YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM2
Organism:	Homo sapiens
Length:	95 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 LSM2.

Description	E-value	Query Range	Subject Range
gi\|114606503 - gi\|114606503\|ref\|XP_518362.2\| PREDICTED: similar to snRNP core Sm protein homolog Sm-X5 [Pan troglod...	5.0E-28	[1..95]	[82..176]
gi\|11138539 - gi\|11138539\|gb\|AAG31434.1\|AF204157_1 snRNP core protein SMX5d [Mus musculus]	7.0E-27	[2..95]	[26..119]
gi\|125818555, gi... - gi\|61097894\|ref\|NP_571571.1\| smx5 [Danio rerio], gi\|55715812\|gb\|AAH85441.1\| Smx5 [Danio rerio], gi\|1...	6.0E-26	[1..95]	[1..95]
gi\|92899039 - gi\|92899039\|gb\|ABE94505.1\| Like-Sm ribonucleoprotein, eukaryotic and archaea-type, core [Medicago tr...	9.0E-26	[1..94]	[1..89]
gi\|109509736, gi... - gi\|46237602\|emb\|CAE83980.1\| LSM2 homolog, U6 small nuclear RNA associated [S. cerevisiae] [Rattus no...	1.0E-25	[2..95]	[38..131]
gi\|226372864 - gi\|226372864\|gb\|ACO52057.1\| U6 snRNA-associated Sm-like protein LSm2 [Rana catesbeiana] gi\|163838653, gi... - gi\|62871721\|gb\|AAH94397.1\| Lsm2 protein [Xenopus laevis], gi\|163838653\|ref\|NP_001106211.1\| LSM2 homo... gi\|62858431, gi\|... - gi\|89273744\|emb\|CAJ81423.1\| LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Xenopus t...	2.0E-25	[1..95]	[1..95]
gi\|90306422, gi\|... - gi\|90306422\|gb\|EAS36053.1\| hypothetical protein CIMG_01407 [Coccidioides immitis RS], gi\|119194065\|r...	3.0E-25	[1..93]	[81..173]
gi\|110760170 - gi\|110760170\|ref\|XP_001120188.1\| PREDICTED: similar to CG10418-PA [Apis mellifera]	7.0E-25	[1..95]	[1..95]
gi\|109123961 - gi\|109123961\|ref\|XP_001115319.1\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm4 (Gly...	2.0E-24	[1..79]	[124..201]

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Predicted Domain #1

Region A:
Residues: [1-95]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFYSFFKSL VGKDVVVELK NDLSICGTLH SVDQYLNIKL TDISVTDPEK YPHMLSVKNC  60
   61 FIRGSVVRYV QLPADEVDTQ LLQDAARKEA LQQKQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.0
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	5.81718051012035	bayes_pls_golite062009
nucleic acid binding	3.79237851568526	bayes_pls_golite062009
binding	2.63965180938967	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
protein binding	0.418315253537627	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: