Detailed view for Rv3465
Basic information
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
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
Network
Pfam domains
Gene Ontology
GO:0009103 lipopolysaccharide biosynthetic process
Metabolic Pathways
Streptomycin biosynthesis (KEGG)
Polyketide sugar unit biosynthesis (KEGG)
Global map (KEGG)
Biosynthesis of antibiotics (KEGG)
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 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 |
-
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
| Gene/Ortholog | Organism | Phenotype | Source Study |
|---|---|---|---|
| mtu3526 this record | Mycobacterium tuberculosis | essential | nmpdr |
| b2038 | Escherichia coli | non-essential | goodall |
-
blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930 -
alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924 -
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 -
keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection -
shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan -
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 -
yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
Phenotypes and Validation (curated)
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
Associated compounds / Druggability
Known modulators for this target
| Compound | Source | Reference |
|---|---|---|
| References |
Predicted associations
By orthology with druggable targets
By sequence similarity to non orthologous druggable targets
Obtained from network model
Assayability
Assay information
- ChEMBL
- Inhibition of Mycobacterium tuberculosis RmlC/RmlD expressed in Escherichia coli by spectrophotometry
Reagent availability
Bibliographic References
4 literature references were collected for this gene.