YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB5
Organism:	Saccharomyces cerevisiae
Length:	215 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 RPB5.

Description	E-value	Query Range	Subject Range
gi\|1680605 - gi\|1680605\|gb\|AAC60556.1\|S59774_1 RNA polymerase subunit [Saccharomyces cerevisiae]	1.0E-85	[1..215]	[1..215]
RPAB1_KLUMA - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Kluyveromyces marxianus GN=RPB5 PE=3 S...	2.0E-81	[1..215]	[1..215]
POLR2E - polymerase (RNA) II (DNA directed) polypeptide E, 25kDa tr\|F2Z4J4\|F2Z4J4... - PREDICTED: similar to DNA directed RNA polymerase II polypeptide E isoform 2 [Bos taurus], PREDICTED... gi\|149761124 - gi\|149761124\|ref\|XP_001496313.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide E ... gi\|208967082 - gi\|208967082\|dbj\|BAG73555.1\| polymerase (RNA) II (DNA directed) polypeptide E, 25kDa [synthetic cons...	7.0E-78	[3..214]	[1..209]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-77	[3..214]	[1..209]
gi\|194884129, gi... - gi\|194884129\|ref\|XP_001976148.1\| GG22706 [Drosophila erecta], gi\|190659335\|gb\|EDV56548.1\| GG22706 [D... gi\|195333273, gi... - gi\|195333273\|ref\|XP_002033316.1\| GM20482 [Drosophila sechellia], gi\|194125286\|gb\|EDW47329.1\| GM20482... Rpb5-PA, FBpp0304268 - The gene Rpb5 is referred to in FlyBase by the symbol Dmel\Rpb5 (CG11979, FBgn0033571). It is a prot... gi\|220957602, gi... - gi\|220957602\|gb\|ACL91344.1\| Rpb5-PA [synthetic construct], gi\|220948406\|gb\|ACL86746.1\| Rpb5-PA [synt... gi\|195483584, gi... - gi\|195483584\|ref\|XP_002090346.1\| GE13062 [Drosophila yakuba], gi\|194176447\|gb\|EDW90058.1\| GE13062 [D... gi\|194201932, gi... - gi\|195551744\|ref\|XP_002076283.1\| GD15257 [Drosophila simulans], gi\|194201932\|gb\|EDX15508.1\| GD15257 ...	8.0E-75	[3..214]	[1..209]
rpb5 - DNA-directed RNA polymerase I, II and III subunit Rpb5 RPAB1_SCHPO - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Schizosaccharomyces pombe (strain 972 ...	2.0E-69	[5..214]	[4..209]
RPB5A_ARATH - DNA-directed RNA polymerases II and IV subunit 5A OS=Arabidopsis thaliana GN=NRPB5A PE=1 SV=1	3.0E-67	[3..215]	[1..205]

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Predicted Domain #1

Region A:
Residues: [1-144]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF  60
   61 QANPTEESIS KFPDMGSLWV EFCDEPSVGV KTMKTFVIHI QEKNFQTGIF VYQNNITPSA 120
  121 MKLVPSIPPA TIETFNEAAL VVNI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1265.69897
Match:	1dzfA_
Description:	Eukaryotic RPB5 N-terminal domain; Eukaryotic RPB5 C-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [145-215]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 THHELVPKHI RLSSDEKREL LKRYRLKESQ LPRIQRADPV ALYLGLKRGE VVKIIRKSET  60
   61 SGRYASYRIC M

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1265.69897
Match:	1dzfA_
Description:	Eukaryotic RPB5 N-terminal domain; Eukaryotic RPB5 C-terminal domain
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