Detailed view for Rv1279

Basic information

TDR Targets ID: 7855
Mycobacterium tuberculosis, Probable dehydrogenase FAD flavoprotein GMC oxidoreductase
Source Database / ID:  Tuberculist 

pI: 7.2678 | Length (AA): 528 | MW (Da): 57331 | 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

PF00732   GMC oxidoreductase
PF05199   GMC oxidoreductase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016614   oxidoreductase activity, acting on CH-OH group of donors  
GO:0050660   FAD binding  
GO:0055114   oxidation reduction  
GO:0006066   alcohol metabolic process  

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
1 528 1ju2 (A) 23 515 24.00 0 1 1.1297 0.3
2 527 2jbv (A) 11 527 38.00 0 1 1.41511 -0.41
6 526 5ncc (A) 85 636 41.00 0 1 1.39264 0.02
6 528 5oc1 (A) 4 564 37.00 0 1 1.40943 -0.41

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
Lower 0-20% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_126713)

Species Accession Gene Product
Arabidopsis thaliana AT1G14185   glucose-methanol-choline oxidoreductase-like protein
Arabidopsis thaliana AT3G56060   Glucose-methanol-choline (GMC) oxidoreductase family protein
Arabidopsis thaliana AT1G14190   glucose-methanol-choline oxidoreductase-like protein
Arabidopsis thaliana AT1G73050   Glucose-methanol-choline (GMC) oxidoreductase family protein
Arabidopsis thaliana AT5G51930   Glucose-methanol-choline (GMC) oxidoreductase family protein
Arabidopsis thaliana AT5G51950   Glucose-methanol-choline (GMC) oxidoreductase family protein
Brugia malayi Bm1_39805   GMC oxidoreductase family protein
Caenorhabditis elegans CELE_C34C6.4   Protein C34C6.4
Dictyostelium discoideum DDB_G0287229   choline dehydrogenase
Drosophila melanogaster Dmel_CG45065   CG45065 gene product from transcript CG45065-RA
Drosophila melanogaster Dmel_CG45064   CG45064 gene product from transcript CG45064-RA
Drosophila melanogaster Dmel_CG12398   CG12398 gene product from transcript CG12398-RA
Drosophila melanogaster Dmel_CG9503   CG9503 gene product from transcript CG9503-RA
Drosophila melanogaster Dmel_CG9518   CG9518 gene product from transcript CG9518-RA
Drosophila melanogaster Dmel_CG9514   CG9514 gene product from transcript CG9514-RA
Escherichia coli b0311   choline dehydrogenase, a flavoprotein
Homo sapiens 55349   choline dehydrogenase
Leishmania braziliensis LbrM.35.3450   oxidoreductase, putative
Leishmania donovani LdBPK_363380.1   oxidoreductase, putative
Leishmania infantum LinJ.36.3380   oxidoreductase, putative
Leishmania major LmjF.36.3230   oxidoreductase, putative
Leishmania mexicana LmxM.36.3230   oxidoreductase, putative
Loa Loa (eye worm) LOAG_03547   GMC oxidoreductase
Mus musculus ENSMUSG00000015970   choline dehydrogenase
Mycobacterium tuberculosis Rv1279   Probable dehydrogenase FAD flavoprotein GMC oxidoreductase
Mycobacterium ulcerans MUL_4004   dehydrogenase fad flavoprotein GMC oxidoreductase
Neospora caninum NCLIV_057150   hypothetical protein
Oryza sativa 9266710   Os06g0656000
Oryza sativa 4349162   Os10g0524500
Oryza sativa 4336725   Os04g0573100
Oryza sativa 9271148   Os03g0118700
Oryza sativa 4330311   Os02g0678300
Onchocerca volvulus OVOC5096   Choline dehydrogenase, mitochondrial homolog
Schistosoma japonicum Sjp_0075460   IPR005834,Haloacid dehalogenase-like hydrolase,domain-containing
Schistosoma japonicum Sjp_0213850   Conserved hypothetical protein
Schistosoma japonicum Sjp_0075450   ko:K00108 choline dehydrogenase [EC1.1.99.1], putative
Schistosoma japonicum Sjp_0105830   ko:K00108 choline dehydrogenase [EC1.1.99.1], putative
Schistosoma japonicum Sjp_0315030   Choline dehydrogenase, mitochondrial precursor, putative
Schistosoma mansoni Smp_094500   choline dehydrogenase
Schmidtea mediterranea mk4.009633.03   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.005893.00   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.012411.03   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.034907.01   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.045332.00  
Schmidtea mediterranea mk4.009633.02   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.011185.01   Choline dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.039386.03  
Schmidtea mediterranea mk4.039478.00   Choline dehydrogenase, mitochondrial
Trypanosoma brucei gambiense Tbg972.11.10730   oxidoreductase, putative
Trypanosoma brucei Tb927.11.9560   oxidoreductase, putative
Trypanosoma congolense TcIL3000.11.10030   oxidoreductase, putative
Trypanosoma cruzi TcCLB.511229.20   oxidoreductase, putative
Trypanosoma cruzi TcCLB.511589.170   oxidoreductase, putative
Toxoplasma gondii TGME49_313950   GMC oxidoreductase

Essentiality

Rv1279 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1300 this record Mycobacterium tuberculosis non-essential nmpdr
Tb11.01.1320 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.1320 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.1320 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.1320 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0311 Escherichia coli non-essential goodall
TGME49_313950 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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

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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Gene identifier Rv1279 (Mycobacterium tuberculosis), Probable dehydrogenase FAD flavoprotein GMC oxidoreductase
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