YRC Public Data Repository - Protein Structure Prediction

Protein:	RRP8
Organism:	Saccharomyces cerevisiae
Length:	383 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 RRP8.

Description	E-value	Query Range	Subject Range
RRP8 - Nucleolar protein involved in rRNA processing, pre-rRNA cleavage at site A2; also involved in telome...	1.0E-63	[1..383]	[20..402]
gi\|45201248, gi\|... - gi\|45201248\|ref\|NP_986818.1\| AGR152Wp [Ashbya gossypii ATCC 10895], gi\|44986102\|gb\|AAS54642.1\| AGR15... gi\|44986102 - gi\|44986102\|gb\|AAS54642.1\| AGR152Wp [Ashbya gossypii ATCC 10895]	4.0E-51	[1..381]	[21..391]
gi\|26346719 - gi\|26346719\|dbj\|BAC37008.1\| unnamed protein product [Mus musculus]	4.0E-42	[6..374]	[101..451]
gi\|2662099 - gi\|2662099\|dbj\|BAA23705.1\| KIAA0409 [Homo sapiens]	8.0E-41	[12..374]	[121..464]
UBIE_ECOK1 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O1:K1 / APEC GN=ubi... UBIE_ECOL6 - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Escherichia coli O6 GN=ubiE PE=3 SV=1 gi\|191173929, gi... - gi\|75237632\|ref\|ZP_00721652.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... UBIE_ECOL6 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O6:H1 (strain CFT07... gi\|227888553, gi... - gi\|227888553\|ref\|ZP_04006358.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Escherichia c... UBIE_ECO45 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O45:K1 (strain S88 ... gi\|226903039, gi... - gi\|237702868\|ref\|ZP_04533349.1\| ubiquinone/menaquinone biosynthesis methyltransferase ubiE [Escheric... UBIE_ECO81 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O81 (strain ED1a) G... UBIE_ECOUT - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain UTI89 / UPE... UBIE_ECOL5 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O6:K15:H31 (strain ...	3.0E-39	[153..368]	[7..240]
gi\|15804425, gi\|... - gi\|15804425\|ref\|NP_290465.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Escherichia coli... EG11473 - bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase / S-adenosylmethionine:2-DMK methyltra... gi\|15834017, gi\|... - gi\|15834017\|ref\|NP_312790.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Escherichia coli... UBIE_SHIF8 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella flexneri serotype 5b (strai... UBIE_ECOLI - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE (EC 2.1.1.-) - Escherichia coli gi\|189359289, gi... - gi\|189359289\|gb\|EDU77708.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|168750349, gi... - gi\|188015435\|gb\|EDU53557.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|168768120, gi... - gi\|189362634\|gb\|EDU81053.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|168763964, gi... - gi\|189365986\|gb\|EDU84402.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|24054401, gi\|... - gi\|24115129\|ref\|NP_709639.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Shigella flexner... UBIE_SHIFL - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella flexneri GN=ubiE PE=3 SV=1 UBIE_ECO57 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O157:H7 GN=ubiE PE=... gi\|30064870, gi\|... - gi\|30064870\|ref\|NP_839041.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Shigella flexner... sp\|B7UNG3\|UBIE_ECO27 - Ubiquinone/menaquinone biosynthesis methyltransferase ubiE OS=Escherichia coli O127:H6 (strain E2348... gi\|124499196, gi... - gi\|124530430\|ref\|ZP_01701088.1\| ubiquinone/menaquinone biosynthesis methyltransferases [Escherichia ... UBIE_ECOBW - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain K12 / MC410... gi\|226838737, gi... - gi\|254039046\|ref\|ZP_04873097.1\| ubiquinone/menaquinone biosynthesis methyltransferase ubiE [Escheric... gi\|254595231, gi... - gi\|254795831\|ref\|YP_003080668.1\| bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase [Esc... UBIE_SHISS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella sonnei (strain Ss046) GN=ub... gi\|208814084, gi... - gi\|208814084\|ref\|ZP_03255413.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escheric... UBIE_SHIDS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella dysenteriae serotype 1 (str... gi\|208727266, gi... - gi\|208807465\|ref\|ZP_03249802.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escheric... gi\|193065706, gi... - gi\|75256243\|ref\|ZP_00727921.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... UBIE_ECO5E - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O157:H7 (strain EC4... gi\|188491557, gi... - gi\|75512612\|ref\|ZP_00735124.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... gi\|208819338, gi... - gi\|208819338\|ref\|ZP_03259658.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escheric... UBIE_ECO27 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O127:H6 (strain E23... UBIE_ECOLC - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain ATCC 8739 /... UBIE_ECOSE - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain SE11) GN=ub... UBIE_SHIBS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella boydii serotype 4 (strain S... UBIE_ECO8A - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O8 (strain IAI1) GN... gi\|85676218, gi\|... - gi\|89110187\|ref\|AP_003967.1\| bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-ad... gi\|217325793, gi... - gi\|217325793\|ref\|ZP_03441877.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escheric... UBIE_SHIB3 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Shigella boydii serotype 18 (strain ... gi\|189001430, gi... - gi\|189001430\|gb\|EDU70416.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... UBIE_ECO24 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O139:H28 (strain E2... gi\|168775610, gi... - gi\|187768861\|gb\|EDU32705.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|168801097, gi... - gi\|189376704\|gb\|EDU95120.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|194438661, gi... - gi\|83585906\|ref\|ZP_00924545.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... gi\|168786677, gi... - gi\|189373295\|gb\|EDU91711.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escherichia ... gi\|75230794, gi\|... - gi\|75230794\|ref\|ZP_00717257.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... UBIE_ECOSM - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain SMS-3-5 / S... gi\|75238283, gi\|... - gi\|75238283\|ref\|ZP_00722282.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... UBIE_ECODH - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain K12 / DH10B... UBIE_ECOHS - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O9:H4 (strain HS) G... gi\|195938125 - gi\|195938125\|ref\|ZP_03083507.1\| ubiquinone/menaquinone biosynthesis methyltransferase [Escherichia c... gi\|194412713, gi... - gi\|75209540\|ref\|ZP_00709761.1\| COG2226: Methylase involved in ubiquinone/menaquinone biosynthesis [E... gi\|170769855, gi... - gi\|170769855\|ref\|ZP_02904308.1\| ubiquinone/menaquinone biosynthesis methyltransferase UbiE [Escheric... EG11473 - bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase / S-adenosylmethionine:2-DMK methyltra... UBIE_ECO7I - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O7:K1 (strain IAI39... UBIE_ECO55 - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli (strain 55989 / EAE... UBIE_ECOLU - Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Escherichia coli O17:K52:H18 (strain...	5.0E-39	[153..368]	[7..240]

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Predicted Domain #1

Region A:
Residues: [1-125]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALFNVEGWS IKTKTVAFDN KTNKSSKDKK KNNRKNGKLT REQKLKEETE AELKEQVEDI  60
   61 PSEGSVAKDI PKKNQEKSDQ NETSKKRKHD EEAPLMQVKE NIEKPTKKQL TPLQQKMMAK 120
  121 LTGSR

[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.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [126-383]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FRWINEQLYT ISSDEALKLI KEQPQLFDEY HDGFRSQVQA WPENPVDVFV DQIRYRCMKP  60
   61 VNAPGGLPGL KDSKEIVIAD MGCGEAQLAL EINNFFKNYN KKAKKYLKRR HKVHSFDLKK 120
  121 ANERITVADI RNVPLPDESC TIVVFCLALM GTNFLDFIKE AYRILAPRGE LWIAEIKSRF 180
  181 SDGKGNEFVD ALKLMGFFHK KTFDENKMFT RFEFFKPPAE IIEERRQKLE RRQKFIEVET 240
  241 EKEELEKKRR KIAEENGS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.69897
Match:	1kphA_
Description:	CmaA1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
S-adenosylmethionine-dependent methyltransferase activity	3.15840198589582	bayes_pls_golite062009
methyltransferase activity	3.08059259177729	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	2.99781997782052	bayes_pls_golite062009
rRNA methyltransferase activity	2.89157295612945	bayes_pls_golite062009
RNA methyltransferase activity	2.57273894921779	bayes_pls_golite062009
N-methyltransferase activity	2.26670816231281	bayes_pls_golite062009
tRNA methyltransferase activity	1.55242772787972	bayes_pls_golite062009
catalytic activity	1.25333584501255	bayes_pls_golite062009
rRNA (guanine) methyltransferase activity	1.21404153202137	bayes_pls_golite062009
transferase activity	1.07321114919891	bayes_pls_golite062009
rRNA (adenine) methyltransferase activity	1.03293084629981	bayes_pls_golite062009
rRNA (adenine-N6,N6-)-dimethyltransferase activity	0.954020631547781	bayes_pls_golite062009
transcription regulator activity	0.914549843668268	bayes_pls_golite062009
DNA binding	0.86027591375666	bayes_pls_golite062009
rRNA (uridine) methyltransferase activity	0.742142092552002	bayes_pls_golite062009
nucleic acid binding	0.616949327277483	bayes_pls_golite062009
RNA binding	0.417524996559564	bayes_pls_golite062009
binding	0.383237930789959	bayes_pls_golite062009
rRNA (uridine-2'-O-)-methyltransferase activity	0.15443733645953	bayes_pls_golite062009

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: