YRC Public Data Repository - Protein Structure Prediction

Protein:	cwf29
Organism:	Schizosaccharomyces pombe
Length:	217 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 cwf29.

Description	E-value	Query Range	Subject Range
gi\|73976775 - gi\|73976775\|ref\|XP_539581.2\| PREDICTED: similar to poly(A) binding protein, cytoplasmic 4 isoform 1 ...	164.0	[0..5]	[215..153]
gi\|48734702 - gi\|48734702\|gb\|AAH71591.1\| PABPC4 protein [Homo sapiens]	164.0	[0..5]	[215..153]
gi\|55959639, gi\|... - gi\|66267552\|gb\|AAH94755.1\| PABPC4 protein [Homo sapiens], gi\|55962217\|emb\|CAI12298.1\| poly(A) bindin... gi\|114555673 - gi\|114555673\|ref\|XP_001170937.1\| PREDICTED: poly A binding protein, cytoplasmic 4 isoform 1 [Pan tro...	164.0	[0..5]	[215..153]
gi\|76689271 - gi\|76689271\|ref\|XP_614388.2\| PREDICTED: similar to poly(A) binding protein, cytoplasmic 4 isoform 1 ...	163.0	[0..5]	[215..153]
gi\|109002439 - gi\|109002439\|ref\|XP_001113342.1\| PREDICTED: poly A binding protein, cytoplasmic 4 [Macaca mulatta] CCDS438.1_1 - null	163.0	[0..5]	[215..153]

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Predicted Domain #1

Region A:
Residues: [1-217]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSIRQIERL NEQELDKPFS SSWHQDYSDS AYIYIGNLDF DLNEDDILCV FSEFGEPVDI  60
   61 NLVRDKETGK SKGFAFLKYE DQRSTVLAVD NMTNVKLLDR LVRVDHVASY KVPQKEKEPA 120
  121 NLVPLGESGS SLSVSTINTS NLPDHDYKTI IQNEVEQTLS PKDEKDLLDP MRDYIHREKR 180
  181 RKLKHESSDR SDKSDSNRHS RHHRRHSRSR RHRDLDG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.69897
Match:	1up1A
Description:	UP1, THE TWO RNA-RECOGNITION MOTIF DOMAIN OF HNRNP A1
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
snRNA binding	4.06596327298973	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
binding	3.49612884560266	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
U1 snRNA binding	3.02511982045347	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
protein binding	1.32954276279597	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
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.425042944899091	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009
snoRNA binding	0.0568636182001701	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: