Detailed view for Rv3239c

Basic information

TDR Targets ID: 9026
Mycobacterium tuberculosis, Probable conserved transmembrane transport protein
Source Database / ID:  Tuberculist 

pI: 9.7228 | Length (AA): 1048 | MW (Da): 110199 | Paralog Number: 5

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 15

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

PF00027   Cyclic nucleotide-binding domain
PF01734   Patatin-like phospholipase
PF07690   Major Facilitator Superfamily

Gene Ontology

Mouse over links to read term descriptions.
GO:0046470   phosphatidylcholine metabolic process  
GO:0022857   transmembrane transporter activity  
GO:0004622   lysophospholipase activity  
GO:0016021   integral to membrane  
GO:0015520   tetracycline:hydrogen antiporter activity  
GO:0005215   transporter activity  
GO:0055085   transmembrane transport  
GO:0046677   response to antibiotic  
GO:0015904   tetracycline transport  
GO:0008152   metabolic process  
GO:0006810   transport  
GO:0006629   lipid metabolic process  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 9 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
16 466 4u4v (A) 28 452 18.00 0 0.74 0.446744 0.43
25 204 4lds (A) 8 192 28.00 0.046 0.33 0.174856 1.19
89 364 5i20 (B) 3 286 20.00 0 0.37 0.194759 1.11
508 612 5c8w (A) 161 265 26.00 0.000074 1 0.574291 -1.25
508 632 2pqq (A) 3 134 40.00 0 1 0.608675 -0.8
510 736 3d0s (A) 5 224 28.00 0.00000043 1 0.425703 0.2
510 645 3gyd (A) 22 168 28.00 0.000098 1 0.429871 -0.11
786 1045 5fya (A) 23 311 34.00 0 1 0.650292 -0.52
788 1045 5fya (A) 25 311 31.00 0 1 0.647583 -0.54

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
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_126664)

Species Accession Gene Product
Candida albicans CaO19.7336   one of two genes (CaP19.7554 and CaP19.7336) similar to pichia anomala putative transporter (CAC69145)
Candida albicans CaO19.8888   similar to S. pombe fnx1 (SPBC12C2.13c) MSF-MDR transporter implicated in G0 transition
Candida albicans CaO19.12243   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Candida albicans CaO19.4779   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Candida albicans CaO19.3444   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Candida albicans CaO19.10948   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Candida albicans CaO19.1942   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Candida albicans CaO19.1308   similar to S. pombe fnx1 (SPBC12C2.13c) MSF-MDR transporter implicated in G0 transition
Candida albicans CaO19.9497   one of three related potential transporter genes (CaP19.1942, CaP19.3444 and CaP19.4779) similar to S. cerevisiae YKR105C, YCL06
Dictyostelium discoideum DDB_G0283345   drug resistance transporter, EmrB/QacA subfamily protein
Escherichia coli b2686   multidrug efflux system protein
Escherichia coli b1828   putative transporter
Escherichia coli b2367   putative multidrug efflux system
Giardia lamblia GL50803_8444   MDR-type permease
Giardia lamblia GL50803_16880   Multidrug resistance protein B
Mycobacterium leprae ML1562c   POSSIBLE INTEGRAL MEMBRANE EFFLUX PROTEIN EFPA
Mycobacterium tuberculosis Rv1877   Probable conserved integral membrane protein
Mycobacterium tuberculosis Rv0783c   Possible multidrug resistance integral membrane efflux protein EmrB
Mycobacterium tuberculosis Rv2333c   Integral membrane drug efflux protein Stp
Mycobacterium tuberculosis Rv3239c   Probable conserved transmembrane transport protein
Mycobacterium tuberculosis Rv3728   Probable conserved two-domain membrane protein
Mycobacterium tuberculosis Rv2459   Probable conserved integral membrane transport protein
Mycobacterium ulcerans MUL_0240   hypothetical protein
Mycobacterium ulcerans MUL_3826   hypothetical protein
Mycobacterium ulcerans MUL_1468   integral membrane transport protein
Mycobacterium ulcerans MUL_0542   multidrug resistance integral membrane efflux protein
Mycobacterium ulcerans MUL_0501   integral membrane drug efflux protein
Mycobacterium ulcerans MUL_3729   integral membrane transport protein
Mycobacterium ulcerans MUL_3590   transmembrane transport protein
Saccharomyces cerevisiae YGR224W   Azr1p
Saccharomyces cerevisiae YMR088C   Vba1p
Saccharomyces cerevisiae YCL069W   Vba3p
Saccharomyces cerevisiae YKR105C   Vba5p
Saccharomyces cerevisiae YPR198W   Sge1p
Saccharomyces cerevisiae YDR119W   Vba4p
Schmidtea mediterranea mk4.065124.00  

Essentiality

Rv3239c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu798 Mycobacterium tuberculosis non-essential nmpdr
mtu1907 Mycobacterium tuberculosis non-essential nmpdr
mtu2374 Mycobacterium tuberculosis non-essential nmpdr
mtu2502 Mycobacterium tuberculosis non-essential nmpdr
mtu3298 this record Mycobacterium tuberculosis non-essential nmpdr
b1828 Escherichia coli non-essential goodall
b2367 Escherichia coli non-essential goodall
b2686 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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.

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 Rv3239c (Mycobacterium tuberculosis), Probable conserved transmembrane transport protein
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