Detailed view for Rv2500c

Basic information

TDR Targets ID: 6030
Mycobacterium tuberculosis, Possible acyl-CoA dehydrogenase FadE19 (MMGC)
Source Database / ID:  Tuberculist 

pI: 5.1372 | Length (AA): 394 | MW (Da): 41916 | 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

PF00441   Acyl-CoA dehydrogenase, C-terminal domain
PF02770   Acyl-CoA dehydrogenase, middle domain
PF02771   Acyl-CoA dehydrogenase, N-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016627   oxidoreductase activity, acting on the CH-CH group of donors  
GO:0050660   FAD binding  
GO:0016491   oxidoreductase activity  
GO:0009055   electron carrier activity  
GO:0003995   acyl-CoA dehydrogenase activity  
GO:0055114   oxidation reduction  
GO:0008152   metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 5 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
1 388 3b96 (A) 42 433 38.00 0 1 1.47847 -0.53
12 391 4u83 (A) 2 375 46.00 0 1 1.58187 -0.98
13 391 2jif (A) 57 428 37.00 0 1 1.52463 -1.12
13 391 1jqi (A) 10 382 45.00 0 1 1.59533 -1.04
13 391 2dvl (A) 3 370 41.00 0 1 1.53233 -0.91

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
  • 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_128729)

Species Accession Gene Product
Arabidopsis thaliana AT3G45300   isovaleryl-CoA-dehydrogenase
Caenorhabditis elegans CELE_C02B10.1   Protein IVD-1
Dictyostelium discoideum DDB_G0279827   isovaleryl-CoA dehydrogenase, mitochondrial
Drosophila melanogaster Dmel_CG6638   CG6638 gene product from transcript CG6638-RA
Escherichia coli b0039   crotonobetaine reductase subunit II, FAD-binding
Homo sapiens ENSG00000128928   isovaleryl-CoA dehydrogenase
Leishmania braziliensis LbrM.27.1010   isovaleryl-coA dehydrogenase, putative
Leishmania donovani LdBPK_270790.1   isovaleryl-coA dehydrogenase, putative
Leishmania infantum LinJ.27.0790   isovaleryl-coA dehydrogenase, putative
Leishmania major LmjF.27.0930   isovaleryl-coA dehydrogenase, putative
Leishmania mexicana LmxM.27.0930   isovaleryl-coA dehydrogenase, putative
Mus musculus ENSMUSG00000027332   isovaleryl coenzyme A dehydrogenase
Mycobacterium tuberculosis Rv2500c   Possible acyl-CoA dehydrogenase FadE19 (MMGC)
Mycobacterium ulcerans MUL_3778   acyl-CoA dehydrogenase FadE19
Mycobacterium ulcerans MUL_1705   acyl-CoA dehydrogenase
Neospora caninum NCLIV_020260   isovaleryl-coA dehydrogenase, putative
Oryza sativa 4337676   Os05g0125500
Schmidtea mediterranea mk4.001468.00  
Schmidtea mediterranea mk4.006240.00   Isovaleryl-CoA dehydrogenase, mitochondrial
Trypanosoma brucei gambiense Tbg972.11.1640   isovaleryl-coA dehydrogenase, putative
Trypanosoma brucei Tb927.11.1540   isovaleryl-coA dehydrogenase, putative
Trypanosoma congolense TcIL3000_0_13370   isovaleryl-coA dehydrogenase, putative
Trypanosoma cruzi TcCLB.509829.20   isovaleryl-coA dehydrogenase, putative
Trypanosoma cruzi TcCLB.506629.220   isovaleryl-coA dehydrogenase, putative

Essentiality

Rv2500c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2543 this record Mycobacterium tuberculosis essential nmpdr
Tb11.55.0026 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.55.0026 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb11.55.0026 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.55.0026 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0039 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • 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.
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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
No druggable targets predicted through repurposing network model

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 Rv2500c (Mycobacterium tuberculosis), Possible acyl-CoA dehydrogenase FadE19 (MMGC)
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