YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB11
Organism:	Saccharomyces cerevisiae
Length:	120 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 RPB11.

Description	E-value	Query Range	Subject Range
gi\|73957788 - gi\|73957788\|ref\|XP_546937.2\| PREDICTED: similar to RAS p21 protein activator 4 [Canis familiaris]	167.0	[0..1]	[105..992]
gi\|62088376 - gi\|62088376\|dbj\|BAD92635.1\| MGC13098 protein variant [Homo sapiens]	158.0	[0..1]	[105..23]
gi\|109066247 - gi\|109066247\|ref\|XP_001114618.1\| PREDICTED: similar to DNA-directed RNA polymerase II subunit J (DNA...	157.0	[0..1]	[105..75]
gi\|49525102 - gi\|49525102\|emb\|CAG58715.1\| unnamed protein product [Candida glabrata] gi\|49525102, gi\|... - gi\|50286733\|ref\|XP_445796.1\| unnamed protein product [Candida glabrata], gi\|49525102\|emb\|CAG58715.1\|...	156.0	[0..1]	[120..1]
gi\|114612984 - gi\|114612984\|ref\|XP_001135267.1\| PREDICTED: similar to MGC13098 protein [Pan troglodytes]	154.0	[0..1]	[105..240]

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Predicted Domain #1

Region A:
Residues: [1-120]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA  60
   61 YKVEHPFFAR FKLRIQTTEG YDPKDALKNA CNSIINKLGA LKTNFETEWN LQTLAADDAF 120
  121

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.0
Match:	1i3qK
Description:	RPB11
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