YRC Public Data Repository - Protein Structure Prediction

Protein:	lsm3
Organism:	Schizosaccharomyces pombe
Length:	93 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 lsm3.

Description	E-value	Query Range	Subject Range
gi\|47211209 - gi\|47211209\|emb\|CAF90166.1\| unnamed protein product [Tetraodon nigroviridis]	99.0	[0..4]	[93..6]
gi\|112305, gi\|206694 - gi\|206694\|gb\|AAA42059.1\| snRNP-associated polypeptide N, pir\|\|A35448 small nuclear ribonucleoprotein...	99.0	[0..7]	[93..2]
gi\|5870130 - gi\|5870130\|gb\|AAD54489.1\| small nuclear ribonucleoprotein B' [Homo sapiens]	99.0	[0..7]	[93..2]
gi\|109080354, gi... - gi\|109080356\|ref\|XP_001107037.1\| PREDICTED: similar to small nuclear ribonucleoparticle-associated p...	98.0	[0..5]	[93..3]
gi\|86438323 - gi\|86438323\|gb\|AAI12635.1\| SNRPB protein [Bos taurus]	98.0	[0..7]	[93..2]
gi\|46096383, gi\|... - gi\|71005460\|ref\|XP_757396.1\| hypothetical protein UM01249.1 [Ustilago maydis 521], ref\|XP_398864.1\| ...	98.0	[0..5]	[91..21]

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Predicted Domain #1

Region A:
Residues: [1-93]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MESAQAVAEP LDLVRLSLDE IVYVKLRGDR ELNGRLHAYD EHLNMVLGDA EEIVTIFDDE  60
   61 ETDKDKALKT IRKHYEMLFV RGDSVILIAP PRN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.09691
Match:	1d3bB
Description:	B 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	2.69031444148163	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
binding	2.04681172391952	bayes_pls_golite062009
protein binding	0.187097443004706	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: