YRC Public Data Repository - Protein Structure Prediction

Protein:	RPAB2_YEAST
Organism:	Saccharomyces cerevisiae S288c
Length:	155 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 RPAB2_YEAST.

Description	E-value	Query Range	Subject Range
gi\|190408109 - gi\|190408109\|gb\|EDV11374.1\| RNA polymerases I [Saccharomyces cerevisiae RM11-1a] RPO26 - RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III; part of central core; simila... RPAB2_YEAST - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Saccharomyces cerevisiae (strain ATCC ... gi\|151942957 - gi\|151942957\|gb\|EDN61303.1\| ABC23 [Saccharomyces cerevisiae YJM789]	6.0E-48	[1..155]	[1..155]
rpb6 - DNA-directed RNA polymerase I, II and III subunit Rpb6 RPAB2_SCHPO - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Schizosaccharomyces pombe (strain 972 ...	2.0E-34	[1..152]	[1..142]
gi\|7494191 - pir\|\|T18424 hypothetical protein C0155c - malaria parasite (Plasmodium falciparum) gi\|3647353, gi\|1... - gi\|3647353\|emb\|CAB10577.1\| DNA-directed RNA polymerase subunit I, putative [Plasmodium falciparum 3D...	3.0E-31	[12..154]	[15..163]
RPD6A_ARATH - DNA-directed RNA polymerases II, IV and V subunit 6A OS=Arabidopsis thaliana GN=NRPB6A PE=1 SV=1	3.0E-31	[12..154]	[3..134]
gi\|14578297 - gi\|14578297\|gb\|AAF99463.1\| PV1H14085_P [Plasmodium vivax]	6.0E-31	[1..154]	[1..157]
gi\|546863 - gi\|546863\|gb\|AAB30834.1\| RNA polymerase common subunit RPB6 [Cricetinae] RPB6_PONPY, RPAB... - DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP... gi\|55661193 - gi\|55661193\|ref\|XP_515126.1\| PREDICTED: similar to RNA Polymerase II subunit 14.4 kD isoform 2 [Pan ... HGNC:9193\|MIM:60... - (RNA) II (DNA directed) polypeptide F gi\|208965372, gi... - gi\|208965372\|dbj\|BAG72700.1\| polymerase (RNA) II (DNA directed) polypeptide F [synthetic construct],... gi\|109094151 - gi\|109094151\|ref\|XP_001090989.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide F ... gi\|119893172 - gi\|119893172\|ref\|XP_001251505.1\| PREDICTED: polymerase (RNA) II (DNA directed) polypeptide F [Bos ta... CCDS13963.1_1 - null tr\|G1T2J1\|G1T2J1... - pep:novel scaffold:oryCun2:GL018972:212613:222716:1 gene:ENSOCUG00000012064 transcript:ENSOCUT000000... RPAB2_PONAB - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii GN=POLR2F PE=2 SV=1 RPAB2_CRIGR - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Cricetulus griseus GN=POLR2F PE=2 SV=1 ENSCJAT00000023683 - null POLR2F - polymerase (RNA) II (DNA directed) polypeptide F	2.0E-30	[11..153]	[1..125]
gi\|194037227 - gi\|194037227\|ref\|XP_001925706.1\| PREDICTED: similar to RNA polymerase II [Sus scrofa] RPAB2_MOUSE - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Mus musculus GN=Polr2f PE=2 SV=1 RPAB2_RAT - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Rattus norvegicus GN=Polr2f PE=1 SV=1	2.0E-30	[11..153]	[1..125]
gi\|113611118, gi... - gi\|50936931\|ref\|XP_477993.1\| putative DNA-directed RNA polymerase Iia [Oryza sativa (japonica cultiv... gi\|125558240 - gi\|125558240\|gb\|EAZ03776.1\| hypothetical protein OsI_25904 [Oryza sativa Indica Group]	2.0E-30	[4..154]	[2..132]
gi\|19170947, gi\|... - gi\|19173358\|ref\|NP_597161.1\| DNA-DIRECTED RNA POLYMERASE I [Encephalitozoon cuniculi GB-M1], gi\|1917... gi\|19173358 - gi\|19173358\|ref\|NP_597161.1\| DNA-DIRECTED RNA POLYMERASE I [Encephalitozoon cuniculi GB-M1]	6.0E-30	[42..153]	[30..138]

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Predicted Domain #1

Region A:
Residues: [1-155]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ  60
   61 HEQIRRKTLK EKAIPKDQRA TTPYMTKYER ARILGTRALQ ISMNAPVFVD LEGETDPLRI 120
  121 AMKELAEKKI PLVIRRYLPD GSFEDWSVEE LIVDL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	815.68867
Match:	1i3qF_
Description:	RPB6
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	8.95763217796707	bayes_pls_golite062009
RNA polymerase activity	8.95763217796707	bayes_pls_golite062009
nucleotidyltransferase activity	6.40098308297479	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	4.33401073482737	bayes_pls_golite062009
transferase activity	3.84777794959854	bayes_pls_golite062009
binding	2.4602171483686	bayes_pls_golite062009
DNA binding	1.9558633290744	bayes_pls_golite062009
nucleic acid binding	1.91068858292286	bayes_pls_golite062009
catalytic activity	0.902495165806215	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: