Detailed view for Rv1872c

Basic information

TDR Targets ID: 6321
Mycobacterium tuberculosis, Possible L-lactate dehydrogenase (cytochrome) LldD2

Source Database / ID:  Tuberculist 

pI: 10.1459 | Length (AA): 414 | MW (Da): 45342 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

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

PF01070   FMN-dependent dehydrogenase

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0010181   FMN binding  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0008152   metabolic process  

Metabolic Pathways

Structural information

Modbase 3D models:

There are 3 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
20 414 1kbi (A) 108 492 31.00 0 1 1.21621 0.19
31 403 6gmc (A) 2 362 34.00 0 1 1.33007 -0.38
33 401 1gox (A) 2 354 37.00 0 1 1.3034 -0.31

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
Mid 40-60% percentile Dormant phase. 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_126945)

Species Accession Gene Product
Arabidopsis thaliana AT3G14150   Aldolase-type TIM barrel family protein
Arabidopsis thaliana AT3G14420   peroxisomal (S)-2-hydroxy-acid oxidase GLO1
Arabidopsis thaliana AT3G14415   peroxisomal (S)-2-hydroxy-acid oxidase GLO2
Arabidopsis thaliana AT3G14130   Aldolase-type TIM barrel family protein
Candida albicans CaO19.12467   cytochrome b2 precursor
Candida albicans CaO19.5000   cytochrome b2 precursor
Caenorhabditis elegans CELE_F41E6.5   Protein F41E6.5, isoform A
Dictyostelium discoideum DDB_G0291814   hydroxyacid oxidase
Drosophila melanogaster Dmel_CG18003   CG18003 gene product from transcript CG18003-RB
Escherichia coli b3605   L-lactate dehydrogenase, FMN-linked
Homo sapiens ENSG00000116882   hydroxyacid oxidase 2 (long chain)
Homo sapiens ENSG00000101323   hydroxyacid oxidase (glycolate oxidase) 1
Mycobacterium leprae ML2046   POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2
Mus musculus ENSMUSG00000027261   hydroxyacid oxidase 1, liver
Mus musculus ENSMUSG00000027870   hydroxyacid oxidase 2
Mycobacterium tuberculosis Rv1872c   Possible L-lactate dehydrogenase (cytochrome) LldD2
Mycobacterium ulcerans MUL_3002   L-lactate dehydrogenase (cytochrome) LldD2
Oryza sativa 9266434   Os08g0198700
Oryza sativa 4337048   Os04g0623500
Oryza sativa 4343908   Os07g0616500
Oryza sativa 9266366   Os04g0623600
Oryza sativa 4334349   Os03g0786100
Oryza sativa 4342420   Os07g0152900
Saccharomyces cerevisiae YML054C   Cyb2p
Schmidtea mediterranea mk4.009795.02  
Schmidtea mediterranea mk4.009795.01  
Treponema pallidum TP0291   hypothetical protein

Essentiality

Rv1872c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1902 this record Mycobacterium tuberculosis non-essential nmpdr
b3605 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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
Species Known druggable target Linked compounds Reference
Homo sapiens hydroxyacid oxidase (glycolate oxidase) 1 Compounds References
Rattus norvegicus Hydroxyacid oxidase 2 Compounds References
Homo sapiens hydroxyacid oxidase 2 (long chain) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets

Obtained from network model

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.1438 1 1
0.0209 0.5 0.5
0.0454 0.4821 0.608
0.02 0.651 1
0.017 0.5661 1
0.0378 0.4645 0.8799
0.017 0.5225 1
0.1105 1 1
0.0209 0.37 0.5
0.017 0.2858 0.5736
0.018 0.7746 1
0.0533 1 0.5
0.0359 0.9829 1
0.1322 0.3575 0.9206
0.0378 0.4645 0.8799
0.1051 1 1
0.2638 0.3277 1
0.1418 1 0.5
0.0168 0.3276 1
0.0545 0.6751 1
0.0325 0.6994 1
0.0338 0.587 0.584
0.0176 0.288 0.5
0.0366 0.3221 0.3185
0.0666 1 1
0.0333 1 0.5
0.0341 0.475 1
0.0545 0.6751 1
0.0585 1 0.5
0.0454 0.4821 0.608
0.0709 1 1
0.0178 0.4679 1
0.0174 0.6703 0.5
0.0924 1 1
0.1438 1 1
0.0338 1 1
0.0924 1 1
0.0371 1 1
0.0552993 1 0.5
0.1438 1 1
0.0209 0.9062 1
0.1584 1 1
0.0666 1 1
0.0532 0.6223 1
0.0209 0.5 0.5
0.0359 0.9829 1
0.0344 0.3422 0.5
0.0209 1 0.5
0.017 0.2978 0.894
0.0559 0.5596 1
0.051 1 1
0.0209 0.2945 1
0.0209 0.4077 0.5
0.0366 0.3221 0.3185
0.2892 1 1
0.0209 1 0.5
0.0209 0.5 0.5
0.0209 1 0.5
0.0209 0.5116 0.5
0.0534 0.5 0.5
0.0341 0.475 1
0.0209 0.2945 1
0.1438 1 1
0.2638 0.3277 1
0.0341 0.475 1
0.1073 0.4485 1
0.1322 0.3575 0.9206
0.0527 0.6648 1
0.0182 0.3837 0.5
0.1426 0.37 1
0.017 0.2978 0.894
0.0209 0.2638 0.5

Assayability

Assay information

  • Assay for L-Lactic Dehydrogenase - Cytochrome (1.1.2.3 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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 Rv1872c (Mycobacterium tuberculosis), Possible L-lactate dehydrogenase (cytochrome) LldD2
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