Detailed view for Rv3564

Basic information

TDR Targets ID: 6046
Mycobacterium tuberculosis, Probable acyl-CoA dehydrogenase FadE33
Source Database / ID:  Tuberculist 

pI: 4.77 | Length (AA): 318 | MW (Da): 33558 | Paralog Number: 2

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
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  

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
1 318 3mkh (A) 5 417 22.00 0.0000000000067 1 0.8779 1.05
1 318 4x28 (D) 3 372 30.00 0 1 1.2149 0.38
2 318 4x28 (D) 4 372 35.00 0 1 1.20156 0.18
5 281 4kto (A) 12 349 33.00 0.0000000000067 1 1.03777 0.36

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:

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

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_156898)

Species Accession Gene Product
Mycobacterium tuberculosis Rv3563   Probable acyl-CoA dehydrogenase FadE32
Mycobacterium tuberculosis Rv3564   Probable acyl-CoA dehydrogenase FadE33
Mycobacterium tuberculosis Rv1933c   Probable acyl-CoA dehydrogenase FadE18
Mycobacterium ulcerans MUL_2176   acyl-CoA dehydrogenase FadE18
Mycobacterium ulcerans MUL_3840   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_2756   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_3682   acyl-CoA dehydrogenase FadE18
Mycobacterium ulcerans MUL_0361   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_2893   acyl-CoA dehydrogenase FadE18
Mycobacterium ulcerans MUL_4128   acyl-CoA dehydrogenase FadE32
Mycobacterium ulcerans MUL_0319   acyl-CoA dehydrogenase
Mycobacterium ulcerans MUL_4129   acyl-CoA dehydrogenase FadE33

Essentiality

Rv3564 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3625 this record Mycobacterium tuberculosis essential nmpdr
Show/Hide essentiality data references
  • 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
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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
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 Rv3564 (Mycobacterium tuberculosis), Probable acyl-CoA dehydrogenase FadE33
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