Detailed view for Rv0499

Basic information

TDR Targets ID: 7406
Mycobacterium tuberculosis, Conserved hypothetical protein
Source Database / ID:  Tuberculist 

pI: 6.3751 | Length (AA): 291 | MW (Da): 30670 | 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

PF13622   Thioesterase-like superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0016301   kinase activity  
GO:0004143   diacylglycerol kinase activity  
GO:0007205   activation of protein kinase C activity  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 5 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
1 120 1zki (A) 10 128 21.00 0.28 0.75 0.686571 -0.4
1 117 2cy9 (B) 12 135 20.00 0 0.66 0.611362 -0.32
3 288 3bbj (A) 5 269 24.00 0 0.99 1.23902 0.02
5 289 3bbj (A) 7 270 28.00 0 1 1.21568 0.21
114 209 1g2o (A) 41 127 36.00 0.49 0.45 0.541397 0.15

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 Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. murphy
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_129103)

Species Accession Gene Product
Arabidopsis thaliana AT1G04290   thioesterase-like protein
Brugia malayi Bm1_56475   Hypothetical UPF0152 protein F42H10.6 in chromosome III
Brugia malayi Bm1_46645   thioesterase family protein
Caenorhabditis elegans CELE_C25H3.14   Protein C25H3.14
Caenorhabditis elegans CELE_F42H10.6   Protein F42H10.6
Caenorhabditis elegans CELE_C25H3.3   Protein C25H3.3
Dictyostelium discoideum DDB_G0276419   thioesterase superfamily protein
Dictyostelium discoideum DDB_G0295733   thioesterase superfamily protein
Dictyostelium discoideum DDB_G0289161   hypothetical protein
Drosophila melanogaster Dmel_CG16985   CG16985 gene product from transcript CG16985-RA
Drosophila melanogaster Dmel_CG16986   CG16986 gene product from transcript CG16986-RA
Homo sapiens ENSG00000112304   acyl-CoA thioesterase 13
Mus musculus ENSMUSG00000006717   acyl-CoA thioesterase 13
Mycobacterium tuberculosis Rv0499   Conserved hypothetical protein
Mycobacterium ulcerans MUL_4569   hypothetical protein
Mycobacterium ulcerans MUL_4450   hypothetical protein
Oryza sativa 4324995   Os01g0882100
Oryza sativa 4335905   Os04g0436100
Onchocerca volvulus OVOC9331   Putative esterase
Schistosoma japonicum Sjp_0201810   Thioesterase superfamily member 2, putative
Schmidtea mediterranea mk4.001257.03  
Schmidtea mediterranea mk4.052381.02  

Essentiality

Rv0499 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
this record Mycobacterium tuberculosis non-essential nmpdr
CELE_C25H3.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C25H3.14 Caenorhabditis elegans embryonic lethal wormbase
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

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

No literature references available for this target.

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User comments

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Gene identifier Rv0499 (Mycobacterium tuberculosis), Conserved hypothetical protein
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