Detailed view for Rv2540c

Basic information

TDR Targets ID: 981044
Mycobacterium tuberculosis, Probable chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase)
Source Database / ID:  Tuberculist 

pI: 6.51 | Length (AA): 401 | MW (Da): 41760 | 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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 392 4bai (A) 1 392 99.99 0 1 2.08816 -0.55

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_128304)

Species Accession Gene Product
Arabidopsis thaliana AT1G48850   chorismate synthase
Candida albicans CaO19.3489   chorismate synthase
Candida albicans CaO19.1986   Chorismate synthase
Chlamydia trachomatis CT_368   chorismate synthase
Escherichia coli b2329   chorismate synthase
Mycobacterium leprae ML0516   Chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase).
Mycobacterium tuberculosis Rv2540c   Probable chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase)
Mycobacterium ulcerans MUL_1759   chorismate synthase
Neospora caninum NCLIV_023120   Chorismate synthase (EC 4.2.3.5), related
Oryza sativa 4332286   Os03g0254800
Plasmodium berghei PBANKA_1121900   chorismate synthase, putative
Plasmodium falciparum PF3D7_0623000   chorismate synthase
Plasmodium knowlesi PKNH_1127200   chorismate synthase, putative
Plasmodium vivax PVX_114265   chorismate synthase
Plasmodium yoelii PY04071   chorismate synthase, putative
Saccharomyces cerevisiae YGL148W   bifunctional chorismate synthase/riboflavin reductase [NAD(P)H] ARO2
Toxoplasma gondii TGME49_201380   chorismate synthase, putative

Essentiality

Rv2540c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2329 Escherichia coli non-essential goodall
PBANKA_1121900 Plasmodium berghei Dispensable plasmo
TGME49_201380 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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.
  • 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
  • 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.

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
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) Chorismate synthase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0171 0.3741 0.5
0.2372 0.4917 1
0.0171 0.3741 0.5
0.2192 0.4924 1
0.0106 0.4752 0.5
0.1072 0.2604 1
0.1996 0.4923 1
0.1806 0.4837 1
0.1853 0.4894 1
0.2007 0.4919 1
0.2464 0.3554 1
0.1483 0.4749 1
0.1589 0.4926 1
0.23 0.4916 1
0.2372 0.4917 1
0.0708 0.4891 1
0.2466 0.3279 1
0.1684 0.4906 1
0.1711 0.3964 1
0.087 0.4884 1
0.0887 0.4818 1
0.0348 0.4863 1
0.0527 0.488 1
0.2908 0.4922 1
0.2464 0.3554 1
0.235 0.391 1
0.2372 0.4917 1
0.1806 0.4837 1
0.2464 0.3554 1
0.0344 0.4278 1
0.1494 0.2761 1
0.2464 0.3554 1
0.0708 0.4891 1
0.1075 0.2634 1
0.1997 0.4915 1
0.1565 0.4578 0.5
0.1065 0.4916 1
0.0438 0.4776 1
0.1068 0.4912 1
0.0345 0.3385 1
0.1742 0.4917 1
0.2372 0.4917 1
0.0887 0.4818 1
0.215 0.4919 1
0.0881 0.2658 1
0.0327 0.3768 1
0.0973 0.2858 1
0.2452 0.4255 1
0.2464 0.3554 1
0.1303 0.4832 1
0.2466 0.3275 1
0.1068 0.4912 1
0.2162 0.4922 1
0.1141 0.3396 1
0.2266 0.4918 1
0.2825 0.405 1
0.1705 0.4913 1
0.0966 0.2686 0.5
0.1997 0.4915 1
0.1814 0.4908 1
0.2041 0.4919 1
0.2466 0.3275 1
0.2041 0.4919 1
0.0272 0.4368 0.429
0.0902 0.4904 1
0.0523 0.4882 1
0.1076 0.4918 1
0.1294 0.4901 1
0.2103 0.492 1
0.2402 0.4914 1
0.165 0.483 1
0.2382 0.3584 1
0.0101 0.2597 0.5
0.1689 0.4863 1
0.2464 0.3554 1
0.2322 0.4918 1
0.1479 0.4622 1
0.235 0.391 1
0.2464 0.3554 1
0.098 0.4661 0.5624
0.1483 0.4749 1
0.0327 0.3768 1
0.035 0.4436 1

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 Rv2540c (Mycobacterium tuberculosis), Probable chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase)
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