YRC Public Data Repository - Protein Structure Prediction

Protein:	rpb5
Organism:	Schizosaccharomyces pombe
Length:	210 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 rpb5.

Description	E-value	Query Range	Subject Range
RPB5_ASHGO, RPAB... - DNA-directed RNA polymerases II 24 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 5) - Ashb... RPAB1_ASHGO - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Ashbya gossypii (strain ATCC 10895 / C...	299.0	[0..3]	[209..4]
rpb-5 - RNA polymerase status:Confirmed UniProt:Q9N5K2 protein_id:AAF39906.1	296.0	[0..1]	[209..1]
gi\|157747715 - gi\|157747715\|ref\|XP_001668952.1\| Hypothetical protein CBG12745 [Caenorhabditis briggsae AF16] RPAB1_CAEBR - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Caenorhabditis briggsae GN=rpb-5 PE=3 ...	293.0	[0..1]	[209..1]
gi\|38051843, gi\|... - gi\|38051843\|gb\|AAH60467.1\| MGC68604 protein [Xenopus laevis], gi\|148225220\|ref\|NP_001083516.1\| hypot... gi\|89272916, gi\|... - gi\|89272916\|emb\|CAJ82278.1\| polymerase (RNA) II (DNA directed) polypeptide E [Xenopus tropicalis], g...	291.0	[0..3]	[209..2]
gi\|47216655 - gi\|47216655\|emb\|CAG04853.1\| unnamed protein product [Tetraodon nigroviridis]	290.0	[0..3]	[209..2]
gi\|48124579 - gi\|48124579\|ref\|XP_396561.1\| PREDICTED: similar to Rpb5 CG11979-PA [Apis mellifera]	290.0	[0..3]	[209..2]
gi\|190408693 - gi\|190408693\|gb\|EDV11958.1\| 25 kDa RNA polymerase subunit [Saccharomyces cerevisiae RM11-1a] gi\|151946543 - gi\|151946543\|gb\|EDN64765.1\| 25 kDa RNA polymerase subunit [Saccharomyces cerevisiae YJM789] gi\|207347621 - gi\|207347621\|gb\|EDZ73732.1\| YBR154Cp-like protein [Saccharomyces cerevisiae AWRI1631] RPAB1_YEAST - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Saccharomyces cerevisiae (strain ATCC ... RPB5 - RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III; contacts DNA and affects tra...	290.0	[0..3]	[209..4]
gi\|57525846, gi\|... - gi\|57525846\|ref\|NP_001003564.1\| polymerase (RNA) II (DNA directed) polypeptide E [Danio rerio], gi\|5...	290.0	[0..3]	[209..2]
gi\|91087261 - gi\|91087261\|ref\|XP_975533.1\| PREDICTED: similar to AGAP010064-PA [Tribolium castaneum]	290.0	[0..3]	[209..2]
gi\|54035366 - gb\|AAH83992.1\| Unknown (protein for MGC:98112) [Xenopus laevis] RPAB1_RAT - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus GN=Polr2e PE=2 SV=1 RPAB1_MOUSE - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus GN=Polr2e PE=1 SV=1	289.0	[0..3]	[209..2]

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Predicted Domain #1

Region A:
Residues: [1-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSAEEKNIVR VFRAWKTAHQ LVHDRGYGVS QAELDLTLDQ FKAMHCGMGR NLDRTTLSFY  60
   61 AKPSNDSNKG TIYIEFAKEP SVGIKEMRTF VHTLGDHNHK TGILIYANSM TPSAAKIIAT 120
  121 VTGQFTIETF QESDLIVNIT HHELVPKHIL LSPDEKKELL DRYKLRETQL PRIQLADPVA 180
  181 RYLGLKRGEV VKIVRRSETS GRYNSYRICA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	78.69897
Match:	1dzfA
Description:	Eukaryotic RPB5 N-terminal domain; Eukaryotic RPB5 C-terminal domain
Matching Structure (courtesy of the PDB):

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