YRC Public Data Repository - Protein Structure Prediction

Protein:	lsm-1
Organism:	Caenorhabditis elegans
Length:	125 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 lsm-1.

Description	E-value	Query Range	Subject Range
gi\|39597338, gi\|... - gi\|39597338\|emb\|CAE59566.1\| Hypothetical protein CBG02963 [Caenorhabditis briggsae], gi\|187036983\|em... gi\|157751226 - gi\|157751226\|ref\|XP_001679325.1\| Hypothetical protein CBG02963 [Caenorhabditis briggsae AF16]	127.0	[0..1]	[125..1]
LSM1B_ARATH - Sm-like protein LSM1B OS=Arabidopsis thaliana GN=LSM1B PE=1 SV=1	106.0	[0..10]	[116..11]
gi\|113564476, gi... - gi\|222628944\|gb\|EEE61076.1\| hypothetical protein OsJ_14946 [Oryza sativa Japonica Group], gi\|1154586... gi\|218194932 - gi\|218194932\|gb\|EEC77359.1\| hypothetical protein OsI_16058 [Oryza sativa Indica Group]	103.0	[0..4]	[116..7]
gi\|85091383 - gi\|85091383\|ref\|XP_958875.1\| hypothetical protein [Neurospora crassa OR74A] gi\|28920264, gi\|... - gi\|32414377\|ref\|XP_327668.1\| hypothetical protein [Neurospora crassa], gi\|28920264\|gb\|EAA29639.1\| hy...	103.0	[0..3]	[124..59]
gi\|92868138 - gi\|92868138\|gb\|ABE78228.1\| Like-Sm ribonucleoprotein-related, core [Medicago truncatula]	103.0	[0..4]	[116..6]
gi\|73979315 - gi\|73979315\|ref\|XP_532806.2\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm1 (Small n...	103.0	[0..2]	[119..84]
gi\|112305, gi\|206694 - gi\|206694\|gb\|AAA42059.1\| snRNP-associated polypeptide N, pir\|\|A35448 small nuclear ribonucleoprotein...	100.0	[0..7]	[110..2]

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Predicted Domain #1

Region A:
Residues: [1-125]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDLPDPYLPG AISLFEQLDK KLLVVLRDGR KLIGFLRSID QFANLILEDV VERTFVEKYF  60
   61 CETGQGFMLI RGENVELAGE IDDTIETGLT QVSPEEFRRL EDEYIAKNPP KFLKRQAEKT 120
  121 EEHDA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.522879
Match:	1b34A
Description:	D1 core SNRNP protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.863258635994511	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: