YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM4_MOUSE
Organism:	Mus musculus
Length:	137 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 LSM4_MOUSE.

Description	E-value	Query Range	Subject Range
gi\|13161882 - gi\|13161882\|emb\|CAC33027.1\| Lsm4 protein [Takifugu rubripes]	128.0	[0..1]	[135..1]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	122.0	[0..1]	[121..1]
LSM4_FAGSY - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica GN=LSM4 PE=2 SV=1	121.0	[0..1]	[130..1]
FBpp0293054, CG1... - This gene is referred to in FlyBase by the symbol Dmel\CG17768 (CG17768, FBgn0032240). It is a prote...	119.0	[0..1]	[135..1]
gi\|38047763 - gi\|38047763\|gb\|AAR09784.1\| similar to Drosophila melanogaster CG17768 [Drosophila yakuba]	117.0	[0..3]	[135..1]
gi\|47217413 - gi\|47217413\|emb\|CAG00773.1\| unnamed protein product [Tetraodon nigroviridis]	115.0	[0..2]	[98..2]
gi\|12834762 - gi\|12834762\|dbj\|BAB23033.1\| unnamed protein product [Mus musculus]	114.0	[0..1]	[87..1]
gi\|54311207, gi\|... - gi\|54311207\|gb\|AAH84779.1\| LOC495318 protein [Xenopus laevis], gi\|147902804\|ref\|NP_001088454.1\| hypo...	113.0	[0..1]	[137..1]
gi\|39849973, gi\|... - gi\|52078460\|gb\|AAH82491.1\| LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Xenopus tr...	113.0	[0..1]	[137..1]

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Predicted Domain #1

Region A:
Residues: [1-137]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLPLSLLKTA QNHPMLVELK NGETYNGHLV SCDNWMNINL REVICTSRDG DKFWRMPECY  60
   61 IRGSTIKYLR IPDEIIDMVR EEAAKGRGRG GPQQKQQKGR GMGGAGRGVF GGRGRGGIPG 120
  121 AGRGQPEKKP GRQAGKQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.221849
Match:	1b34A
Description:	D1 core SNRNP protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
	9.36615441177233	bayes_pls_golite062009
RNA binding	5.1274062744119	bayes_pls_golite062009
nucleic acid binding	2.69031444148163	bayes_pls_golite062009
mRNA binding	2.56885776197912	bayes_pls_golite062009
binding	2.04681172391952	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: