Detailed view for Tb927.6.2770

Basic information

TDR Targets ID: 14240
Trypanosoma brucei, Vacuolar assembly protein vps41
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.9768 | Length (AA): 1092 | MW (Da): 121971 | 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

PF01476   LysM domain
PF10367   Vacuolar sorting protein 39 domain 2

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  
GO:0005488   binding  
GO:0016998   cell wall catabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 6 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
100 244 4wjs (A) 162 318 24.00 0.000068 0.51 0.299884 0.32
598 840 1b89 (A) 1191 1413 15.00 0 1 0.241927 0.32
854 883 1e0g (A) 3 32 37.00 0 0.87 0.518872 -0.53
856 886 5bum (A) 6 36 32.00 0 0.69 0.472788 -0.74
972 1030 3s2k (C) 185 245 37.00 0.87 0.59 0.197129 1.74
995 1044 5d0i (A) 264 334 18.00 0.61 0.4 0.190688 0.03

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 Bloodstream Form. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Procyclic. 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_128765)

Species Accession Gene Product
Arabidopsis thaliana AT1G08190   vacuolar protein sorting-associated protein 41
Brugia malayi Bm1_34430   Vacuolar assembly protein VPS41 homolog
Brugia malayi Bm1_20740   hypothetical protein
Candida albicans CaO19.4858   similar to N terminus of protein involved in vacuolar assembly
Candida albicans CaO19.4860   hypothetical protein
Candida albicans CaO19.4859   similar to internal portion of VPS41 protein involved in vacuolar assembly
Candida albicans CaO19.12323   hypothetical protein
Candida albicans CaO19.12322   similar to internal portion of VPS41 protein involved in vacuolar assembly
Candida albicans CaO19.12321   similar to N terminus of protein involved in vacuolar assembly
Caenorhabditis elegans CELE_F32A6.3   Protein VPS-41, isoform B
Dictyostelium discoideum DDB_G0286803   7-fold repeat in clathrin and VPS proteins repeat-containing protein
Drosophila melanogaster Dmel_CG18028   light
Echinococcus granulosus EgrG_000123800   vacuolar protein sorting associated protein 41
Echinococcus multilocularis EmuJ_000123800   vacuolar protein sorting associated protein 41
Homo sapiens ENSG00000006715   vacuolar protein sorting 41 homolog (S. cerevisiae)
Leishmania braziliensis LbrM.30.1410   vacuolar assembly protein vps41, putative
Leishmania donovani LdBPK_301350.1   vacuolar assembly protein vps41, putative
Leishmania infantum LinJ.30.1350   vacuolar assembly protein vps41, putative
Leishmania major LmjF.30.1280   vacuolar assembly protein vps41, putative
Leishmania mexicana LmxM.29.1280   vacuolar assembly protein vps41, putative
Loa Loa (eye worm) LOAG_01302   hypothetical protein
Loa Loa (eye worm) LOAG_01303   hypothetical protein
Mus musculus ENSMUSG00000041236   vacuolar protein sorting 41 (yeast)
Oryza sativa 4335134   Os04g0195000
Saccharomyces cerevisiae YDR080W   Vps41p
Schistosoma japonicum Sjp_0077560   Vacuolar protein sorting-associated protein 41 homolog, putative
Schistosoma mansoni Smp_073110   vacuolar protein sorting vps41
Schistosoma mansoni Smp_073100   vacuolar protein sorting vps41
Schmidtea mediterranea mk4.001034.01  
Trypanosoma brucei gambiense Tbg972.6.2540   vacuolar assembly protein vps41, putative
Trypanosoma brucei Tb927.6.2770   Vacuolar assembly protein vps41
Trypanosoma congolense TcIL3000_6_2230   vacuolar assembly protein vps41, putative
Trypanosoma congolense TcIL3000_0_18920   vacuolar assembly protein vps41, putative
Trypanosoma cruzi TcCLB.507923.30   vacuolar assembly protein vps41, putative
Trypanosoma cruzi TcCLB.463359.9   vacuolar assembly protein vps41, putative
Trypanosoma cruzi TcCLB.511753.140   vacuolar assembly protein vps41, putative

Essentiality

Tb927.6.2770 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.2770 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.2770 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.6.2770 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.2770 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F32A6.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F32A6.3 Caenorhabditis elegans larval arrest wormbase
Show/Hide essentiality data references
  • 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.
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) normal (PATO:0000461) 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: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
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 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 Tb927.6.2770 (Trypanosoma brucei), Vacuolar assembly protein vps41
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