YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB8
Organism:	Saccharomyces cerevisiae
Length:	146 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 RPB8.

Description	E-value	Query Range	Subject Range
gi\|195495435, gi... - gi\|195495435\|ref\|XP_002095266.1\| GE19787 [Drosophila yakuba], gi\|195476786\|ref\|XP_002086242.1\| GE230... gi\|194122367, gi... - gi\|195348643\|ref\|XP_002040857.1\| GM22401 [Drosophila sechellia], gi\|194122367\|gb\|EDW44410.1\| GM22401... gi\|220952982, gi... - gi\|220952982\|gb\|ACL89034.1\| Rpb8-PA [synthetic construct], gi\|220942882\|gb\|ACL83984.1\| Rpb8-PA [synt... gi\|195592244, gi... - gi\|195592244\|ref\|XP_002085845.1\| GD14989 [Drosophila simulans], gi\|194197854\|gb\|EDX11430.1\| GD14989 ... gi\|54642281, gi\|... - gi\|54642281\|gb\|EAL31030.1\| GA10862 [Drosophila pseudoobscura pseudoobscura], gi\|125978971\|ref\|XP_001... gi\|125978971\|ref... - GA10862-PA [Drosophila pseudoobscura], GA10862 [Drosophila pseudoobscura pseudoobscura] Rpb8-PA - The gene Rpb8 is referred to in FlyBase by the symbol Dmel\Rpb8 (CG11246, FBgn0037121). It is a prot... gi\|194118457, gi... - gi\|195160970\|ref\|XP_002021344.1\| GL24857 [Drosophila persimilis], gi\|194118457\|gb\|EDW40500.1\| GL2485... gi\|190655459, gi... - gi\|194875877\|ref\|XP_001973676.1\| GG16218 [Drosophila erecta], gi\|190655459\|gb\|EDV52702.1\| GG16218 [D...	206.0	[0..1]	[146..1]
gi\|62204372, gi\|... - gi\|62955177\|ref\|NP_001017600.1\| hypothetical protein LOC550263 [Danio rerio], gi\|62204372\|gb\|AAH9285...	199.0	[0..1]	[146..1]
POLR2H - polymerase (RNA) II (DNA directed) polypeptide H gi\|62658151, gi\|... - gi\|62658151\|ref\|XP_573313.1\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide H ... gi\|90077816 - gi\|90077816\|dbj\|BAE88588.1\| unnamed protein product [Macaca fascicularis] gi\|126314756 - gi\|126314756\|ref\|XP_001363950.1\| PREDICTED: similar to RNA polymerase II subunit hRPB17 [Monodelphis... tr\|G1SSB5\|G1SSB5... - pep:novel chromosome:oryCun2:14:81347861:81353351:-1 gene:ENSOCUG00000007078 transcript:ENSOCUT00000... tr\|M3W8E3\|M3W8E3... - RNA polymerase II subunit H OS=Felis catus GN=POLR2H PE=4 SV=1 gi\|61887551 - gi\|61887551\|ref\|XP_581913.1\| PREDICTED: polymerase (RNA) II (DNA directed) polypeptide H isoform 1 [... gi\|57109920 - gi\|57109920\|ref\|XP_535826.1\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide H ... gi\|167774183, gi... - gi\|208967086\|dbj\|BAG73557.1\| polymerase (RNA) II (DNA directed) polypeptide H [synthetic construct],... tr\|G3I303\|G3I303... - DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Cricetulus griseus GN=I79_017801 PE=4 ... gi\|50752375 - gi\|50752375\|ref\|XP_422761.1\| PREDICTED: similar to RNA polymerase II subunit hRPB17 isoform 2 [Gallu... ENSCJAT00000029117 - null CCDS3264.1_1 - null RPAB3_MOUSE - DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Mus musculus GN=Polr2h PE=1 SV=3 gi\|542151990\|ref... - PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC3 isoform X1 [Zonotrichia albico... gi\|149731172 - gi\|149731172\|ref\|XP_001498295.1\| PREDICTED: similar to RNA polymerase II, polypeptide H [Equus cabal... gi\|149442170 - gi\|149442170\|ref\|XP_001511382.1\| PREDICTED: similar to RNA polymerase II subunit hRPB17 [Ornithorhyn...	198.0	[0..1]	[146..1]
gi\|47220948 - gi\|47220948\|emb\|CAG03481.1\| unnamed protein product [Tetraodon nigroviridis]	198.0	[0..1]	[146..1]
gi\|62859379 - gi\|62859379\|ref\|NP_001016113.1\| polymerase (RNA) II (DNA directed) polypeptide H [Xenopus (Silurana)...	197.0	[0..1]	[146..1]
gi\|148232948, gi... - gi\|49117881\|gb\|AAH72811.1\| MGC80152 protein [Xenopus laevis], gi\|148232948\|ref\|NP_001085470.1\| MGC80...	195.0	[0..1]	[146..1]
gi\|82942471, gi\|... - gi\|94393926\|ref\|XP_986091.1\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide H ...	193.0	[0..1]	[146..1]
gi\|66508630 - gi\|66508630\|ref\|XP_394557.2\| PREDICTED: similar to Rpb8 CG11246-PA isoform 1 [Apis mellifera]	191.0	[0..1]	[146..1]
RPB8A_ARATH - DNA-directed RNA polymerases II and V subunit 8A OS=Arabidopsis thaliana GN=NRPB8A PE=1 SV=1	190.0	[0..4]	[146..6]

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Predicted Domain #1

Region A:
Residues: [1-146]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA  60
   61 SSLNLEDTPA NDSSATRSWR PPQAGDRSLA DDYDYVMYGT AYKFEEVSKD LIAVYYSFGG 120
  121 LLMRLEGNYR NLNNLKQENA YLLIRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	58.69897
Match:	1a1dA
Description:	YEAST RNA POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY
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