Detailed view for TcCLB.503881.20

Basic information

TDR Targets ID: 45215
Trypanosoma cruzi, GDP-mannose 4,6 dehydratase, putative

Source Database / ID:  TriTrypDB  GeneDB

pI: 6.9313 | Length (AA): 378 | MW (Da): 43477 | Paralog Number: 3

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

Druggability Group : DG2

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

PF16363   GDP-mannose 4,6 dehydratase

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  

Structural information

Modbase 3D models:

There are 7 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
16 372 1wvg (A) 6 353 20.00 0 1 1 -0.88
22 354 1oc2 (A) 5 330 40.00 0 1 1.4 -1.39
23 357 1kew (A) 2 345 33.00 0 1 1.38 -1.71
20 356 2hun (A) 3 321 40.00 0 1 1.37093 -0.86
22 367 1z45 (A) 12 396 23.00 0 1 1.14214 0.05
23 357 4egb (A) 2 321 41.00 0 1 1.36314 -0.95
23 357 1kew (A) 2 345 34.00 0 1 1.31664 -1.17

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 epimastigote. Smircich P
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile metacyclic. Smircich P
Show/Hide expression data references
  • Smircich P Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi.

Orthologs

Ortholog group members (OG5_127949)

Species Accession Gene Product
Arabidopsis thaliana AT3G14790   rhamnose biosynthetic enzyme 3
Arabidopsis thaliana AT1G78570   UDP-L-rhamnose synthase
Arabidopsis thaliana AT1G53500   putative NDP-L-rhamnose synthase
Brugia malayi Bm1_42170   NAD dependent epimerase/dehydratase family protein
Candida albicans CaO19.3674   dTDP glucose-6-dehydratase
Candida albicans CaO19.11158   dTDP glucose-6-dehydratase
Caenorhabditis elegans CELE_C01F1.3   Protein C01F1.3, isoform B
Caenorhabditis elegans CELE_F53B1.4   Protein F53B1.4
Dictyostelium discoideum DDB_G0279465   hypothetical protein
Escherichia coli b2041   dTDP-glucose 4,6 dehydratase, NAD(P)-binding
Escherichia coli b3788   dTDP-glucose 4,6-dehydratase
Entamoeba histolytica EHI_174070   dTDP-D-glucose 4,6-dehydratase, putative
Entamoeba histolytica EHI_125700   dTDP-D-glucose 4,6-dehydratase, putative
Homo sapiens ENSG00000088451   TDP-glucose 4,6-dehydratase
Leishmania braziliensis LbrM.26.2150   GDP-mannose 4,6 dehydratase, putative
Leishmania donovani LdBPK_262240.1   GDP-mannose 4,6 dehydratase, putative
Leishmania infantum LinJ.26.2240   GDP-mannose 4,6 dehydratase, putative
Leishmania major LmjF.26.2230   GDP-mannose 4,6 dehydratase, putative
Leishmania mexicana LmxM.26.2230   GDP-mannose 4,6 dehydratase, putative
Loa Loa (eye worm) LOAG_03637   hypothetical protein
Mycobacterium leprae ML1964   dTDP-GLUCOSE 4,6-DEHYDRATASE RMLB
Mus musculus ENSMUSG00000022130   TDP-glucose 4,6-dehydratase
Mycobacterium tuberculosis Rv3464   dTDP-glucose 4,6-dehydratase RmlB
Mycobacterium ulcerans MUL_0840   dTDP-glucose-4,6-dehydratase, RmlB
Mycobacterium ulcerans MUL_2058   hypothetical protein
Oryza sativa 4332425   Os03g0278200
Schmidtea mediterranea mk4.032167.03   dTDP-D-glucose 4,6-dehydratase
Trypanosoma cruzi TcCLB.508119.120   GDP-mannose 4,6 dehydratase, putative
Trypanosoma cruzi TcCLB.503881.20   GDP-mannose 4,6 dehydratase, putative
Trypanosoma cruzi TcCLB.507039.41   hypothetical protein, conserved
Trypanosoma cruzi TcCLB.511019.84   GDP-mannose 4,6 dehydratase, putative
Trichomonas vaginalis TVAG_414560   DTDP-glucose 4,6-dehydratase, putative

Essentiality

TcCLB.503881.20 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3525 Mycobacterium tuberculosis essential nmpdr
b2041 Escherichia coli non-essential goodall
b3788 Escherichia coli non-essential goodall
CELE_C01F1.3 Caenorhabditis elegans larval arrest wormbase
CELE_C01F1.3 Caenorhabditis elegans larval lethal wormbase
Show/Hide essentiality data references
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

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
Species Target Length Identity Alignment span Linked Drugs Reference
Mycobacterium tuberculosis 3-beta-hydroxysteroid dehydrogenase 370 aa 21.8% 376 aa Compounds References

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

No literature references available for this target.

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 TcCLB.503881.20 (Trypanosoma cruzi), GDP-mannose 4,6 dehydratase, putative
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