Detailed view for MUL_4157

Basic information

TDR Targets ID: 955134
Mycobacterium ulcerans, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Source Database / ID:  KEGG  

pI: 5.9611 | Length (AA): 159 | MW (Da): 16287 | Paralog Number: 0

Signal peptide: N | GPI Anchor: Y | 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

PF02542   YgbB family

Gene Ontology

Mouse over links to read term descriptions.
GO:0008685   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity  
GO:0016114   terpenoid biosynthetic process  

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
1 151 2uzh (A) 6 156 72.00 0 1 1.87439 -1.23

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_130616)

Species Accession Gene Product
Arabidopsis thaliana AT1G63970   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Babesia bovis BBOV_IV002810   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative
Chlamydia trachomatis CT_434   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Escherichia coli b2746   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Mycobacterium leprae ML0322   Probable 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (MECPS) (MECDP-synthase )
Mycobacterium tuberculosis Rv3581c   Probable 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (MECPS)
Mycobacterium ulcerans MUL_4157   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Neospora caninum NCLIV_029230   hypothetical protein
Oryza sativa 4330320   Os02g0680600
Plasmodium berghei PBANKA_0306400   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative
Plasmodium falciparum PF3D7_0209300   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Plasmodium knowlesi PKNH_0411800   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative
Plasmodium vivax PVX_003920   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative
Plasmodium yoelii PY00321   YgbB family, putative
Toxoplasma gondii TGME49_255690   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase domain-containing protein
Treponema pallidum TP0512   hypothetical protein
Theileria parva TP03_0365   2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0409   2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Essentiality

MUL_4157 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2746 Escherichia coli essential goodall
TGME49_255690 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
Species Known druggable target Linked compounds Reference
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Compounds References
Arabidopsis thaliana 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Compounds References
Mycobacterium tuberculosis Probable 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (MECPS) 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
0.0658 1 1
0.1068 0.2803 1
0.1046 0.2772 1
0.0744 0.2509 1
0.1071 0.2793 1
0.0668 0.3071 1
0.1075 0.2822 1
0.107 0.2914 1
0.1065 0.2883 1
0.0592 0.4733 0.4699
0.0744 0.3186 1
0.1046 0.2772 1
0.1058 0.4548 1
0.066 0.3051 1
0.1065 0.2884 1
0.1058 0.3556 1
0.1071 0.2793 1
0.0742 0.2521 1
0.0657 0.3029 1
0.1065 0.2884 1
0.1068 0.2548 1
0.1068 0.3162 1
0.0652 0.3015 1
0.1068 0.3549 1
0.0592 0.4733 0.4699

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 MUL_4157 (Mycobacterium ulcerans), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
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