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 are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no 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