Detailed view for Tb927.11.10000

Basic information

TDR Targets ID: 15228
Trypanosoma brucei, Charged multivesicular body protein 3, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.5094 | Length (AA): 219 | MW (Da): 25146 | 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

PF03357   Snf7

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0016020   membrane  
GO:0005545   phosphatidylinositol binding  
GO:0015031   protein transport  
GO:0007034   vacuolar transport  
GO:0016192   vesicle-mediated transport  

Metabolic Pathways

Endocytosis (KEGG)

Structural information

Modbase 3D models:

There are 2 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
9 179 2gd5 (B) 10 180 42.00 0.000000017 1 1.15952 -0.07
12 211 5cwo (A) 13 207 15.00 0 0.69 1.04164 -0.63

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 80-100% 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_129145)

Species Accession Gene Product
Arabidopsis thaliana AT5G22950   vacuolar protein sorting-associated protein 24-1
Brugia malayi Bm1_56555   SNF7 family protein
Candida albicans CaO19.9579   sorting of proteins in pre-vacuolar endosome
Candida albicans CaO19.2031   sorting of proteins in pre-vacuolar endosome
Caenorhabditis elegans CELE_T27F7.1   Protein T27F7.1
Dictyostelium discoideum DDB_G0284769   SNF7 family protein
Drosophila melanogaster Dmel_CG9779   Vacuolar protein sorting 24
Echinococcus granulosus EgrG_000238400   charged multivesicular body protein 3
Echinococcus multilocularis EmuJ_000049300   transfer RNA-Arg
Echinococcus multilocularis EmuJ_000238400   charged multivesicular body protein 3
Echinococcus multilocularis EmuJ_000048800   transfer RNA-Ile
Echinococcus multilocularis EmuJ_000560500   transfer RNA-Trp
Homo sapiens ENSG00000115561   charged multivesicular body protein 3
Homo sapiens ENSG00000249884   RNF103-CHMP3 readthrough
Leishmania braziliensis LbrM.35.3670   SNF7-like protein
Leishmania donovani LdBPK_363600.1   Charged multivesicular body protein 3, putative
Leishmania infantum LinJ.36.3600   SNF7-like protein
Leishmania major LmjF.36.3440   SNF7-like protein
Leishmania mexicana LmxM.36.3440   SNF7-like protein
Loa Loa (eye worm) LOAG_01290   SNF7 family protein
Mus musculus ENSMUSG00000053119   charged multivesicular body protein 3
Oryza sativa 4331337   Os03g0108400
Oryza sativa 4343227   Os07g0479400
Saccharomyces cerevisiae YKL041W   ESCRT-III subunit protein VPS24
Schistosoma japonicum Sjp_0133290   IPR005024,Snf7,domain-containing
Schistosoma japonicum Sjp_0027500   Charged multivesicular body protein 3, putative
Schistosoma mansoni Smp_032150   neuroendocrine differentiation factor
Schmidtea mediterranea mk4.003826.01   Charged multivesicular body protein 3
Trypanosoma brucei gambiense Tbg972.11.11230   class-E vacuolar protein-sorting protein 24 (Vps24p), putative,SNF7-like protein, putative
Trypanosoma brucei Tb927.11.10000   Charged multivesicular body protein 3, putative
Trypanosoma congolense TcIL3000.11.10520   Charged multivesicular body protein 3, putative
Trypanosoma cruzi TcCLB.503675.20   class-E vacuolar protein-sorting protein 24 (Vps24p), putative
Trypanosoma cruzi TcCLB.506337.30   Charged multivesicular body protein 3, putative
Trichomonas vaginalis TVAG_396200   neuroendocrine differentiation factor, putative

Essentiality

Tb927.11.10000 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.1760 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.1760 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.1760 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.1760 this record Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T27F7.1 Caenorhabditis elegans adult lethal wormbase
CELE_T27F7.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_T27F7.1 Caenorhabditis elegans larval arrest wormbase
CELE_T27F7.1 Caenorhabditis elegans larval lethal wormbase
CELE_T27F7.1 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.

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) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in procyclic forms . 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 Tb927.11.10000 (Trypanosoma brucei), Charged multivesicular body protein 3, putative
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