Detailed view for Rv1607

Basic information

TDR Targets ID: 5746
Mycobacterium tuberculosis, Probable ionic transporter integral membrane protein ChaA
Source Database / ID:  Tuberculist 

pI: 6.9905 | Length (AA): 360 | MW (Da): 36772 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 11

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

PF01699   Sodium/calcium exchanger protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0016021   integral to membrane  
GO:0055085   transmembrane transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 2 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
1 359 4k1c (A) 34 394 22.00 0 1 1.24252 0.01
3 359 4k1c (A) 38 397 18.00 0 0.84 1.23417 -0.08

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 20-40% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_128780)

Species Accession Gene Product
Arabidopsis thaliana AT1G55720   cation exchanger 6
Arabidopsis thaliana AT3G13320   low affinity calcium antiporter CAX2
Arabidopsis thaliana AT2G38170   vacuolar cation/proton exchanger 1
Arabidopsis thaliana AT1G55730   vacuolar cation/proton exchanger 5
Arabidopsis thaliana AT3G51860   vacuolar cation/proton exchanger 3
Candida albicans CaO19.405   Calcium transport protein of the vacuolar membrane
Candida albicans CaO19.8035   Calcium transport protein of the vacuolar membrane
Cryptosporidium hominis Chro.10296   calcium antiporter
Cryptosporidium parvum cgd1_2620   calcium antiporter, Na/Ca exchange associated membrane protein with 11 transmembrane domains
Escherichia coli b1216   calcium/sodium:proton antiporter
Leishmania donovani LdBPK_140270.1   hypothetical protein, conserved
Leishmania infantum LinJ.14.0270   hypothetical protein, conserved
Leishmania major LmjF.14.0270   hypothetical protein, conserved
Leishmania mexicana LmxM.14.0270   hypothetical protein, conserved
Mycobacterium leprae ML1267   Probable ionic transporter integral membrane protein ChaA
Mycobacterium tuberculosis Rv1607   Probable ionic transporter integral membrane protein ChaA
Neospora caninum NCLIV_002830   Calcium/proton antiporter, related
Oryza sativa 4339806   Os05g0594200
Oryza sativa 9271552   Os02g0138900
Oryza sativa 4333044   Os03g0397400
Oryza sativa 4337242   Os04g0653200
Oryza sativa 4324573   Os01g0557500
Plasmodium berghei PBANKA_0102300   cation/H+ antiporter
Plasmodium falciparum PF3D7_0603500   cation/H+ antiporter
Plasmodium knowlesi PKNH_1147200   cation/H+ antiporter, putative
Plasmodium vivax PVX_113340   cation/H+ antiporter, putative
Plasmodium yoelii PY00061   calcium/proton exchanger, putative
Saccharomyces cerevisiae YDL128W   Vcx1p
Schmidtea mediterranea mk4.058979.00  
Toxoplasma gondii TGME49_207910   manganese resistance 1 protein, putative

Essentiality

Rv1607 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1635 this record Mycobacterium tuberculosis non-essential nmpdr
b1216 Escherichia coli non-essential goodall
TGME49_207910 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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.
  • 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
  • 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

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

Druggability index (range: 0 to 1): 0.1

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 Rv1607 (Mycobacterium tuberculosis), Probable ionic transporter integral membrane protein ChaA
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