YRC Public Data Repository - Protein Structure Prediction

Protein:	PRP40
Organism:	Saccharomyces cerevisiae
Length:	583 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 PRP40.

Description	E-value	Query Range	Subject Range
PRP40 - U1 snRNP protein involved in splicing, interacts with the branchpoint-binding protein during the for... gi\|151941533 - gi\|151941533\|gb\|EDN59896.1\| U1 snRNP protein [Saccharomyces cerevisiae YJM789] PRP40_YEAST - Pre-mRNA-processing protein PRP40 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRP40 ...	4.0E-91	[1..583]	[1..583]
gi\|15636898 - gi\|15636898\|dbj\|BAB68206.1\| formin binding protein 11-related protein [Gallus gallus]	6.0E-63	[2..549]	[303..908]
CG3542-PB - This gene is referred to in FlyBase by the symbol Dmel\CG3542 (CG3542, FBgn0031492). It is a protein...	1.0E-61	[3..553]	[6..585]
gi\|37535504, gi\|... - gi\|37535504\|ref\|NP_922054.1\| hypothetical protein [Oryza sativa (japonica cultivar-group)], gb\|AAP54...	1.0E-58	[2..566]	[491..1016]
gi\|7767653 - gi\|7767653\|gb\|AAF69150.1\|AC007915_2 F27F5.2 [Arabidopsis thaliana]	3.0E-58	[2..550]	[189..778]
usp104 - U1 snRNP-associated protein Usp104 PRP40_SCHPO - Pre-mRNA-processing protein prp40 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=prp40 PE...	2.0E-56	[2..551]	[34..600]
CE03847 - WW\/rsp5\/WWP domain containing proteins (2 domains) status:Partially_confirmed UniProt:P34600 prote...	9.0E-56	[2..560]	[82..640]
gi\|5081610, gi\|1... - gi\|9055244\|ref\|NP_061256.1\| huntington yeast partner C [Mus musculus], gi\|5081610\|gb\|AAD39464.1\|AF13...	1.0E-55	[4..551]	[98..681]

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Predicted Domain #1

Region A:
Residues: [1-33]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSIWKEAKDA SGRIYYYNTL TKKSTWEKPK ELI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.31133
Match:	1e0lA_
Description:	Formin binding protein FBP28 domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.16402927467227	bayes_pls_golite062009
binding	2.02935060794966	bayes_pls_golite062009
transcription cofactor activity	1.56045209816163	bayes_pls_golite062009
transcription coactivator activity	1.54071619149498	bayes_pls_golite062009
transcription activator activity	1.50941346594353	bayes_pls_golite062009
transcription factor binding	1.46474521462806	bayes_pls_golite062009
protein binding	0.772594643545448	bayes_pls_golite062009
catalytic activity	0.210712504691113	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [34-82]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SQEELLLREN GWKAAKTADG KVYYYNPTTR ETSWTIPAFE KKVEPIAEQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.30103
Match:	1i5hW_
Description:	Ubiquitin ligase NEDD4 WWIII domain
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [83-153]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KHDTVSHAQV NGNRIALTAG EKQEPGRTIN EEESQYANNS KLLNVRRRTK EEAEKEFITM  60
   61 LKENQVDSTW S

[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 #4

Region A:
Residues: [154-494]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FSRIISELGT RDPRYWMVDD DPLWKKEMFE KYLSNRSADQ LLKEHNETSK FKEAFQKMLQ  60
   61 NNSHIKYYTR WPTAKRLIAD EPIYKHSVVN EKTKRQTFQD YIDTLIDTQK ESKKKLKTQA 120
  121 LKELREYLNG IITTSSSETF ITWQQLLNHY VFDKSKRYMA NRHFKVLTHE DVLNEYLKIV 180
  181 NTIENDLQNK LNELRLRNYT RDRIARDNFK SLLREVPIKI KANTRWSDIY PHIKSDPRFL 240
  241 HMLGRNGSSC LDLFLDFVDE QRMYIFAQRS IAQQTLIDQN FEWNDADSDE ITKQNIEKVL 300
  301 ENDRKFDKVD KEDISLIVDG LIKQRNEKIQ QKLQNERRIL E

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.69897
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [495-583]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKKHYFWLLL QRTYTKTGKP KPSTWDLASK ELGESLEYKA LGDEDNIRRQ IFEDFKPESS  60
   61 APTAESATAN LTLTASKKRH LTPAVELDY

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	11.537602
Match:	PF01846
Description:	FF domain

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

Found no confident structure predictions for this domain.

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

Predicted functions: