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View Structure Prediction Details

Protein: LSM4
Organism: Saccharomyces cerevisiae
Length: 187 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 LSM4.

Description E-value Query
Range		 Subject
Range
gi|605651 - gi|605651|gb|AAA58257.1| regulatory protein [Saccharomyces cerevisiae]
gi|207345878 - gi|207345878|gb|EDZ72558.1| YER112Wp-like protein [Saccharomyces cerevisiae AWRI1631]
gi|190405674 - gi|190405674|gb|EDV08941.1| U6 snRNA associated protein [Saccharomyces cerevisiae RM11-1a]
 6.0E-36 [1..187] [1..187]
LSM4_TOBAC - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Nicotiana tabacum PE=2 SV=1
 3.0E-30 [1..116] [1..106]
gi|34902916, gi|... - gi|6016876|dbj|BAA85219.1| unnamed protein product [Oryza sativa (japonica cultivar-group)], gi|3490...
 5.0E-26 [1..107] [1..116]
LSM4_FAGSY - Probable U6 snRNA-associated Sm-like protein LSm4 OS=Fagus sylvatica GN=LSM4 PE=2 SV=1
 1.0E-25 [1..102] [1..92]
gi|13161882 - gi|13161882|emb|CAC33027.1| Lsm4 protein [Takifugu rubripes]
 1.0E-25 [1..128] [1..118]
LSM4_MOUSE - U6 snRNA-associated Sm-like protein LSm4 OS=Mus musculus GN=Lsm4 PE=1 SV=1
 4.0E-25 [1..108] [1..98]
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)
 2.0E-24 [1..107] [1..116]
LSM4_ARATH - Sm-like protein LSM4 OS=Arabidopsis thaliana GN=LSM4 PE=1 SV=1
 3.0E-24 [1..102] [1..91]

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Predicted Domain #1
Region A:
Residues: [1-111] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLPLYLLTNA KGQQMQIELK NGEIIQGILT NVDNWMNLTL SNVTEYSEES AINSEDNAES  60
   61 SKAVKLNEIY IRGTFIKFIK LQDNIIDKVK QQINSNNNSN SNGPGHKRYY N

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 55.94696
Match: 1d3bA_
Description: D3 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 2.69031444148163 bayes_pls_golite062009
mRNA binding 2.57166143288861 bayes_pls_golite062009
binding 2.49177223698264 bayes_pls_golite062009
protein binding 0.625703802792387 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [112-187] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NRDSNNNRGN YNRRNNNNGN SNRRPYSQNR QYNNSNSSNI NNSINSINSN NQNMNNGLGG  60
   61 SVQHHFNSSS PQKVEF

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

    MCM
Score		 GO
Score		 GO
Term		 SCOP
Match		 SCOP Description
View Download 0.819 0.053 rRNA processing a.60.2 RuvA domain 2-like

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle