Detailed view for Rv3842c

Basic information

TDR Targets ID: 6160
Mycobacterium tuberculosis, Probable glycerophosphoryl diester phosphodiesterase GlpQ1 (glycerophosphodiester phosphodiesterase)

Source Database / ID:  Tuberculist 

pI: 7.5597 | Length (AA): 274 | MW (Da): 29917 | Paralog Number: 1

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

PF03009   Glycerophosphoryl diester phosphodiesterase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0008889   glycerophosphodiester phosphodiesterase activity  
GO:0008081   phosphoric diester hydrolase activity  
GO:0006629   lipid metabolic process  
GO:0006071   glycerol metabolic process  

Metabolic Pathways

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
3 266 2oog (A) 45 310 26.00 0 1 1.3548 -0.62
6 266 3l12 (A) 8 306 36.00 0 1 1.10375 0.42
10 273 3ks6 (A) 0 249 17.00 0.05 1 1.1548 -0.02
195 274 3rlg (A) 191 271 18.00 0.067 0.98 0.624271 -0.75

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. hasan
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. murphy
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_127726)

Species Accession Gene Product
Arabidopsis thaliana AT1G71340   glycerophosphodiester phosphodiesterase
Brugia malayi Bm1_01870   Glycerophosphoryl diester phosphodiesterase family protein
Caenorhabditis elegans CELE_T12B3.3   Protein T12B3.3
Dictyostelium discoideum DDB_G0271374   hypothetical protein
Drosophila melanogaster Dmel_CG14883   CG14883 gene product from transcript CG14883-RA
Escherichia coli b3449   glycerophosphodiester phosphodiesterase, cytosolic
Entamoeba histolytica EHI_113970   glycerophosphoryl diester phosphodiesterase, putative
Homo sapiens ENSG00000006007   glycerophosphodiester phosphodiesterase 1
Leishmania braziliensis LbrM.24.2240   hypothetical protein, conserved
Leishmania donovani LdBPK_242250.1   Glycerophosphoryl diester phosphodiesterase family, putative
Leishmania infantum LinJ.24.2250   hypothetical protein, conserved
Leishmania major LmjF.24.2160   hypothetical protein, conserved
Leishmania mexicana LmxM.24.2160   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_12305   hypothetical protein
Mycobacterium leprae ML0074   Probable glycerophosphoryl diester phosphodiesterase GlpQ1 (glycerophosphodiester phosphodiesterase)
Mus musculus ENSMUSG00000033917   glycerophosphodiester phosphodiesterase 1
Mycobacterium tuberculosis Rv3842c   Probable glycerophosphoryl diester phosphodiesterase GlpQ1 (glycerophosphodiester phosphodiesterase)
Mycobacterium tuberculosis Rv0317c   Possible glycerophosphoryl diester phosphodiesterase GlpQ2 (glycerophosphodiester phosphodiesterase)
Mycobacterium ulcerans MUL_5015   glycerophosphoryl diester phosphodiesterase
Mycobacterium ulcerans MUL_1157   glycerophosphoryl diester phosphodiesterase
Oryza sativa 4350150   Os11g0236000
Onchocerca volvulus OVOC5492   Glycerophosphodiester phosphodiesterase 1 homolog
Schmidtea mediterranea mk4.035731.01  
Trypanosoma brucei gambiense Tbg972.8.6110   hypothetical protein, conserved
Trypanosoma brucei Tb927.8.6080   Glycerophosphoryl diester phosphodiesterase family, putative
Trypanosoma cruzi TcCLB.511901.30   Glycerophosphoryl diester phosphodiesterase family, putative
Trypanosoma cruzi TcCLB.511071.100   Present in the outer mitochondrial membrane proteome 42

Essentiality

Rv3842c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3909 this record Mycobacterium tuberculosis non-essential nmpdr
Tb927.8.6080 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.6080 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.6080 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb927.8.6080 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3449 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv3842c (Mycobacterium tuberculosis), Probable glycerophosphoryl diester phosphodiesterase GlpQ1 (glycerophosphodiester phosphodiesterase)
Title for this comment
Comment