YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM8
Organism:	Saccharomyces cerevisiae
Length:	128 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 LSM8.

Description	E-value	Query Range	Subject Range
gi\|73979315 - gi\|73979315\|ref\|XP_532806.2\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm1 (Small n...	107.0	[0..18]	[126..90]
lsm-1 - Yeast J0714 like status:Confirmed UniProt:Q20229 protein_id:CAA93263.1	99.0	[0..18]	[128..8]
RSMB_MACEU - Small nuclear ribonucleoprotein-associated protein B' OS=Macropus eugenii GN=SNRPB PE=2 SV=1	99.0	[0..16]	[107..1]
gi\|47217413 - gi\|47217413\|emb\|CAG00773.1\| unnamed protein product [Tetraodon nigroviridis]	98.0	[0..24]	[113..7]
gi\|114656016 - gi\|114656016\|ref\|XP_523182.2\| PREDICTED: hypothetical protein [Pan troglodytes]	98.0	[0..16]	[104..38]
RSMN_MOUSE - Small nuclear ribonucleoprotein-associated protein N OS=Mus musculus GN=Snrpn PE=2 SV=1 gi\|386203 - gi\|386203\|gb\|AAB27138.1\| SmN [Mus sp.] gi\|109080390, gi... - gi\|109080390\|ref\|XP_001108068.1\| PREDICTED: similar to small nuclear ribonucleoparticle-associated p... RSMN_MACFA - Small nuclear ribonucleoprotein-associated protein N OS=Macaca fascicularis GN=SNRPN PE=2 SV=1 RSMN_PONPY - Small nuclear ribonucleoprotein-associated protein N - Pongo pygmaeus (Orangutan) SNRPN - small nuclear ribonucleoprotein polypeptide N RSMN_RAT - Small nuclear ribonucleoprotein-associated protein N OS=Rattus norvegicus GN=Snrpn PE=2 SV=1 RSMN_PONAB - Small nuclear ribonucleoprotein-associated protein N OS=Pongo abelii GN=SNRPN PE=2 SV=1 gi\|123987597, gi... - gi\|123999102\|gb\|ABM87134.1\| small nuclear ribonucleoprotein polypeptide N [synthetic construct], gi\|...	98.0	[0..16]	[104..1]
gi\|86438323 - gi\|86438323\|gb\|AAI12635.1\| SNRPB protein [Bos taurus]	98.0	[0..16]	[104..1]

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Predicted Domain #1

Region A:
Residues: [1-128]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDQQAAYSTP YKKNTLSCTM SATLKDYLNK RVVIIKVDGE CLIASLNGFD KNTNLFITNV  60
   61 FNRISKEFIC KAQLLRGSEI ALVGLIDAEN DDSLAPIDEK KVPMLKDTKN KIENEHVIWE 120
  121 KVYESKTK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.522879
Match:	1d3bB
Description:	B core SNRNP protein
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