YRC Public Data Repository - Protein Structure Prediction

Protein:	RPAB1_RAT
Organism:	Rattus norvegicus
Length:	210 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 RPAB1_RAT.

Description	E-value	Query Range	Subject Range
gi\|38051843, gi\|... - gi\|38051843\|gb\|AAH60467.1\| MGC68604 protein [Xenopus laevis], gi\|148225220\|ref\|NP_001083516.1\| hypot... gi\|89272916, gi\|... - gi\|89272916\|emb\|CAJ82278.1\| polymerase (RNA) II (DNA directed) polypeptide E [Xenopus tropicalis], g...	315.0	[0..1]	[210..1]
gi\|47216655 - gi\|47216655\|emb\|CAG04853.1\| unnamed protein product [Tetraodon nigroviridis]	314.0	[0..1]	[210..1]
gi\|57525846, gi\|... - gi\|57525846\|ref\|NP_001003564.1\| polymerase (RNA) II (DNA directed) polypeptide E [Danio rerio], gi\|5...	313.0	[0..1]	[210..1]
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...	313.0	[0..1]	[210..1]
RPB5_PONPY, RPAB... - DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (RPB5) (RPABC1) - Pongo pygma... RPAB1_PONAB - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii GN=POLR2E PE=2 SV=1	312.0	[0..1]	[210..1]
gi\|48124579 - gi\|48124579\|ref\|XP_396561.1\| PREDICTED: similar to Rpb5 CG11979-PA [Apis mellifera]	311.0	[0..1]	[209..1]
RPAB1_BOVIN - DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Bos taurus GN=POLR2E PE=1 SV=1	310.0	[0..1]	[210..1]

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Predicted Domain #1

Region A:
Residues: [1-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV  60
   61 LVAHNDDPTD QMFVFFPEEP KVGIKTIKVY CQRMQEENIT RALIVVQQGM TPSAKQSLVD 120
  121 MAPKYVLEQF LQQELLINIT EHELVPEHVV MTKEEVTELL ARYKLRESQL PRIQAGDPVA 180
  181 RYFGIKRGQV VKIIRPSETA GRYITYRLVQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.0
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