YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB7
Organism:	Saccharomyces cerevisiae
Length:	171 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

[What does the above image mean?]

[Show Ginzu Version Information]

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.

Description	E-value	Query Range	Subject Range
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...	3.0E-35	[2..171]	[3..172]
gi\|13359203 - gi\|13359203\|dbj\|BAB33335.1\| KIAA1665 protein [Homo sapiens]	5.0E-34	[1..171]	[14..211]
rpb-7 - status:Partially_confirmed UniProt:Q9N3C9 protein_id:AAF59550.1	2.0E-33	[1..170]	[24..193]
RPOE_SULAC - DNA-directed RNA polymerase subunit E OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JC... RPOE_SULAC - DNA-directed RNA polymerase subunit E OS=Sulfolobus acidocaldarius GN=rpoE PE=1 SV=2	8.0E-33	[1..170]	[1..170]
gi\|223640159, gi... - gi\|241948197\|ref\|XP_002416821.1\| DNA-directed RNA polymerase II 19 kda polypeptide, putative; DNA-di... gi\|12655858 - gi\|12655858\|gb\|AAK00627.1\| RNA polymerase II subunit 7 [Candida albicans] gi\|68475644, gi\|... - gi\|68475644\|ref\|XP_718170.1\| likely RNA Pol II core complex subunit [Candida albicans SC5314], gi\|68...	3.0E-32	[1..170]	[1..170]
gi\|15621365, gi\|... - gi\|15920582\|ref\|NP_376251.1\| DNA-directed RNA polymerase subunit E' [Sulfolobus tokodaii str. 7], gi...	3.0E-32	[1..171]	[1..171]
RPC8_MOUSE - DNA-directed RNA polymerase III subunit RPC8 OS=Mus musculus GN=Polr3h PE=1 SV=2 gi\|149065819, gi... - gi\|27662966\|ref\|XP_216998.1\| PREDICTED: similar to polymerase (RNA) III (DNA directed) polypeptide H...	4.0E-32	[1..171]	[1..198]
gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase [Escherichia coli O157:H7], gi\|13363518\|db... gi\|74313701, gi\|... - gi\|74313701\|ref\|YP_312120.1\| polynucleotide phosphorylase/polyadenylase [Shigella sonnei Ss046], gi\|... gi\|209920641, gi... - gi\|209920641\|ref\|YP_002294725.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli SE11],... gi\|209758380, gi... - pir\|\|H85979 polynucleotide phosphorylase [imported] - Escherichia coli (strain O157:H7, substrain E... gi\|218353603, gi... - gi\|218696871\|ref\|YP_002404538.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli 55989]... gi\|218701935, gi... - gi\|218701935\|ref\|YP_002409564.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli IAI39]... gi\|12517775, gi\|... - gi\|15803706\|ref\|NP_289740.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 ED... gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 st...	2.0E-31	[2..162]	[555..713]
EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... gi\|194422295, gi... - gi\|83585805\|ref\|ZP_00924446.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_ECOBW - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=pnp ... PNP_ECOHS - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O9:H4 (strain HS) GN=pnp PE=3 SV=1 gi\|253323044, gi... - gi\|253772000\|ref\|YP_003034831.1\| Polyribonucleotide nucleotidyltransferase [Escherichia coli BL21(DE... gi\|254038330, gi... - gi\|254038330\|ref\|ZP_04872388.1\| polynucleotide phosphorylase/polyadenylase [Escherichia sp. 1_1_43],... PNP_ECOLI - Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (Polynucleotide phosphorylase) (PNPase) - Esc... PNP_ECODH - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / DH10B) GN=pnp PE=3 SV=2	2.0E-31	[2..162]	[532..690]

Back

Predicted Domain #1

Region A:
Residues: [1-79]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR  60
   61 ILPTDGSAEF NVKYRAVVF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	116.228787
Match:	1go3E_
Description:	C-terminal domain of RNA polymerase II subunit RBP4 (RpoE); N-terminal, heterodimerisation domain of RBP4 (RpoE)
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

Predicted Domain #2

Region A:
Residues: [80-171]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI  60
   61 KSRIRVKIEG CISQVSSIHA IGSIKEDYLG AI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	116.228787
Match:	1go3E_
Description:	C-terminal domain of RNA polymerase II subunit RBP4 (RpoE); N-terminal, heterodimerisation domain of RBP4 (RpoE)
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

Predicted functions: