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View Structure Prediction Details

Protein: RRP40
Organism: Saccharomyces cerevisiae
Length: 240 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 RRP40.

Description E-value Query
Range		 Subject
Range
gi|12839296 - gi|12839296|dbj|BAB24501.1| unnamed protein product [Mus musculus]
 9.0E-59 [12..229] [27..239]
gi|15010706, gi|... - gi|23308267|gb|AAN18103.1| At2g25350/F13B15.1 [Arabidopsis thaliana], gi|20198061|gb|AAM15377.1| Exp...
 7.0E-57 [5..233] [17..237]
RRP40_SCHPO - Exosome complex component rrp40 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp40 PE=3...
SPAC22A12.12c - exosome subunit Rrp40
 1.0E-54 [3..224] [11..231]
gi|114627214 - gi|114627214|ref|XP_001166030.1| PREDICTED: hypothetical protein isoform 4 [Pan troglodytes]
gi|208966240, gi... - gi|208966240|dbj|BAG73134.1| exosome component 2 [synthetic construct], gi|157928498|gb|ABW03545.1| ...
EXOSC2 - exosome component 2
 4.0E-51 [2..222] [24..231]
ECR1_THEAC - Probable exosome complex RNA-binding protein 1 OS=Thermoplasma acidophilum GN=Ta1292 PE=3 SV=1
RRP4_THEAC - Exosome complex component Rrp4 OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 ...
 8.0E-51 [2..239] [8..227]
ECR1_THEVO - Probable exosome complex RNA-binding protein 1 OS=Thermoplasma volcanium GN=TV0309 PE=3 SV=1
RRP4_THEVO - Exosome complex component Rrp4 OS=Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / ...
 4.0E-49 [2..239] [8..227]
exos-3 - status:Confirmed UniProt:Q93830 protein_id:CAB01875.1
 4.0E-49 [3..229] [2..218]
RRP4_PYRFU - Exosome complex component Rrp4 OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1...
ECR1_PYRFU - Probable exosome complex RNA-binding protein 1 OS=Pyrococcus furiosus GN=PF1569 PE=3 SV=1
 6.0E-49 [2..237] [9..236]

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Predicted Domain #1
Region A:
Residues: [1-146] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS GVQTAYIDYS  60
   61 SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM AFPNASKKNR PTLQVGDLVY 120
  121 ARVCTAEKEL EAEIECFDST TGRDAG

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 8.74
Match: 1e3hA
Description: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted Domain #2
Region A:
Residues: [147-240] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FGILEDGMII DVNFNFARQL LFNNDFPLLK VLAAHTKFEV AIGLNGKIWV KCEELSNTLA  60
   61 CYRTIMECCQ KNDTAAFKDI AKRQFKEILT VKEE

[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.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.845 0.025 mRNA catabolic process d.58.10 Acylphosphatase-like

Predicted functions:

Term Confidence Notes
ribonuclease activity 7.42330864261751 bayes_pls_golite062009
exoribonuclease activity 6.76241588209982 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 6.73428326869965 bayes_pls_golite062009
3'-5'-exoribonuclease activity 5.13367897180134 bayes_pls_golite062009
3'-5' exonuclease activity 3.51306349336452 bayes_pls_golite062009
nucleic acid binding 3.194200758646 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 3.07263153665399 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 2.73968547121328 bayes_pls_golite062009
DNA binding 2.71213098011194 bayes_pls_golite062009
exonuclease activity 2.66053639652924 bayes_pls_golite062009
RNA binding 2.41160981373213 bayes_pls_golite062009
binding 2.24181355929217 bayes_pls_golite062009
structure-specific DNA binding 1.81524862921454 bayes_pls_golite062009
single-stranded DNA binding 1.62996999055328 bayes_pls_golite062009
structural constituent of ribosome 1.4075750746354 bayes_pls_golite062009
aminoacyl-tRNA ligase activity 1.35850109411274 bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds 1.35845277283398 bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds 1.35845277283398 bayes_pls_golite062009
1.2099360907571 bayes_pls_golite062009
exoribonuclease II activity 1.18248519339188 bayes_pls_golite062009
structural molecule activity 1.06009055746922 bayes_pls_golite062009
transcription regulator activity 0.996884322431837 bayes_pls_golite062009
hydrolase activity 0.724860465280978 bayes_pls_golite062009
nuclease activity 0.57381531077345 bayes_pls_golite062009
mRNA binding 0.4162128308402 bayes_pls_golite062009
ligase activity 0.346041081217685 bayes_pls_golite062009
sequence-specific DNA binding 0.32084431704638 bayes_pls_golite062009
transcription factor activity 0.298729064067577 bayes_pls_golite062009
translation regulator activity 0.22908707234671 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.179682348023561 bayes_pls_golite062009
aspartate-tRNA ligase activity 0.151650064901878 bayes_pls_golite062009
translation initiation factor activity 0.11625379846973 bayes_pls_golite062009
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle