YRC Public Data Repository - Protein Structure Prediction

Protein:	rpb-11
Organism:	Caenorhabditis elegans
Length:	122 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-11.

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]	165.0	[0..1]	[116..992]
gi\|62088376 - gi\|62088376\|dbj\|BAD92635.1\| MGC13098 protein variant [Homo sapiens]	160.0	[0..1]	[104..23]
gi\|157752764 - gi\|157752764\|ref\|XP_001680094.1\| Hypothetical protein CBG20834 [Caenorhabditis briggsae AF16] RPB11_CAEBR - Probable DNA-directed RNA polymerase II subunit RPB11 OS=Caenorhabditis briggsae GN=rpb-11 PE=3 SV=1	154.0	[0..1]	[122..1]
gi\|109066247 - gi\|109066247\|ref\|XP_001114618.1\| PREDICTED: similar to DNA-directed RNA polymerase II subunit J (DNA...	154.0	[0..1]	[116..75]
gi\|46097891, gi\|... - gi\|71011575\|ref\|XP_758471.1\| hypothetical protein UM02324.1 [Ustilago maydis 521], ref\|XP_399939.1\| ...	150.0	[0..2]	[115..3]
gi\|114612984 - gi\|114612984\|ref\|XP_001135267.1\| PREDICTED: similar to MGC13098 protein [Pan troglodytes]	146.0	[0..1]	[104..240]

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Predicted Domain #1

Region A:
Residues: [1-122]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNAPAAFESF LLLDDKKFYI EKDTKVPNAA IFTIMKEDHT LGNMLKIQLL KDPEVLFAGY  60
   61 KNPHPLEHKI LLRIQTTNNT TPADALTTAI TDLVGELSLL EHRIDAAIKK CTQSGDQERG 120
  121 YN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	32.30103
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