Detailed view for Rv2496c

Basic information

TDR Targets ID: 6658
Mycobacterium tuberculosis, Probable branched-chain keto acid dehydrogenase E1 component, beta subunit BkdB
Source Database / ID:  Tuberculist 

pI: 4.9822 | Length (AA): 348 | MW (Da): 38064 | Paralog Number: 0

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

PF02779   Transketolase, pyrimidine binding domain
PF02780   Transketolase, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 4 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
19 346 1ik6 (A) 1 325 46.00 0 1 1.39993 -0.65
22 346 1qs0 (B) 2 338 43.00 0 1 1.44871 -0.52
25 346 1w85 (B) 2 323 47.00 0 1 1.60909 -1.21
26 345 1umd (B) 4 322 49.00 0 1 1.57594 -1.04

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, Dormant phase. hasan murphy
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_128323)

Species Accession Gene Product
Arabidopsis thaliana AT1G55510   branched-chain alpha-keto acid decarboxylase E1 beta subunit
Arabidopsis thaliana AT3G13450   branched chain alpha-keto acid dehydrogenase E1 beta
Babesia bovis BBOV_IV008190   branched-chain alpha-keto acid dehydrogenase E1 component beta subunit, putative
Brugia malayi Bm1_56495   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor
Caenorhabditis elegans CELE_F27D4.5   Protein TAG-173
Chlamydia trachomatis CT_340   oxoisovalerate dehydrogenase subunits alpha/beta
Dictyostelium discoideum DDB_G0268020   3-methyl-2-oxobutanoate dehydrogenase
Drosophila melanogaster Dmel_CG17691   CG17691 gene product from transcript CG17691-RC
Homo sapiens ENSG00000083123   branched chain keto acid dehydrogenase E1, beta polypeptide
Leishmania braziliensis LbrM.34.0090   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Leishmania donovani LdBPK_350050.1   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Leishmania infantum LinJ.35.0050   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Leishmania major LmjF.35.0050   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Leishmania mexicana LmxM.34.0050   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Loa Loa (eye worm) LOAG_04489   2-oxoisovalerate dehydrogenase subunit beta
Mus musculus ENSMUSG00000032263   branched chain ketoacid dehydrogenase E1, beta polypeptide
Mycobacterium tuberculosis Rv2496c   Probable branched-chain keto acid dehydrogenase E1 component, beta subunit BkdB
Mycobacterium ulcerans MUL_3774   pyruvate dehydrogenase E1 component subunit PdhB
Neospora caninum NCLIV_057460   Transketolase central region, related
Oryza sativa 4342508   Os07g0170100
Plasmodium berghei PBANKA_1104200   2-oxoisovalerate dehydrogenase subunit beta, mitochondrial, putative
Plasmodium falciparum PF3D7_0504600   2-oxoisovalerate dehydrogenase subunit beta, mitochondrial, putative
Plasmodium knowlesi PKNH_1029000   2-oxoisovalerate dehydrogenase subunit beta, mitochondrial, putative
Plasmodium vivax PVX_097790   2-oxoisovalerate dehydrogenase subunit beta, mitochondrial, putative
Plasmodium yoelii PY03843   Drosophila melanogaster RE25729p
Schmidtea mediterranea mk4.017287.00  
Schmidtea mediterranea mk4.004369.02   2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Trypanosoma brucei gambiense Tbg972.10.5390   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Trypanosoma brucei Tb10.v4.0043   chrX additional, unordered contigs
Trypanosoma brucei Tb927.10.4330   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Trypanosoma congolense TcIL3000_10_3620   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Trypanosoma cruzi TcCLB.511469.100   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Trypanosoma cruzi TcCLB.506295.160   2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor, putative
Toxoplasma gondii TGME49_314400   pyruvate dehydrogenase E1 component, beta subunit, putative
Theileria parva TP01_0956   pyruvate dehydrogenase E1 component beta subunit, mitochondrial, putative

Essentiality

Rv2496c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2539 this record Mycobacterium tuberculosis non-essential nmpdr
CELE_F27D4.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F27D4.5 Caenorhabditis elegans slow growth wormbase
CELE_F27D4.5 Caenorhabditis elegans sterile wormbase
PBANKA_1104200 Plasmodium berghei Slow plasmo
TGME49_314400 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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

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
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
0.0056 0.5952 0.5
0.0035 0.6302 0.5
0.0053 0.5529 0.5
0.0052 0.553 0.5
0.031 0.4555 0.4555
0.0035 0.3052 0.5
0.0035 0.6302 0.5
0.0078 0.3014 0
0.0035 0.6302 0.5
0.0054 0.3152 0.5
0.027 0.4515 0
0.0053 0.2736 0.5
0.0054 0.2543 0.5
0.0035 0.6302 0.5
0.0035 0.6302 0.5
0.027 0.4515 0
0.0036 0.6302 0.5
0.0042 0.6302 0.5
0.0052 0.553 0.5
0.0292 0.3014 0
0.0035 0.4707 0.5
0.0055 0.5529 0.5
0.0053 0.5509 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv2496c (Mycobacterium tuberculosis), Probable branched-chain keto acid dehydrogenase E1 component, beta subunit BkdB
Title for this comment
Comment