Detailed view for Rv0906

Basic information

TDR Targets ID: 7640
Mycobacterium tuberculosis, Conserved protein
Source Database / ID:  Tuberculist 

pI: 6.5486 | Length (AA): 372 | MW (Da): 40641 | Paralog Number: 0

Signal peptide: Y | 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

PF12706   Beta-lactamase superfamily domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0070290   GO:N-acylphosphatidylethanolamine-specific phospholipase D activity  

GO:0008270   zinc ion binding  

Metabolic Pathways

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

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
46 362 4qn9 (A) 57 388 30.00 0 1 1.22485 -0.23
46 359 4qn9 (A) 57 385 37.00 0 1 1.26119 -0.45
105 359 3x30 (A) 1 225 28.00 0.0000001 1 0.946284 -0.81

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
Mid 40-60% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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_128466)

Species Accession Gene Product
Babesia bovis BBOV_I004470   conserved hypothetical protein
Candida albicans CaO19.6061   similar to S. cerevisiae FMP30 (YPL103C) mitochondrial protein
Candida albicans CaO19.13482   similar to S. cerevisiae FMP30 (YPL103C) mitochondrial protein
Caenorhabditis elegans CELE_Y37E11AR.3   Protein NAPE-2, isoform A
Caenorhabditis elegans CELE_Y37E11AR.4   Protein NAPE-1
Dictyostelium discoideum DDB_G0271270   beta-lactamase-like domain-containing protein
Dictyostelium discoideum DDB_G0293392   beta-lactamase-like domain-containing protein
Echinococcus granulosus EgrG_002071000   3'partial|5'partial|n acyl phosphatidylethanolamine hydrolyzing
Echinococcus granulosus EgrG_000144800   n acyl phosphatidylethanolamine hydrolyzing
Echinococcus granulosus EgrG_000124500   n acyl phosphatidylethanolamine hydrolyzing
Echinococcus multilocularis EmuJ_000144800   n acyl phosphatidylethanolamine hydrolyzing
Homo sapiens ENSG00000161048   N-acyl phosphatidylethanolamine phospholipase D
Leishmania donovani LdBPK_131290.1   Beta-lactamase superfamily domain containing protein, putative
Leishmania infantum LinJ.13.1290   hypothetical protein, conserved
Leishmania major LmjF.13.1390   hypothetical protein, conserved
Leishmania mexicana LmxM.13.1390   hypothetical protein, conserved
Mus musculus ENSMUSG00000044968   N-acyl phosphatidylethanolamine phospholipase D
Mycobacterium tuberculosis Rv0906   Conserved protein
Mycobacterium ulcerans MUL_0235   hypothetical protein
Neospora caninum NCLIV_009780   Beta-lactamase domain protein (Precursor), related
Neospora caninum NCLIV_031520   hypothetical protein, conserved
Plasmodium berghei PBANKA_0905200   conserved Plasmodium protein, unknown function
Plasmodium berghei PBANKA_1026400   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1143800   conserved Plasmodium protein, unknown function
Plasmodium falciparum PF3D7_1416300   conserved protein, unknown function
Plasmodium knowlesi PKNH_0941700   conserved Plasmodium protein, unknown function
Plasmodium knowlesi PKNH_1341800   conserved Plasmodium protein, unknown function
Plasmodium vivax PVX_085635   hypothetical protein, conserved
Plasmodium vivax PVX_092795   hypothetical protein, conserved
Plasmodium yoelii PY06610   hypothetical protein
Plasmodium yoelii PY02609   hypothetical protein
Saccharomyces cerevisiae YPL103C   Fmp30p
Schmidtea mediterranea mk4.075769.00   N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Schmidtea mediterranea mk4.011893.00   N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Toxoplasma gondii TGME49_320490   N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D family protein
Toxoplasma gondii TGME49_231150   hypothetical protein
Theileria parva TP01_0189   hypothetical protein
Trichomonas vaginalis TVAG_334240   conserved hypothetical protein
Trichomonas vaginalis TVAG_453240   conserved hypothetical protein
Trichomonas vaginalis TVAG_223500   conserved hypothetical protein
Trichomonas vaginalis TVAG_290900   conserved hypothetical protein

Essentiality

Rv0906 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu922 this record Mycobacterium tuberculosis non-essential nmpdr
PBANKA_0905200 Plasmodium berghei Dispensable plasmo
TGME49_320490 Toxoplasma gondii Probably essential sidik
TGME49_231150 Toxoplasma gondii Probably essential sidik
TGME49_320490 Toxoplasma gondii Probably non-essential sidik
TGME49_231150 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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
Mus musculus N-acyl phosphatidylethanolamine phospholipase D Compounds References
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 Rv0906 (Mycobacterium tuberculosis), Conserved protein
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