Detailed view for TcCLB.457339.10

Basic information

TDR Targets ID: 32647
Trypanosoma cruzi, U6 snRNA-associated Sm-like protein LSm4, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 11.3942 | Length (AA): 164 | MW (Da): 18281 | Paralog Number: 1

Signal peptide: Y | GPI Anchor: N | Predicted trans-membrane segments: 1

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF01423   LSM domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0000956   nuclear-transcribed mRNA catabolic process  
GO:0000398   nuclear mRNA splicing, via spliceosome  
GO:0006396   RNA processing  

Metabolic Pathways

RNA degradation (KEGG)
Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 5 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
60 130 1i4k (A) 5 74 34.00 0 1 0.88 -1.16
60 128 1h64 (1) 5 72 28.00 0 0.94 0.89 -1.19
60 128 1i4k (A) 5 72 35.00 0.0000000047 1 0.954432 -1.01
60 134 4xq3 (A) 8 83 28.00 0 1 0.841517 -0.51
69 128 4emh (A) 12 71 43.00 0.0000000022 1 0.983754 -0.93

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128255)

Species Accession Gene Product
Arabidopsis thaliana AT5G27720   U6 snRNA-associated Sm-like protein LSm4
Babesia bovis BBOV_I004760   U6 snRNA-associated Sm-like protein LSm4, putative
Brugia malayi Bm1_14590   Probable U6 snRNA-associated Sm-like protein LSm4, putative
Candida albicans CaJ7_s010   hypothetical protein
Caenorhabditis elegans CELE_F32A5.7   Protein LSM-4
Cryptosporidium hominis Chro.40305   ENSANGP00000016613
Cryptosporidium parvum cgd4_2710   hypothetical protein
Dictyostelium discoideum DDB_G0287053   LSM domain-containing protein
Drosophila melanogaster Dmel_CG17768   CG17768 gene product from transcript CG17768-RA
Echinococcus granulosus EgrG_000672500   u6 snRNA associated Sm protein LSm4
Entamoeba histolytica EHI_049370   LSM domain containing protein
Echinococcus multilocularis EmuJ_000672500   u6 snRNA associated Sm protein LSm4
Echinococcus multilocularis EmuJ_000505700   expressed conserved protein
Homo sapiens ENSG00000130520   LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Leishmania braziliensis LbrM.32.0800   U6 snRNA-associated Sm-like protein LSm4p
Leishmania donovani LdBPK_320750.1   U6 snRNA-associated Sm-like protein LSm4p
Leishmania infantum LinJ.32.0750   U6 snRNA-associated Sm-like protein LSm4p
Leishmania major LmjF.32.0715   U6 snRNA-associated Sm-like protein LSm4p
Leishmania mexicana LmxM.31.0715   U6 snRNA-associated Sm-like protein LSm4p
Loa Loa (eye worm) LOAG_09541   hypothetical protein
Mus musculus ENSMUSG00000031848   LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Neospora caninum NCLIV_067060   hypothetical protein
Oryza sativa 4326227   Os01g0256900
Plasmodium berghei PBANKA_0939900   U6 snRNA-associated Sm-like protein LSm4, putative
Plasmodium falciparum PF3D7_1107000   U6 snRNA-associated Sm-like protein LSm4, putative
Plasmodium knowlesi PKNH_0904600   U6 snRNA-associated Sm-like protein LSm4, putative
Plasmodium vivax PVX_091025   U6 snRNA-associated Sm-like protein LSm4, putative
Plasmodium yoelii PY07662   Sm protein, putative
Saccharomyces cerevisiae YER112W   Lsm4p
Schistosoma japonicum Sjp_0084410   U6 snRNA-associated Sm-like protein LSm4, putative
Schistosoma japonicum Sjp_0313320   IPR001478,PDZ/DHR/GLGF,domain-containing
Schistosoma japonicum Sjp_0109100   expressed protein
Schistosoma japonicum Sjp_0313550   expressed protein
Schistosoma mansoni Smp_157680   U6 snrna-associated sm-like protein lsm4
Schistosoma mansoni Smp_157670   hypothetical protein
Schmidtea mediterranea mk4.006672.00   Probable U6 snRNA-associated Sm-like protein LSm4
Schmidtea mediterranea mk4.015978.00   Probable U6 snRNA-associated Sm-like protein LSm4
Trypanosoma brucei gambiense Tbg972.11.15590   U6 snRNA-associated Sm-like protein LSm4p,small nucleolar ribonucleoprotein-like protein
Trypanosoma brucei Tb927.11.13960   U6 snRNA-associated Sm-like protein LSm4p
Trypanosoma cruzi TcCLB.457339.10   U6 snRNA-associated Sm-like protein LSm4, putative
Trypanosoma cruzi TcCLB.504643.40   U6 snRNA-associated Sm-like protein LSm4, putative
Toxoplasma gondii TGME49_278950   LSM domain-containing protein
Theileria parva TP03_0516   U6 snRNA-associated protein, putative

Essentiality

TcCLB.457339.10 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F32A5.7 Caenorhabditis elegans embryonic lethal wormbase
CELE_F32A5.7 Caenorhabditis elegans slow growth wormbase
YER112W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0939900 Plasmodium berghei Essential plasmo
TGME49_278950 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier TcCLB.457339.10 (Trypanosoma cruzi), U6 snRNA-associated Sm-like protein LSm4, putative
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