YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB3
Organism:	Saccharomyces cerevisiae
Length:	318 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 RPB3.

Description	E-value	Query Range	Subject Range
gi\|172213 - gi\|172213\|gb\|AAA34889.1\| RNA polymerase II (EC 2.7.7.6)	3.0E-96	[1..318]	[1..318]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-82	[2..313]	[12..319]
RPB3_SCHPO - DNA-directed RNA polymerase II subunit RPB3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G... rpb3 - DNA-directed RNA polymerase II subunit 3	3.0E-73	[1..306]	[1..295]
gi\|1834323 - gi\|1834323\|dbj\|BAA09316.1\| RNA polymerase II subunit 3 [Schizosaccharomyces pombe]	1.0E-72	[1..306]	[1..295]
POLR2C - polymerase (RNA) II (DNA directed) polypeptide C, 33kDa gi\|114662810 - gi\|114662810\|ref\|XP_001148305.1\| PREDICTED: DNA directed RNA polymerase II polypeptide C isoform 1 [... gi\|123981016, gi... - gi\|60823189\|gb\|AAX36635.1\| polymerase II polypeptide C [synthetic construct], gi\|208967078\|dbj\|BAG73... gi\|90079489 - gi\|90079489\|dbj\|BAE89424.1\| unnamed protein product [Macaca fascicularis] gi\|109128647, gi... - gi\|109128647\|ref\|XP_001098417.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide C ... ENSCJAT00000023359 - null	7.0E-67	[6..270]	[7..271]

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Predicted Domain #1

Region A:
Residues: [1-180]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD  60
   61 EFIAHRLGLI PLQSMDIEQL EYSRDCFCED HCDKCSVVLT LQAFGESEST TNVYSKDLVI 120
  121 VSNLMGRNIG HPIIQDKEGN GVLICKLRKG QELKLTCVAK KGIAKEHAKW GPAAAIEFEY 180
  181

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [225-318]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ADTFYMNVES VGSIPVDQVV VRGIDTLQKK VASILLALTQ MDQDKVNFAS GDNNTASNML  60
   61 GSNEDVMMTG AEQDPYSNAS QMGNTGSGGY DNAW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10097.0
Match:	1k83C_
Description:	RPB3
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [181-224]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPWNKLKHTD YWYEQDSAKE WPQSKNCEYE DPPNEGDPFD YKAQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10097.0
Match:	1k83C_
Description:	RPB3
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