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View Structure Prediction Details

Protein: RAD5
Organism: Saccharomyces cerevisiae
Length: 1169 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 RAD5.

Description E-value Query
Range		 Subject
Range
RAD5_YEAST - DNA repair protein RAD5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD5 PE=1 SV=1
RAD5 - DNA helicase proposed to promote replication fork regression during postreplication repair by templa...
 0.0 [1..1169] [1..1169]
SM3L2_ARATH - Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member...
 0.0 [85..1168] [1..1028]
kis-PA - The gene kismet is referred to in FlyBase by the symbol Dmel\kis (CG3696, FBgn0086902). It is a prot...
 0.0 [13..1026] [1539..2495]
RAD5_SCHPO - DNA repair protein rad8 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad8 PE=1 SV=1
rad8 - ubiquitin-protein ligase E3
 0.0 [60..1169] [108..1132]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 0.0 [60..1107] [108..1070]
gi|6329728 - gi|6329728|dbj|BAA86436.1| KIAA1122 protein [Homo sapiens]
 0.0 [7..1027] [32..1021]
gi|996018, gi|45... - gi|996018|emb|CAA62831.1| BRG1 protein [Gallus gallus], gi|45384232|ref|NP_990390.1| BRG1 protein [G...
 0.0 [136..1069] [423..1254]

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Predicted Domain #1
Region A:
Residues: [1-378] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSHIEQEERK RFFNDDLDTS ETSLNFKSEN KESFLFANSH NDDDDDVVVS VSDTTEGEGD  60
   61 RSIVPVRREI EEEGQNQFIT ELLRIIPEMP KDLVMELNEK FGSQEEGLSL ALSHYFDHNS 120
  121 GTSISKIPSS PNQLNTLSDT SNSTLSPSSF HPKRRRIYGF RNQTRLEDKV TWKRFIGALQ 180
  181 VTGMATRPTV RPLKYGSQMK LKRSSEEISA TKVYDSRGRK KASMASLVRI FDIQYDREIG 240
  241 RVSEDIAQIL YPLLSSHEIS FEVTLIFCDN KRLSIGDSFI LQLDCFLTSL IFEERNDGES 300
  301 LMKRRRTEGG NKREKDNGNF GRTLTETDEE LESRSKRLAL LKLFDKLRLK PILDEQKALE 360
  361 KHKIELNSDP EIIDLDND

[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 #2
Region A:
Residues: [379-476] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EICSNQVTEV HNNLRDTQHE EETMNLNQLK TFYKAAQSSE SLKSLPETEP SRDVFKLELR  60
   61 NYQKQGLTWM LRREQEFAKA ASDGEASETG ANMINPLW

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 11.29
Match: 1gm5A
Description: RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3
Region A:
Residues: [477-819] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KQFKWPNDMS WAAQNLQQDH VNVEDGIFFY ANLHSGEFSL AKPILKTMIK GGILSDEMGL  60
   61 GKTVAAYSLV LSCPHDSDVV DKKLFDIENT AVSDNLPSTW QDNKKPYASK TTLIVVPMSL 120
  121 LTQWSNEFTK ANNSPDMYHE VYYGGNVSSL KTLLTKTKTP PTVVLTTYGI VQNEWTKHSK 180
  181 GRMTDEDVNI SSGLFSVNFY RIIIDEGHNI RNRTTVTSKA VMALQGKCKW VLTGTPIINR 240
  241 LDDLYSLVKF LELDPWRQIN YWKTFVSTPF ESKNYKQAFD VVNAILEPVL LRRTKQMKDK 300
  301 DGKPLVELPP KEVVIKRLPF SKSQDLLYKF LLDKAEVSVK SGI

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 11.29
Match: 1gm5A
Description: RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [820-921] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ARGDLLKKYS TILVHILRLR QVCCHPGLIG SQDENDEDLS KNNKLVTEQT VELDSLMRVV  60
   61 SERFDNSFSK EELDAMIQRL KVKYPDNKSF QSLECSICTT EP

[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 functions:

Term Confidence Notes
DNA-dependent ATPase activity 2.72462789867829 bayes_pls_golite062009
DNA helicase activity 2.2817164193758 bayes_pls_golite062009
binding 2.05253348982328 bayes_pls_golite062009
ATP-dependent DNA helicase activity 1.88455339138556 bayes_pls_golite062009
nucleoside-triphosphatase activity 1.84050240798436 bayes_pls_golite062009
pyrophosphatase activity 1.81138802583782 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides 1.78927528875848 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 1.78903889318615 bayes_pls_golite062009
helicase activity 1.70242731830224 bayes_pls_golite062009
microtubule motor activity 1.35938517416356 bayes_pls_golite062009
motor activity 1.32129340699286 bayes_pls_golite062009
protein-DNA loading ATPase activity 1.29640539057136 bayes_pls_golite062009
hydrolase activity 1.29419296935491 bayes_pls_golite062009
structure-specific DNA binding 1.2539059700735 bayes_pls_golite062009
purine NTP-dependent helicase activity 1.19311444180077 bayes_pls_golite062009
ATP-dependent helicase activity 1.19311444180077 bayes_pls_golite062009
ATPase activity 1.18431260772292 bayes_pls_golite062009
DNA-directed DNA polymerase activity 1.17617511072239 bayes_pls_golite062009
DNA polymerase activity 1.14104131900023 bayes_pls_golite062009
DNA clamp loader activity 1.12431517057397 bayes_pls_golite062009
double-stranded DNA binding 1.117585097627 bayes_pls_golite062009
nucleic acid binding 1.08697924060619 bayes_pls_golite062009
catalytic activity 1.00104173493322 bayes_pls_golite062009
DNA binding 0.702147676354075 bayes_pls_golite062009
single-stranded DNA binding 0.568457189190858 bayes_pls_golite062009
mismatched DNA binding 0.31144582840038 bayes_pls_golite062009
transcription regulator activity 0.287777990975748 bayes_pls_golite062009
DNA strand annealing activity 0.283577486331079 bayes_pls_golite062009
nucleotide binding 0.114848452385726 bayes_pls_golite062009
purine nucleotide binding 0.10713474095071 bayes_pls_golite062009
purine ribonucleotide binding 0.0916519414118148 bayes_pls_golite062009
ribonucleotide binding 0.0915913646217636 bayes_pls_golite062009
3'-5' DNA helicase activity 0.0769112340058804 bayes_pls_golite062009

Predicted Domain #5
Region A:
Residues: [922-975] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDLDKALFTE CGHSFCEKCL FEYIEFQNSK NLGLKCPNCR NQIDACRLLA LVQT

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.458 0.972 nuclear chromatin a.4.1 Homeodomain-like

Predicted Domain #6
Region A:
Residues: [976-1169] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSNSKNLEFK PYSPASKSSK ITALLKELQL LQDSSAGEQV VIFSQFSTYL DILEKELTHT  60
   61 FSKDVAKIYK FDGRLSLKER TSVLADFAVK DYSRQKILLL SLKAGGVGLN LTCASHAYMM 120
  121 DPWWSPSMED QAIDRLHRIG QTNSVKVMRF IIQDSIEEKM LRIQEKKRTI GEAMDTDEDE 180
  181 RRKRRIEEIQ MLFE

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 2.522879
Match: 1d9xA_
Description: Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle