TB Genome Annotation Portal

Rv3140 (fadE23)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: acyl-CoA dehydrogenase
  • REFSEQ: acyl-CoA dehydrogenase FADE23
  • PATRIC: Probable acyl-CoA dehydrogenase (EC 1.3.99.3)
  • TUBERCULIST: Probable acyl-CoA dehydrogenase FadE23
  • NCBI: Probable acyl-CoA dehydrogenase FadE23
  • updated information (H37Rv4):
    • gene name: fadE23
    • function:
    • reference:
• Type: Not Target
• Start: 3506790
• End: 3507995
• Operon:


• Trans-membrane region:
  
• Role: I.A.3 - Fatty acids
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0050660 - flavin adenine dinucleotide binding (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • MK[c] + PROPIONYLCOA[c] -> MKH2[c] + ACRCOA[c]
  • MK[c] + 2MBUTCOA[c] -> MKH2[c] + 2MBECOA[c]
  • MK[c] + 3MBUTCOA[c] -> MKH2[c] + 3MBECOA[c]
  • MK[c] + IBUTCOA[c] -> MKH2[c] + MACRCOA[c]
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  4L1F	37%	Acidaminococcus fermentans	Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a mechanism of flavin-based electron bifurcation
  2VIG	37%	HOMO SAPIENS	Crystal structure of human short-chain acyl CoA dehydrogenase
  3MDE	37%	Sus scrofa	CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE
  3MDD	37%	Sus scrofa	CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE
  1UDY	37%	Sus scrofa	Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA
  1JQI	37%	Rattus norvegicus	Crystal Structure of Rat Short Chain Acyl-CoA Dehydrogenase Complexed With Acetoacetyl-CoA
  5LNX	35%	Bacillus subtilis (strain 168)	Crystal structure of MmgC, an acyl-CoA dehydrogenase from bacillus subtilis.
  5OL2	35%	Clostridioides difficile	The electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile
  5IDU	35%	Burkholderia phymatum	Crystal structure of an acyl-CoA dehydrogenase domain protein from Burkholderia phymatum bound to FAD
  1BUC	35%	Megasphaera elsdenii	THREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII

• Links to additional information on fadE23:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.649 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MAINLELPRKLQAIIVKTHQGAAEMMRPIARKYDLKEHAYPVELDTLINLFEGAAESFNFAGAHSLRDEDEGKDENHNGANMAAVVQTMEASWGDVAMML
SLPYQGLGNAAISAVATDEQLERLGKVWAAMAITEPEFGSDSAAVSTTATLDGDEYVINGEKIFVTAGSRATHIVVWATLDKSLGRPAIKSFIVPREHPG
VTVERLEHKLGIKGSDTAVIRFDNARIPKGNLLGNPEIEVGKGFAGVMETFDNTRPIVAAMAVGIGRAALEEIRSVLTGAGVEISYDKPSHTQSAAAAEF
LRMEADWEASYLLSLRAAWQADNNIPNSKEASMSKAKAGRMASDVTCKTVELAGTTGYSEQSLLEKWARDSKILDIFEGTQQIQQLVVARRLLGLSSSEL
K

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.29 (0.19)	1.96 (0.92)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link