YRC Public Data Repository - Protein Structure Prediction

Protein:	LSM2
Organism:	Saccharomyces cerevisiae
Length:	95 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 LSM2.

Description	E-value	Query Range	Subject Range
gi\|11138539 - gi\|11138539\|gb\|AAG31434.1\|AF204157_1 snRNP core protein SMX5d [Mus musculus]	7.0E-27	[2..95]	[26..119]
gi\|109509738, gi... - gi\|149028025\|gb\|EDL83476.1\| rCG38360, isoform CRA_b [Rattus norvegicus], gi\|109509738\|ref\|XP_0010608... LSM2 - LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) gi\|178056596, gi... - gi\|178056596\|ref\|NP_001116608.1\| LSM2 homolog, U6 small nuclear RNA associated [Sus scrofa], gi\|1472... gi\|109070461 - gi\|109070461\|ref\|XP_001105870.1\| PREDICTED: LSM2 homolog, U6 small nuclear RNA associated (S. cerevi... CCDS4722.1_1 - null ENSCJAT00000004970 - null ENSPTRT00000033228 - null tr\|G1SHV1\|G1SHV1... - pep:novel chromosome:oryCun2:12:20606176:20612202:-1 gene:ENSOCUG00000002583 transcript:ENSOCUT00000... LSM2_MOUSE - U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus GN=Lsm2 PE=1 SV=1 gi\|226443174, gi... - gi\|226443174\|ref\|NP_001140070.1\| U6 snRNA-associated Sm-like protein LSm2 [Salmo salar], gi\|22122167... gi\|151557081, gi... - gi\|76650929\|ref\|XP_581859.2\| PREDICTED: similar to snRNP core Sm protein homolog Sm-X5 [Bos taurus],... gi\|73972304 - gi\|73972304\|ref\|XP_532081.2\| PREDICTED: similar to U6 snRNA-associated Sm-like protein LSm2 (SnRNP c... gi\|124000059, gi... - gi\|208968015\|dbj\|BAG73846.1\| U6 snRNA-associated Sm-like protein LSm2 [synthetic construct], gi\|1240...	9.0E-25	[1..95]	[1..95]
CG10418-PA - This gene is referred to in FlyBase by the symbol Dmel\CG10418 (CG10418, FBgn0036277). It is a prote... gi\|220951570 - gi\|220951570\|gb\|ACL88328.1\| CG10418-PA [synthetic construct] gi\|195493810, gi... - gi\|195493810\|ref\|XP_002094573.1\| GE21899 [Drosophila yakuba], gi\|194180674\|gb\|EDW94285.1\| GE21899 [D... gi\|195589798, gi... - gi\|195589798\|ref\|XP_002084636.1\| GD14374 [Drosophila simulans], gi\|194196645\|gb\|EDX10221.1\| GD14374 ... gi\|194119204, gi... - gi\|195327103\|ref\|XP_002030261.1\| GM25341 [Drosophila sechellia], gi\|194119204\|gb\|EDW41247.1\| GM25341... gi\|195376259, gi... - gi\|195376259\|ref\|XP_002046914.1\| GJ13149 [Drosophila virilis], gi\|194154072\|gb\|EDW69256.1\| GJ13149 [...	7.0E-24	[1..95]	[1..95]
gi\|34902916, gi\|... - gi\|6016876\|dbj\|BAA85219.1\| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi\|3490...	3.0E-23	[1..92]	[1..89]
gi\|2113818 - gi\|2113818\|emb\|CAB05859.1\| AmphiBrf43 [Branchiostoma floridae]	1.0E-22	[1..91]	[1..91]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1	3.0E-22	[1..94]	[1..90]
gi\|13161882 - gi\|13161882\|emb\|CAC33027.1\| Lsm4 protein [Takifugu rubripes]	3.0E-22	[1..92]	[1..90]
LSM4_FAGSY - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica GN=LSM4 PE=2 SV=1	4.0E-22	[1..94]	[1..90]

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Predicted Domain #1

Region A:
Residues: [1-95]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK YPHLGSVRNI  60
   61 FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.69897
Match:	1b34A_
Description:	D1 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	3.79237851568526	bayes_pls_golite062009
binding	2.63965180938967	bayes_pls_golite062009
mRNA binding	2.57166143288861	bayes_pls_golite062009
protein binding	0.418315253537627	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: