YRC Public Data Repository - Protein Structure Prediction

Protein:	GBP2
Organism:	Saccharomyces cerevisiae
Length:	427 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 GBP2.

Description	E-value	Query Range	Subject Range
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[13..426]	[12..371]
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	[13..426]	[12..370]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[13..426]	[12..370]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[13..426]	[12..370]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[13..426]	[12..370]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	0.0	[13..426]	[12..370]

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Predicted Domain #1

Region A:
Residues: [1-112]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MERELGMYGN DRSRSRSPVR RRLSDDRDRY DDYNDSSSNN GNGSRRQRRD RGSRFNDRYD  60
   61 QSYGGSRYHD DRNWPPRRGG RGRGGSRSFR GGRGGGRGRT LGPIVERDLE RQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	4.92126426323641	bayes_pls_golite062009
	4.08350076268185	bayes_pls_golite062009
binding	3.64400841800969	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
structural molecule activity	2.78501986457503	bayes_pls_golite062009
poly-pyrimidine tract binding	2.47215943693079	bayes_pls_golite062009
telomeric DNA binding	2.04976561275235	bayes_pls_golite062009
transcription regulator activity	1.92450390013691	bayes_pls_golite062009
DNA binding	1.8021593476478	bayes_pls_golite062009
transcription factor activity	1.15127506309683	bayes_pls_golite062009
snRNA binding	1.12690941758278	bayes_pls_golite062009
protein binding	1.12215421354121	bayes_pls_golite062009
mRNA 3'-UTR binding	0.824614388276642	bayes_pls_golite062009
structure-specific DNA binding	0.43716526938634	bayes_pls_golite062009
transporter activity	0.417047632648771	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	bayes_pls_golite062009
translation regulator activity	0.38120065819101	bayes_pls_golite062009
transmembrane transporter activity	0.288804044686487	bayes_pls_golite062009
single-stranded DNA binding	0.2202184446161	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.128616879457381	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.00171911393626201	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [113-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FDATKRNFEN SIFVRNLTFD CTPEDLKELF GTVGEVVEAD IITSKGHHRG MGTVEFTKNE  60
   61 SVQDAISKFD GALFMDRKLM VRQDNPPPEA AKEFSKKA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [211-329]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TREEIDNGFE VFIINLPYSM NWQSLKDMFK ECGHVLRADV ELDFNGFSRG FGSVIYPTED  60
   61 EMIRAIDTFN GMEVEGRVLE VREGRFNKRK NNDRYNQRRE DLEDTRGTEP GLAQDAAVH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	116.045757
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	4.92126426323641	bayes_pls_golite062009
	4.08350076268185	bayes_pls_golite062009
binding	3.64400841800969	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
structural molecule activity	2.78501986457503	bayes_pls_golite062009
poly-pyrimidine tract binding	2.47215943693079	bayes_pls_golite062009
telomeric DNA binding	2.04976561275235	bayes_pls_golite062009
transcription regulator activity	1.92450390013691	bayes_pls_golite062009
DNA binding	1.8021593476478	bayes_pls_golite062009
transcription factor activity	1.15127506309683	bayes_pls_golite062009
snRNA binding	1.12690941758278	bayes_pls_golite062009
protein binding	1.12215421354121	bayes_pls_golite062009
mRNA 3'-UTR binding	0.824614388276642	bayes_pls_golite062009
structure-specific DNA binding	0.43716526938634	bayes_pls_golite062009
transporter activity	0.417047632648771	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	bayes_pls_golite062009
translation regulator activity	0.38120065819101	bayes_pls_golite062009
transmembrane transporter activity	0.288804044686487	bayes_pls_golite062009
single-stranded DNA binding	0.2202184446161	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.128616879457381	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.00171911393626201	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [330-427]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IDETAAKFTE GVNPGGDRNC FIYCSNLPFS TARSDLFDLF GPIGKINNAE LKPQENGQPT  60
   61 GVAVVEYENL VDADFCIQKL NNYNYGGCSL QISYARRD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	16.39794
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: