YRC Public Data Repository - Protein Structure Prediction

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

Found no confident structure predictions for this domain.

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 is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

		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

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: