YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB9
Organism:	Saccharomyces cerevisiae
Length:	122 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 RPB9.

Description	E-value	Query Range	Subject Range
RPB9 - RNA polymerase II subunit B12.6; contacts DNA; mutations affect transcription start site selection a... ORFP:8599 - YGL070C, Contig c21 27068-27436 gi\|151943735 - gi\|151943735\|gb\|EDN62045.1\| RNA polymerase B [Saccharomyces cerevisiae YJM789] RPB9_YEAST - DNA-directed RNA polymerase II subunit RPB9 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)... gi\|190407029 - gi\|190407029\|gb\|EDV10296.1\| RNA polymerase II core subunit [Saccharomyces cerevisiae RM11-1a]	9.0E-32	[1..122]	[1..122]
gi\|149721893 - gi\|149721893\|ref\|XP_001493833.1\| PREDICTED: similar to RNA Polymerase II subunit 14.5 kD [Equus caba... tr\|M3X8K0\|M3X8K0... - DNA-directed RNA polymerase subunit OS=Felis catus GN=POLR2I PE=3 SV=1 POLR2I - polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa tr\|G1TAL1\|G1TAL1... - pep:novel scaffold:oryCun2:GL018786:846736:847756:-1 gene:ENSOCUG00000013044 transcript:ENSOCUT00000... gi\|76641410 - gi\|76641410\|ref\|XP_871092.1\| PREDICTED: similar to DNA-directed RNA polymerase II 14.5 kDa polypepti... RPB9_MOUSE - DNA-directed RNA polymerase II subunit RPB9 OS=Mus musculus GN=Polr2i PE=1 SV=1 CCDS12487.1_1 - null RPB9_PIG - DNA-directed RNA polymerase II subunit RPB9 OS=Sus scrofa GN=POLR2I PE=3 SV=1 gi\|126329203 - gi\|126329203\|ref\|XP_001364276.1\| PREDICTED: similar to RNA Polymerase II subunit 14.5 kD [Monodelphi... gi\|73947834 - gi\|73947834\|ref\|XP_853642.1\| PREDICTED: similar to DNA-directed RNA polymerase II 14.5 kDa polypepti... gi\|114676836 - gi\|114676836\|ref\|XP_001162834.1\| PREDICTED: DNA directed RNA polymerase II polypeptide I [Pan troglo... gi\|208967088, gi... - gi\|208967088\|dbj\|BAG73558.1\| polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa [synthetic co... ENSCJAT00000018746 - null gi\|149056348, gi... - gi\|34855683\|ref\|XP_214895.2\| PREDICTED: similar to DNA-directed RNA polymerase II 14.5 kDa polypepti... gi\|109124448 - gi\|109124448\|ref\|XP_001102318.1\| PREDICTED: similar to DNA-directed RNA polymerase II 14.5 kDa polyp...	2.0E-28	[4..112]	[14..125]
gi\|7327286 - gi\|7327286\|gb\|AAB29028.2\| RNA polymerase II subunit 9 [Drosophila melanogaster]	2.0E-27	[4..112]	[18..129]
gi\|18893037, gi\|... - gi\|18977358\|ref\|NP_578715.1\| DNA-directed RNA polymerase subunit M [Pyrococcus furiosus DSM 3638], g...	6.0E-27	[4..112]	[2..108]
rpb-9 - status:Partially_confirmed UniProt:Q965S0 protein_id:AAK85514.1	7.0E-27	[4..112]	[56..167]
RPB9A_ARATH - DNA-directed RNA polymerases II, IV and V subunit 9A OS=Arabidopsis thaliana GN=NRPB9A PE=1 SV=1	1.0E-26	[1..112]	[1..114]
TFS_THECE - Transcription factor S OS=Thermococcus celer GN=tfs PE=1 SV=1	1.0E-26	[4..112]	[1..108]
rpb9 - DNA-directed RNA polymerase II complex subunit Rpb9 RPB9_SCHPO - DNA-directed RNA polymerase II subunit RPB9 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G...	3.0E-26	[1..112]	[1..112]

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Predicted Domain #1

Region A:
Residues: [1-45]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	632.39794
Match:	1k83I_
Description:	RBP9 subunit of RNA polymerase II
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [46-122]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HELITNIGET AGVVQDIGSD PTLPRSDREC PKCHSRENVF FQSQQRRKDT SMVLFFVCLS  60
   61 CSHIFTSDQK NKRTQFS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	632.39794
Match:	1k83I_
Description:	RBP9 subunit of RNA polymerase II
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