YRC Public Data Repository - Protein Structure Prediction

Protein:	RPE1_METJA, RPOE...
Organism:	Methanocaldococcus jannaschii
Length:	187 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 RPE1_METJA, RPOE....

Description	E-value	Query Range	Subject Range
gi\|229354854, gi... - gi\|229507349\|ref\|ZP_04396854.1\| ribonuclease R [Vibrio cholerae BX 330286], gi\|229354854\|gb\|EEO19775... gi\|227082716, gi... - gi\|227082716\|ref\|YP_002811267.1\| ribonuclease R [Vibrio cholerae M66-2], gi\|227010604\|gb\|ACP06816.1\|... gi\|229606855, gi... - gi\|229606855\|ref\|YP_002877503.1\| ribonuclease R [Vibrio cholerae MJ-1236], gi\|229369510\|gb\|ACQ59933.... gi\|229516852, gi... - gi\|229516852\|ref\|ZP_04406298.1\| ribonuclease R [Vibrio cholerae RC9], gi\|229345915\|gb\|EEO10887.1\| ri... RNR_VIBCH - Ribonuclease R OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rnr PE=3 ... gi\|153225383, gi... - gi\|153225383\|ref\|ZP_01954739.1\| ribonuclease R [Vibrio cholerae MAK 757], gi\|124117330\|gb\|EAY36073.1... gi\|153824007, gi... - gi\|229509728\|ref\|ZP_04399209.1\| ribonuclease R [Vibrio cholerae B33], gi\|229353202\|gb\|EEO18141.1\| ri... RNR_VIBCH - Ribonuclease R OS=Vibrio cholerae GN=rnr PE=3 SV=1	163.0	[0..11]	[186..577]
gi\|254851139, gi... - gi\|254851139\|ref\|ZP_05240489.1\| ribonuclease R [Vibrio cholerae MO10], gi\|254846844\|gb\|EET25258.1\| r... tr\|C6YKQ8\|C6YKQ8... - Ribonuclease R OS=Vibrio cholerae MO10 GN=rnr PE=3 SV=1	163.0	[0..11]	[186..577]
gi\|121728988, gi... - gi\|75814697\|ref\|ZP_00745255.1\| COG0557: Exoribonuclease R [Vibrio cholerae V52], gi\|121728988\|ref\|ZP... gi\|147675348, gi... - gi\|75827850\|ref\|ZP_00757285.1\| COG0557: Exoribonuclease R [Vibrio cholerae O395], gi\|227119038\|ref\|Y... gi\|229527471, gi... - gi\|229527471\|ref\|ZP_04416863.1\| ribonuclease R [Vibrio cholerae 12129(1)], gi\|229335103\|gb\|EEO00588.... gi\|153214904, gi... - gi\|153214904\|ref\|ZP_01949702.1\| ribonuclease R [Vibrio cholerae 1587], gi\|124115063\|gb\|EAY33883.1\| r... gi\|148873499, gi... - gi\|153831021\|ref\|ZP_01983688.1\| ribonuclease R [Vibrio cholerae 623-39], gi\|148873499\|gb\|EDL71634.1\|... gi\|153827410, gi... - gi\|153827410\|ref\|ZP_01980077.1\| ribonuclease R [Vibrio cholerae MZO-2], gi\|149738683\|gb\|EDM53025.1\| ... gi\|229341259, gi... - gi\|229521665\|ref\|ZP_04411083.1\| ribonuclease R [Vibrio cholerae TM 11079-80], gi\|229341259\|gb\|EEO062... gi\|229349399, gi... - gi\|229513522\|ref\|ZP_04402986.1\| ribonuclease R [Vibrio cholerae TMA 21], gi\|229349399\|gb\|EEO14355.1\|...	163.0	[0..11]	[186..577]
gi\|68517562, gi\|... - gi\|68544732\|ref\|ZP_00584344.1\| Exoribonuclease II [Shewanella baltica OS155], gi\|68517562\|gb\|EAN4121...	162.0	[0..11]	[187..276]
gi\|59712921, gi\|... - gi\|59712921\|ref\|YP_205697.1\| exoribonuclease R, RNase R [Vibrio fischeri ES114], gi\|59481022\|gb\|AAW8...	159.0	[0..11]	[187..577]
gi\|37199996, gi\|... - gi\|37681245\|ref\|NP_935854.1\| exoribonuclease R [Vibrio vulnificus YJ016], gi\|37199996\|dbj\|BAC95825.1...	158.0	[0..11]	[177..579]
gi\|82718443, gi\|... - gi\|82744208\|ref\|ZP_00906794.1\| Exoribonuclease II [Shewanella sp. W3-18-1], gi\|82718443\|gb\|EAP53423....	158.0	[0..11]	[187..195]
gi\|27364704, gi\|... - gi\|27364704\|ref\|NP_760232.1\| exoribonuclease R [Vibrio vulnificus CMCP6], gi\|27360849\|gb\|AAO09759.1\|...	158.0	[0..11]	[177..577]
gi\|113887634, gi... - gi\|78692299\|ref\|ZP_00856848.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Shewanella s...	156.0	[0..11]	[187..569]
gi\|82494752, gi\|... - gi\|82494752\|ref\|ZP_00880331.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Shewanella s...	156.0	[0..11]	[187..569]

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Predicted Domain #1

Region A:
Residues: [1-187]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MYKILEIADV VKVPPEEFGK DLKETVKKIL MEKYEGRLDK DVGFVLSIVD VKDIGEGKVV  60
   61 HGDGSAYHPV VFETLVYIPE MYELIEGEVV DVVEFGSFVR LGPLDGLIHV SQIMDDYVSY 120
  121 DPKREAIIGK ETGKVLEIGD YVRARIVAIS LKAERKRGSK IALTMRQPYL GKLEWIEEEK 180
  181 AKKQNQE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	34.69897
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
nucleic acid binding	3.87899047526266	bayes_pls_golite062009
DNA binding	3.47278447192966	bayes_pls_golite062009
binding	3.35781855253373	bayes_pls_golite062009
RNA polymerase activity	3.02898635943078	bayes_pls_golite062009
DNA-directed RNA polymerase activity	3.02898635943078	bayes_pls_golite062009
transcription regulator activity	2.10110937001387	bayes_pls_golite062009
structure-specific DNA binding	1.81524862921454	bayes_pls_golite062009
single-stranded DNA binding	1.62996999055328	bayes_pls_golite062009
structural constituent of ribosome	1.51215866188241	bayes_pls_golite062009
ribonuclease activity	1.19236946227657	bayes_pls_golite062009
structural molecule activity	1.16496993393687	bayes_pls_golite062009
transcription factor activity	0.937752547283357	bayes_pls_golite062009
nucleotidyltransferase activity	0.775557023642925	bayes_pls_golite062009
sequence-specific DNA binding	0.76825863122436	bayes_pls_golite062009
protein binding	0.767256907671421	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.583085644017496	bayes_pls_golite062009
nuclease activity	0.57381531077345	bayes_pls_golite062009
translation regulator activity	0.31332179848255	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.263197317040851	bayes_pls_golite062009
translation initiation factor activity	0.2080607201312	bayes_pls_golite062009
RNA binding	0.18502033889261	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.125256208482441	bayes_pls_golite062009
exoribonuclease activity	0.109774918833391	bayes_pls_golite062009
chromatin binding	0.0075451629397203	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: