YRC Public Data Repository - Protein Structure Prediction

Protein:	RPC40
Organism:	Saccharomyces cerevisiae
Length:	335 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 RPC40.

Description	E-value	Query Range	Subject Range
RPC40 - RNA polymerase subunit AC40, common to RNA polymerase I and III gi\|151942887 - gi\|151942887\|gb\|EDN61233.1\| AC40 [Saccharomyces cerevisiae YJM789] RPAC1_YEAST - DNA-directed RNA polymerases I and III subunit RPAC1 OS=Saccharomyces cerevisiae (strain ATCC 204508...	0.0	[1..335]	[1..335]
gi\|627869, gi\|57... - gi\|6677787\|ref\|NP_033111.1\| RNA polymerase 1-1 [Mus musculus], gi\|627869\|pir\|\|A55082 DNA-directed RN...	0.0	[1..330]	[19..347]
ENSPTRT00000033663 - null POLR1C - polymerase (RNA) I polypeptide C, 30kDa	0.0	[1..330]	[10..338]
gi\|68401632, gi\|... - gi\|68401632\|ref\|XP_685461.1\| PREDICTED: similar to RNA polymerase 1-1 isoform 1 [Danio rerio], gi\|41...	0.0	[1..325]	[11..334]
rpc40 - DNA-directed RNA polymerase I and III subunit Rpc40 RPAC1_SCHPO - DNA-directed RNA polymerases I and III subunit RPAC1 OS=Schizosaccharomyces pombe (strain 972 / ATCC...	0.0	[2..330]	[8..340]
gi\|1914859 - gi\|1914859\|emb\|CAA71570.1\| homologous to 40kD subunit of RNA-polymerase I and III [Cricetulus griseu...	0.0	[2..330]	[7..339]
gi\|32422577, gi\|... - gi\|32422577\|ref\|XP_331732.1\| hypothetical protein [Neurospora crassa], gi\|28927476\|gb\|EAA36428.1\| DN... gi\|85119573 - gi\|85119573\|ref\|XP_965664.1\| DNA-directed RNA polymerases I and III 40 kDa polypeptide [Neurospora c...	0.0	[2..329]	[25..370]

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Predicted Domain #1

Region A:
Residues: [1-229]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID  60
   61 TSIANAFRRI MISEVPSVAA EYVYFFNNTS VIQDEVLAHR IGLVPLKVDP DMLTWVDSNL 120
  121 PDDEKFTDEN TIVLSLNVKC TRNPDAPKGS TDPKELYNNA HVYARDLKFE PQGRQSTTFA 180
  181 DCPVVPADPD ILLAKLRPGQ EISLKAHCIL GIGGDHAKFS PVSTASYRL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [295-335]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RNHFIFNVES AGAMTPEEIF FKSVRILKNK AEYLKNCPIT Q

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	228.211549
Match:	1i3qC_
Description:	RPB3
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [230-294]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPQINILQPI KGESARRFQK CFPPGVIGID EGSDEAYVKD ARKDTVSREV LRYEEFADKV  60
   61 KLGRV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	228.211549
Match:	1i3qC_
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