YRC Public Data Repository - Protein Structure Prediction

Protein:	POP4
Organism:	Saccharomyces cerevisiae
Length:	279 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 POP4.

Description	E-value	Query Range	Subject Range
POP4_YEAST - RNases MRP/P 32.9 kDa subunit OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=POP4 PE=1 ... POP4 - Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursor... gi\|207347488 - gi\|207347488\|gb\|EDZ73642.1\| YBR257Wp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|190408592 - gi\|190408592\|gb\|EDV11857.1\| RNases MRP/P 32.9 kDa subunit [Saccharomyces cerevisiae RM11-1a] gi\|151946644 - gi\|151946644\|gb\|EDN64866.1\| RNase MRP subunit [Saccharomyces cerevisiae YJM789]	0.0	[1..279]	[1..279]
gi\|123992762, gi... - gi\|123999500\|gb\|ABM87306.1\| processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae) [s... POP4 - processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae)	6.0E-57	[63..273]	[9..220]
RPP29_MOUSE - Ribonuclease P protein subunit p29 OS=Mus musculus GN=Pop4 PE=2 SV=1	4.0E-55	[64..273]	[10..221]
CG8038-PA - This gene is referred to in FlyBase by the symbol Dmel\CG8038 (CG8038, FBgn0035831). It is a protein...	4.0E-31	[130..266]	[65..199]
CE18505 - status:Partially_confirmed UniProt:Q9XVT1 protein_id:CAB02730.1	2.0E-29	[135..269]	[61..178]
gi\|18406178, gi\|... - gi\|21554179\|gb\|AAM63258.1\| unknown [Arabidopsis thaliana], gi\|20197152\|gb\|AAC64308.2\| expressed prot...	4.0E-27	[133..256]	[184..290]
RNP1_PYRFU - Ribonuclease P protein component 1 OS=Pyrococcus furiosus GN=rnp1 PE=1 SV=1 RNP1_PYRFU - Ribonuclease P protein component 1 OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 /...	2.0E-26	[171..266]	[41..126]
RNP1_PYRAB - Ribonuclease P protein component 1 OS=Pyrococcus abyssi GN=rnp1 PE=3 SV=1 RNP1_PYRAB - Ribonuclease P protein component 1 OS=Pyrococcus abyssi (strain GE5 / Orsay) GN=rnp1 PE=3 SV=1	2.0E-26	[171..266]	[41..125]
RNP1_PYRHO - Ribonuclease P protein component 1 OS=Pyrococcus horikoshii GN=rnp1 PE=1 SV=1 RNP1_PYRHO - Ribonuclease P protein component 1 OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 99...	4.0E-26	[171..266]	[41..125]

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Predicted Domain #1

Region A:
Residues: [1-162]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDRTQTFIKD CLFTKCLEDP EKPFNENRFQ DTLLLLPTDG GLTSRLQRQQ RKSKLNLDNL  60
   61 QKVSQLESAD KQLEKRDYQR INKNSKIALR EYINNCKKNT KKCLKLAYEN KITDKEDLLH 120
  121 YIEEKHPTIY ESLPQYVDFV PMYKELWINY IKELLNITKN LK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.486	d.19.1	MHC antigen-recognition domain
View	Download	0.486	d.19.1	MHC antigen-recognition domain
View	Download	0.480	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.480	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.351	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.351	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.395	d.19.1	MHC antigen-recognition domain
View	Download	0.371	d.19.1	MHC antigen-recognition domain
View	Download	0.320	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.262	a.24.3	Cytochromes
View	Download	0.235	a.26.1	4-helical cytokines
View	Download	0.228	a.97.1	An anticodon-binding domain of class I aminoacyl-tRNA synthetases
View	Download	0.216	d.58.26	GHMP Kinase, C-terminal domain
View	Download	0.214	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.212	c.45.1	(Phosphotyrosine protein) phosphatases II
View	Download	0.202	d.95.2	Homing endonucleases

Predicted Domain #2

Region A:
Residues: [163-279]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TFNGSLALLK LSMADYNGAL LRVTKSKNKT LIGLQGIVIW DSQKFFIMIV KGNIIDEIKC  60
   61 IPKKGTVFQF EIPISDDDDS ALRYSILGDR FKYRSVDRAG RKFKSRRCDD MLYYIQN

[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	0.519	0.231	ribonuclease P activity	b.1.18	E set domains
View	Download	0.559	0.187	ribonuclease P activity	b.60.1	Lipocalins
View	Download	0.564	0.120	ribonuclease P activity	d.93.1	SH2 domain
View	Download	0.629	0.019	ribonuclease P activity	b.61.1	Avidin/streptavidin
View	Download	0.567	N/A	N/A	b.24.1	Hyaluronate lyase-like, C-terminal domain
View	Download	0.517	N/A	N/A	d.233.1	Inhibitor of vertebrate lysozyme, Ivy
View	Download	0.465	N/A	N/A	d.199.1	DNA-binding C-terminal domain of the transcription factor MotA
View	Download	0.454	N/A	N/A	d.58.35	Pseudouridine synthase
View	Download	0.426	N/A	N/A	b.24.1	Hyaluronate lyase-like, C-terminal domain
View	Download	0.416	N/A	N/A	c.51.3	B12-dependend dehydatases associated subunit
View	Download	0.416	N/A	N/A	c.52.1	Restriction endonuclease-like
View	Download	0.414	N/A	N/A	b.63.1	Oncogene products
View	Download	0.370	N/A	N/A	d.21.1	Diaminopimelate epimerase-like
View	Download	0.351	N/A	N/A	d.24.1	Pili subunits
View	Download	0.348	N/A	N/A	d.85.1	RNA bacteriophage capsid protein
View	Download	0.341	N/A	N/A	b.1.18	E set domains
View	Download	0.338	N/A	N/A	c.23.1	CheY-like
View	Download	0.332	N/A	N/A	d.129.1	TATA-box binding protein-like
View	Download	0.282	N/A	N/A	b.63.1	Oncogene products
View	Download	0.271	N/A	N/A	b.61.3	D-aminopeptidase, middle and C-terminal domains
View	Download	0.271	N/A	N/A	d.32.1	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
View	Download	0.268	N/A	N/A	d.93.1	SH2 domain
View	Download	0.260	N/A	N/A	c.51.2	TolB, N-terminal domain
View	Download	0.257	N/A	N/A	c.23.4	Succinyl-CoA synthetase domains
View	Download	0.252	N/A	N/A	b.1.10	Clathrin adaptor appendage domain
View	Download	0.250	N/A	N/A	a.72.1	Functional domain of the splicing factor Prp18
View	Download	0.242	N/A	N/A	b.60.1	Lipocalins
View	Download	0.232	N/A	N/A	b.1.1	Immunoglobulin
View	Download	0.229	N/A	N/A	b.8.1	TRAF domain-like
View	Download	0.227	N/A	N/A	d.110.1	Profilin (actin-binding protein)
View	Download	0.225	N/A	N/A	d.129.1	TATA-box binding protein-like
View	Download	0.222	N/A	N/A	d.21.1	Diaminopimelate epimerase-like
View	Download	0.212	N/A	N/A	b.60.1	Lipocalins
View	Download	0.212	N/A	N/A	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.210	N/A	N/A	b.18.1	Galactose-binding domain-like
View	Download	0.208	N/A	N/A	b.71.1	Glycosyl hydrolase domain
View	Download	0.204	N/A	N/A	b.1.1	Immunoglobulin
View	Download	0.203	N/A	N/A	d.58.34	Formiminotransferase domain of formiminotransferase-cyclodeaminase.
View	Download	0.201	N/A	N/A	c.51.1	Anticodon-binding domain of Class II aaRS

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.22645124912591	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: