YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM3
Organism:	Saccharomyces cerevisiae
Length:	89 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 LSM3.

Description	E-value	Query Range	Subject Range
gi\|34902916, gi\|... - gi\|6016876\|dbj\|BAA85219.1\| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi\|3490...	2.0E-20	[4..88]	[3..81]
gi\|151940954 - gi\|151940954\|gb\|EDN59336.1\| snRNP protein [Saccharomyces cerevisiae YJM789] LSM3 - Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytopla... gi\|190405474 - gi\|190405474\|gb\|EDV08741.1\| snRNP protein [Saccharomyces cerevisiae RM11-1a] LSM3_YEAST - U6 snRNA-associated Sm-like protein LSm3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN...	2.0E-19	[1..89]	[1..89]
gi\|190247 - gi\|190247\|gb\|AAA60151.1\| snRNP polypeptide B [Homo sapiens]	7.0E-19	[10..87]	[11..92]
LSM4_FAGSY - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica GN=LSM4 PE=2 SV=1	1.0E-18	[4..88]	[3..81]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	1.0E-18	[4..88]	[3..81]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-18	[10..87]	[11..92]
RSMB_MACEU - Small nuclear ribonucleoprotein-associated protein B' OS=Macropus eugenii GN=SNRPB PE=2 SV=1	3.0E-18	[10..87]	[11..92]
LSM4_ORYSJ - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Oryza sativa subsp. japonica GN=Os01g0256900 PE... LSM4_ORYSA - Probable U6 snRNA-associated Sm-like protein LSm4 - Oryza sativa (Rice)	3.0E-18	[4..88]	[3..81]
gi\|50540540, gi\|... - gi\|8099650\|gb\|AAF72188.1\| snRNP-associated protein; SmB [Danio rerio], gi\|50540540\|ref\|NP_991230.1\| ...	3.0E-18	[10..87]	[11..92]
gi\|3142634 - gi\|3142634\|gb\|AAC78612.1\| small nuclear ribonucleoprotein N [Mus musculus]	3.0E-18	[10..87]	[11..92]

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Predicted Domain #1

Region A:
Residues: [1-89]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 METPLDLLKL NLDERVYIKL RGARTLVGTL QAFDSHCNIV LSDAVETIYQ LNNEELSESE  60
   61 RRCEMVFIRG DTVTLISTPS EDDDGAVEI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	88.533179
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: