YRC Public Data Repository - Protein Structure Prediction

Protein:	HRB1
Organism:	Saccharomyces cerevisiae
Length:	429 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 HRB1.

Description	E-value	Query Range	Subject Range
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[28..428]	[5..371]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[35..428]	[12..370]
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	[35..428]	[12..370]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[35..428]	[12..370]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[35..428]	[12..370]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	0.0	[35..428]	[12..370]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDDHGYERD NHLSRRSGNY NGRRKFADTY RGSRDRGEYR GGRERSDYRE RERFNNRDNP  60
   61 RSRDRYDDRR RGRDVTGRYG NRRDDYPRSF RSRHNTRDDS RRGGFGSSGA RGDYGPLLAR 120
  121 ELD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	109.512579
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [124-222]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STYEEKVNRN YSNSIFVGNL TYDSTPEDLT EFFSQIGKVV RADIITSRGH HRGMGTVEFT  60
   61 NSDDVDRAIR QYDGAFFMDR KIFVRQDNPP PSNNIKERK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.770868
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.01922154152081	bayes_pls_golite062009
mRNA binding	4.4242122918002	bayes_pls_golite062009
binding	3.19379300171257	bayes_pls_golite062009
nucleic acid binding	2.34356093608328	bayes_pls_golite062009
single-stranded RNA binding	2.32459056139943	bayes_pls_golite062009
poly-pyrimidine tract binding	1.53870607671929	bayes_pls_golite062009
protein binding	1.52056358240529	bayes_pls_golite062009
nucleic acid transmembrane transporter activity	1.11467033780466	bayes_pls_golite062009
RNA transmembrane transporter activity	1.11467033780466	bayes_pls_golite062009
transporter activity	0.417047632648771	bayes_pls_golite062009
mRNA 3'-UTR binding	0.414871108842203	bayes_pls_golite062009
transmembrane transporter activity	0.288804044686487	bayes_pls_golite062009
poly-purine tract binding	0.15653271757169	bayes_pls_golite062009
	0.147515630076636	bayes_pls_golite062009
structural molecule activity	0.106871867442361	bayes_pls_golite062009
poly(A) RNA binding	0.0459878286238641	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.00171911393626201	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [223-337]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ALDRGELRHN RKTHEVIVKN LPASVNWQAL KDIFKECGNV AHADVELDGD GVSTGSGTVS  60
   61 FYDIKDLHRA IEKYNGYSIE GNVLDVKSKE SVHNHSDGDD VDIPMDDSPV NEEAR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.770868
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.01922154152081	bayes_pls_golite062009
mRNA binding	4.4242122918002	bayes_pls_golite062009
binding	3.19379300171257	bayes_pls_golite062009
nucleic acid binding	2.34356093608328	bayes_pls_golite062009
single-stranded RNA binding	2.32459056139943	bayes_pls_golite062009
poly-pyrimidine tract binding	1.53870607671929	bayes_pls_golite062009
protein binding	1.52056358240529	bayes_pls_golite062009
nucleic acid transmembrane transporter activity	1.11467033780466	bayes_pls_golite062009
RNA transmembrane transporter activity	1.11467033780466	bayes_pls_golite062009
transporter activity	0.417047632648771	bayes_pls_golite062009
mRNA 3'-UTR binding	0.414871108842203	bayes_pls_golite062009
transmembrane transporter activity	0.288804044686487	bayes_pls_golite062009
poly-purine tract binding	0.15653271757169	bayes_pls_golite062009
	0.147515630076636	bayes_pls_golite062009
structural molecule activity	0.106871867442361	bayes_pls_golite062009
poly(A) RNA binding	0.0459878286238641	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.00171911393626201	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [338-429]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KFTENVVGGG ERNRLIYCSN LPFSTAKSDL YDLFETIGKV NNAELRYDSK GAPTGIAVVE  60
   61 YDNVDDADVC IERLNNYNYG GCDLDISYAK RL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.9794
Match:	2mssA_
Description:	Neural RNA-binding protein Musashi-1
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: