YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB7_RAT
Organism:	Rattus norvegicus
Length:	172 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 RPB7_RAT.

Description	E-value	Query Range	Subject Range
rpb-7 - status:Partially_confirmed UniProt:Q9N3C9 protein_id:AAF59550.1	157.0	[0..1]	[170..24]
gi\|157746383 - gi\|157746383\|ref\|XP_001668287.1\| Hypothetical protein CBG04195 [Caenorhabditis briggsae AF16] gi\|187036345, gi... - gi\|39595528\|emb\|CAE60566.1\| Hypothetical protein CBG04195 [Caenorhabditis briggsae], gi\|187036345\|em...	154.0	[0..1]	[170..24]
gi\|90081264 - gi\|90081264\|dbj\|BAE90112.1\| unnamed protein product [Macaca fascicularis] gi\|109105730 - gi\|109105730\|ref\|XP_001116154.1\| PREDICTED: similar to polymerase (RNA) II (DNA directed) polypeptid...	150.0	[0..5]	[172..54]
gi\|38567178 - gi\|38567178\|emb\|CAE76471.1\| probable DNA-directed RNA polymerase II chain Rpb7 [Neurospora crassa]	150.0	[0..1]	[169..1]
gi\|114638047 - gi\|114638047\|ref\|XP_001142605.1\| PREDICTED: similar to RNA polymerase II subunit hsRPB7 [Pan troglod...	150.0	[0..4]	[172..57]
gi\|89266814, gi\|... - gi\|89266814\|emb\|CAJ83494.1\| polymerase (RNA) II (DNA directed) polypeptide G [Xenopus tropicalis], g... RPB7_DANRE - DNA-directed RNA polymerase II subunit RPB7 OS=Danio rerio GN=polr2g PE=2 SV=1 gi\|147900153, gi... - gi\|147900153\|ref\|NP_001091291.1\| hypothetical protein LOC100037112 [Xenopus laevis], gi\|123959696\|gb...	149.0	[0..1]	[172..1]
rpb7 - DNA-directed RNA polymerase complex II subunit Rpb7 RPB7_SCHPO - DNA-directed RNA polymerase II subunit rpb7 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G...	148.0	[0..2]	[171..3]
gi\|115973786, gi... - gi\|72013666\|ref\|XP_780458.1\| PREDICTED: similar to Polymerase (RNA) II (DNA directed) polypeptide G-...	148.0	[0..1]	[172..1]
gi\|73586691 - gi\|73586691\|gb\|AAI03081.1\| Polymerase (RNA) II (DNA directed) polypeptide G [Bos taurus]	146.0	[0..1]	[172..1]
gi\|42544433, gi\|... - gi\|46108676\|ref\|XP_381396.1\| hypothetical protein FG01220.1 [Gibberella zeae PH-1], gi\|42544433\|gb\|E...	146.0	[0..1]	[172..1]

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Predicted Domain #1

Region A:
Residues: [1-172]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ  60
   61 PGRGFVLYPV KYKAIVFRPF KGEVVDAVVT QVNKVGLFTE IGPMSCFISR HSIPSEMEFD 120
  121 PNSNPPCYKT MDEDIVIQQD DEIRLKIVGT RVDKNDIFAI GSLMDDYLGL VS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.522879
Match:	2c35B
Description:	Subunits Rpb4 and Rpb7 of human RNA polymerase II
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA polymerase activity	8.99678434167899	bayes_pls_golite062009
DNA-directed RNA polymerase activity	8.99678434167899	bayes_pls_golite062009
nucleotidyltransferase activity	6.44182740737882	bayes_pls_golite062009
structural constituent of ribosome	5.1118741250402	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	4.85462508375149	bayes_pls_golite062009
structural molecule activity	4.51553901145182	bayes_pls_golite062009
transferase activity	3.90847350895308	bayes_pls_golite062009
ribonuclease activity	3.83159232224897	bayes_pls_golite062009
DNA binding	3.53568546959418	bayes_pls_golite062009
RNA binding	3.49834780836233	bayes_pls_golite062009
	2.80746531284205	bayes_pls_golite062009
nucleic acid binding	2.41557476646435	bayes_pls_golite062009
exoribonuclease activity	2.41262897171619	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	2.38378389593693	bayes_pls_golite062009
transcription regulator activity	2.10110937001387	bayes_pls_golite062009
binding	1.9712766790272	bayes_pls_golite062009
structure-specific DNA binding	1.81524862921454	bayes_pls_golite062009
mRNA binding	1.660993824641	bayes_pls_golite062009
single-stranded DNA binding	1.62996999055328	bayes_pls_golite062009
protein binding	1.55473080522232	bayes_pls_golite062009
translation regulator activity	1.46320772716954	bayes_pls_golite062009
translation factor activity, nucleic acid binding	1.40718318783582	bayes_pls_golite062009
translation initiation factor activity	1.27539679024898	bayes_pls_golite062009
transcription activator activity	1.09079153283893	bayes_pls_golite062009
catalytic activity	1.02941336036162	bayes_pls_golite062009
transcription factor activity	0.937752547283357	bayes_pls_golite062009
sequence-specific DNA binding	0.85691075793641	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.83268201349295	bayes_pls_golite062009
hydrolase activity	0.724860465280978	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.583085644017496	bayes_pls_golite062009
nuclease activity	0.57381531077345	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.474251377131502	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.47336621289748	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.47336621289748	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.223941674251642	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: