YRC Public Data Repository - Protein Structure Prediction

Protein:	RpII33-PA
Organism:	Drosophila melanogaster
Length:	275 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 RpII33-PA.

Description	E-value	Query Range	Subject Range
gi\|125854879, gi... - gi\|41053985\|ref\|NP_956215.1\| polymerase (RNA) II (DNA directed) polypeptide C [Danio rerio], gi\|2827...	289.0	[0..1]	[275..1]
gi\|125984946, gi... - gi\|54644558\|gb\|EAL33299.1\| GA20659 [Drosophila pseudoobscura pseudoobscura], gi\|125984946\|ref\|XP_001... gi\|195164762, gi... - gi\|195164762\|ref\|XP_002023215.1\| GL21238 [Drosophila persimilis], gi\|194105300\|gb\|EDW27343.1\| GL2123... gi\|125984946\|ref... - GA20659-PA [Drosophila pseudoobscura], GA20659 [Drosophila pseudoobscura pseudoobscura]	287.0	[0..1]	[275..1]
gi\|47221930 - gi\|47221930\|emb\|CAF98942.1\| unnamed protein product [Tetraodon nigroviridis]	286.0	[0..1]	[275..1]
gi\|89266865, gi\|... - gi\|89266865\|emb\|CAJ83921.1\| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Xenopus tropica...	285.0	[0..1]	[275..1]
RPB3_BOVIN - DNA-directed RNA polymerase II subunit RPB3 OS=Bos taurus GN=POLR2C PE=1 SV=1 gi\|73949776 - gi\|73949776\|ref\|XP_535283.2\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptide C ... gi\|149699174 - gi\|149699174\|ref\|XP_001494261.1\| PREDICTED: similar to Polymerase (RNA) II (DNA directed) polypeptid...	285.0	[0..1]	[275..1]
POLR2C - polymerase (RNA) II (DNA directed) polypeptide C, 33kDa gi\|114662810 - gi\|114662810\|ref\|XP_001148305.1\| PREDICTED: DNA directed RNA polymerase II polypeptide C isoform 1 [... gi\|123981016, gi... - gi\|60823189\|gb\|AAX36635.1\| polymerase II polypeptide C [synthetic construct], gi\|208967078\|dbj\|BAG73... gi\|90079489 - gi\|90079489\|dbj\|BAE89424.1\| unnamed protein product [Macaca fascicularis] gi\|109128647, gi... - gi\|109128647\|ref\|XP_001098417.1\| PREDICTED: similar to DNA directed RNA polymerase II polypeptide C ... ENSCJAT00000023359 - null	285.0	[0..1]	[275..1]
gi\|47682270, gi\|... - gi\|47682270\|gb\|AAH70601.1\| MGC81245 protein [Xenopus laevis], gi\|148234336\|ref\|NP_001084998.1\| hypot...	284.0	[0..1]	[275..1]
gi\|59808391, gi\|... - gi\|60223073\|ref\|NP_001012491.1\| polymerase II polypeptide C [Rattus norvegicus], gi\|59808391\|gb\|AAH8... gi\|74213568, gi\|... - gi\|74213568\|dbj\|BAE35592.1\| unnamed protein product [Mus musculus], gi\|74191349\|dbj\|BAE30257.1\| unna... tr\|G3I3K9\|G3I3K9... - DNA-directed RNA polymerase II subunit RPB3 OS=Cricetulus griseus GN=I79_018018 PE=4 SV=1	284.0	[0..1]	[275..1]
gi\|50753469 - gi\|50753469\|ref\|XP_414001.1\| PREDICTED: hypothetical protein [Gallus gallus]	284.0	[0..1]	[275..1]

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Predicted Domain #1

Region A:
Residues: [1-275]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPYANQPSVQ ITELTDDNVK FVLEDTELSV ANSLRRVFIA ETPTLAIDWV QLEANSTVLS  60
   61 DEFLAHRIGL IPLISDDVVE RLQYTRDCIC LDFCPECSVE FTLDVKCSEE QTRHVTTADL 120
  121 KSSNAKVLPV TSRNQGEEDN EYGESNDEIL IIKLRKGQEL KLRAYAKKGF GKEHAKWNPT 180
  181 AGVCFEYDPD NSMRHTLYPK PDEWPKSEHT ELEDDQYEAP YNWEAKPNKF FFNVESAGAL 240
  241 KPENIVVMGV QVLKNKLSNL QTQLSHESQN DALAV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	61.045757
Match:	1i3qC
Description:	RPB3
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