YRC Public Data Repository - Protein Structure Prediction

Protein:	rpb-6
Organism:	Caenorhabditis elegans
Length:	137 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 rpb-6.

Description	E-value	Query Range	Subject Range
gi\|71020411, gi\|... - gi\|71020411\|ref\|XP_760436.1\| hypothetical protein UM04289.1 [Ustilago maydis 521], ref\|XP_401904.1\| ...	167.0	[0..4]	[136..1]
RPAB2_CAEBR - Probable DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Caenorhabditis briggsae GN=rp... gi\|157751064 - gi\|157751064\|ref\|XP_001679244.1\| Hypothetical protein CBG03063 [Caenorhabditis briggsae AF16]	158.0	[0..1]	[137..1]
orf19.2643, orf1... - orf19.2643 CGDID:CAL0003456 Assembly 19, Contig19-10155 (15691, 15218) CDS, reverse complemented, tr... gi\|238882727 - gi\|238882727\|gb\|EEQ46365.1\| DNA-directed RNA polymerases I [Candida albicans WO-1] gi\|46433385, gi\|... - gi\|68488216\|ref\|XP_712026.1\| potential subunit common to RNA polymerase I, II and III [Candida albic...	153.0	[0..5]	[134..14]
gi\|113611118, gi... - gi\|50936931\|ref\|XP_477993.1\| putative DNA-directed RNA polymerase Iia [Oryza sativa (japonica cultiv... gi\|125558240 - gi\|125558240\|gb\|EAZ03776.1\| hypothetical protein OsI_25904 [Oryza sativa Indica Group]	148.0	[0..4]	[136..3]
AGAP005873-PA - DNA-directed RNA polymerases I, II, and III subunit RPABC2\|protein_coding\|2L:22716242:22716721:1\|gen... gi\|55238688, gi\|... - gi\|58387910\|ref\|XP_315900.2\| AGAP005873-PA [Anopheles gambiae str. PEST], gi\|55238688\|gb\|EAA11626.2\|...	147.0	[0..30]	[136..25]
gi\|190408109 - gi\|190408109\|gb\|EDV11374.1\| RNA polymerases I [Saccharomyces cerevisiae RM11-1a] RPO26 - RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III; part of central core; simila... RPAB2_YEAST - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Saccharomyces cerevisiae (strain ATCC ... gi\|151942957 - gi\|151942957\|gb\|EDN61303.1\| ABC23 [Saccharomyces cerevisiae YJM789]	146.0	[0..4]	[134..1]
gi\|108880924, gi... - gi\|157137087\|ref\|XP_001663881.1\| DNA-directed RNA polymerase subunit rpb6 [Aedes aegypti], gi\|108880...	146.0	[0..30]	[136..25]
RPD6A_ARATH - DNA-directed RNA polymerases II, IV and V subunit 6A OS=Arabidopsis thaliana GN=NRPB6A PE=1 SV=1	146.0	[0..1]	[136..1]
gi\|56759040 - gi\|56759040\|gb\|AAW27660.1\| SJCHGC05009 protein [Schistosoma japonicum]	145.0	[0..1]	[136..1]

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Predicted Domain #1

Region A:
Residues: [1-137]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MADEDDYQDM DNDDFVDDNE MEDVIEEDPQ RPDNEDEDDD NVDENFELFD QGKAVPTSEH  60
   61 VTTPFMTKYE RARVLGTRAL QIAMGAPVMV ELEGETDPLE IARKELKQRR IPIIVRRYLP 120
  121 DGSYEDWPTD QLQLADW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.0
Match:	1i3qF
Description:	RPB6
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	0.372436499192166	bayes_pls_golite062009

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

Predicted functions: