Detailed view for Rv3465

Basic information

TDR Targets ID: 7015
Mycobacterium tuberculosis, dTDP-4-dehydrorhamnose 3,5-epimerase RmlC (dTDP-4-keto-6-deoxyglucose 3,5-epimerase) (dTDP-L-rhamnose synthetase) (thymidine dip

Source Database / ID:  Tuberculist 

pI: 4.7367 | Length (AA): 202 | MW (Da): 22314 | 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

PF00908   dTDP-4-dehydrorhamnose 3,5-epimerase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008830   dTDP-4-dehydrorhamnose 3,5-epimerase activity  
GO:0009103   lipopolysaccharide 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
1 201 1upi (A) 1 201 99.99 0 1 2.21285 -1.33

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:

  • 1PM7:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 1UPI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2IXC:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% 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_132926)

Species Accession Gene Product
Brugia malayi Bm1_32635   dTDP-4-dehydrorhamnose 3,5-epimerase
Caenorhabditis elegans CELE_C14F11.6   Protein C14F11.6
Escherichia coli b2038   dTDP-4-deoxyrhamnose-3,5-epimerase
Loa Loa (eye worm) LOAG_00105   dTDP-4-dehydrorhamnose 3,5-epimerase
Mycobacterium leprae ML1965   dTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE RMLC (dTDP-4-KETO-6-DEOXYGLUCOSE 3,5-EPIMERASE) (dTDP-L-RHAMNOSE SYNTHETASE) (THYMIDINE DIP
Mycobacterium tuberculosis Rv3465   dTDP-4-dehydrorhamnose 3,5-epimerase RmlC (dTDP-4-keto-6-deoxyglucose 3,5-epimerase) (dTDP-L-rhamnose synthetase) (thymidine dip
Mycobacterium ulcerans MUL_0839   dTDP-4-dehydrorhamnose 3,5-epimerase, RmlC
Onchocerca volvulus OVOC3044  
Schmidtea mediterranea mk4.040374.01  
Schmidtea mediterranea mk4.059329.02  
Trichomonas vaginalis TVAG_313960   conserved hypothetical protein
Trichomonas vaginalis TVAG_340730   DTDP-4-dehydrorhamnose 3,5-epimerase, putative

Essentiality

Rv3465 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3526 this record Mycobacterium tuberculosis essential nmpdr
b2038 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection

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

Compound Source Reference
References

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

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0291 0.2854 1
0.0314 0.2764 1
0.0314 0.2764 1
0.0289 0.2689 1
0.0274 0.2689 1
0.0305 0.3227 1
0.0373956 1 1

Assayability

Assay information

  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis RmlC/RmlD expressed in Escherichia coli by spectrophotometry

Reagent availability

No reagent availability information for this target.

Bibliographic References

4 literature references were collected for this gene.

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 Rv3465 (Mycobacterium tuberculosis), dTDP-4-dehydrorhamnose 3,5-epimerase RmlC (dTDP-4-keto-6-deoxyglucose 3,5-epimerase) (dTDP-L-rhamnose synthetase) (thymidine dip
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