Detailed view for Tb927.10.9360

Basic information

TDR Targets ID: 12971
Trypanosoma brucei, L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 9.1831 | Length (AA): 520 | MW (Da): 57475 | Paralog Number: 0

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

Druggability Group : DG3

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

PF01266   FAD dependent oxidoreductase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0055114   oxidation reduction  

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
52 113 2oln (A) 3 61 42.00 0.081 0.39 0.344131 1.46
52 89 3e1t (A) 6 41 42.00 0 0.35 0.397677 0.52
54 515 3dme (A) 5 368 30.00 0 1 0.912062 0.84
54 87 5fs7 (A) 132 165 32.00 0 0.15 0.389985 -0.12

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
Mid 40-60% 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_127956)

Species Accession Gene Product
Arabidopsis thaliana AT3G56840   FAD-dependent oxidoreductase-like protein
Brugia malayi Bm1_52090   cDNA sequence BC016226
Candida albicans CaO19.13618   similar to several predicted dehydrogenases
Candida albicans CaO19.6238   similar to several predicted dehydrogenases
Caenorhabditis elegans CELE_Y45G12B.3   Protein Y45G12B.3
Dictyostelium discoideum DDB_G0267656   hypothetical protein
Drosophila melanogaster Dmel_CG10639   CG10639 gene product from transcript CG10639-RA
Escherichia coli b2660   L-2-hydroxyglutarate oxidase
Entamoeba histolytica EHI_161010   anaerobic glycerol-3-phosphate dehydrogenase subunit A, putative
Entamoeba histolytica EHI_099700   NAD(FAD)-dependent dehydrogenase, putative
Giardia lamblia GL50803_16125   Glycerol-3-phosphate dehydrogenase
Homo sapiens ENSG00000087299   L-2-hydroxyglutarate dehydrogenase
Leishmania braziliensis LbrM.35.5720   hypothetical protein, conserved
Leishmania donovani LdBPK_365700.1   L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
Leishmania infantum LinJ.36.5700   hypothetical protein, conserved
Leishmania major LmjF.36.5460   hypothetical protein, conserved
Leishmania mexicana LmxM.36.5460   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_00810   hypothetical protein
Mus musculus ENSMUSG00000020988   L-2-hydroxyglutarate dehydrogenase
Oryza sativa 4327565   Os01g0809900
Schistosoma mansoni Smp_050080   NAD dehydrogenase
Schmidtea mediterranea mk4.004701.07   NAD dehydrogenase, putative
Trypanosoma brucei gambiense Tbg972.10.11450   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.9360   L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
Trypanosoma congolense TcIL3000_10_8120   L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
Trypanosoma cruzi TcCLB.509799.140   L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
Trypanosoma cruzi TcCLB.511037.20   L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative

Essentiality

Tb927.10.9360 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.9360 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.9360 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.9360 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.9360 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2660 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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

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 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 Tb927.10.9360 (Trypanosoma brucei), L-2-hydroxyglutarate dehydrogenase, mitochondrial, putative
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