YRC Public Data Repository - Protein Structure Prediction

Protein:	SMX3
Organism:	Saccharomyces cerevisiae
Length:	86 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 SMX3.

Description	E-value	Query Range	Subject Range
gi\|190408104 - gi\|190408104\|gb\|EDV11369.1\| small nuclear ribonucleoprotein F [Saccharomyces cerevisiae RM11-1a] gi\|151942952 - gi\|151942952\|gb\|EDN61298.1\| Sm F [Saccharomyces cerevisiae YJM789] RUXF_YEAST - Small nuclear ribonucleoprotein F OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SMX3 P... SMX3 - Core Sm protein Sm F; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and ...	2.0E-21	[1..86]	[1..86]
DebB-PA - The gene Developmental embryonic B is referred to in FlyBase by the symbol Dmel\DebB (CG16792, FBgn0... gi\|194177214, gi... - gi\|195485487\|ref\|XP_002091113.1\| GE13467 [Drosophila yakuba], gi\|194177214\|gb\|EDW90825.1\| GE13467 [D... gi\|194201964, gi... - gi\|195551862\|ref\|XP_002076315.1\| DebB [Drosophila simulans], gi\|195551853\|ref\|XP_002076311.1\| GD1524... gi\|220956990 - gi\|220956990\|gb\|ACL91038.1\| DebB-PA [synthetic construct] gi\|54635536, gi\|... - gi\|54635536\|gb\|EAL24939.1\| GA14154 [Drosophila pseudoobscura pseudoobscura], gi\|125807333\|ref\|XP_001... gi\|125807333\|ref... - GA14154-PA [Drosophila pseudoobscura], GA14154 [Drosophila pseudoobscura pseudoobscura] gi\|190620658, gi... - gi\|194754150\|ref\|XP_001959360.1\| GF12081 [Drosophila ananassae], gi\|190620658\|gb\|EDV36182.1\| GF12081... gi\|194883764, gi... - gi\|194883764\|ref\|XP_001975970.1\| GG22599 [Drosophila erecta], gi\|190659157\|gb\|EDV56370.1\| GG22599 [D... gi\|195056665, gi... - gi\|195056665\|ref\|XP_001995140.1\| GH22983 [Drosophila grimshawi], gi\|193899346\|gb\|EDV98212.1\| GH22983... gi\|195122320, gi... - gi\|195122320\|ref\|XP_002005660.1\| GI18952 [Drosophila mojavensis], gi\|193910728\|gb\|EDW09595.1\| GI1895... gi\|195149774, gi... - gi\|195149774\|ref\|XP_002015830.1\| GL11267 [Drosophila persimilis], gi\|194109677\|gb\|EDW31720.1\| GL1126... gi\|194125468, gi... - gi\|195333646\|ref\|XP_002033498.1\| GM20378 [Drosophila sechellia], gi\|194125468\|gb\|EDW47511.1\| GM20378... gi\|195381309, gi... - gi\|195381309\|ref\|XP_002049395.1\| GJ21558 [Drosophila virilis], gi\|194144192\|gb\|EDW60588.1\| GJ21558 [... gi\|194162173, gi... - gi\|195436262\|ref\|XP_002066088.1\| GK22120 [Drosophila willistoni], gi\|194162173\|gb\|EDW77074.1\| GK2212...	3.0E-19	[7..86]	[1..79]
snr-5 - small nuclear ribonucleoprotein Sm F (snRNP core protein F) status:Confirmed UniProt:P34659 protein_...	3.0E-19	[7..85]	[1..78]
LSM6A_ARATH - Sm-like protein LSM6A OS=Arabidopsis thaliana GN=LSM6A PE=1 SV=1	5.0E-19	[1..84]	[1..83]
gi\|34902916, gi\|... - gi\|6016876\|dbj\|BAA85219.1\| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi\|3490...	5.0E-17	[13..86]	[1..74]
gi\|27573934, gi\|... - gi\|27573935\|pdb\|1MGQ\|G Chain G, Crystal Structure Of A Heptameric Sm-Like Protein From Methanobacter...	7.0E-17	[3..83]	[1..83]
gi\|49900002, gi\|... - gi\|89273434\|emb\|CAJ82339.1\| small nuclear ribonucleoprotein polypeptide F [Xenopus tropicalis], gi\|5... RUXF_BOVIN - Small nuclear ribonucleoprotein F OS=Bos taurus GN=SNRPF PE=3 SV=2 RUXF_MOUSE - Small nuclear ribonucleoprotein F OS=Mus musculus GN=Snrpf PE=1 SV=1 gi\|109481861, gi... - gi\|186910249\|ref\|NP_001119563.1\| small nuclear ribonucleoprotein polypeptide F [Rattus norvegicus], ... gi\|542143322\|ref... - PREDICTED: small nuclear ribonucleoprotein F [Zonotrichia albicollis] ENSCJAT00000005183 - null ENSMMUT000000130... - null, null ENSPTRT00000009771 - null RUXF_XENLA - Small nuclear ribonucleoprotein F OS=Xenopus laevis GN=snrpf PE=3 SV=1 CCDS9055.1_1 - null tr\|F7CC29\|F7CC29... - Small nuclear ribonucleoprotein polypeptide F OS=Equus caballus OX=9796 GN=SNRPF PE=3 SV=1 SNRPF - small nuclear ribonucleoprotein polypeptide F gi\|118082523 - gi\|118082523\|ref\|XP_416157.2\| PREDICTED: similar to SNRPF protein [Gallus gallus]	8.0E-17	[9..84]	[1..75]

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Predicted Domain #1

Region A:
Residues: [1-86]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV  60
   61 AGVSHGTLGE IFIRCNNVLY IRELPN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.69897
Match:	1i81A_
Description:	Archaeal homoheptameric Sm protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	9.36615441177233	bayes_pls_golite062009
RNA binding	5.81718051012035	bayes_pls_golite062009
nucleic acid binding	2.69031444148163	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
binding	2.44117021254507	bayes_pls_golite062009
protein binding	0.318488892917007	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: