YRC Public Data Repository - Protein Structure Prediction

Protein:	NOP13
Organism:	Saccharomyces cerevisiae
Length:	403 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 NOP13.

Description	E-value	Query Range	Subject Range
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 ...	0.0	[37..400]	[12..358]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[37..400]	[12..358]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[37..400]	[12..358]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[37..400]	[12..359]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[37..400]	[12..358]
gi\|13540314 - gi\|13540314\|gb\|AAK29408.1\|AF338225_1 embryonic poly(A) binding protein [Xenopus laevis]	0.0	[37..400]	[12..358]

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Predicted Domain #1

Region A:
Residues: [1-112]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSETELSKED AVTKKDNEEQ VKKALLDPTK KRKAEDEIEI DLKSSIPLSK KQKRLLRRGK  60
   61 VTLEELNAKY NIDPKSIEEY KEDAEKKKSG ASEKDAQGEE STINTPTGDE SG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.218487
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.04120049976231	bayes_pls_golite062009
mRNA binding	4.29904003387927	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
	3.36965439092178	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.32565125258004	bayes_pls_golite062009
poly-pyrimidine tract binding	1.99190411806363	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	0.89093640300829	bayes_pls_golite062009
snoRNA binding	0.87536768969411	bayes_pls_golite062009
snRNA binding	0.45487108214667	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [113-227]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EVVKKKKKDE NKYGVWIGNL SFDTTKDDLV RFFIAKTKDN EDEKSRVTEQ DITRLSMPRV  60
   61 AAKNSNAMKN KGFCYMFFKN VEQMKAVLEL SESHLNGRNM LIKDSENYSG RPDKD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.512579
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.04120049976231	bayes_pls_golite062009
mRNA binding	4.29904003387927	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
	3.36965439092178	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.32565125258004	bayes_pls_golite062009
poly-pyrimidine tract binding	1.99190411806363	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	0.89093640300829	bayes_pls_golite062009
snoRNA binding	0.87536768969411	bayes_pls_golite062009
snRNA binding	0.45487108214667	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [228-328]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DLVAMSKNPP SRILFVGNLS FDVTDDLLRK HFQHCGDIVK IRMATFEDSG KCKGFAFIDF  60
   61 KNEEGSTNEL KDKSCRKIAG RPLRMEYGED RSKRQVRKKV E

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	113.512579
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [329-403]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NVSRNNSSSF DISNNKGYDR AGQDNGSKPE YKRSNANRRP PVDSNNRTKS SVALATAQRG  60
   61 SAAIVPSQGK KVKFD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	34.39794
Match:	1b7fA_
Description:	Sex-lethal protein
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:

Predicted functions: