YRC Public Data Repository - Protein Structure Prediction

Protein:	RIO2
Organism:	Saccharomyces cerevisiae
Length:	425 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 RIO2.

Description	E-value	Query Range	Subject Range
gi\|151944337 - gi\|151944337\|gb\|EDN62615.1\| right open reading frame [Saccharomyces cerevisiae YJM789] RIO2 - Essential serine kinase involved in the processing of the 20S pre-rRNA into mature 18S rRNA; has sim... RIO2_YEAST - Serine/threonine-protein kinase RIO2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIO... gi\|190409181 - gi\|190409181\|gb\|EDV12446.1\| serine/threonine-protein kinase RIO2 [Saccharomyces cerevisiae RM11-1a] gi\|207341824 - gi\|207341824\|gb\|EDZ69771.1\| YNL207Wp-like protein [Saccharomyces cerevisiae AWRI1631]	0.0	[1..425]	[1..425]
RIOK2 - RIO kinase 2 (yeast)	3.0E-93	[2..419]	[3..381]
gi\|14789753 - gi\|14789753\|gb\|AAH10781.1\| RIO kinase 2 (yeast) [Mus musculus]	2.0E-91	[2..419]	[3..381]
CDC2_OXYRB - Cell division control protein 2 homolog OS=Oxybasis rubra GN=CDC2 PE=2 SV=1	8.0E-89	[93..397]	[2..288]
gi\|3123614 - gi\|3123614\|emb\|CAA76700.1\| cyclin-dependent protein kinase p34cdc2 [Solanum lycopersicum]	5.0E-88	[93..397]	[2..288]
gi\|9885803 - gi\|9885803\|gb\|AAG01534.1\|AF289467_1 cyclin-dependent kinase A:4 [Nicotiana tabacum]	5.0E-88	[93..397]	[2..288]
CDC2_MAIZE - Cell division control protein 2 homolog OS=Zea mays GN=CDC2 PE=2 SV=1	8.0E-88	[95..397]	[4..288]

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Predicted Domain #1

Region A:
Residues: [1-67]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKLDTSHMRY LTTDDFRVLQ AVEQGSRSHE VVPTPLIHQI SGMRSQSGTN RAISDLAKLS  60
   61 LISKMRN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.610	0.456	cytosol	a.77.1	DEATH domain
View	Download	0.524	0.219	nucleus	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.311	0.014	nucleus	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.308	0.001	cytosol	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.516	N/A	N/A	a.77.1	DEATH domain
View	Download	0.301	N/A	N/A	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.248	N/A	N/A	a.144.1	PABC (PABP) domain
View	Download	0.242	N/A	N/A	d.58.36	Sulfite reductase, domains 1 and 3
View	Download	0.239	N/A	N/A	a.150.1	Anti-sigma factor AsiA
View	Download	0.230	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.222	N/A	N/A	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.211	N/A	N/A	a.4.1	Homeodomain-like

Predicted Domain #2

Region A:
Residues: [68-425]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VKYDGYRLTY NGIDYLALKT MLNRDTVYSV GNTIGVGKES DIYKVSDKNG NPRVMKIHRL  60
   61 GRTSFHSVRN NRDYLKKSNQ GANWMHLSRL AANKEYQFMS MLYSKGFKVP EPFDNSRHIV 120
  121 VMELIEGYPM RRLRKHKNIP KLYSDLMCFI VDLANSGLIH CDFNEFNIMI KDKLEDENDC 180
  181 GFVVIDFPQC ISIQHQDADY YFQRDVDCIR RFFKKKLKYE PKPDSSMLDT EGFGDGYKYA 240
  241 YPDFKRDVKR TDNLDELVQA SGFSKKHPGD RGLETAVESM RNAVYNSDDD MSNDEAEEEN 300
  301 GEGDYSEEDE YYDSELDNES SEDDSEDAQE EENERIIEAL SSGVENLKMD KLGNYILE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	54.69897
Match:	1jnk__
Description:	c-jun N-terminal kinase (jnk3s)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
phosphotransferase activity, alcohol group as acceptor	2.32531951245217	bayes_pls_golite062009
protein kinase activity	2.28862009982746	bayes_pls_golite062009
kinase activity	2.161759445077	bayes_pls_golite062009
binding	2.15579529579992	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	2.11128976205756	bayes_pls_golite062009
transferase activity	1.80001061545783	bayes_pls_golite062009
protein serine/threonine kinase activity	1.76101721812142	bayes_pls_golite062009
catalytic activity	1.21655087018101	bayes_pls_golite062009
protein binding	0.994439669854616	bayes_pls_golite062009
transcription regulator activity	0.463264466764216	bayes_pls_golite062009
nucleic acid binding	0.363413065857089	bayes_pls_golite062009
DNA binding	0.347750642152652	bayes_pls_golite062009
transcription factor activity	0.265590485407466	bayes_pls_golite062009
RNA binding	0.202560498527088	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.149958560815481	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.149958560815481	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.14842991990838	bayes_pls_golite062009
ATP binding	0.0978219864504931	bayes_pls_golite062009
adenyl ribonucleotide binding	0.0611476803427368	bayes_pls_golite062009
adenyl nucleotide binding	0.050750946930082	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: