YRC Public Data Repository - Protein Structure Prediction

Protein:	DBP2
Organism:	Saccharomyces cerevisiae
Length:	546 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 DBP2.

Description	E-value	Query Range	Subject Range
DBP2_YEAST - ATP-dependent RNA helicase DBP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DBP2 PE=... DBP2 - Essential ATP-dependent RNA helicase of the DEAD-box protein family, involved in nonsense-mediated m...	0.0	[1..546]	[1..546]
gi\|45382259, gi\|... - gi\|5114446\|gb\|AAD40318.1\|AF158370_1 DEAD-box RNA helicase [Gallus gallus], gi\|45382259\|ref\|NP_990158...	0.0	[32..545]	[3..524]
DDX5 - DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 gi\|109116805 - gi\|109116805\|ref\|XP_001109860.1\| PREDICTED: DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 [Macaca mulatta... gi\|119912544 - gi\|119912544\|ref\|XP_613184.3\| PREDICTED: DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 isoform 1 [Bos tau... ENSPTRT00000017501 - null gi\|73965213 - gi\|73965213\|ref\|XP_850467.1\| PREDICTED: similar to Probable RNA-dependent helicase p68 (DEAD-box pro... CCDS11659.1_1 - null gi\|168277560, gi... - gi\|61362310\|gb\|AAX42198.1\| DEAD box polypeptide 5 [synthetic construct], gi\|61362303\|gb\|AAX42197.1\| ...	0.0	[24..545]	[7..520]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	0.0	[39..545]	[2..500]
DBP2_SCHPO - ATP-dependent RNA helicase dbp2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=dbp2 PE=2 ... dbp2 - ATP-dependent RNA helicase Dbp2	0.0	[3..495]	[12..504]
gi\|5270 - gi\|5270\|emb\|CAA36873.1\| p68 protein [Schizosaccharomyces pombe]	0.0	[3..495]	[12..504]
gi\|8163810, gi\|1... - gi\|8163810\|gb\|AAF73861.1\|AF218580_1 p68 RNA helicase [Xenopus laevis], gi\|148229654\|ref\|NP_001084230...	0.0	[21..545]	[3..525]
DDX3Y_MOUSE - ATP-dependent RNA helicase DDX3Y OS=Mus musculus GN=Ddx3y PE=1 SV=2	0.0	[2..531]	[72..611]
gi\|10177293 - gi\|10177293\|dbj\|BAB10554.1\| ATP-dependent RNA helicase-like protein [Arabidopsis thaliana]	0.0	[5..495]	[27..518]

Back

Predicted Domain #1

Region A:
Residues: [1-80]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTYGGRDQQY NKTNYKSRGG DFRGGRNSDR NSYNDRPQGG NYRGGFGGRS NYNQPQELIK  60
   61 PNWDEELPKL PTFEKNFYVE

[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: [81-327]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HESVRDRSDS EIAQFRKENE MTISGHDIPK PITTFDEAGF PDYVLNEVKA EGFDKPTGIQ  60
   61 CQGWPMALSG RDMVGIAATG SGKTLSYCLP GIVHINAQPL LAPGDGPIVL VLAPTRELAV 120
  121 QIQTECSKFG HSSRIRNTCV YGGVPKSQQI RDLSRGSEIV IATPGRLIDM LEIGKTNLKR 180
  181 VTYLVLDEAD RMLDMGFEPQ IRKIVDQIRP DRQTLMWSAT WPKEVKQLAA DYLNDPIQVQ 240
  241 VGSLELS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	730.0103
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [328-546]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ASHNITQIVE VVSDFEKRDR LNKYLETASQ DNEYKTLIFA STKRMCDDIT KYLREDGWPA  60
   61 LAIHGDKDQR ERDWVLQEFR NGRSPIMVAT DVAARGIDVK GINYVINYDM PGNIEDYVHR 120
  121 IGRTGRAGAT GTAISFFTEQ NKGLGAKLIS IMREANQNIP PELLKYDRRS YGGGHPRYGG 180
  181 GRGGRGGYGR RGGYGGGRGG YGGNRQRDGG WGNRGRSNY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	730.0103
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits