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View Structure Prediction Details

Protein: DOA4
Organism: Saccharomyces cerevisiae
Length: 926 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 DOA4.

Description E-value Query
Range
Subject
Range
DOA4 - Ubiquitin isopeptidase, required for recycling ubiquitin from proteasome-bound ubiquitinated interme...
UBP4_YEAST - Ubiquitin carboxyl-terminal hydrolase 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...
0.0 [1..926] [1..926]
UBP4_KLULA - Ubiquitin carboxyl-terminal hydrolase 4 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 7...
UBP4_KLULA - Ubiquitin carboxyl-terminal hydrolase 4 OS=Kluyveromyces lactis GN=DOA4 PE=3 SV=1
0.0 [14..494] [2..442]
UBP21_MOUSE - Ubiquitin carboxyl-terminal hydrolase 21 OS=Mus musculus GN=Usp21 PE=1 SV=1
5.0E-99 [344..921] [7..557]
gi|6492126, gi|5... - gi|6492126|gb|AAF14190.1|AF106659_1 deubiquitinating enzyme Ubp69 [Rattus norvegicus], gi|51592088|r...
4.0E-96 [342..921] [82..610]

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Predicted Domain #1
Region A:
Residues: [1-184]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEQNIISTIR DECIRHRSKY LTIAQLTAIA EAKINEFIIT GKAKDQDLSS LLDKCIDILS  60
   61 IYKKNSKDIK NIISCKNKGA MISSNSVMII QLNYVYYKVI HIIVTTNIPH LSEFAKIKLH 120
  121 KSTSDEGNGN NNNNEFQLMN IYNTLLETLL KDENIAKIKS FIKSSIKQTK LNHEQEECNL 180
  181 MRTG

[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.

Found no confident structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [185-335]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SYITSNQLNS LISSSANSAS SQMEILLIDI RSRLEFNKSH IDTKNIICLE PISFKMSYSD  60
   61 HDLEKKSLIT SPNSEIKMFQ SRNLFKFIIL YTDANEYNVK QQSVLLDILV NHSFEKPISD 120
  121 DFTKIFILES GFPGWLKSNY GRQVSSSFPS N

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 14.0
Match: 1d5vA_
Description: Adipocyte-transcription factor FREAC-11 (s12, fkh-14)
Matching Structure (courtesy of the PDB):

Predicted Domain #3
Region A:
Residues: [336-561]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNIKDDSVYI NGNTSGLSLQ HLPKMSPSIR HSMDDSMKEM LVAPTPLNHL QQQQQQQSDN  60
   61 DHVLKRSSSF KKLFSNYTSP NPKNSNSNLY SISSLSISSS PSPLPLHSPD PVKGNSLPIN 120
  121 YPETPHLWKN SETDFMTNQR EQLNHNSFAH IAPINTKAIT SPSRTATPKL QRFPQTISMN 180
  181 LNMNSNGHSS ATSTIQPSCL SLSNNDSLDH TDVTPTSSHN YDLDFA

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 7.33
Match: 1ldvA
Description: No description for 1ldvA was found.

Predicted functions:

Term Confidence Notes
transcription regulator activity 5.29569167054278 bayes_pls_golite062009
DNA binding 4.90756541371868 bayes_pls_golite062009
nucleic acid binding 4.69183445184264 bayes_pls_golite062009
transcription factor activity 4.14166958134441 bayes_pls_golite062009
binding 3.52874320222492 bayes_pls_golite062009
sequence-specific DNA binding 2.48053910222825 bayes_pls_golite062009
hydrolase activity 2.30467124306022 bayes_pls_golite062009
transcription activator activity 2.29614125067822 bayes_pls_golite062009
transcription repressor activity 2.19033875364989 bayes_pls_golite062009
RNA polymerase II transcription factor activity 1.48055533524841 bayes_pls_golite062009
small conjugating protein ligase activity 1.27763700765562 bayes_pls_golite062009
ubiquitin-protein ligase activity 1.12147035668008 bayes_pls_golite062009
transcription factor binding 0.83705247708153 bayes_pls_golite062009
acid-amino acid ligase activity 0.754042916649094 bayes_pls_golite062009
protein binding 0.753698599635855 bayes_pls_golite062009
structure-specific DNA binding 0.379762425417023 bayes_pls_golite062009
structural molecule activity 0.272316540117209 bayes_pls_golite062009
signal transducer activity 0.120341737642948 bayes_pls_golite062009
molecular transducer activity 0.120341737642948 bayes_pls_golite062009
structural constituent of ribosome 0.0912115683429473 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [562-753]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VGLENLGNSC YMNCIIQCIL GTHELTQIFL DDSYAKHINI NSKLGSKGIL AKYFARLVHM  60
   61 MYKEQVDGSK KISISPIKFK LACGSVNSLF KTASQQDCQE FCQFLLDGLH EDLNQCGSNP 120
  121 PLKELSQEAE ARREKLSLRI ASSIEWERFL TTDFSVIVDL FQGQYASRLK CKVCSHTSTT 180
  181 YQPFTVLSIP IP

[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 #5
Region A:
Residues: [754-926]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KKNSRNNITI EDCFREFTKC ENLEVDEQWL CPHCEKRQPS TKQLTITRLP RNLIVHLKRF  60
   61 DNLLNKNNDF VIYPFLLDLT PFWANDFDGV FPPGVNDDEL PIRGQIPPFK YELYGVACHF 120
  121 GTLYGGHYTA YVKKGLKKGW LYFDDTKYKP VKNKADAINS NAYVLFYHRV YGV

[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.


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