YRC Public Data Repository - Protein Structure Prediction

Protein:	SNP1
Organism:	Saccharomyces cerevisiae
Length:	300 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 SNP1.

Description	E-value	Query Range	Subject Range
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	2.0E-65	[2..290]	[105..387]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	2.0E-65	[2..290]	[105..387]
PABP1_BOVIN - Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1 gi\|109087089 - gi\|109087089\|ref\|XP_001098239.1\| PREDICTED: poly(A) binding protein, cytoplasmic 1 isoform 2 [Macaca... gi\|123993665, gi... - gi\|168278070\|dbj\|BAG11013.1\| polyadenylate-binding protein 1 [synthetic construct], gi\|123999981\|gb\|... gi\|194036975 - gi\|194036975\|ref\|XP_001927782.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-bind... PABPC1 - poly(A) binding protein, cytoplasmic 1 gi\|73974130, gi\|... - gi\|73974178\|ref\|XP_857695.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-binding ...	2.0E-65	[2..290]	[105..387]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	8.0E-63	[2..290]	[105..392]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	1.0E-62	[2..293]	[105..396]

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Predicted Domain #1

Region A:
Residues: [1-90]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNYNLSKYPD DVSRLFKPRP PLSYKRPTDY PYAKRQTNPN ITGVANLLST SLKHYMEEFP  60
   61 EGSPNNHLQR YEDIKLSKIK NAQLLDRRLQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	99.9691
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
	6.62953239642182	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
U1 snRNA binding	4.22094068431436	bayes_pls_golite062009
snRNA binding	4.06596327298973	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
protein binding	0.872515134876947	bayes_pls_golite062009
ligase activity	0.633198446266208	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [91-187]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NWNPNVDPHI KDTDPYRTIF IGRLPYDLDE IELQKYFVKF GEIEKIRIVK DKITQKSKGY  60
   61 AFIVFKDPIS SKMAFKEIGV HRGIQIKDRI CIVDIER

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	99.9691
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [188-300]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRTVKYFKPR RLGGGLGGRG YSNRDSRLPG RFASASTSNP AERNYAPRLP RRETSSSAYS  60
   61 ADRYGSSTLD ARYRGNRPLL SAATPTAAVT SVYKSRNSRT RESQPAPKEA PDY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	80.30103
Match:	1fxlA_
Description:	Hu antigen D (Hud)
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

Predicted functions: