Detailed view for Rv0654

Basic information

TDR Targets ID: 7501
Mycobacterium tuberculosis, Probable dioxygenase
Source Database / ID:  Tuberculist 

pI: 6.0219 | Length (AA): 501 | MW (Da): 54944 | 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

PF03055   Retinal pigment epithelial membrane protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0016702   oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen  
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
2 498 3npe (A) 115 594 29.00 0 1 1.14682 0.26
4 500 4ou9 (A) 11 490 30.00 0 1 1.17612 0.17
7 499 5v2d (A) 4 480 26.00 0 1 1.18983 0.05
138 227 2hjv (A) 255 319 48.00 0.32 0.35 0.222741 0.43

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 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. hasan
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_128633)

Species Accession Gene Product
Arabidopsis thaliana AT4G32810   carotenoid cleavage dioxygenase 8
Caenorhabditis elegans CELE_F53C3.12   Protein BCMO-2
Caenorhabditis elegans CELE_Y46G5A.24   Protein BCMO-1
Drosophila melanogaster Dmel_CG9347   neither inactivation nor afterpotential B
Homo sapiens ENSG00000197580   beta-carotene oxygenase 2
Homo sapiens ENSG00000135697   beta-carotene oxygenase 1
Mus musculus ENSMUSG00000031845   beta-carotene oxygenase 1
Mus musculus ENSMUSG00000032066   beta-carotene oxygenase 2
Mycobacterium tuberculosis Rv0654   Probable dioxygenase
Mycobacterium ulcerans MUL_0744   dioxygenase
Oryza sativa 4327933   Os01g0566500
Oryza sativa 4326177   Os01g0746400
Oryza sativa 9267333   Os08g0293900
Schmidtea mediterranea mk4.000205.07   Carotenoid isomerooxygenase
Schmidtea mediterranea mk4.000205.05  

Essentiality

Rv0654 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu666 this record Mycobacterium tuberculosis non-essential nmpdr
CELE_Y46G5A.24 Caenorhabditis elegans slow growth wormbase
CELE_F53C3.12 Caenorhabditis elegans slow growth wormbase
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
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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.

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 Rv0654 (Mycobacterium tuberculosis), Probable dioxygenase
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