Detailed view for Rv3398c

Basic information

TDR Targets ID: 6246
Mycobacterium tuberculosis, Probable multifunctional geranylgeranyl pyrophosphate synthetase IdsA1 (GGPP synthetase) (ggppsase) (geranylgeranyl diphosphate
Source Database / ID:  Tuberculist 

pI: 6.2691 | Length (AA): 359 | MW (Da): 38852 | Paralog Number: 1

Signal peptide: N | 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

PF00348   Polyprenyl synthetase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008299   isoprenoid biosynthetic process  

Structural information

Modbase 3D models:

There are 2 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
23 355 3nf2 (A) 39 374 49.00 0 1 1.61488 -1.07
23 358 3p8r (A) 1 293 31.00 0 1 0.916233 0.8

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 20-40% percentile Dormant phase. hasan
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_130660)

Species Accession Gene Product
Arabidopsis thaliana AT3G14530   geranylgeranyl pyrophosphate synthase 9
Arabidopsis thaliana AT3G14550   geranylgeranyl pyrophosphate synthase 3
Arabidopsis thaliana AT3G29430   geranylgeranyl pyrophosphate synthase 11
Arabidopsis thaliana AT3G14510   putative geranylgeranyl pyrophosphate synthase 8
Arabidopsis thaliana AT4G36810   geranylgeranyl pyrophosphate synthase 1
Arabidopsis thaliana AT2G23800   geranylgeranyl pyrophosphate synthase 2
Arabidopsis thaliana AT2G18640   geranylgeranyl pyrophosphate synthase 4
Arabidopsis thaliana AT2G18620   geranylgeranyl pyrophosphate synthase 7
Arabidopsis thaliana AT3G32040   geranylgeranyl pyrophosphate synthase 12
Chlamydia trachomatis CT_628   geranylgeranyl pyrophosphate synthase
Escherichia coli b0421   geranyltranstransferase
Mycobacterium tuberculosis Rv3398c   Probable multifunctional geranylgeranyl pyrophosphate synthetase IdsA1 (GGPP synthetase) (ggppsase) (geranylgeranyl diphosphate
Mycobacterium tuberculosis Rv3383c   Possible polyprenyl synthetase IdsB (polyprenyl transferase) (polyprenyl diphosphate synthase)
Mycobacterium ulcerans MUL_3197   polyprenyl synthetase IdsB
Oryza sativa 4343721   Os07g0580900
Oryza sativa 9272383   Os01g0248701
Schmidtea mediterranea mk4.043315.00  
Wolbachia endosymbiont of Brugia malayi Wbm0737   geranylgeranyl pyrophosphate synthase

Essentiality

Rv3398c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3459 this record Mycobacterium tuberculosis essential nmpdr
mtu3443 Mycobacterium tuberculosis non-essential nmpdr
b0421 Escherichia coli essential goodall
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • 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

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

Druggability index (range: 0 to 1): 0.1

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
Escherichia coli geranyltranstransferase Compounds References
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Trypanosoma cruzi solanesyl-diphosphate synthase, putative 292 aa 33.2% 250 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0729 0.2699 0.2699
0.0456 0.3534 0.3233
0.0693 0.2649 0.315
0.0704 0.3928 0.3922
0.0191 0.3456 0
0.0729 0.2699 0.2699
0.0261 0.2812 0.2877
0.0693 0.2649 0.315
0.8894 0.2959 0.2959
0.0411 0.2525 0.2784
0.0498 0.3247 0.3125
0.0635 0.2606 0
0.0377 0.3464 0.3416
0.0743 0.2834 0.2825
0.0693 0.2649 0.315
0.0498 0.3247 0.3125
0.0693 0.2649 0.315
0.0743 0.2834 0.2825
0.05 0.2528 0.2449
0.0411 0.2525 0.2784
0.0715 0.3347 0.2814
0.0411 0.2525 0.2784
0.0519 0.3461 0.3285
0.0715 0.3347 0.2814
0.0128 0.288 0
0.0953 0.2702 0.2699
0.0517 0.2702 0
0.1374 0.2627 0.2562
0.0693 0.2649 0.315
0.8894 0.2959 0.2959
0.0332 0.2653 0.2653
0.0905 0.2782 0.2724
0.026 0.2585 0.245
0.0706 0.2737 0.272
0.8894 0.2959 0.2959
0.0788 0.2789 0.227
0.7818 0.3027 0.3027
0.0519 0.2681 0.2607
0.053 0.3396 0.3396
0.0663 0.273 0.2708
0.0365 0.2945 0.2945
0.0729 0.2699 0.2699
0.0433 0.267 0.256
0.0743 0.2834 0.2825
0.1063 0.2647 0.2596
0.0327 0.2716 0
0.4164 0.2924 0.2924
0.1179 0.3053 0.295
0.0403 0.2639 0.2347
0.4428 0.2931 0.293
0.0519 0.3461 0.3285
0.0715 0.3347 0.2814
0.0118 0.3145 0
0.0673 0.2639 0.263
0.0743 0.2834 0.2825
0.0436 0.3099 0.3
0.0711 0.2728 0.2728
0.0365 0.2945 0.2945
0.0416 0.3269 0
0.0743 0.2834 0.2825
0.0537 0.3254 0.3185
0.0498 0.3247 0.3125
0.0533 0.3405 0.3164
0.0094 0.3186 0.3186
0.0693 0.2649 0.315
0.1685 0.2666 0.0917
0.0254 0.2727 0.2591
0.0169 0.3173 0
0.0518 0.3339 0.327
0.0905 0.2782 0.2724
0.0583 0.3069 0.3067
0.1888 0.2671 0.2665
0.0715 0.3347 0.2814
0.0545 0.2666 0
0.047 0.2506 0
0.0663 0.273 0.2708
0.013 0.2786 1
0.0495 0.3464 0.3385
0.4164 0.2924 0.2924
0.0494 0.29 0
0.0693 0.2649 0.315
0.1063 0.2647 0.2596
0.0433 0.267 0.256
0.0693 0.2649 0.315
0.0715 0.3347 0.2814
0.0094 0.2984 0.1422
0.026 0.2585 0.245
0.417 0.2929 0.2929

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 Rv3398c (Mycobacterium tuberculosis), Probable multifunctional geranylgeranyl pyrophosphate synthetase IdsA1 (GGPP synthetase) (ggppsase) (geranylgeranyl diphosphate
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