YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB4
Organism:	Saccharomyces cerevisiae
Length:	221 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 RPB4.

Description	E-value	Query Range	Subject Range
gi\|190409366 - gi\|190409366\|gb\|EDV12631.1\| RNA polymerase II fourth largest subunit [Saccharomyces cerevisiae RM11-... RPB4_YEAST - DNA-directed RNA polymerase II subunit RPB4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c)... gi\|151944986 - gi\|151944986\|gb\|EDN63241.1\| RNA polymerase B [Saccharomyces cerevisiae YJM789] RPB4 - RNA polymerase II subunit B32; forms two subunit dissociable complex with Rpb7p; involved recruitmen...	1.0E-70	[1..221]	[1..221]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	5.0E-38	[117..220]	[45..143]
gi\|109507081, gi... - gi\|62664161\|ref\|XP_344660.2\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide D ... gi\|73984138 - gi\|73984138\|ref\|XP_540983.2\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide D ... POLR2D - polymerase (RNA) II (DNA directed) polypeptide D RPB4_MOUSE - DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=1 SV=2 ENSPTRT00000023093 - null ENSCJAT00000042799 - null tr\|M3WUR6\|M3WUR6... - RNA polymerase II subunit D OS=Felis catus GN=POLR2D PE=4 SV=1 gi\|208967080 - gi\|208967080\|dbj\|BAG73554.1\| polymerase (RNA) II (DNA directed) polypeptide D [synthetic construct]	1.0E-30	[117..219]	[42..139]
NRPB4_ARATH - DNA-directed RNA polymerase II subunit 4 OS=Arabidopsis thaliana GN=NRPB4 PE=1 SV=1	1.0E-29	[120..215]	[34..132]
gi\|19170992, gi\|... - gi\|19173403\|ref\|NP_597206.1\| DNA-DIRECTED RNA POLYMERASE II 16KDA POLYPEPTIDE [Encephalitozoon cunic... gi\|19173403 - gi\|19173403\|ref\|NP_597206.1\| DNA-DIRECTED RNA POLYMERASE II 16KDA POLYPEPTIDE [Encephalitozoon cunic...	2.0E-26	[125..217]	[12..103]
RPB4_SCHPO - DNA-directed RNA polymerase II subunit rpb4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G... rpb4 - DNA-directed RNA polymerase II complex subunit Rpb4	9.0E-24	[140..218]	[54..131]
gi\|124800957, gi... - gi\|3845133\|gb\|AAC71838.1\| DNA-directed RNA polymerase II 16 kDa subunit, putative [Plasmodium falcip... gi\|7494425 - pir\|\|H71619 RNA polymerase 16kD subunit, RPB4-like PFB0245c - malaria parasite (Plasmodium falciparu...	7.0E-21	[142..218]	[52..128]
gi\|16082290 - gi\|16082290\|ref\|NP_394753.1\| hypothetical protein Ta1298 [Thermoplasma acidophilum DSM 1728] gi\|10640642 - gi\|10640642\|emb\|CAC12420.1\| hypothetical protein [Thermoplasma acidophilum]	0.005	[142..218]	[28..104]

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Predicted Domain #1

Region A:
Residues: [1-122]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK  60
   61 EALVERRRAF KRSQKKHKKK HLKHENANDE TTAVEDEDDD LDEDDVNADD DDFMHSETRE 120
  121 KE

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	28.552842
Match:	PF03874
Description:	RNA polymerase Rpb4

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [123-221]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LESIDVLLEQ TTGGNNKDLK NTMQYLTNFS RFRDQETVGA VIQLLKSTGL HPFEVAQLGS  60
   61 LACDTADEAK TLIPSLNNKI SDDELERILK ELSNLETLY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.54
Match:	1go3F
Description:	RNA polymerase II subunit RBP7 (RpoF)
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