YRC Public Data Repository - Protein Structure Prediction

Protein:	RPAB2_RAT
Organism:	Rattus norvegicus
Length:	127 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 RPAB2_RAT.

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\| ...	163.0	[0..3]	[127..15]
RPAB2_BOVIN - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Bos taurus GN=POLR2F PE=1 SV=1	158.0	[0..1]	[127..1]
gi\|57092769 - gi\|57092769\|ref\|XP_531740.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide F isof... tr\|M3VZ62\|M3VZ62... - RNA polymerase II subunit F OS=Felis catus GN=POLR2F PE=4 SV=1	157.0	[0..1]	[127..1]
gi\|546863 - gi\|546863\|gb\|AAB30834.1\| RNA polymerase common subunit RPB6 [Cricetinae] RPB6_PONPY, RPAB... - DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPABC14.4) (RP... gi\|55661193 - gi\|55661193\|ref\|XP_515126.1\| PREDICTED: similar to RNA Polymerase II subunit 14.4 kD isoform 2 [Pan ... HGNC:9193\|MIM:60... - (RNA) II (DNA directed) polypeptide F gi\|208965372, gi... - gi\|208965372\|dbj\|BAG72700.1\| polymerase (RNA) II (DNA directed) polypeptide F [synthetic construct],... gi\|109094151 - gi\|109094151\|ref\|XP_001090989.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide F ... gi\|119893172 - gi\|119893172\|ref\|XP_001251505.1\| PREDICTED: polymerase (RNA) II (DNA directed) polypeptide F [Bos ta... CCDS13963.1_1 - null tr\|G1T2J1\|G1T2J1... - pep:novel scaffold:oryCun2:GL018972:212613:222716:1 gene:ENSOCUG00000012064 transcript:ENSOCUT000000... RPAB2_PONAB - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii GN=POLR2F PE=2 SV=1 RPAB2_CRIGR - DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Cricetulus griseus GN=POLR2F PE=2 SV=1 ENSCJAT00000023683 - null POLR2F - polymerase (RNA) II (DNA directed) polypeptide F	156.0	[0..1]	[127..1]
gi\|74225195 - gi\|74225195\|dbj\|BAE38285.1\| unnamed protein product [Mus musculus]	156.0	[0..1]	[127..1]
gi\|47217008 - gi\|47217008\|emb\|CAG01636.1\| unnamed protein product [Tetraodon nigroviridis]	155.0	[0..1]	[127..1]
gi\|6522686, gi\|4... - gi\|6522686\|emb\|CAB62065.1\| RNA polymerase common subunit RPB6 [Gallus gallus], gi\|45382031\|ref\|NP_99...	155.0	[0..1]	[127..1]

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Predicted Domain #1

Region A:
Residues: [1-127]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY  60
   61 ERARVLGTRA LQIAMCAPVM VELEGETDPL LIAMKELKAR KIPIIIRRYL PDGSYEDWGV 120
  121 DELIISD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.0
Match:	1qklA
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: