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View Structure Prediction Details

Protein: gi|190405867
Organism: Saccharomyces cerevisiae RM11-1a
Length: 523 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 gi|190405867.

Description E-value Query
Range		 Subject
Range
NAM8_YEAST - Protein NAM8 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NAM8 PE=1 SV=2
NAM8 - RNA binding protein, component of the U1 snRNP protein; mutants are defective in meiotic recombinati...
gi|190405867 - gi|190405867|gb|EDV09134.1| RNA-binding protein [Saccharomyces cerevisiae RM11-1a]
gi|207344656 - gi|207344656|gb|EDZ71726.1| YHR086Wp-like protein [Saccharomyces cerevisiae AWRI1631]
 0.0 [1..523] [1..523]
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 [44..507] [1..487]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1
 0.0 [44..507] [1..487]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2
 0.0 [44..507] [1..487]
PAB1_XENLA, PABP... - (P20965) Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1), (P20965) Polyadenylat...
 0.0 [44..507] [1..486]
gi|19526272 - gi|19526272|gb|AAL89666.1|AF411956_7 polyA-binding protein [Takifugu rubripes]
 9.0E-95 [51..511] [8..493]

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Predicted Domain #1
Region A:
Residues: [1-164] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSYKQTTYYP SRGNLVRNDS SPYTNTISSE TNNSSTSVLS LQGASNVSLG TTGNQLYMGD  60
   61 LDPTWDKNTV RQIWASLGEA NINVRMMWNN TLNNGSRSSM GPKNNQGYCF VDFPSSTHAA 120
  121 NALLKNGMLI PNFPNKKLKL NWATSSYSNS NNSLNNVKSG NNCS

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 126.67837
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
6.62953239642182 bayes_pls_golite062009
mRNA binding 5.29759606920196 bayes_pls_golite062009
nucleic acid binding 4.92126426323641 bayes_pls_golite062009
U1 snRNA binding 4.22094068431436 bayes_pls_golite062009
snRNA binding 4.06596327298973 bayes_pls_golite062009
binding 3.64400841800969 bayes_pls_golite062009
poly-pyrimidine tract binding 3.11990160533699 bayes_pls_golite062009
single-stranded RNA binding 2.93798024346416 bayes_pls_golite062009
structural molecule activity 2.78501986457503 bayes_pls_golite062009
protein binding 2.17260848225967 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
transcription activator activity 1.12833244388568 bayes_pls_golite062009
transcription repressor activity 0.998305828880243 bayes_pls_golite062009
mRNA 3'-UTR binding 0.824614388276642 bayes_pls_golite062009
mRNA 5'-UTR binding 0.625848256054783 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.461000905454505 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: [165-303] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IFVGDLAPNV TESQLFELFI NRYASTSHAK IVHDQVTGMS KGYGFVKFTN SDEQQLALSE  60
   61 MQGVFLNGRA IKVGPTSGQQ QHVSGNNDYN RSSSSLNNEN VDSRFLSKGQ SFLSNGNNNM 120
  121 GFKRNHMSQF IYPVQQQPS

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 14.522879
Match: 1qm9A_
Description: Polypyrimidine tract-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
mRNA binding 5.29759606920196 bayes_pls_golite062009
nucleic acid binding 4.92126426323641 bayes_pls_golite062009
U1 snRNA binding 4.22094068431436 bayes_pls_golite062009
snRNA binding 4.06596327298973 bayes_pls_golite062009
binding 3.64400841800969 bayes_pls_golite062009
poly-pyrimidine tract binding 3.11990160533699 bayes_pls_golite062009
single-stranded RNA binding 2.93798024346416 bayes_pls_golite062009
structural molecule activity 2.78501986457503 bayes_pls_golite062009
protein binding 2.17260848225967 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
transcription activator activity 1.12833244388568 bayes_pls_golite062009
transcription repressor activity 0.998305828880243 bayes_pls_golite062009
mRNA 3'-UTR binding 0.824614388276642 bayes_pls_golite062009
mRNA 5'-UTR binding 0.625848256054783 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.461000905454505 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 #3
Region A:
Residues: [304-396] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LNHFTDPNNT TVFIGGLSSL VTEDELRAYF QPFGTIVYVK IPVGKCCGFV QYVDRLSAEA  60
   61 AIAGMQGFPI ANSRVRLSWG RSAKQTALLQ QAM

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 14.522879
Match: 1qm9A_
Description: Polypyrimidine tract-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [397-523] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSNSLQVQQQ QPGLQQPNYG YIPSSTCEAP VLPDNNVSST MLPGCQILNY SNPYANANGL  60
   61 GSNNFSFYSN NNATNTQATS LLADTSSMDL SGTGGQQVIM QGSEAVVNST NAMLNRLEQG 120
  121 SNGFMFA

[Run NCBI BLAST on this sequence.]

Detection Method: MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle