YRC Public Data Repository - Protein Structure Prediction

Protein:	POL2
Organism:	Saccharomyces cerevisiae
Length:	2222 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 POL2.

Description	E-value	Query Range	Subject Range
CE17767 - DNA polymerase family B (3 domains) status:Partially_confirmed UniProt:O62218 protein_id:CAB04263.1	0.0	[33..2212]	[18..2132]
gi\|56584977, gi\|... - gi\|56584977\|gb\|AAH87613.1\| POLE protein [Homo sapiens], gi\|14043221\|gb\|AAH07599.1\|AAH07599 Unknown (...	0.0	[1489..2218]	[1..786]
gi\|6579197, gi\|1... - gi\|6579197\|gb\|AAF18240.1\|AC011438_2 T23G18.11 [Arabidopsis thaliana], gi\|15223158\|ref\|NP_172303.1\| E...	0.0	[20..2218]	[3..2263]
gi\|1045247 - gi\|1045247\|emb\|CAA63235.1\| POL2 [Saccharomyces cerevisiae]	0.0	[1..2221]	[1..2221]
gi\|5565875 - gi\|5565875\|gb\|AAD45244.1\|AF123502_1 DNA polymerase epsilon catalytic subunit [Mus musculus]	0.0	[8..2218]	[5..2273]
gi\|4102990 - gi\|4102990\|gb\|AAD01637.1\| DNA polymerase epsilon homolog [Aspergillus nidulans]	0.0	[3..2220]	[9..2203]
DPOE_SCHPO - DNA polymerase epsilon catalytic subunit A OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN... cdc20 - DNA polymerase epsilon catalytic subunit a Pol2	0.0	[3..2220]	[21..2194]

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Predicted Domain #1

Region A:
Residues: [1-100]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MMFGKKKNNG GSSTARYSAG NKYNTLSNNY ALSAQQLLNA SKIDDIDSMM GFERYVPPQY  60
   61 NGRFDAKDID QIPGRVGWLT NMHATLVSQE TLSSGSNGGG

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.225	c.47.1	Thioredoxin-like
View	Download	0.421	a.77.1	DEATH domain
View	Download	0.232	d.26.1	FKBP-like

Predicted Domain #2

Region A:
Residues: [101-136]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSNDGERVTT NQGISGVDFY FLDEEGGSFK STVVYD

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [246-534]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DVPYHVRVSI DKDIRVGKWY KVTQQGFIED TRKIAFADPV VMAFDIETTK PPLKFPDSAV  60
   61 DQIMMISYMI DGEGFLITNR EIISEDIEDF EYTPKPEYPG FFTIFNENDE VALLQRFFEH 120
  121 IRDVRPTVIS TFNGDFFDWP FIHNRSKIHG LDMFDEIGFA PDAEGEYKSS YCSHMDCFRW 180
  181 VKRDSYLPQG SQGLKAVTQS KLGYNPIELD PELMTPYAFE KPQHLSEYSV SDAVATYYLY 240
  241 MKYVHPFIFS LCTIIPLNPD ETLRKGTGTL CEMLLMVQAY QHNILLPNK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	274.0
Match:	1tgoA_
Description:	Exonuclease domain of family B (archaeal and phage) DNA polymerases; T4-like DNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [137-245]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PYFFIACNDE SRVNDVEELV KKYLESCLKS LQIIRKEDLT MDNHLLGLQK TLIKLSFVNS  60
   61 NQLFEARKLL RPILQDNANN NVQRNIYNVA ANGSEKVDAK HLIEDIREY

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [535-555]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HTDPIERFYD GHLLESETYV G

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [575-678]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KIDPSAIDEL LQELPEALKF SVEVENKSSV DKVTNFEEIK NQITQKLLEL KENNIRNELP  60
   61 LIYHVDVASM YPNIMTTNRL QPDSIKAERD CASCDFNRPG KTCA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	274.0
Match:	1tgoA_
Description:	Exonuclease domain of family B (archaeal and phage) DNA polymerases; T4-like DNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [556-574]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GHVESLEAGV FRSDLKNEF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [679-857]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RKLKWAWRGE FFPSKMDEYN MIKRALQNET FPNKNKFSKK KVLTFDELSY ADQVIHIKKR  60
   61 LTEYSRKVYH RVKVSEIVER EAIVCQRENP FYVDTVKSFR DRRYEFKGLA KTWKGNLSKI 120
  121 DPSDKHARDE AKKMIVLYDS LQLAHKVILN SFYGYVMRKG SRWYSMEMAG ITCLTGATI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	274.0
Match:	1tgoA_
Description:	Exonuclease domain of family B (archaeal and phage) DNA polymerases; T4-like DNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [858-1098]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IQMARALVER VGRPLELDTD GIWCILPKSF PETYFFTLEN GKKLYLSYPC SMLNYRVHQK  60
   61 FTNHQYQELK DPLNYIYETH SENTIFFEVD GPYKAMILPS SKEEGKGIKK RYAVFNEDGS 120
  121 LAELKGFELK RRGELQLIKN FQSDIFKVFL EGDTLEGCYS AVASVCNRWL DVLDSHGLML 180
  181 EDEDLVSLIC ENRSMSKTLK EYEGQKSTSI TTARRLGDFL GEDMVKDKGL QCKYIISSKP 240
  241 F

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.0
Match:	1b1fR_
Description:	No description for 1b1fR_ was found.

Predicted Domain #6

Region A:
Residues: [1099-1232]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NAPVTERAIP VAIFSADIPI KRSFLRRWTL DPSLEDLDIR TIIDWGYYRE RLGSAIQKII  60
   61 TIPAALQGVS NPVPRVEHPD WLKRKIATKE DKFKQTSLTK FFSKTKNVPT MGKIKDIEDL 120
  121 FEPTVEEDNA KIKI

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
DNA-directed DNA polymerase activity	10.6911520838834	bayes_pls_golite062009
DNA polymerase activity	10.645713605123	bayes_pls_golite062009
nucleotidyltransferase activity	8.39147983801981	bayes_pls_golite062009
DNA primase activity	6.94341770434315	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	4.49699229430126	bayes_pls_golite062009
endonuclease activity	4.05835176777658	bayes_pls_golite062009
endodeoxyribonuclease activity	4.04079853250282	bayes_pls_golite062009
transferase activity	3.80228208941612	bayes_pls_golite062009
DNA binding	2.64619844447089	bayes_pls_golite062009
nucleic acid binding	2.6018293992859	bayes_pls_golite062009
deoxyribonuclease activity	2.53877834217178	bayes_pls_golite062009
RNA polymerase activity	2.39159655026329	bayes_pls_golite062009
DNA-directed RNA polymerase activity	2.39159655026329	bayes_pls_golite062009
transcription regulator activity	2.22832306273638	bayes_pls_golite062009
ribonuclease activity	2.21640837000075	bayes_pls_golite062009
binding	1.84871443682239	bayes_pls_golite062009
exonuclease activity	1.38951646742998	bayes_pls_golite062009
transcription factor activity	1.18792852183348	bayes_pls_golite062009
exoribonuclease activity	0.985835839433199	bayes_pls_golite062009
catalytic activity	0.985794797454925	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.91438167081716	bayes_pls_golite062009
damaged DNA binding	0.903519456111979	bayes_pls_golite062009
mismatch repair complex binding	0.893434681603753	bayes_pls_golite062009
chromatin binding	0.891218870764102	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.589620648556852	bayes_pls_golite062009
structure-specific DNA binding	0.431057665208185	bayes_pls_golite062009
3'-5' exonuclease activity	0.427833022898625	bayes_pls_golite062009
MutLalpha complex binding	0.419053137349237	bayes_pls_golite062009
protein binding	0.366887851366715	bayes_pls_golite062009
	0.300511724300705	bayes_pls_golite062009
DNA helicase activity	0.280008381637593	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	0.244405458380391	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.213302068277253	bayes_pls_golite062009
single-stranded DNA binding	0.170862363182338	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.152950127352174	bayes_pls_golite062009
nuclease activity	0.126991239633667	bayes_pls_golite062009
transcription activator activity	0.0924765766526223	bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity	0.024241485627603	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [1233-1924]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ARTTKKKAVS KRKRNQLTNE EDPLVLPSEI PSMDEDYVGW LNYQKIKWKI QARDRKRRDQ  60
   61 LFGNTNSSRE RSALGSMIRK QAESYANSTW EVLQYKDSGE PGVLEVFVTI NGKVQNITFH 120
  121 IPKTIYMKFK SQTMPLQKIK NCLIEKSSAS LPNNPKTSNP AGGQLFKITL PESVFLEEKE 180
  181 NCTSIFNDEN VLGVFEGTIT PHQRAIMDLG ASVTFRSKAM GALGKGIQQG FEMKDLSMAE 240
  241 NERYLSGFSM DIGYLLHFPT SIGYEFFSLF KSWGDTITIL VLKPSNQAQE INASSLGQIY 300
  301 KQMFEKKKGK IETYSYLVDI KEDINFEFVY FTDISKLYRR LSQETTKLKE ERGLQFLLLL 360
  361 QSPFITKLLG TIRLLNQMPI VKLSLNEVLL PQLNWQPTLL KKLVNHVLSS GSWISHLIKL 420
  421 SQYSNIPICN LRLDSMDYII DVLYARKLKK ENIVLWWNEK APLPDHGGIQ NDFDLNTSWI 480
  481 MNDSEFPKIN NSGVYDNVVL DVGVDNLTVN TILTSALIND AEGSDLVNNN MGIDDKDAVI 540
  541 NSPSEFVHDA FSNDALNVLR GMLKEWWDEA LKENSTADLL VNSLASWVQN PNAKLFDGLL 600
  601 RYHVHNLTKK ALLQLVNEFS ALGSTIVYAD RNQILIKTNK YSPENCYAYS QYMMKAVRTN 660
  661 PMFSYLDLNI KRYWDLLIWM DKFNFSGLAC IE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #8

Region A:
Residues: [1925-2222]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IEEKENQDYT AVSQWQLKKF LSPIYQPEFE DWMMIILDSM LKTKQSYLKL NSGTQRPTQI  60
   61 VNVKKQDKED SVENSLNGFS HLFSKPLMKR VKKLFKNQQE FILDPQYEAD YVIPVLPGSH 120
  121 LNVKNPLLEL VKSLCHVMLL SKSTILEIRT LRKELLKIFE LREFAKVAEF KDPSLSLVVP 180
  181 DFLCEYCFFI SDIDFCKAAP ESIFSCVRCH KAFNQVLLQE HLIQKLRSDI ESYLIQDLRC 240
  241 SRCHKVKRDY MSAHCPCAGA WEGTLPRESI VQKLNVFKQV AKYYGFDILL SCIADLTI

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

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: