Detailed view for Tb927.3.1780

Basic information

TDR Targets ID: 12198
Trypanosoma brucei, U6 snRNA-associated Sm-like protein LSm8p
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.8604 | Length (AA): 129 | MW (Da): 14023 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

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:0046540   U4/U6 x U5 tri-snRNP complex  
GO:0030629   U6 snRNA 3'-end binding  
GO:0000398   nuclear mRNA splicing, via spliceosome  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
1 69 3pgg (A) 32 112 23.00 0.0000073 0.62 0.893684 -0.85
2 120 1m5q (A) 16 131 22.00 0.000025 0.27 1.01628 0.55
2 91 1d3b (B) 9 80 26.00 0 0.82 0.812974 -0.49
3 110 4c92 (B) 8 89 22.00 0.017 1 0.854009 -0.15
4 123 4c92 (A) 48 135 35.00 0 0.7 0.949033 0.33

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

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_128730)

Species Accession Gene Product
Arabidopsis thaliana AT1G65700   Small nuclear ribonucleoprotein family protein
Babesia bovis BBOV_IV002350   U6 snRNA-associated Sm-like protein LSm8, putative
Brugia malayi Bm1_31260   U6 snRNA-associated Sm-like protein LSm8
Caenorhabditis elegans CELE_Y73B6BL.32   Protein LSM-8
Cryptosporidium hominis Chro.70595   u6 snRNA-associated sm-like protein
Cryptosporidium parvum cgd7_5350   conserved hypothetical protein
Dictyostelium discoideum DDB_G0288479   LSM domain-containing protein
Drosophila melanogaster Dmel_CG2021   CG2021 gene product from transcript CG2021-RA
Entamoeba histolytica EHI_188020   LSM domain containing protein
Homo sapiens 51691   LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Leishmania braziliensis LbrM.25.2290   hypothetical protein, conserved
Leishmania donovani LdBPK_251780.1   LSM domain containing protein, putative
Leishmania infantum LinJ.25.1780   hypothetical protein, conserved
Leishmania major LmjF.25.1705   hypothetical protein, conserved
Leishmania mexicana LmxM.25.1705   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_00762   U6 snRNA-associated Sm-like protein LSm8
Mus musculus ENSMUSG00000044155   LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Neospora caninum NCLIV_034680   U6 snRNA-associated protein LSm8-like protein, related
Oryza sativa 4339810   Os05g0594900
Plasmodium berghei PBANKA_0701400   U6 snRNA-associated Sm-like protein LSm8, putative
Plasmodium falciparum PF3D7_0829300   U6 snRNA-associated Sm-like protein LSm8, putative
Plasmodium knowlesi PKNH_1323500   U6 snRNA-associated Sm-like protein LSm8, putative
Plasmodium vivax PVX_088885   U6 snRNA-associated Sm-like protein LSm8, putative
Schistosoma japonicum Sjp_0094510   U6 snRNA-associated Sm-like protein LSm8, putative
Schistosoma japonicum Sjp_0094530   U6 snRNA-associated Sm-like protein LSm8, putative
Schistosoma mansoni Smp_175550   lsm1
Schmidtea mediterranea mk4.005302.05   Putative lsm1
Trypanosoma brucei gambiense Tbg972.3.1630   U6 snRNA-associated Sm-like protein LSm8p
Trypanosoma brucei Tb927.3.1780   U6 snRNA-associated Sm-like protein LSm8p
Trypanosoma congolense TcIL3000_3_880   U6 snRNA-associated Sm-like protein LSm8p
Trypanosoma cruzi TcCLB.510091.70   U6 snRNA-associated Sm-like protein LSm8, putative
Trypanosoma cruzi TcCLB.510421.314   U6 snRNA-associated Sm-like protein LSm8p
Toxoplasma gondii TGME49_272630   U6 snRNA-associated Sm family protein LSm8, putative
Theileria parva TP03_0418   U6 snRNA-associated Sm-like protein LSm8, putative

Essentiality

Tb927.3.1780 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.1780 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.1780 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.1780 this record Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.3.1780 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_272630 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) decreased (PATO:0000468) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) decreased (PATO:0000468) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: decreased cell proliferation (significant loss of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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

1 literature reference was collected for this gene.

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Gene identifier Tb927.3.1780 (Trypanosoma brucei), U6 snRNA-associated Sm-like protein LSm8p
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