YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|253326546, gi...
Organism:	Escherichia coli BL21(DE3)
Length:	928 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|253326546, gi....

Description	E-value	Query Range	Subject Range
gi\|191173870, gi... - gi\|75237829\|ref\|ZP_00721844.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|110345795, gi... - gi\|110644203\|ref\|YP_671933.1\| DNA polymerase I [Escherichia coli 536], gi\|110345795\|gb\|ABG72032.1\| D...	1002.0	[0..1]	[928..1]
gi\|81247619, gi\|... - gi\|82546208\|ref\|YP_410155.1\| DNA polymerase I [Shigella boydii Sb227], gi\|81247619\|gb\|ABB68327.1\| DN...	1001.0	[0..1]	[928..1]
gi\|194433216, gi... - gi\|83569864\|ref\|ZP_00921313.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	1000.0	[0..1]	[928..1]
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...	999.0	[0..1]	[928..1]
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...	999.0	[0..1]	[928..1]
gi\|75197739, gi\|... - gi\|75197739\|ref\|ZP_00707809.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	997.0	[0..1]	[928..1]
gi\|110617000, gi... - gi\|110807452\|ref\|YP_690972.1\| DNA polymerase I [Shigella flexneri 5 str. 8401], gi\|110617000\|gb\|ABF0...	997.0	[0..1]	[928..1]
gi\|81243110, gi\|... - gi\|82778962\|ref\|YP_405311.1\| DNA polymerase I [Shigella dysenteriae Sd197], gi\|81243110\|gb\|ABB63820....	995.0	[0..1]	[928..1]
gi\|37524397, gi\|... - gi\|37524397\|ref\|NP_927741.1\| DNA polymerase I [Photorhabdus luminescens subsp. laumondii TTO1], gi\|3...	991.0	[0..1]	[928..1]
gi\|77960492, gi\|... - gi\|77960492\|ref\|ZP_00824361.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ...	991.0	[0..1]	[928..1]

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Predicted Domain #1

Region A:
Residues: [1-316]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVQIPQNPLI LVDGSSYLYR AYHAFPPLTN SAGEPTGAMY GVLNMLRSLI MQYKPTHAAV  60
   61 VFDAKGKTFR DELFEHYKSH RPPMPDDLRA QIEPLHAMVK AMGLPLLAVS GVEADDVIGT 120
  121 LAREAEKAGR PVLISTGDKD MAQLVTPNIT LINTMTNTIL GPEEVVNKYG VPPELIIDFL 180
  181 ALMGDSSDNI PGVPGVGEKT AQALLQGLGG LDTLYAEPEK IAGLSFRGAK TMAAKLEQNK 240
  241 EVAYLSYQLA TIKTDVELEL TCEQLEVQQP AAEELLGLFK KYEFKRWTAD VEAGKWLQAK 300
  301 GAKPAAKPQE TSVADE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.30103
Match:	1ul1X
Description:	Crystal structure of the human FEN1-PCNA complex
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed DNA polymerase activity	6.33250010226773	bayes_pls_golite062009
DNA polymerase activity	6.29823284530384	bayes_pls_golite062009
nucleotidyltransferase activity	4.44991185075403	bayes_pls_golite062009
endodeoxyribonuclease activity	4.07340135619133	bayes_pls_golite062009
deoxyribonuclease activity	4.00347149381256	bayes_pls_golite062009
exonuclease activity	3.72933728353267	bayes_pls_golite062009
endonuclease activity	3.34452870782409	bayes_pls_golite062009
flap endonuclease activity	3.33299970358696	bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity	3.0212856936199	bayes_pls_golite062009
hydrolase activity	2.80884894948531	bayes_pls_golite062009
nuclease activity	2.68985366534382	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	2.66071760609476	bayes_pls_golite062009
5'-3' exonuclease activity	2.59274910747636	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	2.50398903419616	bayes_pls_golite062009
exodeoxyribonuclease activity	2.49591627688404	bayes_pls_golite062009
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	2.35681599762087	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.30898087880859	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.81733387652368	bayes_pls_golite062009
transferase activity	1.74257249090689	bayes_pls_golite062009
5'-3' exodeoxyribonuclease activity	1.57727010389968	bayes_pls_golite062009
single-stranded DNA specific endodeoxyribonuclease activity	1.4168915851726	bayes_pls_golite062009
double-stranded DNA specific exodeoxyribonuclease activity	1.37762008199118	bayes_pls_golite062009
catalytic activity	1.37534898662234	bayes_pls_golite062009
5'-flap endonuclease activity	1.1643154824625	bayes_pls_golite062009
nucleic acid binding	1.15438701346212	bayes_pls_golite062009
DNA binding	0.977616139642209	bayes_pls_golite062009
binding	0.835604503331911	bayes_pls_golite062009
damaged DNA binding	0.632303740950726	bayes_pls_golite062009
endodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.620251812982006	bayes_pls_golite062009
single-stranded DNA specific 5'-3' exodeoxyribonuclease activity	0.547465794501352	bayes_pls_golite062009
structure-specific DNA binding	0.325190032018196	bayes_pls_golite062009
protein binding	0.236485289446406	bayes_pls_golite062009
ribonuclease activity	0.00329622574140309	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [317-928]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APEVTATVIS YDNYVTILDE ETLKAWIAKL EKAPVFAFDT ETDSLDNISA NLVGLSFAIE  60
   61 PGVAAYIPVA HDYLDAPDQI SRERALELLK PLLEDEKALK VGQNLKYDRG ILANYGIELR 120
  121 GIAFDTMLES YILNSVAGRH DMDSLAERWL KHKTITFEEI AGKGKNQLTF NQIALEEAGR 180
  181 YAAEDADVTL QLHLKMWPDL QKHKGPLNVF ENIEMPLVPV LSRIERNGVK IDPKVLHNHS 240
  241 EELTLRLAEL EKKAHEIAGE EFNLSSTKQL QTILFEKQGI KPLKKTPGGA PSTSEEVLEE 300
  301 LALDYPLPKV ILEYRGLAKL KSTYTDKLPL MINPKTGRVH TSYHQAVTAT GRLSSTDPNL 360
  361 QNIPVRNEEG RRIRQAFIAP EDYVIVSADY SQIELRIMAH LSRDKGLLTA FAEGKDIHRA 420
  421 TAAEVFGLPL ETVTSEQRRS AKAINFGLIY GMSAFGLARQ LNIPRKEAQK YMDLYFERYP 480
  481 GVLEYMERTR AQAKEQGYVE TLDGRRLYLP DIKSSNGARR AAAERAAINA PMQGTAADII 540
  541 KRAMIAVDAW LQAEQPRVRM IMQVHDELVF EVHKDDVDAV AKQIHQLMEN CTRLDVPLLV 600
  601 EVGSGENWDQ AH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1dpiA
Description:	STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP
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
ribonuclease activity	2.97887080014447	bayes_pls_golite062009
exonuclease activity	2.86892175148145	bayes_pls_golite062009
nuclease activity	2.84202779131927	bayes_pls_golite062009
hydrolase activity	2.78602644579272	bayes_pls_golite062009
endonuclease activity	2.57451891632839	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.43032491532703	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
exoribonuclease activity	1.78601534260605	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	1.6669463825155	bayes_pls_golite062009
transferase activity	1.47288345517763	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
3'-5'-exoribonuclease activity	1.22355734630669	bayes_pls_golite062009
endoribonuclease activity	1.13158139596857	bayes_pls_golite062009
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	0.91511342646401	bayes_pls_golite062009
ribonuclease H activity	0.869940880547909	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
nucleic acid binding	0.251640316483416	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:

Predicted functions: