YRC Public Data Repository - Protein Structure Prediction

Protein:	PUB1
Organism:	Saccharomyces cerevisiae
Length:	453 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 PUB1.

Description	E-value	Query Range	Subject Range
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[66..453]	[2..420]
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	[66..452]	[2..417]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[66..452]	[2..417]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[66..452]	[2..417]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	0.0	[66..453]	[2..417]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[71..452]	[7..416]

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Predicted Domain #1

Region A:
Residues: [1-152]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSENNEEQHQ QQQQQQPVAV ETPSAVEAPA SADPSSEQSV AVEGNSEQAE DNQGENDPSV  60
   61 VPANAITGGR ETSDRVLYVG NLDKAITEDI LKQYFQVGGP IANIKIMIDK NNKNVNYAFV 120
  121 EYHQSHDANI ALQTLNGKQI ENNIVKINWA FQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	261.211549
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
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
general RNA polymerase II transcription factor activity	0.425042944899091	bayes_pls_golite062009
hydrolase activity	0.389390547875764	bayes_pls_golite062009
sequence-specific DNA binding	0.383589644462932	bayes_pls_golite062009
translation regulator activity	0.38120065819101	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.128616879457381	bayes_pls_golite062009
snoRNA binding	0.0568636182001701	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [153-275]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SQQSSSDDTF NLFVGDLNVN VDDETLRNAF KDFPSYLSGH VMWDMQTGSS RGYGFVSFTS  60
   61 QDDAQNAMDS MQGQDLNGRP LRINWAAKRD NNNNNNYQQR RNYGNNNRGG FRQYNSNNNN 120
  121 NMN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	261.211549
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [276-331]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGMNMNMNMN MNNSRGMPPS SMGMPIGAMP LPSQGQPQQS QTIGLPPQVN PQAVDH

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.335	g.18.1	Complement control module/SCR domain
View	Download	0.268	a.60.1	SAM/Pointed domain
View	Download	0.281	g.3.7	Scorpion toxin-like

Predicted Domain #4

Region A:
Residues: [332-453]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IIRSAPPRVT TAYIGNIPHF ATEADLIPLF QNFGFILDFK HYPEKGCCFI KYDTHEQAAV  60
   61 CIVALANFPF QGRNLRTGWG KERSNFMPQQ QQQGGQPLIM NDQQQPVMSE QQQQQQQQQQ 120
  121 QQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.045757
Match:	1bnyA_
Description:	No description for 1bnyA_ was found.

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: