YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|123981016, gi...
Organism:	synthetic construct
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 gi|123981016, gi....

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...	3.0E-82	[1..275]	[1..275]
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...	1.0E-81	[1..275]	[1..275]
gi\|47221930 - gi\|47221930\|emb\|CAF98942.1\| unnamed protein product [Tetraodon nigroviridis]	1.0E-81	[1..275]	[1..275]
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	2.0E-81	[1..275]	[1..275]
gi\|47682270, gi\|... - gi\|47682270\|gb\|AAH70601.1\| MGC81245 protein [Xenopus laevis], gi\|148234336\|ref\|NP_001084998.1\| hypot...	4.0E-81	[1..275]	[1..275]
gi\|50753469 - gi\|50753469\|ref\|XP_414001.1\| PREDICTED: hypothetical protein [Gallus gallus]	4.0E-81	[1..275]	[1..275]
gi\|89266865, gi\|... - gi\|89266865\|emb\|CAJ83921.1\| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Xenopus tropica...	5.0E-81	[1..275]	[1..275]
gi\|2920709, gi\|2... - gi\|337497\|gb\|AAA36586.1\| RNA polymerase subunit hRPB 33, gi\|2920711\|emb\|CAA11843.1\| RNA polymerase s...	7.0E-81	[1..275]	[1..275]

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Predicted Domain #1

Region A:
Residues: [1-275]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH  60
   61 DEFIAHRLGL IPLISDDIVD KLQYSRDCTC EEFCPECSVE FTLDVRCNED QTRHVTSRDL 120
  121 ISNSPRVIPV TSRNRDNDPN DYVEQDDILI VKLRKGQELR LRAYAKKGFG KEHAKWNPTA 180
  181 GVAFEYDPDN ALRHTVYPKP EEWPKSEYSE LDEDESQAPY DPNGKPERFY YNVESCGSLR 240
  241 PETIVLSALS GLKKKLSDLQ TQLSHEIQSD VLTIN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	63.522879
Match:	1i3qC
Description:	RPB3
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	8.95763217796707	bayes_pls_golite062009
RNA polymerase activity	8.95763217796707	bayes_pls_golite062009
nucleotidyltransferase activity	6.40098308297479	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	4.33401073482737	bayes_pls_golite062009
transferase activity	3.84777794959854	bayes_pls_golite062009
DNA binding	1.9558633290744	bayes_pls_golite062009
nucleic acid binding	1.91068858292286	bayes_pls_golite062009
binding	1.8068389543514	bayes_pls_golite062009
catalytic activity	0.902495165806215	bayes_pls_golite062009
protein binding	0.505707524948553	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: