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View Structure Prediction Details

Protein: RAD2
Organism: Saccharomyces cerevisiae
Length: 1031 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 RAD2.

Description E-value Query
Range		 Subject
Range
RAD2 - Single-stranded DNA endonuclease, cleaves single-stranded DNA during nucleotide excision repair to e...
RAD2_YEAST - DNA repair protein RAD2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD2 PE=1 SV=2
 0.0 [1..1031] [1..1031]
ERCC5_XENLA - DNA repair protein complementing XP-G cells homolog OS=Xenopus laevis GN=ercc5 PE=2 SV=1
 0.0 [1..1030] [1..1057]
ERCC5_MOUSE, XPG... - (P35689) DNA-repair protein complementing XP-G cells homolog (Xeroderma pigmentosum group G compleme...
 0.0 [1..1030] [1..1026]
ERCC5 - excision repair cross-complementing rodent repair deficiency, complementation group 5
 0.0 [1..1030] [1..1027]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 0.0 [1..1030] [1..1027]
rad13 - DNA repair nuclease Rad13
RAD13_SCHPO - DNA repair protein rad13 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad13 PE=2 SV=2
 0.0 [1..1027] [1..1018]
gi|5712619 - gi|5712619|gb|AAD47568.1|AF125578_1 DNA repair endonuclease [Drosophila melanogaster]
 0.0 [1..1026] [1..1123]

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Predicted Domain #1
Region A:
Residues: [1-195] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGVHSFWDIA GPTARPVRLE SLEDKRMAVD ASIWIYQFLK AVRDQEGNAV KNSHITGFFR  60
   61 RICKLLYFGI RPVFVFDGGV PVLKRETIRQ RKERRQGKRE SAKSTARKLL ALQLQNGSND 120
  121 NVKNSTPSSG SSVQIFKPQD EWDLPDIPGF KYDKEDARVN SNKTFEKLMN SINGDGLEDI 180
  181 DLDTINPASA EFEEL

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 12.55
Match: 1bgxT
Description: 5' to 3' exonuclease domain of DNA polymerase Taq; Exonuclease domain of prokaryotic DNA polymerase; DNA polymerase I (Klenow fragment)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
single-stranded DNA specific endodeoxyribonuclease activity 8.219187336366 bayes_pls_golite062009
endodeoxyribonuclease activity 7.26787266873051 bayes_pls_golite062009
deoxyribonuclease activity 6.75316483671775 bayes_pls_golite062009
endonuclease activity 6.39053146471031 bayes_pls_golite062009
exonuclease activity 3.46607201774246 bayes_pls_golite062009
flap endonuclease activity 3.35117165021395 bayes_pls_golite062009
DNA binding 2.74395891269151 bayes_pls_golite062009
hydrolase activity 2.60874360745066 bayes_pls_golite062009
binding 2.58539672241253 bayes_pls_golite062009
nucleic acid binding 2.54722210455433 bayes_pls_golite062009
5'-3' exonuclease activity 2.50129811584994 bayes_pls_golite062009
nuclease activity 2.49612885073648 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 2.20867470281829 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 2.11221521670814 bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters 2.01491211227289 bayes_pls_golite062009
exodeoxyribonuclease activity 2.00804590500192 bayes_pls_golite062009
damaged DNA binding 1.82833131243547 bayes_pls_golite062009
5'-3' exodeoxyribonuclease activity 1.59902329953921 bayes_pls_golite062009
structure-specific DNA binding 1.57088273902548 bayes_pls_golite062009
double-stranded DNA specific exodeoxyribonuclease activity 1.46817649825808 bayes_pls_golite062009
catalytic activity 1.27951740231695 bayes_pls_golite062009
5'-flap endonuclease activity 1.13738790511505 bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity 1.06918533266108 bayes_pls_golite062009
double-stranded DNA binding 0.550147498650064 bayes_pls_golite062009
single-stranded DNA specific 5'-3' exodeoxyribonuclease activity 0.496731274592508 bayes_pls_golite062009
endodeoxyribonuclease activity, producing 5'-phosphomonoesters 0.330551387282259 bayes_pls_golite062009
protein binding 0.235717056815183 bayes_pls_golite062009
3'-5' exonuclease activity 0.175191448555725 bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.0756835782024594 bayes_pls_golite062009
DNA-directed DNA polymerase activity 0.00167240601151697 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [196-647] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PKATQYLILS SLRLKSRLRM GYSKEQLETI FPNSMDFSRF QIDMVKRRNF FTQKLINTTG  60
   61 FQDGGASKLN EEVINRISGQ KSKEYKLTKT NNGWILGLGA NDGSDAQKAI VIDDKDAGAL 120
  121 VKQLDSNAED GDVLRWDDLE DNSLKIVRHE SSNATTAPQK RSNRSEDEGC DSDECEWEEV 180
  181 ELKPKNVKFV EDFSLKAARL PYMGQSLNNA GSKSFLDKRH DQASPSKTTP TMRISRISVE 240
  241 DDDEDYLKQI EEIEMMEAVQ LSKMEKKPEA DDKSKIAKPV TSKGTEARPP IVQYGLLGAQ 300
  301 PDSKQPYHVT NLNSKSESVI KRTSKTVLSE FRPPSQQEDK GAILTEGEQN LNFISHKIPQ 360
  361 FDFNNENSLL FQKNTESNVS QEATKEKSPI PEMPSWFSST ASQQLYNPYN TTNFVEDKNV 420
  421 RNEQESGAET TNKGSSYELL TGLNATEILE RE

[Run NCBI BLAST on this sequence.]

Detection Method: MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3
Region A:
Residues: [648-1031] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SEKESSNDEN KDDDLEVLSE ELFEDVPTKS QISKEAEDND SRKVESINKE HRKPLIFDYD  60
   61 FSEDEEDNIV ENMIKEQEEF DTFKNTTLST SAERNVAENA FVEDELFEQQ MKDKRDSDEV 120
  121 TMDMIKEVQE LLSRFGIPYI TAPMEAEAQC AELLQLNLVD GIITDDSDVF LFGGTKIYKN 180
  181 MFHEKNYVEF YDAESILKLL GLDRKNMIEL AQLLGSDYTN GLKGMGPVSS IEVIAEFGNL 240
  241 KNFKDWYNNG QFDKRKQETE NKFEKDLRKK LVNNEIILDD DFPSVMVYDA YMRPEVDHDT 300
  301 TPFVWGVPDL DMLRSFMKTQ LGWPHEKSDE ILIPLIRDVN KRKKKGKQKR INEFFPREYI 360
  361 SGDKKLNTSK RISTATGKLK KRKM

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 166.9897
Match: 1a76__
Description: Flap endonuclease-1 (Fen-1 nuclease)
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [671-1031] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDVPTKSQIS KEAEDNDSRK VESINKEHRK PLIFDYDFSE DEEDNIVENM IKEQEEFDTF  60
   61 KNTTLSTSAE RNVAENAFVE DELFEQQMKD KRDSDEVTMD MIKEVQELLS RFGIPYITAP 120
  121 MEAEAQCAEL LQLNLVDGII TDDSDVFLFG GTKIYKNMFH EKNYVEFYDA ESILKLLGLD 180
  181 RKNMIELAQL LGSDYTNGLK GMGPVSSIEV IAEFGNLKNF KDWYNNGQFD KRKQETENKF 240
  241 EKDLRKKLVN NEIILDDDFP SVMVYDAYMR PEVDHDTTPF VWGVPDLDML RSFMKTQLGW 300
  301 PHEKSDEILI PLIRDVNKRK KKGKQKRINE FFPREYISGD KKLNTSKRIS TATGKLKKRK 360
  361 M

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 72.522879
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 endodeoxyribonuclease activity 8.51020676030278 bayes_pls_golite062009
endodeoxyribonuclease activity 7.84678654948641 bayes_pls_golite062009
deoxyribonuclease activity 7.26876236760767 bayes_pls_golite062009
endonuclease activity 6.8680936339396 bayes_pls_golite062009
flap endonuclease activity 4.10438637013244 bayes_pls_golite062009
exonuclease activity 3.99717729574528 bayes_pls_golite062009
5'-3' exonuclease activity 3.19536858640519 bayes_pls_golite062009
nuclease activity 2.9643999717473 bayes_pls_golite062009
DNA binding 2.84879111682833 bayes_pls_golite062009
hydrolase activity 2.80884894948531 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 2.66071760609476 bayes_pls_golite062009
nucleic acid binding 2.62833003756567 bayes_pls_golite062009
binding 2.59149897255998 bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters 2.50398903419616 bayes_pls_golite062009
exodeoxyribonuclease activity 2.49591627688404 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 2.45364009363271 bayes_pls_golite062009
5'-3' exodeoxyribonuclease activity 2.26658239783943 bayes_pls_golite062009
damaged DNA binding 2.10834170214137 bayes_pls_golite062009
double-stranded DNA specific exodeoxyribonuclease activity 2.09057967200253 bayes_pls_golite062009
5'-flap endonuclease activity 1.81850767854435 bayes_pls_golite062009
structure-specific DNA binding 1.70042864382698 bayes_pls_golite062009
single-stranded DNA specific exodeoxyribonuclease activity 1.61167902830399 bayes_pls_golite062009
catalytic activity 1.37534898662234 bayes_pls_golite062009
single-stranded DNA specific 5'-3' exodeoxyribonuclease activity 1.15948049342759 bayes_pls_golite062009
endodeoxyribonuclease activity, producing 5'-phosphomonoesters 0.901965019685213 bayes_pls_golite062009
double-stranded DNA binding 0.626785110524684 bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.512509234493511 bayes_pls_golite062009
3'-5' exonuclease activity 0.50487165366129 bayes_pls_golite062009
protein binding 0.236485289446406 bayes_pls_golite062009
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity 0.14861832363159 bayes_pls_golite062009
DNA-directed DNA polymerase activity 0.0941467407417242 bayes_pls_golite062009
DNA polymerase activity 0.0691107435153178 bayes_pls_golite062009
3'-5'-exodeoxyribonuclease activity 0.0205129272358 bayes_pls_golite062009
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle