Detailed view for Rv3061c

Basic information

TDR Targets ID: 6034
Mycobacterium tuberculosis, Probable acyl-CoA dehydrogenase FadE22

Source Database / ID:  Tuberculist 

pI: 5.2005 | Length (AA): 721 | MW (Da): 76741 | Paralog Number: 5

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 8 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
4 114 5gj8 (D) 9 119 22.00 0 0.63 0.406153 -0.54
4 511 2uxw (A) 93 616 21.00 0 1 0.720777 0.65
31 263 1r2j (A) 17 278 31.00 0.0000001 1 0.591762 0.15
240 712 6es9 (A) 45 550 22.00 0 1 0.852533 0.24
253 300 4x8w (H) 1 307 44.00 0.01 0.15 0.175074 3.37
360 716 4x28 (A) 8 397 31.00 0 1 0.785746 0.23
379 711 2dvl (A) 35 370 25.00 0 1 0.766359 -0.24
430 563 5ys9 (A) 126 277 22.00 0.00000073 0.98 0.418353 -0.74

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:

  • 4X28:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

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_145209)

Species Accession Gene Product
Mycobacterium tuberculosis Rv3573c   Probable acyl-CoA dehydrogenase FadE34
Mycobacterium tuberculosis Rv1934c   Probable acyl-CoA dehydrogenase FadE17
Mycobacterium tuberculosis Rv3061c   Probable acyl-CoA dehydrogenase FadE22
Mycobacterium tuberculosis Rv3560c   Probable acyl-CoA dehydrogenase FadE30
Mycobacterium tuberculosis Rv0271c   Probable acyl-CoA dehydrogenase FadE6
Mycobacterium tuberculosis Rv3562   Probable acyl-CoA dehydrogenase FadE31
Mycobacterium ulcerans MUL_4958   acyl-CoA dehydrogenase FadE6
Mycobacterium ulcerans MUL_3411   acyl-CoA dehydrogenase FadE22
Mycobacterium ulcerans MUL_0322   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_4144   acyl-CoA dehydrogenase FadE34
Mycobacterium ulcerans MUL_3842   acyl-CoA dehydrogenase FadE17
Mycobacterium ulcerans MUL_4125   acyl-CoA dehydrogenase FadE30
Mycobacterium ulcerans MUL_3681   acyl-CoA dehydrogenase FadE17
Mycobacterium ulcerans MUL_2757   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_0360   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_1194   acyl-CoA dehydrogenase FadE6
Mycobacterium ulcerans MUL_4127   acyl-CoA dehydrogenase FadE31
Mycobacterium ulcerans MUL_3874   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_3854   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_2892   acyl-CoA dehydrogenase FadE17

Essentiality

Rv3061c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3114 this record Mycobacterium tuberculosis non-essential nmpdr
mtu3621 Mycobacterium tuberculosis non-essential nmpdr
mtu274 Mycobacterium tuberculosis non-essential nmpdr
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • 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
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

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 Rv3061c (Mycobacterium tuberculosis), Probable acyl-CoA dehydrogenase FadE22
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