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View Structure Prediction Details

Protein: POL1
Organism: Saccharomyces cerevisiae
Length: 1468 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 POL1.

Description E-value Query
Range		 Subject
Range
DPOLA_MOUSE - DNA polymerase alpha catalytic subunit OS=Mus musculus GN=Pola1 PE=1 SV=2
 0.0 [3..1464] [33..1459]
gi|172209 - gi|172209|gb|AAA34888.1| polymerase I
 0.0 [1..1468] [1..1468]
DPOLA_XENLA - DNA polymerase alpha catalytic subunit OS=Xenopus laevis GN=pola1 PE=1 SV=1
 0.0 [2..1463] [17..1451]
gi|8393995, gi|1... - gi|8393995|ref|NP_058633.1| polymerase (DNA-directed), alpha [Homo sapiens], pir||DJHUAC DNA-directe...
 0.0 [3..1464] [27..1456]
DPOLA_RAT - DNA polymerase alpha catalytic subunit (Fragment) OS=Rattus norvegicus GN=Pola1 PE=2 SV=1
 0.0 [3..1453] [33..1451]
DPOLA_OXYTR - DNA polymerase alpha catalytic subunit OS=Oxytricha trifallax PE=3 SV=1
 0.0 [26..1466] [20..1507]
DPOLA_STENO - DNA polymerase alpha catalytic subunit OS=Sterkiella nova PE=3 SV=1
 0.0 [29..1466] [7..1478]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 0.0 [4..1464] [17..1475]
DNApol-alpha180-PA - The gene DNA polymerase Ã?ŽÃ?± 180kD is referred to in FlyBase by the symbol Dmel\DNApol-Ã?&#1...
 0.0 [4..1464] [17..1475]

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Predicted Domain #1
Region A:
Residues: [1-338] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSKSEKLEK LRKLQAARNG TSIDDYEGDE SDGDRIYDEI DEKEYRARKR QELLHDDFVV  60
   61 DDDGVGYVDR GVEEDWREVD NSSSDEDTGN LASKDSKRKK NIKREKDHQI TDMLRTQHSK 120
  121 STLLAHAKKS QKKSIPIDNF DDILGEFESG EVEKPNILLP SKLRENLNSS PTSEFKSSIK 180
  181 RVNGNDESSH DAGISKKVKI DPDSSTDKYL EIESSPLKLQ SRKLRYANDV QDLLDDVENS 240
  241 PVVATKRQNV LQDTLLANPP SAQSLADEED DEDSDEDIIL KRRTMRSVTT TRRVNIDSRS 300
  301 NPSTSPFVTA PGTPIGIKGL TPSKSLQSNT DVATLAVN

[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 Domain #2
Region A:
Residues: [339-390] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VKKEDVVDPE TDTFQMFWLD YCEVNNTLIL FGKVKLKDDN CVSAMVQING LC

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [479-813] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SNIFESFVIQ NRIMGPCWLD IKGADFNSIR NASHCAVEVS VDKPQNITPT TTKTMPNLRC  60
   61 LSLSIQTLMN PKENKQEIVS ITLSAYRNIS LDSPIPENIK PDDLCTLVRP PQSTSFPLGL 120
  121 AALAKQKLPG RVRLFNNEKA MLSCFCAMLK VEDPDVIIGH RLQNVYLDVL AHRMHDLNIP 180
  181 TFSSIGRRLR RTWPEKFGRG NSNMNHFFIS DICSGRLICD IANEMGQSLT PKCQSWDLSE 240
  241 MYQVTCEKEH KPLDIDYQNP QYQNDVNSMT MALQENITNC MISAEVSYRI QLLTLTKQLT 300
  301 NLAGNAWAQT LGGTRAGRNE YILLHEFSRN GFIVP

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1450.0
Match: 1qhtA_
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: [391-478] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RELFFLPREG KTPTDIHEEI IPLLMDKYGL DNIRAKPQKM KYSFELPDIP SESDYLKVLL  60
   61 PYQTPKSSRD TIPSDLSSDT FYHVFGGN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [814-846] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DKEGNRSRAQ KQRQNEENAD APVNSKKAKY QGG

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [867-975] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLYPSIIQEF NICFTTVDRN KEDIDELPSV PPSEVDQGVL PRLLANLVDR RREVKKVMKT  60
   61 ETDPHKRVQC DIRQQALKLT ANSMYGCLGY VNSRFYAKPL AMLVTNKGR

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1450.0
Match: 1qhtA_
Description: Exonuclease domain of family B (archaeal and phage) DNA polymerases; T4-like DNA polymerase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
DNA primase activity 8.57378684936335 bayes_pls_golite062009
DNA-directed DNA polymerase activity 6.156872069104 bayes_pls_golite062009
DNA polymerase activity 6.10801780003354 bayes_pls_golite062009
nucleotidyltransferase activity 4.59418010473269 bayes_pls_golite062009
ribonuclease activity 2.10426652514018 bayes_pls_golite062009
exonuclease activity 1.68989335095363 bayes_pls_golite062009
nucleic acid binding 1.62213678119562 bayes_pls_golite062009
RNA polymerase activity 1.60828797652808 bayes_pls_golite062009
DNA-directed RNA polymerase activity 1.60828797652808 bayes_pls_golite062009
DNA binding 1.55767764828811 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 1.44884785815263 bayes_pls_golite062009
binding 1.23825244840872 bayes_pls_golite062009
damaged DNA binding 1.08077297289305 bayes_pls_golite062009
catalytic activity 1.04899053677564 bayes_pls_golite062009
endonuclease activity 0.991569665925888 bayes_pls_golite062009
transcription regulator activity 0.863544378011356 bayes_pls_golite062009
exoribonuclease activity 0.85780161294346 bayes_pls_golite062009
3'-5' exonuclease activity 0.78558451404229 bayes_pls_golite062009
transferase activity 0.784455099927681 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 0.78013028675591 bayes_pls_golite062009
endodeoxyribonuclease activity 0.48776342704945 bayes_pls_golite062009
structure-specific DNA binding 0.433956339585542 bayes_pls_golite062009
3'-5'-exoribonuclease activity 0.43313823287883 bayes_pls_golite062009
chromatin binding 0.382725239240319 bayes_pls_golite062009
protein binding 0.377121823388117 bayes_pls_golite062009
nuclease activity 0.332024848299731 bayes_pls_golite062009
DNA helicase activity 0.283883977748512 bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.262305398570872 bayes_pls_golite062009
single-stranded DNA binding 0.206750180223289 bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity 0.19596408995795 bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters 0.193854882336037 bayes_pls_golite062009
5'-3' exonuclease activity 0.154583332107704 bayes_pls_golite062009
transcription factor activity 0.093362945686819 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [847-866] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LVFEPEKGLH KNYVLVMDFN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [976-1069] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EILMNTRQLA ESMNLLVVYG DTDSVMIDTG CDNYADAIKI GLGFKRLVNE RYRLLEIDID  60
   61 NVFKKLLLHA KKKYAALTVN LDKNGNGTTV LEVK

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1450.0
Match: 1qhtA_
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: [1070-1299] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GLDMKRREFC PLSRDVSIHV LNTILSDKDP EEALQEVYDY LEDIRIKVET NNIRIDKYKI  60
   61 NMKLSKDPKA YPGGKNMPAV QVALRMRKAG RVVKAGSVIT FVITKQDEID NAADTPALSV 120
  121 AERAHALNEV MIKSNNLIPD PQYYLEKQIF APVERLLERI DSFNVVRLSE ALGLDSKKYF 180
  181 RREGGNNNGE DINNLQPLET TITDVERFKD TVTLELSCPS CDKRFPFGGI

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 1450.0
Match: 1qhtA_
Description: Exonuclease domain of family B (archaeal and phage) DNA polymerases; T4-like DNA polymerase
Matching Structure (courtesy of the PDB):

Predicted Domain #6
Region A:
Residues: [1300-1468] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VSSNYYRVSY NGLQCKHCEQ LFTPLQLTSQ IEHSIRAHIS LYYAGWLQCD DSTCGIVTRQ  60
   61 VSVFGKRCLN DGCTGVMRYK YSDKQLYNQL LYFDSLFDCE KNKKQELKPI YLPDDLDYPK 120
  121 EQLTESSIKA LTEQNRELME TGRSVVQKYL NDCGRRYVDM TSIFDFMLN

[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		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.259 0.956 DNA replication initiation a.4.5 "Winged helix" DNA-binding domain
View Download 0.270 0.956 DNA replication initiation b.88.1 Mss4-like
View Download 0.330 0.956 DNA replication initiation a.24.1 Apolipoprotein
View Download 0.252 0.956 DNA replication initiation f.35.1 Multidrug efflux transporter AcrB transmembrane domain
View Download 0.239 0.956 DNA replication initiation a.24.1 Apolipoprotein
View Download 0.214 0.956 DNA replication initiation a.25.1 Ferritin-like

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle