108781429\|gb\|ABG15487.1... gi\|167427044, gi... - gi\|167427044\|ref\|ZP_02318797.1\| DNA polymerase I [Yersinia pestis biovar Mediaevalis str. K1973002],... gi\|165911860, gi... - gi\|89102783\|ref\|ZP_01175393.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	408.0	[0..23]	[566..6]
Q66GG4\|Q66GG4_YERPS - DNA polymerase A - Yersinia pseudotuberculosis gi\|186696389, gi... - gi\|186893363\|ref\|YP_001870475.1\| DNA polymerase I [Yersinia pseudotuberculosis PB1/+], gi\|186696389\|... gi\|51587658, gi\|... - gi\|51594376\|ref\|YP_068567.1\| DNA polymerase I [Yersinia pseudotuberculosis IP 32953], gi\|51587658\|em...	408.0	[0..23]	[566..6]
gi\|238726143, gi... - gi\|77976788\|ref\|ZP_00832259.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	406.0	[0..23]	[566..6]
gi\|217325868, gi... - gi\|217325868\|ref\|ZP_03441952.1\| DNA polymerase I [Escherichia coli O157:H7 str. TW14588], gi\|2173220... gi\|13364262, gi\|... - gi\|15834040\|ref\|NP_312813.1\| DNA polymerase I [Escherichia coli O157:H7 str. Sakai], gi\|13364262\|dbj... gi\|209400301, gi... - gi\|209400301\|ref\|YP_002273378.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4115], gi\|2091617... gi\|208738936, gi... - gi\|208818813\|ref\|ZP_03259133.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4042], gi\|20873893... gi\|13364262, gi\|... - gi\|15834040\|ref\|NP_312813.1\| DNA polymerase I [Escherichia coli O157:H7], gi\|13364262\|dbj\|BAB38209.1... gi\|254595254, gi... - gi\|254795854\|ref\|YP_003080691.1\| DNA polymerase I [Escherichia coli O157:H7 str. TW14359], gi\|254595... gi\|209752838, gi... - pir\|\|H86073 DNA polymerase I [similarity] - Escherichia coli (strain O157:H7, substrain EDL933), pi... gi\|254039074, gi... - gi\|254039074\|ref\|ZP_04873124.1\| DNA polymerase I [Escherichia sp. 1_1_43], gi\|226838510\|gb\|EEH70539.... gi\|15804448, gi\|... - gi\|15804448\|ref\|NP_290488.1\| DNA polymerase I [Escherichia coli O157:H7 EDL933], gi\|12518742\|gb\|AAG5... gi\|168755528, gi... - gi\|189357227\|gb\|EDU75646.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4401], gi\|168755528\|re... gi\|208733927, gi... - gi\|208812650\|ref\|ZP_03253979.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4045], gi\|20873392... gi\|208728682, gi... - gi\|208808881\|ref\|ZP_03251218.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4206], gi\|20872868... gi\|189001592, gi... - gi\|189001592\|gb\|EDU70578.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4076], gi\|168780763\|re... gi\|189362585, gi... - gi\|189362585\|gb\|EDU81004.1\| DNA polymerase I [Escherichia coli O157:H7 str. EC4486], gi\|168768145\|re...	406.0	[0..23]	[565..6]
gi\|75176751, gi\|... - gi\|75176751\|ref\|ZP_00696879.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|157080273, gi... - gi\|75188598\|ref\|ZP_00701865.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... EG10746 - 5' to 3' DNA polymerase and 3' to 5' /5' to 3' exonuclease / DNA polymerase I; required for plasmid r... gi\|194420903, gi... - gi\|83584518\|ref\|ZP_00923195.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|193068096, gi... - gi\|75238306\|ref\|ZP_00722305.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|75258154, gi\|... - gi\|75258154\|ref\|ZP_00729615.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|194430447, gi... - gi\|75208255\|ref\|ZP_00708615.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... DPO1_ECOLI - DNA polymerase I (EC 2.7.7.7) (POL I) - Escherichia coli gi\|190900509, gi... - gi\|75227237\|ref\|ZP_00714035.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|253975716, gi... - gi\|254163815\|ref\|YP_003046923.1\| DNA polymerase I [Escherichia coli B str. REL606], gi\|253975716\|gb\|... gi\|253326546, gi... - gi\|254290565\|ref\|YP_003056313.1\| DNA polymerase I [Escherichia coli BL21(DE3)], gi\|253979872\|gb\|ACT4... gi\|242379401, gi... - gi\|251787128\|ref\|YP_003001432.1\| hypothetical protein B21_03698 [Escherichia coli BL21], gi\|24237940... EG10746 - 5' to 3' DNA polymerase and 3' to 5' /5' to 3' exonuclease / DNA polymerase I; required for plasmid r... gi\|238860827, gi... - gi\|238902931\|ref\|YP_002928727.1\| DNA polymerase I [Escherichia coli BW2952], gi\|238860827\|gb\|ACR6282... gi\|85676195, gi\|... - gi\|89110164\|ref\|AP_003944.1\| fused DNA polymerase I 5'->3' exonuclease, 3'->5' polymerase and 3'->5'... gi\|169757050, gi... - gi\|170022122\|ref\|YP_001727076.1\| DNA polymerase I [Escherichia coli ATCC 8739], gi\|169757050\|gb\|ACA7... gi\|169891171, gi... - gi\|170083336\|ref\|YP_001732656.1\| DNA polymerase I [Escherichia coli str. K-12 substr. DH10B], gi\|169... gi\|124501229, gi... - gi\|124527527\|ref\|ZP_01698992.1\| DNA polymerase I [Escherichia coli B], gi\|124501229\|gb\|EAY48694.1\| D... gi\|188488957, gi... - gi\|75513987\|ref\|ZP_00736340.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|209921336, gi... - gi\|209921336\|ref\|YP_002295420.1\| DNA polymerase I [Escherichia coli SE11], gi\|209914595\|dbj\|BAG79669... gi\|74314369, gi\|... - gi\|74314369\|ref\|YP_312788.1\| DNA polymerase I [Shigella sonnei Ss046], gi\|73857846\|gb\|AAZ90553.1\| DN... gi\|218363191, gi... - gi\|218556422\|ref\|YP_002389336.1\| DNA polymerase I [Escherichia coli IAI1], gi\|218363191\|emb\|CAR00833... gi\|218697577, gi... - gi\|218697577\|ref\|YP_002405244.1\| DNA polymerase I [Escherichia coli 55989], gi\|218354309\|emb\|CAV0102...	405.0	[0..23]	[565..6]
gi\|218560939, gi... - gi\|218560939\|ref\|YP_002393852.1\| DNA polymerase I [Escherichia coli S88], gi\|218367708\|emb\|CAR05497.... gi\|91213409, gi\|... - gi\|91213409\|ref\|YP_543395.1\| DNA polymerase I [Escherichia coli UTI89], gi\|91074983\|gb\|ABE09864.1\| D... gi\|117626137, gi... - gi\|117626137\|ref\|YP_859460.1\| DNA polymerase I [Escherichia coli APEC O1], gi\|115515261\|gb\|ABJ03336.... gi\|226902830, gi... - gi\|237702893\|ref\|ZP_04533374.1\| DNA polymerase I [Escherichia sp. 3_2_53FAA], gi\|226902830\|gb\|EEH890...	405.0	[0..23]	[565..6]

Back

Predicted Domain #1

Region A:
Residues: [1-385]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGIKGLLGLL KPMQKSSHVE EFSGKTLGVD GYVWLHKAVF TCAHELAFNK ETDKYLKYAI  60
   61 HQALMLQYYG VKPLIVFDGG PLPCKASTEQ KRKERRQEAF ELGKKLWDEG KKSQAIMQFS 120
  121 RCVDVTPEMA WKLIIALREH GIESIVAPYE ADAQLVYLEK ENIIDGIITE DSDMLVFGAQ 180
  181 TVLFKMDGFG NCITIRRNDI ANAQDLNLRL PIEKLRHMAI FSGCDYTDGV AGMGLKTALR 240
  241 YLQKYPEPRA AIRAMRLDKS LKVPVSFEKE FALADLAFRH QRVYCPKDKT LVHLSPPERE 300
  301 LSVHEDAFIG SFFDNQLAID IAEGRSNPIT KCAFDIKDSS MQSFTKTTIT ISKRKGISKT 360
  361 DISNFFMKSI PPSKRPTKST SLIDV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	73.69897
Match:	1ul1X
Description:	Crystal structure of the human FEN1-PCNA complex
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	4.19173394038227	bayes_pls_golite062009
flap endonuclease activity	4.10438637013244	bayes_pls_golite062009
exonuclease activity	3.55065728618765	bayes_pls_golite062009
endonuclease activity	3.40075034200919	bayes_pls_golite062009
endodeoxyribonuclease activity	3.29138075959109	bayes_pls_golite062009
deoxyribonuclease activity	3.25110450559975	bayes_pls_golite062009
5'-3' exonuclease activity	3.19536858640519	bayes_pls_golite062009
hydrolase activity	2.92353053808585	bayes_pls_golite062009
nuclease activity	2.50181033811809	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.45364009363271	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	2.3324415860722	bayes_pls_golite062009
5'-3' exodeoxyribonuclease activity	2.26658239783943	bayes_pls_golite062009
double-stranded DNA specific exodeoxyribonuclease activity	2.09057967200253	bayes_pls_golite062009
exodeoxyribonuclease activity	2.0005433655378	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	1.9833086883205	bayes_pls_golite062009
binding	1.86985246794396	bayes_pls_golite062009
5'-flap endonuclease activity	1.81850767854435	bayes_pls_golite062009
DNA binding	1.67328600485167	bayes_pls_golite062009
nucleic acid binding	1.61574912542722	bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity	1.61167902830399	bayes_pls_golite062009
damaged DNA binding	1.42836853175021	bayes_pls_golite062009
catalytic activity	1.37534898662234	bayes_pls_golite062009
structure-specific DNA binding	1.16717206930423	bayes_pls_golite062009
single-stranded DNA specific 5'-3' exodeoxyribonuclease activity	1.15948049342759	bayes_pls_golite062009
single-stranded DNA specific endodeoxyribonuclease activity	1.10463550341524	bayes_pls_golite062009
endodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.901965019685213	bayes_pls_golite062009
protein binding	0.389020243587168	bayes_pls_golite062009
ribonuclease activity	0.198926730726347	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.176453677293411	bayes_pls_golite062009
double-stranded DNA binding	0.0978227645302046	bayes_pls_golite062009
3'-5'-exodeoxyribonuclease activity	0.0205129272358	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [386-571]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TNVKVQRTHL ANDISSEKQS IKSANEKAYV TPKSNSLKPG FGKSLSDISN SATKNENVPF  60
   61 LPPRTGVSKY FKLQKNTEKE IDEQVPSQSN NTTPTSAKSD SASPQNWFSS FSYQTPNSAS 120
  121 PPFSSLSHTL PISALAKIGH DALNRKNHAS LPSRRIVYKP PSSPSTPISM NPRPKGILSL 180
  181 QQYKFR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.0
Match:	1dpiA
Description:	STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP
Matching Structure (courtesy of the PDB):

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: