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View Structure Prediction Details

Protein: RAD54
Organism: Saccharomyces cerevisiae
Length: 898 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 RAD54.

Description E-value Query
Range
Subject
Range
RAD54 - DNA-dependent ATPase, stimulates strand exchange by modifying the topology of double-stranded DNA; i...
RAD54_YEAST - DNA repair and recombination protein RAD54 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ...
0.0 [1..898] [1..898]
gi|119604570, gi... - gi|192807323|ref|NP_001122321.1| SWI/SNF-related matrix-associated actin-dependent regulator of chro...
0.0 [27..846] [491..1268]
gi|996018, gi|45... - gi|996018|emb|CAA62831.1| BRG1 protein [Gallus gallus], gi|45384232|ref|NP_990390.1| BRG1 protein [G...
0.0 [27..834] [489..1255]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
0.0 [33..826] [496..1248]
gi|447739 - gi|447739|prf||1915304A nylB upstream ORF
0.0 [33..826] [496..1248]
rhp54 - Rad54 homolog Rhp54
RAD54_SCHPO - DNA repair protein rhp54 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rhp54 PE=1 SV=2
0.0 [17..898] [13..852]

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Predicted Domain #1
Region A:
Residues: [1-223]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MARRRLPDRP PNGIGAGERP RLVPRPINVQ DSVNRLTKPF RVPYKNTHIP PAAGRIATGS  60
   61 DNIVGGRSLR KRSATVCYSG LDINADEAEY NSQDISFSQL TKRRKDALSA QRLAKDPTRL 120
  121 SHIQYTLRRS FTVPIKGYVQ RHSLPLTLGM KKKITPEPRP LHDPTDEFAI VLYDPSVDGE 180
  181 MIVHDTSMDN KEEESKKMIK STQEKDNINK EKNSQEERPT QRI

[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: [224-275]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRHPALMTNG VRNKPLRELL GDSENSAENK KKFASVPVVI DPKLAKILRP HQ

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 13.09
Match: 1gm5A
Description: RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
transcription repressor activity 3.46705970365511 bayes_pls_golite062009
transcription regulator activity 3.2394894333307 bayes_pls_golite062009
binding 3.06758476214113 bayes_pls_golite062009
chromatin binding 2.9265077396229 bayes_pls_golite062009
histone binding 2.00388175060339 bayes_pls_golite062009
nucleic acid binding 1.7870619298179 bayes_pls_golite062009
DNA binding 1.72304410722296 bayes_pls_golite062009
protein binding 1.61683263008775 bayes_pls_golite062009
methylated histone residue binding 1.03331560428208 bayes_pls_golite062009
general transcriptional repressor activity 0.49996033797134 bayes_pls_golite062009
nucleoside-triphosphatase activity 0.356338632175355 bayes_pls_golite062009
satellite DNA binding 0.327386416436959 bayes_pls_golite062009
pyrophosphatase activity 0.309377712814897 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides 0.296839540568239 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.29636000593974 bayes_pls_golite062009
catalytic activity 0.14067200158938 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [276-583]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEGVRFLYRC VTGLVMKDYL EAEAFNTSSE DPLKSDEKAL TESQKTEQNN RGAYGCIMAD  60
   61 EMGLGKTLQC IALMWTLLRQ GPQGKRLIDK CIIVCPSSLV NNWANELIKW LGPNTLTPLA 120
  121 VDGKKSSMGG GNTTVSQAIH AWAQAQGRNI VKPVLIISYE TLRRNVDQLK NCNVGLMLAD 180
  181 EGHRLKNGDS LTFTALDSIS CPRRVILSGT PIQNDLSEYF ALLSFSNPGL LGSRAEFRKN 240
  241 FENPILRGRD ADATDKEITK GEAQLQKLST IVSKFIIRRT NDILAKYLPC KYEHVIFVNL 300
  301 KPLQNELY

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 13.09
Match: 1gm5A
Description: RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
microtubule motor activity 3.4297361345158 bayes_pls_golite062009
nucleoside-triphosphatase activity 3.0989886302218 bayes_pls_golite062009
pyrophosphatase activity 3.01886747063507 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides 2.99763530427224 bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 2.99650240285889 bayes_pls_golite062009
binding 2.64537357529343 bayes_pls_golite062009
motor activity 2.60481158518321 bayes_pls_golite062009
nucleic acid binding 2.11222585187695 bayes_pls_golite062009
DNA binding 1.7904783386531 bayes_pls_golite062009
hydrolase activity 1.77231681433173 bayes_pls_golite062009
ATPase activity 1.76238574289941 bayes_pls_golite062009
transcription regulator activity 1.68903321260301 bayes_pls_golite062009
ATPase activity, coupled 1.57826779898847 bayes_pls_golite062009
cytoskeletal protein binding 1.50574672650697 bayes_pls_golite062009
structural constituent of ribosome 1.47858140861683 bayes_pls_golite062009
microfilament motor activity 1.28029120876672 bayes_pls_golite062009
DNA-dependent ATPase activity 1.2155186842031 bayes_pls_golite062009
helicase activity 1.16085745407703 bayes_pls_golite062009
tubulin binding 1.01673904002272 bayes_pls_golite062009
catalytic activity 1.00104173493322 bayes_pls_golite062009
microtubule binding 0.902404986889887 bayes_pls_golite062009
actin binding 0.875514430441177 bayes_pls_golite062009
structural molecule activity 0.86514677273731 bayes_pls_golite062009
plus-end-directed microtubule motor activity 0.773586048423911 bayes_pls_golite062009
DNA helicase activity 0.72881469450553 bayes_pls_golite062009
purine nucleotide binding 0.725611289205392 bayes_pls_golite062009
structure-specific DNA binding 0.720649395550746 bayes_pls_golite062009
nucleotide binding 0.717697610309727 bayes_pls_golite062009
purine ribonucleotide binding 0.713814218071151 bayes_pls_golite062009
ribonucleotide binding 0.713752628021599 bayes_pls_golite062009
transcription factor activity 0.603758349693077 bayes_pls_golite062009
purine NTP-dependent helicase activity 0.59513742813869 bayes_pls_golite062009
ATP-dependent helicase activity 0.59513742813869 bayes_pls_golite062009
double-stranded DNA binding 0.58862275163252 bayes_pls_golite062009
structural constituent of muscle 0.559419947521782 bayes_pls_golite062009
telomeric DNA binding 0.40354211833657 bayes_pls_golite062009
transcription repressor activity 0.244736544804496 bayes_pls_golite062009
ATP-dependent DNA helicase activity 0.22150712609541 bayes_pls_golite062009
ATP binding 0.19169045543599 bayes_pls_golite062009
protein binding 0.170837278876362 bayes_pls_golite062009
adenyl ribonucleotide binding 0.165732470448462 bayes_pls_golite062009
adenyl nucleotide binding 0.162060759063149 bayes_pls_golite062009
substrate-specific transporter activity 0.144154288308693 bayes_pls_golite062009
active transmembrane transporter activity 0.114463153989353 bayes_pls_golite062009
GTPase activity 0.105546189348878 bayes_pls_golite062009
guanyl nucleotide binding 0.0289841199143713 bayes_pls_golite062009
translation regulator activity 0.0269721463618237 bayes_pls_golite062009
guanyl ribonucleotide binding 0.0187537754688351 bayes_pls_golite062009
GTP binding 0.0171298013679982 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.0028386101905622 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [584-640]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NKLIKSREVK KVVKGVGGSQ PLRAIGILKK LCNHPNLLNF EDEFDDEDDL ELPDDYN

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 8.221849
Match: 1hv8A_
Description: Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [641-898]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPGSKARDVQ TKYSAKFSIL ERFLHKIKTE SDDKIVLISN YTQTLDLIEK MCRYKHYSAV  60
   61 RLDGTMSINK RQKLVDRFND PEGQEFIFLL SSKAGGCGIN LIGANRLILM DPDWNPAADQ 120
  121 QALARVWRDG QKKDCFIYRF ISTGTIEEKI FQRQSMKMSL SSCVVDAKED VERLFSSDNL 180
  181 RQLFQKNENT ICETHETYHC KRCNAQGKQL KRAPAMLYGD ATTWNHLNHD ALEKTNDHLL 240
  241 KNEHHYNDIS FAFQYISH

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 7.045757
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