Detailed view for Tb927.4.380

Basic information

TDR Targets ID: 18749
Trypanosoma brucei, WD domain, G-beta repeat, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 4.717 | Length (AA): 333 | MW (Da): 35613 | 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

PF00400   WD domain, G-beta repeat

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
17 211 3uvk (A) 40 218 24.00 0.2 1 0.810786 -0.27
64 163 3fgb (A) 274 378 13.00 0 0.26 0.4201 -0.38
87 196 1erj (A) 500 605 38.00 0.015 0.98 0.62353 0.13
259 333 1r5m (A) 358 431 11.00 0.075 0.02 0.247925 0.52

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:

PDB tag
  • 4V8M:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
NA% 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_132184)

Species Accession Gene Product
Echinococcus granulosus EgrG_000930200   wd40 repeat
Echinococcus multilocularis EmuJ_000930200   wd40 repeat
Giardia lamblia GL50803_7807   WD-40 repeat protein
Leishmania braziliensis LbrM.20.4040   hypothetical protein, conserved
Leishmania donovani LdBPK_344210.1   hypothetical protein, conserved
Leishmania infantum LinJ.34.4210   hypothetical protein, conserved
Leishmania major LmjF.34.4580   hypothetical protein, conserved
Leishmania mexicana LmxM.33.4580   hypothetical protein, conserved
Trypanosoma brucei gambiense Tbg972.4.100   hypothetical protein, conserved
Trypanosoma brucei Tb927.4.380   WD domain, G-beta repeat, putative
Trypanosoma congolense TcIL3000_4_40   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.510689.80   WD domain, G-beta repeat, putative
Trypanosoma cruzi TcCLB.507873.40   WD domain, G-beta repeat, putative
Trichomonas vaginalis TVAG_002950   peroxisomal targeting signal 2 receptor, putative
Trichomonas vaginalis TVAG_421680   WD repeat domain, putative
Trichomonas vaginalis TVAG_393250   WD-repeat protein, putative
Trichomonas vaginalis TVAG_334310   WD-repeat protein, putative
Trichomonas vaginalis TVAG_174550   WD-repeat protein, putative

Essentiality

Tb927.4.380 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.380 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.380 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.380 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.380 this record Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) 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: increased cell proliferation (significant gain 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) increased (PATO:0000470) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier Tb927.4.380 (Trypanosoma brucei), WD domain, G-beta repeat, putative
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