YRC Public Data Repository - Protein Structure Prediction

Protein:	RRP6
Organism:	Saccharomyces cerevisiae
Length:	733 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 RRP6.

Description	E-value	Query Range	Subject Range
RRP6_YEAST - Exosome complex exonuclease RRP6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP6 PE... RRP6 - Nuclear exosome exonuclease component; has 3'-5' exonuclease activity; involved in RNA processing, m...	0.0	[1..733]	[1..733]
gi\|56204111, gi\|... - gi\|56204111\|emb\|CAI22106.1\| exosome component 10 [Homo sapiens], gi\|4505917\|ref\|NP_002676.1\| exosome...	0.0	[10..732]	[40..801]
EXOSX_MOUSE, PMC... - (P56960) Polymyositis/scleroderma autoantigen 100 kDa (Exosome component 10) (Autoantigen PM/Scl 2) ...	0.0	[10..732]	[40..828]
gi\|14250912 - gi\|14250912\|emb\|CAC39261.1\| Rrp6p homologue [Trypanosoma brucei]	0.0	[17..687]	[23..669]
RRP6_SCHPO - Exosome complex exonuclease rrp6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp6 PE=3... rrp6 - exosome subunit Rrp6	6.0E-99	[9..521]	[6..528]
gi\|15239221 - gi\|15239221\|ref\|NP_198440.1\| 3'-5' exonuclease domain-containing protein / helicase and RNase D C-te...	9.0E-84	[10..571]	[29..579]
gi\|75176751, gi\|... - gi\|75176751\|ref\|ZP_00696879.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|157080273, gi... - gi\|75188598\|ref\|ZP_00701865.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... EG10746 - 5' to 3' DNA polymerase and 3' to 5' /5' to 3' exonuclease / DNA polymerase I; required for plasmid r... gi\|194420903, gi... - gi\|83584518\|ref\|ZP_00923195.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|193068096, gi... - gi\|75238306\|ref\|ZP_00722305.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|75258154, gi\|... - gi\|75258154\|ref\|ZP_00729615.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|194430447, gi... - gi\|75208255\|ref\|ZP_00708615.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... DPO1_ECOLI - DNA polymerase I (EC 2.7.7.7) (POL I) - Escherichia coli gi\|190900509, gi... - gi\|75227237\|ref\|ZP_00714035.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|253975716, gi... - gi\|254163815\|ref\|YP_003046923.1\| DNA polymerase I [Escherichia coli B str. REL606], gi\|253975716\|gb\|... gi\|253326546, gi... - gi\|254290565\|ref\|YP_003056313.1\| DNA polymerase I [Escherichia coli BL21(DE3)], gi\|253979872\|gb\|ACT4... gi\|242379401, gi... - gi\|251787128\|ref\|YP_003001432.1\| hypothetical protein B21_03698 [Escherichia coli BL21], gi\|24237940... EG10746 - 5' to 3' DNA polymerase and 3' to 5' /5' to 3' exonuclease / DNA polymerase I; required for plasmid r... gi\|238860827, gi... - gi\|238902931\|ref\|YP_002928727.1\| DNA polymerase I [Escherichia coli BW2952], gi\|238860827\|gb\|ACR6282... gi\|85676195, gi\|... - gi\|89110164\|ref\|AP_003944.1\| fused DNA polymerase I 5'->3' exonuclease, 3'->5' polymerase and 3'->5'... gi\|169757050, gi... - gi\|170022122\|ref\|YP_001727076.1\| DNA polymerase I [Escherichia coli ATCC 8739], gi\|169757050\|gb\|ACA7... gi\|169891171, gi... - gi\|170083336\|ref\|YP_001732656.1\| DNA polymerase I [Escherichia coli str. K-12 substr. DH10B], gi\|169... gi\|124501229, gi... - gi\|124527527\|ref\|ZP_01698992.1\| DNA polymerase I [Escherichia coli B], gi\|124501229\|gb\|EAY48694.1\| D... gi\|188488957, gi... - gi\|75513987\|ref\|ZP_00736340.1\| COG0749: DNA polymerase I - 3'-5' exonuclease and polymerase domains ... gi\|209921336, gi... - gi\|209921336\|ref\|YP_002295420.1\| DNA polymerase I [Escherichia coli SE11], gi\|209914595\|dbj\|BAG79669... gi\|74314369, gi\|... - gi\|74314369\|ref\|YP_312788.1\| DNA polymerase I [Shigella sonnei Ss046], gi\|73857846\|gb\|AAZ90553.1\| DN... gi\|218363191, gi... - gi\|218556422\|ref\|YP_002389336.1\| DNA polymerase I [Escherichia coli IAI1], gi\|218363191\|emb\|CAR00833... gi\|218697577, gi... - gi\|218697577\|ref\|YP_002405244.1\| DNA polymerase I [Escherichia coli 55989], gi\|218354309\|emb\|CAV0102...	3.0E-82	[4..440]	[113..579]

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Predicted Domain #1

Region A:
Residues: [1-187]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI  60
   61 DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG 120
  121 KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP 180
  181 HPYEYEI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.69897
Match:	1j5fA_
Description:	No description for 1j5fA_ was found.

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	8.897633904438	bayes_pls_golite062009
exoribonuclease activity	8.06617873723494	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	7.94412552409677	bayes_pls_golite062009
3'-5'-exoribonuclease activity	6.42138754551191	bayes_pls_golite062009
exonuclease activity	5.51415931494501	bayes_pls_golite062009
3'-5' exonuclease activity	5.26222975375789	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	5.22368891565602	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	4.91798726616235	bayes_pls_golite062009
nuclease activity	3.11657409772275	bayes_pls_golite062009
ribonuclease H activity	2.91966688044755	bayes_pls_golite062009
hydrolase activity	2.78602644579272	bayes_pls_golite062009
	2.73492915653996	bayes_pls_golite062009
endonuclease activity	2.63074055051349	bayes_pls_golite062009
endoribonuclease activity	2.59247838057313	bayes_pls_golite062009
binding	1.92623883978176	bayes_pls_golite062009
transcription regulator activity	1.7470402498426	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	1.74431545836806	bayes_pls_golite062009
nucleic acid binding	1.73824903971928	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	1.59628511603826	bayes_pls_golite062009
DNA binding	1.46904214736532	bayes_pls_golite062009
RNA binding	1.43996903907704	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
transcription factor activity	0.857419485352409	bayes_pls_golite062009
deoxyribonuclease activity	0.24906263529692	bayes_pls_golite062009
DNA polymerase activity	0.0189279348688405	bayes_pls_golite062009
5'-3' exonuclease activity	0.00858768379909414	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [188-420]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DHQEYSPEIL QIREEIPSKS WDDSVPIWVD TSTELESMLE DLKNTKEIAV DLEHHDYRSY  60
   61 YGIVCLMQIS TRERDYLVDT LKLRENLHIL NEVFTNPSIV KVFHGAFMDI IWLQRDLGLY 120
  121 VVGLFDTYHA SKAIGLPRHS LAYLLENFAN FKTSKKYQLA DWRIRPLSKP MTAYARADTH 180
  181 FLLNIYDQLR NKLIESNKLA GVLYESRNVA KRRFEYSKYR PLTPSSEVYS PIE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1049.09691
Match:	1m0yA_
Description:	No description for 1m0yA_ was found.

Predicted Domain #3

Region A:
Residues: [421-527]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV  60
   61 IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSET

[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	0.949	0.256	3'-5'-exoribonuclease activity	a.74.1	Cyclin-like
View	Download	0.941	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.924	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.822	N/A	N/A	a.60.8	HRDC-like
View	Download	0.411	N/A	N/A	a.25.1	Ferritin-like
View	Download	0.363	N/A	N/A	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.342	N/A	N/A	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.342	N/A	N/A	a.118.8	TPR-like
View	Download	0.336	N/A	N/A	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.329	N/A	N/A	d.2.1	Lysozyme-like
View	Download	0.310	N/A	N/A	d.52.2	GMP synthetase C-terminal dimerisation domain
View	Download	0.299	N/A	N/A	a.118.8	TPR-like
View	Download	0.290	N/A	N/A	c.30.1	PreATP-grasp domain
View	Download	0.287	N/A	N/A	a.5.3	N-terminal domain of phosphatidylinositol transfer protein sec14p
View	Download	0.283	N/A	N/A	a.4.3	ARID-like
View	Download	0.282	N/A	N/A	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.282	N/A	N/A	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.275	N/A	N/A	a.3.1	Cytochrome c
View	Download	0.273	N/A	N/A	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.252	N/A	N/A	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.245	N/A	N/A	a.118.11	Cytochrome c oxidase subunit E
View	Download	0.243	N/A	N/A	a.29.4	RecG, N-terminal domain
View	Download	0.242	N/A	N/A	a.91.1	Regulator of G-protein signalling, RGS
View	Download	0.233	N/A	N/A	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.232	N/A	N/A	a.61.1	Retroviral matrix proteins
View	Download	0.232	N/A	N/A	a.1.1	Globin-like
View	Download	0.232	N/A	N/A	a.142.1	PTS-regulatory domain, PRD
View	Download	0.228	N/A	N/A	c.114.1	YchN-like
View	Download	0.228	N/A	N/A	a.23.4	Mitochondrial import receptor subunit Tom20
View	Download	0.218	N/A	N/A	d.95.2	Homing endonucleases
View	Download	0.217	N/A	N/A	a.4.12	TrpR-like
View	Download	0.215	N/A	N/A	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.214	N/A	N/A	a.41.1	Domain of poly(ADP-ribose) polymerase
View	Download	0.205	N/A	N/A	a.185.1	Gametocyte protein Pfg27
View	Download	0.205	N/A	N/A	d.224.1	SufE-like
View	Download	0.205	N/A	N/A	c.45.1	(Phosphotyrosine protein) phosphatases II
View	Download	0.203	N/A	N/A	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.201	N/A	N/A	f.14.1	Voltage-gated potassium channels

Predicted Domain #4

Region A:
Residues: [528-733]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KADGILLETI SVPQIRDVME RFSVLCNSNI SKSRAKPVTN SSILLGKILP REEHDIAYSK  60
   61 DGLPNKVKTE DIRIRAQNFK SALANLEDII FEIEKPLVVP VKLEEIKTVD PASAPNHSPE 120
  121 IDNLDDLVVL KKKNIQKKQP AKEKGVTEKD AVDYSKIPNI LSNKPGQNNR QQKKRRFDPS 180
  181 SSDSNGPRAA KKRRPAAKGK NLSFKR

[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.

Found no structure predictions for this domain.

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: