engineered_reactions.yaml

# Below are the added reactions for Pyrococcus fuuiosus engineered strains

# add reactions for CODH (CODH is inserted to Pfu OE-AdhF strain in order to increase ethanol production (Gina's work))
- id: CODH
  name: carbon monoxide dehydrogenase (CODH)
  genes: engineered_CODH
  #equation: C00237[c] + C00001[c] + (2) C00139[c] => C00011[c] + (2) C00138[c] + (2) C00080[c]
  equation: C00237[c] + C00001[c] + C01330[c] => C00011[c] + C00282[c] + C01330[e]
  ec: 1.2.7.4
  pmid: 25368184
  comment: This equation is based on Brednda ("https://www.brenda-enzymes.org/all_enzymes.php?ecno=1.2.7.4"). CODH complex include three subunits (CODH, mbh and mrp). "mbh" and "mrp" are already in the native Pfu model, so they are not shown here. JV update - The three enzymes form a single large complex, see [pmid:25461503]; I modified the formula to do the sodium pumping from mbh+mrp domains, and to produce hydrogen instead of protons. Left the old formula commented for reference
- id: TP_CO
  name: CO diffusion (Non-enzymatic)
  equation: C00237[c] <=> C00237[e]