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View Structure Prediction Details

Protein: RRP4
Organism: Saccharomyces cerevisiae
Length: 359 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 RRP4.

Description E-value Query
Range		 Subject
Range
SPAC2F7.14c - exosome subunit Rrp4
RRP4_SCHPO - Exosome complex component rrp4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp4 PE=3 S...
 9.0E-76 [4..349] [1..328]
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
 1.0E-71 [35..347] [7..283]
EXOS2_MOUSE - Exosome complex component RRP4 OS=Mus musculus GN=Exosc2 PE=1 SV=1
 2.0E-68 [38..347] [10..283]
Rrp4-PA, FBpp0309932 - The gene Rrp4 is referred to in FlyBase by the symbol Dmel\Rrp4 (CG3931, FBgn0034879). It is a prote...
 1.0E-61 [45..345] [20..286]
exos-2 - status:Confirmed UniProt:Q95XD0 protein_id:AAK68595.1
 9.0E-51 [39..339] [16..282]
RRP4_ARATH - Exosome complex component RRP4 homolog OS=Arabidopsis thaliana GN=RRP4 PE=1 SV=1
 1.0E-48 [34..326] [19..289]
RRP4_PYRAB - Exosome complex component Rrp4 OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=rrp4 PE=3 SV=1
ECR1_PYRAB - Probable exosome complex RNA-binding protein 1 OS=Pyrococcus abyssi GN=PYRAB06090 PE=3 SV=1
 9.0E-48 [45..294] [2..250]
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
 1.0E-47 [45..295] [2..251]
RRP4_PYRHO - Exosome complex component Rrp4 OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 /...
ECR1_PYRHO - Probable exosome complex RNA-binding protein 1 OS=Pyrococcus horikoshii GN=PH1551 PE=3 SV=1
 4.0E-46 [45..280] [2..238]
RS1_CHLMU - 30S ribosomal protein S1 OS=Chlamydia muridarum GN=rpsA PE=1 SV=2
RS1_CHLMU - 30S ribosomal protein S1 OS=Chlamydia muridarum (strain MoPn / Nigg) GN=rpsA PE=3 SV=2
 1.0E-42 [34..314] [150..409]

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Predicted Domain #1
Region A:
Residues: [1-189] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES DSQIVTPGEL  60
   61 VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL KGRYAPETGD HVVGRIAEVG 120
  121 NKRWKVDIGG KQHAVLMLGS VNLPGGILRR KSESDELQMR SFLKEGDLLN AEVQSLFQDG 180
  181 SASLHTRSL

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 23.69897
Match: 1e3pA_
Description: Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; 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 functions:

Term Confidence Notes
RNA binding 5.18414740305744 bayes_pls_golite062009
exoribonuclease activity 4.57899887224013 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 4.54136587416505 bayes_pls_golite062009
ribonuclease activity 4.53127626527286 bayes_pls_golite062009
structural constituent of ribosome 3.89236528662255 bayes_pls_golite062009
mRNA binding 3.82977088614136 bayes_pls_golite062009
nucleic acid binding 3.68444148122352 bayes_pls_golite062009
structural molecule activity 3.54418030121155 bayes_pls_golite062009
3'-5'-exoribonuclease activity 3.40736445988244 bayes_pls_golite062009
binding 2.8667878224392 bayes_pls_golite062009
1.63970610538963 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 1.62417180482862 bayes_pls_golite062009
3'-5' exonuclease activity 1.55351486913613 bayes_pls_golite062009
transcription regulator activity 1.43703138180882 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 1.42151567812515 bayes_pls_golite062009
aminoacyl-tRNA ligase activity 1.35850109411274 bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds 1.35845277283398 bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds 1.35845277283398 bayes_pls_golite062009
exonuclease activity 1.25488463068335 bayes_pls_golite062009
DNA binding 1.20852534725468 bayes_pls_golite062009
exoribonuclease II activity 1.18248519339188 bayes_pls_golite062009
protein binding 0.934192915895039 bayes_pls_golite062009
hydrolase activity 0.704891843968224 bayes_pls_golite062009
mRNA 3'-UTR binding 0.489176583045793 bayes_pls_golite062009
transcription factor activity 0.386248501195543 bayes_pls_golite062009
ligase activity 0.346041081217685 bayes_pls_golite062009
structure-specific DNA binding 0.32222928997178 bayes_pls_golite062009
poly-pyrimidine tract binding 0.30467150200016 bayes_pls_golite062009
catalytic activity 0.161830442565647 bayes_pls_golite062009
aspartate-tRNA ligase activity 0.151650064901878 bayes_pls_golite062009
translation initiation factor activity 0.11625379846973 bayes_pls_golite062009
single-stranded DNA binding 0.1069917291606 bayes_pls_golite062009
DNA-directed RNA polymerase activity 0.0740938021136293 bayes_pls_golite062009
RNA polymerase activity 0.0740938021136293 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [190-287] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KYGKLRNGMF CQVPSSLIVR AKNHTHNLPG NITVVLGVNG YIWLRKTSQM DLARDTPSAN  60
   61 NSSSIKSTGP TGAVSLNPSI TRLEEESSWQ IYSDENDP

[Run NCBI BLAST on this sequence.]

Detection Method: MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.528 0.367 mRNA catabolic process a.3.1 Cytochrome c
View Download 0.444 0.161 mRNA catabolic process d.93.1 SH2 domain
View Download 0.408 0.042 mRNA catabolic process a.74.1 Cyclin-like
View Download 0.582 N/A N/A d.56.1 GroEL-intermediate domain like
View Download 0.361 N/A N/A d.137.1 Monooxygenase (hydroxylase) regulatory protein
View Download 0.352 N/A N/A d.50.2 Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
View Download 0.352 N/A N/A b.1.18 E set domains
View Download 0.330 N/A N/A a.4.12 TrpR-like
View Download 0.327 N/A N/A d.58.17 Metal-binding domain
View Download 0.314 N/A N/A d.49.1 Signal recognition particle alu RNA binding heterodimer, SRP9/14
View Download 0.281 N/A N/A a.51.1 Cytochrome c oxidase subunit h
View Download 0.273 N/A N/A a.77.1 DEATH domain
View Download 0.266 N/A N/A b.55.1 PH domain-like
View Download 0.247 N/A N/A c.25.1 Ferredoxin reductase-like, C-terminal NADP-linked domain
View Download 0.238 N/A N/A d.58.24 CheY-binding domain of CheA
View Download 0.236 N/A N/A d.131.1 DNA clamp
View Download 0.229 N/A N/A a.26.1 4-helical cytokines
View Download 0.222 N/A N/A d.87.2 CO dehydrogenase flavoprotein C-terminal domain-like
View Download 0.209 N/A N/A d.58.3 Protease propeptides/inhibitors
View Download 0.207 N/A N/A a.2.3 Chaperone J-domain
View Download 0.202 N/A N/A d.58.20 NAD-binding domain of HMG-CoA reductase

Predicted Domain #3
Region A:
Residues: [288-359] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SISNNIRQAI CRYANVIKAL AFCEIGITQQ RIVSAYEASM VYSNVGELIE KNVMESIGSD  60
   61 ILTAEKMRGN GN

[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		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.830 0.688 3'-5'-exoribonuclease activity a.4.9 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View Download 0.695 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.631 0.688 3'-5'-exoribonuclease activity a.3.1 Cytochrome c
View Download 0.659 0.688 3'-5'-exoribonuclease activity a.64.1 Saposin
View Download 0.754 0.688 3'-5'-exoribonuclease activity a.159.1 Protein serine/threonine phosphatase 2C, C-terminal domain
View Download 0.616 0.688 3'-5'-exoribonuclease activity a.64.1 Saposin
View Download 0.608 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.605 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.589 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.580 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.570 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.544 0.688 3'-5'-exoribonuclease activity a.17.1 p8-MTCP1
View Download 0.543 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.537 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.515 0.688 3'-5'-exoribonuclease activity a.52.1 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View Download 0.515 0.688 3'-5'-exoribonuclease activity a.7.6 Ribosomal protein S20
View Download 0.501 0.688 3'-5'-exoribonuclease activity a.60.2 RuvA domain 2-like
View Download 0.496 0.688 3'-5'-exoribonuclease activity a.80.1 DNA polymerase III clamp loader subunits, C-terminal domain
View Download 0.471 0.688 3'-5'-exoribonuclease activity a.36.1 Signal peptide-binding domain
View Download 0.452 0.688 3'-5'-exoribonuclease activity a.64.1 Saposin
View Download 0.411 0.688 3'-5'-exoribonuclease activity a.118.11 Cytochrome c oxidase subunit E
View Download 0.397 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.396 0.688 3'-5'-exoribonuclease activity a.3.1 Cytochrome c
View Download 0.395 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.388 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.368 0.688 3'-5'-exoribonuclease activity a.4.11 RNA polymerase subunit RPB10
View Download 0.364 0.688 3'-5'-exoribonuclease activity a.4.6 C-terminal effector domain of the bipartite response regulators
View Download 0.364 0.688 3'-5'-exoribonuclease activity a.76.1 Iron-dependent represor protein, dimerization domain
View Download 0.357 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.357 0.688 3'-5'-exoribonuclease activity a.1.1 Globin-like
View Download 0.350 0.688 3'-5'-exoribonuclease activity a.77.1 DEATH domain
View Download 0.345 0.688 3'-5'-exoribonuclease activity a.4.13 Sigma3 and sigma4 domains of RNA polymerase sigma factors
View Download 0.345 0.688 3'-5'-exoribonuclease activity a.4.6 C-terminal effector domain of the bipartite response regulators
View Download 0.342 0.688 3'-5'-exoribonuclease activity a.4.6 C-terminal effector domain of the bipartite response regulators
View Download 0.342 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.339 0.688 3'-5'-exoribonuclease activity a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.336 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.331 0.688 3'-5'-exoribonuclease activity a.60.6 DNA polymerase beta, N-terminal domain-like
View Download 0.322 0.688 3'-5'-exoribonuclease activity a.2.8 Eukaryotic DNA topoisomerase I, dispensable insert domain
View Download 0.322 0.688 3'-5'-exoribonuclease activity f.14.1 Voltage-gated potassium channels
View Download 0.322 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.321 0.688 3'-5'-exoribonuclease activity a.60.1 SAM/Pointed domain
View Download 0.319 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.314 0.688 3'-5'-exoribonuclease activity a.4.1 Homeodomain-like
View Download 0.312 0.688 3'-5'-exoribonuclease activity d.95.1 Glucose permease domain IIB
View Download 0.311 0.688 3'-5'-exoribonuclease activity a.1.1 Globin-like
View Download 0.306 0.688 3'-5'-exoribonuclease activity a.16.1 S15/NS1 RNA-binding domain
View Download 0.300 0.688 3'-5'-exoribonuclease activity a.60.5 Barrier-to-autointegration factor, BAF
View Download 0.281 0.688 3'-5'-exoribonuclease activity a.60.2 RuvA domain 2-like
View Download 0.281 0.688 3'-5'-exoribonuclease activity a.28.1 ACP-like
View Download 0.280 0.688 3'-5'-exoribonuclease activity a.3.1 Cytochrome c
View Download 0.279 0.688 3'-5'-exoribonuclease activity a.60.9 lambda integrase-like, N-terminal domain
View Download 0.274 0.688 3'-5'-exoribonuclease activity a.65.1 Annexin
View Download 0.269 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.267 0.688 3'-5'-exoribonuclease activity a.39.1 EF-hand
View Download 0.267 0.688 3'-5'-exoribonuclease activity a.57.1 Protein HNS-dependent expression A; HdeA
View Download 0.266 0.688 3'-5'-exoribonuclease activity a.118.14 FliG
View Download 0.266 0.688 3'-5'-exoribonuclease activity a.27.1 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View Download 0.265 0.688 3'-5'-exoribonuclease activity a.4.12 TrpR-like
View Download 0.257 0.688 3'-5'-exoribonuclease activity d.58.11 EF-G/eEF-2 domains III and V
View Download 0.254 0.688 3'-5'-exoribonuclease activity d.87.2 CO dehydrogenase flavoprotein C-terminal domain-like
View Download 0.252 0.688 3'-5'-exoribonuclease activity d.58.11 EF-G/eEF-2 domains III and V
View Download 0.245 0.688 3'-5'-exoribonuclease activity a.130.1 Chorismate mutase II
View Download 0.244 0.688 3'-5'-exoribonuclease activity a.51.1 Cytochrome c oxidase subunit h
View Download 0.241 0.688 3'-5'-exoribonuclease activity a.4.5 "Winged helix" DNA-binding domain
View Download 0.237 0.688 3'-5'-exoribonuclease activity a.52.1 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View Download 0.237 0.688 3'-5'-exoribonuclease activity a.24.7 FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View Download 0.236 0.688 3'-5'-exoribonuclease activity a.64.1 Saposin
View Download 0.235 0.688 3'-5'-exoribonuclease activity a.56.1 CO dehydrogenase ISP C-domain like
View Download 0.234 0.688 3'-5'-exoribonuclease activity d.48.1 RecA protein, C-terminal domain
View Download 0.229 0.688 3'-5'-exoribonuclease activity d.109.1 Actin depolymerizing proteins
View Download 0.228 0.688 3'-5'-exoribonuclease activity a.23.4 Mitochondrial import receptor subunit Tom20
View Download 0.227 0.688 3'-5'-exoribonuclease activity a.50.1 Anaphylotoxins (complement system)
View Download 0.226 0.688 3'-5'-exoribonuclease activity a.1.1 Globin-like
View Download 0.225 0.688 3'-5'-exoribonuclease activity a.11.1 Acyl-CoA binding protein
View Download 0.223 0.688 3'-5'-exoribonuclease activity a.60.8 HRDC-like
View Download 0.223 0.688 3'-5'-exoribonuclease activity f.17.1 F1F0 ATP synthase subunit C
View Download 0.222 0.688 3'-5'-exoribonuclease activity d.87.2 CO dehydrogenase flavoprotein C-terminal domain-like
View Download 0.217 0.688 3'-5'-exoribonuclease activity a.181.1 Antibiotic binding domain of TipA-like multidrug resistance regulators
View Download 0.217 0.688 3'-5'-exoribonuclease activity a.4.2 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
View Download 0.217 0.688 3'-5'-exoribonuclease activity a.60.1 SAM/Pointed domain
View Download 0.211 0.688 3'-5'-exoribonuclease activity a.74.1 Cyclin-like
View Download 0.208 0.688 3'-5'-exoribonuclease activity d.58.1 4Fe-4S ferredoxins
View Download 0.204 0.688 3'-5'-exoribonuclease activity f.13.1 Family A G protein-coupled receptor-like
View Download 0.203 0.688 3'-5'-exoribonuclease activity a.46.1 Methionine synthase domain
View Download 0.200 0.688 3'-5'-exoribonuclease activity a.45.1 Glutathione S-transferase (GST), C-terminal domain

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