Detailed view for Tb927.4.1540

Basic information

TDR Targets ID: 11963
Trypanosoma brucei, NAD dependent epimerase/dehydratase family, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.197 | Length (AA): 508 | MW (Da): 55241 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 1

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

PF01370   NAD dependent epimerase/dehydratase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0050662   coenzyme binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0044237   cellular metabolic process  
GO:0008152   metabolic 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
14 63 5u3h (A) 32 79 15.00 0.96 0.11 0.271425 -0.68
111 471 4w4t (A) 1130 1513 12.00 0 1 0.80043 0.23
128 468 4r1s (A) 5 319 30.00 0 1 1.02306 -0.61
129 245 1qyd (A) 4 111 29.00 0.29 1 0.550115 -0.79
132 287 1r6d (A) 3 152 25.00 0.014 1 0.530887 0.07
133 196 3i4f (A) 42 103 32.00 0.98 0.8 0.544784 -0.58

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. Siegel TN
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile 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_127062)

Species Accession Gene Product
Arabidopsis thaliana AT5G19440   alcohol dehydrogenase-like protein
Arabidopsis thaliana AT1G09500   alcohol dehydrogenase-like protein
Arabidopsis thaliana AT1G09490   alcohol dehydrogenase
Arabidopsis thaliana AT4G35420   dihydroflavonol 4-reductase-like1
Arabidopsis thaliana AT1G66800   alcohol dehydrogenase-like protein
Arabidopsis thaliana AT1G51410   putative alcohol dehydrogenase
Arabidopsis thaliana AT1G09510   alcohol dehydrogenase-like protein
Arabidopsis thaliana AT1G09480   alcohol dehydrogenase-like protein
Brugia malayi Bm1_54400   oxidoreductase
Candida albicans CaO19.2581   similar to S. cerevisiae dihydroflavonol-4-reductase YGL039W and to GRE2 family
Candida albicans CaO19.10660   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.6868   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.10113   similar to S. cerevisiae dihydroflavonol-4-reductase YGL039W and to GRE2 family
Candida albicans CaO19.14157   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.13054   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.11785   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.4781   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.4309   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.5611   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.3150   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Candida albicans CaO19.12245   one of five C. albicans genes similar to a set of S. cerevisiae reductase-like genes, including stress-induced methylglyoxal red
Caenorhabditis elegans CELE_F13D11.4   Protein F13D11.4
Cryptosporidium hominis Chro.50271   cinnamyl-alcohol dehydrogenase (EC 1.1.1.195)
Cryptosporidium parvum cgd5_1140   cinnamyl-alcohol dehydrogenase-like nucleoside diphosphate sugar epimerase
Dictyostelium discoideum DDB_G0277203   NAD-dependent epimerase/dehydratase family protein
Dictyostelium discoideum DDB_G0287677   hypothetical protein
Dictyostelium discoideum DDB_G0287277   NAD-dependent epimerase/dehydratase family protein
Leishmania braziliensis LbrM.20.2770   hypothetical protein, conserved
Leishmania donovani LdBPK_342970.1   NAD dependent epimerase/dehydratase family, putative
Leishmania infantum LinJ.34.2970   hypothetical protein, conserved
Leishmania major LmjF.34.3190   hypothetical protein, conserved
Leishmania mexicana LmxM.33.3190   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_12547   oxidoreductase
Oryza sativa 4346438   Os09g0127300
Oryza sativa 4347447   Os09g0493500
Oryza sativa 4328509   Os02g0180700
Oryza sativa 4345156   Os08g0277200
Onchocerca volvulus OVOC3176  
Saccharomyces cerevisiae YOL151W   methylglyoxal reductase (NADPH-dependent) GRE2
Saccharomyces cerevisiae YDR541C   carbonyl reductase (NADPH-dependent)
Saccharomyces cerevisiae YGL157W   carbonyl reductase (NADPH-dependent) ARI1
Saccharomyces cerevisiae YGL039W   carbonyl reductase (NADPH-dependent)
Trypanosoma brucei gambiense Tbg972.4.1390   hypothetical protein, conserved
Trypanosoma brucei Tb927.4.1540   NAD dependent epimerase/dehydratase family, putative
Trypanosoma congolense TcIL3000_4_1070   NAD dependent epimerase/dehydratase family, putative
Trypanosoma cruzi TcCLB.504057.40   Present in the outer mitochondrial membrane proteome 27

Essentiality

Tb927.4.1540 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.1540 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.1540 this record Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.1540 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.1540 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

Druggability index (range: 0 to 1): 0.1

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 Tb927.4.1540 (Trypanosoma brucei), NAD dependent epimerase/dehydratase family, putative
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