YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM1
Organism:	Homo sapiens
Length:	133 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 LSM1.

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...	4.0E-33	[1..133]	[87..219]
gi\|109504379, gi... - gi\|157820263\|ref\|NP_001102346.1\| LSM1 homolog, U6 small nuclear RNA associated [Rattus norvegicus], ...	5.0E-30	[1..133]	[1..133]
LSM1_MOUSE - U6 snRNA-associated Sm-like protein LSm1 OS=Mus musculus GN=Lsm1 PE=1 SV=1	5.0E-30	[1..133]	[1..133]
gi\|58332084, gi\|... - gi\|58332084\|ref\|NP_001011191.1\| LSM1 homolog, U6 small nuclear RNA associated [Xenopus (Silurana) tr...	1.0E-29	[1..133]	[1..133]
ENSCJAT00000005029 - null LSM1_BOVIN - U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus GN=LSM1 PE=2 SV=1	2.0E-29	[1..133]	[1..133]
gi\|148227316, gi... - gi\|76779739\|gb\|AAI06458.1\| MGC131170 protein [Xenopus laevis], gi\|148227316\|ref\|NP_001090109.1\| hypo...	2.0E-29	[1..133]	[1..133]
gi\|47209042 - gi\|47209042\|emb\|CAF91744.1\| unnamed protein product [Tetraodon nigroviridis]	9.0E-27	[1..133]	[1..133]
gi\|220679348, gi... - gi\|57525910\|ref\|NP_001003551.1\| Lsm1 protein [Danio rerio], gi\|50417210\|gb\|AAH78334.1\| Zgc:101136 [D...	8.0E-26	[1..133]	[1..133]
gi\|157136994, gi... - gi\|157136994\|ref\|XP_001656966.1\| Sm protein G, putative [Aedes aegypti], gi\|108884233\|gb\|EAT48458.1\|...	9.0E-25	[2..133]	[29..160]
AGAP001686-PA - U6 snRNA-associated Sm-like protein LSm1\|protein_coding\|2R:8447654:8448231:1\|gene:AGAP001686 gi\|118794287, gi... - gi\|118794287\|ref\|XP_321407.3\| AGAP001686-PA [Anopheles gambiae str. PEST], gi\|116116223\|gb\|EAA00900....	4.0E-24	[2..133]	[3..134]

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Predicted Domain #1

Region A:
Residues: [1-133]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNYMPGTASL IEDIDKKHLV LLRDGRTLIG FLRSIDQFAN LVLHQTVERI HVGKKYGDIP  60
   61 RGIFVVRGEN VVLLGEIDLE KESDTPLQQV SIEEILEEQR VEQQTKLEAE KLKVQALKDR 120
  121 GLSIPRADTL DEY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	15.522879
Match:	1i81A
Description:	Archaeal homoheptameric Sm 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: