YRC Public Data Repository - Protein Structure Prediction

Protein:	RNT1
Organism:	Saccharomyces cerevisiae
Length:	471 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

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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 RNT1.

Description	E-value	Query Range	Subject Range
gi\|190408465 - gi\|190408465\|gb\|EDV11730.1\| ribonuclease III [Saccharomyces cerevisiae RM11-1a] RNT1_YEAST - Ribonuclease 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RNT1 PE=1 SV=1 gi\|151945944 - gi\|151945944\|gb\|EDN64176.1\| conserved protein [Saccharomyces cerevisiae YJM789] RNT1 - RNAase III; involved in rDNA transcription and rRNA processing; also cleaves a stem-loop structure a...	0.0	[1..471]	[1..471]
pac1 - double-strand-specific ribonuclease Pac1 PAC1_SCHPO - Double-strand-specific pac1 ribonuclease OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=p...	3.0E-69	[18..443]	[11..363]
gi\|7022183 - gi\|7022183\|dbj\|BAA91511.1\| unnamed protein product [Homo sapiens]	5.0E-67	[158..470]	[465..764]
gi\|4007731, gi\|2... - gi\|4007731\|emb\|CAA22415.1\| ribonuclease III [Streptomyces coelicolor A3(2)], gi\|21223928\|ref\|NP_6297... RNC_STRCO - Ribonuclease 3 OS=Streptomyces coelicolor GN=rnc PE=3 SV=1	1.0E-61	[172..465]	[4..272]
gi\|126509385, gi... - gi\|153820073\|ref\|ZP_01972740.1\| ribonuclease III [Vibrio cholerae NCTC 8457], gi\|126509385\|gb\|EAZ719... gi\|254845291, gi... - gi\|254849586\|ref\|ZP_05238936.1\| ribonuclease III [Vibrio cholerae MO10], gi\|254845291\|gb\|EET23705.1\|... RNC_VIBCH - Ribonuclease 3 OS=Vibrio cholerae GN=rnc PE=3 SV=1 gi\|229512326, gi... - gi\|229512326\|ref\|ZP_04401805.1\| ribonuclease III [Vibrio cholerae B33], gi\|229352291\|gb\|EEO17232.1\| ... RNC_VIBCM - Ribonuclease 3 OS=Vibrio cholerae serotype O1 (strain M66-2) GN=rnc PE=3 SV=1 gi\|229519462, gi... - gi\|229519462\|ref\|ZP_04408905.1\| ribonuclease III [Vibrio cholerae RC9], gi\|229344151\|gb\|EEO09126.1\| ... gi\|229507479, gi... - gi\|229507479\|ref\|ZP_04396984.1\| ribonuclease III [Vibrio cholerae BX 330286], gi\|229354984\|gb\|EEO199... gi\|229606984, gi... - gi\|229606984\|ref\|YP_002877632.1\| ribonuclease III [Vibrio cholerae MJ-1236], gi\|229369639\|gb\|ACQ6006... RNC_VIBCH - Ribonuclease 3 OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rnc PE=3 ... gi\|153222435, gi... - gi\|153222435\|ref\|ZP_01953169.1\| ribonuclease III [Vibrio cholerae MAK 757], gi\|124118872\|gb\|EAY37615... gi\|121590982, gi... - gi\|121590982\|ref\|ZP_01678301.1\| ribonuclease III [Vibrio cholerae 2740-80], gi\|121547159\|gb\|EAX57288...	3.0E-61	[197..437]	[7..224]
gi\|15291861 - gi\|15291861\|gb\|AAK93199.1\| LD29995p [Drosophila melanogaster]	1.0E-60	[157..466]	[681..980]
RNC_PASMU - Ribonuclease 3 OS=Pasteurella multocida (strain Pm70) GN=rnc PE=3 SV=1 RNC_PASMU - Ribonuclease 3 OS=Pasteurella multocida GN=rnc PE=3 SV=1	1.0E-60	[194..438]	[4..225]

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Predicted Domain #1

Region A:
Residues: [1-112]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGSKVAGKKK TQNDNKLDNE NGSQQRENIN TKTLLKGNLK ISNYKYLEVI QLEHAVTKLV  60
   61 ESYNKIIELS PNLVAYNEAV NNQDRVPVQI LPSLSRYQLK LAAELKTLHD LK

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [113-180]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDAILTEITD YENEFDTEQK QPILQEISKA DMEKLEKLEQ VKREKREKID VNVYENLNEK  60
   61 EDEEEDEG

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.823	0.139	ribonuclease III activity	a.65.1	Annexin

Predicted functions:

Term	Confidence	Notes
endoribonuclease activity, producing 5'-phosphomonoesters	2.96839328209237	bayes_pls_golite062009
ribonuclease activity	2.94599627195218	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	2.83903486346863	bayes_pls_golite062009
ribonuclease III activity	2.48909442352541	bayes_pls_golite062009
nuclease activity	2.39439402087394	bayes_pls_golite062009
binding	2.32833343930107	bayes_pls_golite062009
nucleic acid binding	1.98461935735212	bayes_pls_golite062009
endonuclease activity	1.82613111953108	bayes_pls_golite062009
RNA binding	1.43330249905245	bayes_pls_golite062009
catalytic activity	1.04704963996426	bayes_pls_golite062009
endoribonuclease activity	1.01755329276132	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	0.627113558693086	bayes_pls_golite062009
protein binding	0.625556404096386	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [181-359]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDSYDPTKAG DIVKATKWPP KLPEIQDLAI RARVFIHKST IKDKVYLSGS EMINAHNERL  60
   61 EFLGDSILNS VMTLIIYNKF PDYSEGQLST LRMNLVSNEQ IKQWSIMYNF HEKLKTNFDL 120
  121 KDENSNFQNG KLKLYADVFE AYIGGLMEDD PRNNLPKIRK WLRKLAKPVI EEATRNQVA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.69897
Match:	1jfzA_
Description:	RNase III endonuclease catalytic domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	3.81869789149138	bayes_pls_golite062009
nucleic acid binding	3.63840462420908	bayes_pls_golite062009
RNA binding	3.49736268261512	bayes_pls_golite062009
transcription regulator activity	2.36373437225982	bayes_pls_golite062009
DNA binding	2.27199216614247	bayes_pls_golite062009
protein binding	1.64057905923545	bayes_pls_golite062009
double-stranded RNA binding	1.46317494664076	bayes_pls_golite062009
structural constituent of ribosome	1.43500771925528	bayes_pls_golite062009
structural molecule activity	1.28116258970047	bayes_pls_golite062009
transcription factor activity	1.06321736079473	bayes_pls_golite062009
transcription activator activity	0.434769929118334	bayes_pls_golite062009
cytoskeletal protein binding	0.403469167264307	bayes_pls_golite062009
transcription repressor activity	0.184664228687648	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [360-471]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LEKTDKLDMN AKRQLYSLIG YASLRLHYVT VKKPTAVDPN SIVECRVGDG TVLGTGVGRN  60
   61 IKIAGIRAAE NALRDKKMLD FYAKQRAAIP RSESVLKDPS QKNKKRKFSD TS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.154902
Match:	1ekzA_
Description:	Staufen, domain III
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:

Predicted functions: