YRC Public Data Repository - Protein Structure Prediction

Protein:	CBC2
Organism:	Saccharomyces cerevisiae
Length:	208 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 CBC2.

Description	E-value	Query Range	Subject Range
PAB1_MOUSE, PABP... - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=1, (P29341) Polyadenylate-binding ...	3.0E-50	[2..208]	[247..475]
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 ...	3.0E-50	[2..208]	[247..475]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	3.0E-50	[2..208]	[247..475]
gi\|13560783 - gi\|13560783\|gb\|AAK30205.1\|AF349964_1 poly(A)-binding protein [Daucus carota]	4.0E-49	[2..196]	[278..477]

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Predicted Domain #1

Region A:
Residues: [1-208]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLEEFDEVK YDHSTKRLDT PSRYLLRKAR RNPNGLQELR ESMKSSTIYV GNLSFYTSEE  60
   61 QIYELFSKCG TIKRIIMGLD RFKFTPCGFC FIIYSCPDEA LNALKYLSDT KLDEKTITID 120
  121 LDPGFEDGRQ FGRGKSGGQV SDELRFDFDA SRGGFAIPFA ERVGVPHSRF DNSSSQSNTN 180
  181 NYIPPPDAMG TFRPGFDEER EDDNYVPQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	391.156545
Match:	1h2tZ_
Description:	CBP20, 20KDa nuclear cap-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
	6.62953239642182	bayes_pls_golite062009
RNA cap binding	5.43390507836051	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
snRNA binding	3.28448936696877	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
U1 snRNA binding	2.26303528058407	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
protein binding	1.14508556628804	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

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: