Detailed view for Rv2716

Basic information

TDR Targets ID: 8720
Mycobacterium tuberculosis, Conserved protein
Source Database / ID:  Tuberculist 

pI: 4.7478 | Length (AA): 228 | MW (Da): 24574 | 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

PF02567   Phenazine biosynthesis-like protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0003824   catalytic activity  
GO:0009058   biosynthetic 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 99 1qya (A) 1 103 16.00 0.18 0.13 0.639411 -0.58
1 228 1qya (A) 1 296 21.00 0 1 0.9684 -0.13
1 220 1ym5 (A) 3 285 27.00 0 1 1.04331 -0.33
5 228 1xub (A) 4 277 29.00 0 1 1.11686 -0.09

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
Upper 60-80% percentile Dormant phase. hasan
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_128465)

Species Accession Gene Product
Arabidopsis thaliana AT1G03210   Phenazine biosynthesis PhzC/PhzF protein
Arabidopsis thaliana AT4G02850   phenazine biosynthesis PhzC/PhzF family protein
Arabidopsis thaliana AT4G02860   Phenazine biosynthesis PhzC/PhzF protein
Candida albicans CaO19.13065   potential phenazine (antibiotic) PhzC/PhzF biosynthesis-like protein
Candida albicans CaO19.5620   potential phenazine (antibiotic) PhzC/PhzF biosynthesis-like protein
Caenorhabditis elegans CELE_T04A11.5   Protein T04A11.5
Caenorhabditis elegans CELE_T04A11.2   Protein T04A11.2
Escherichia coli b1464   PhzC-PhzF family protein
Homo sapiens ENSG00000108187   phenazine biosynthesis-like protein domain containing
Leishmania braziliensis LbrM.17.0460   hypothetical protein, unknown function
Leishmania donovani LdBPK_170540.1   Phenazine biosynthesis-like protein, putative
Leishmania infantum LinJ.17.0540   hypothetical protein, unknown function
Leishmania major LmjF.17.0480   hypothetical protein, unknown function
Leishmania mexicana LmxM.17.0480   hypothetical protein, unknown function
Mus musculus ENSMUSG00000020072   phenazine biosynthesis-like protein domain containing 2
Mus musculus ENSMUSG00000020072   phenazine biosynthesis-like protein domain containing 1
Mycobacterium tuberculosis Rv2716   Conserved protein
Mycobacterium ulcerans MUL_2768   hypothetical protein
Mycobacterium ulcerans MUL_3359   hypothetical protein
Oryza sativa 4324375   Os01g0266500
Oryza sativa 4333184   Os03g0434400
Saccharomyces cerevisiae YHR029C   Yhi9p
Schmidtea mediterranea mk4.054732.00  
Trichomonas vaginalis TVAG_148550   phenazine biosynthesis protein, putative

Essentiality

Rv2716 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2762 this record Mycobacterium tuberculosis non-essential nmpdr
b1464 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • 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

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 Rv2716 (Mycobacterium tuberculosis), Conserved protein
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