YRC Public Data Repository - Protein Structure Prediction

Protein:	ECM2
Organism:	Saccharomyces cerevisiae
Length:	364 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 ECM2.

Description	E-value	Query Range	Subject Range
ECM2 - Pre-mRNA splicing factor, facilitates the cooperative formation of U2/U6 helix II in association wit... SLT11_YEAST - Pre-mRNA-splicing factor SLT11 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ECM2 PE=1...	4.0E-86	[1..364]	[1..364]
C3H4_ARATH - Zinc finger CCCH domain-containing protein 4 OS=Arabidopsis thaliana GN=At1g07360 PE=2 SV=1	4.0E-80	[10..284]	[20..302]
RBM22 - RNA binding motif protein 22 RBM22_MOUSE - Pre-mRNA-splicing factor RBM22 OS=Mus musculus GN=Rbm22 PE=1 SV=1 gi\|73954184 - gi\|73954184\|ref\|XP_546302.2\| PREDICTED: similar to RNA binding motif protein 22 [Canis familiaris] tr\|M3WPJ5\|M3WPJ5... - RNA binding motif protein 22 OS=Felis catus GN=RBM22 PE=4 SV=1 CCDS34278.1_1 - null gi\|119930522 - gi\|119930522\|ref\|XP_001249809.1\| PREDICTED: similar to Pre-mRNA-splicing factor RBM22 (RNA-binding m... gi\|114602891, gi... - gi\|114602893\|ref\|XP_001167209.1\| PREDICTED: hypothetical protein isoform 1 [Pan troglodytes], gi\|114... RBM22_MACFA - Pre-mRNA-splicing factor RBM22 OS=Macaca fascicularis GN=RBM22 PE=2 SV=1 gi\|208965472, gi... - gi\|60654947\|gb\|AAX32038.1\| RNA binding motif protein 22 [synthetic construct], gi\|208965472\|dbj\|BAG7... gi\|109079367 - gi\|109079367\|ref\|XP_001108861.1\| PREDICTED: similar to RNA binding motif protein 22 isoform 2 [Macac... tr\|G1T1G7\|G1T1G7... - pep:novel chromosome:oryCun2:3:32380281:32388261:-1 gene:ENSOCUG00000011532 transcript:ENSOCUT000000...	1.0E-74	[10..287]	[21..309]
gi\|12858161 - gi\|12858161\|dbj\|BAB31220.1\| unnamed protein product [Mus musculus]	2.0E-74	[10..287]	[21..309]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	7.0E-72	[100..362]	[2..277]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	8.0E-72	[100..362]	[2..276]

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Predicted Domain #1

Region A:
Residues: [1-91]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNDEINEPPP NICEQCLGDE ANIRMTKIPQ GSECKICTLP FTLYHFKTSK RSNNIIKTLI  60
   61 CVRCATQRNI CQCCMLDSRW HIPIQLRDHL I

[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	0.247	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.385	b.60.1	Lipocalins
View	Download	0.389	d.93.1	SH2 domain
View	Download	0.266	a.77.1	DEATH domain
View	Download	0.348	d.129.1	TATA-box binding protein-like
View	Download	0.357	d.45.1	ClpS-like
View	Download	0.583	c.52.2	tRNA splicing endonuclease, C-terminal domain
View	Download	0.427	a.54.1	Domain of early E2A DNA-binding protein, ADDBP
View	Download	0.427	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.323	d.120.1	Cytochrome b5
View	Download	0.307	d.19.1	MHC antigen-recognition domain
View	Download	0.291	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.254	d.93.1	SH2 domain
View	Download	0.242	a.1.1	Globin-like
View	Download	0.234	a.6.1	Putative DNA-binding domain
View	Download	0.233	d.204.1	Ribosome binding protein Y (YfiA homologue)
View	Download	0.232	b.1.1	Immunoglobulin
View	Download	0.220	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.215	b.31.1	EV matrix protein
View	Download	0.208	g.52.1	Inhibitor of apoptosis (IAP) repeat
View	Download	0.207	b.33.1	ISP domain
View	Download	0.205	d.204.1	Ribosome binding protein Y (YfiA homologue)

Predicted functions:

Term	Confidence	Notes
binding	1.74860109511336	bayes_pls_golite062009
catalytic activity	0.223774911842048	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [92-198]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLVNEENVMT EEAKNDMMKR FLSLKNVKLG GAQITSDPSE ADNIVDKLKN ILLRATSDGP  60
   61 STPLIKNTTA LYKNEKGANE VKNLEKYASV DISHILKKLP LNESFLK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.154902
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.73097473547076	bayes_pls_golite062009
	6.62953239642182	bayes_pls_golite062009
mRNA binding	5.29759606920196	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
binding	3.49612884560266	bayes_pls_golite062009
snRNA binding	3.28448936696877	bayes_pls_golite062009
poly-pyrimidine tract binding	3.11990160533699	bayes_pls_golite062009
single-stranded RNA binding	2.93798024346416	bayes_pls_golite062009
U1 snRNA binding	2.26303528058407	bayes_pls_golite062009
protein binding	1.32954276279597	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
mRNA 3'-UTR binding	0.591700155096213	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [199-287]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NPSTKSFFLY NIDASIPEWK ITDTVSQLLG IKKWKDGNSL SLIVNHKAKC GGLRFQSSEL  60
   61 GERFVSKISE TLVTPKGLKR GVLLIDRFR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.154902
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [288-364]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IFIIPWSSGF SAASFGTNTA ENIKLSLSLN KLIQLELGLS FPTKSTDNAK NDKKKTSKKV  60
   61 HKDRSKKSKP RANKLTI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	52.221849
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
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: