Model - Scenario - 3-HBz anaerobic

Version 1

OBJ max BIOMASS
SOLVER glpk
UB BIOMASS 1000
LB BIOMASS 0
# UB anaerobic_aromatic_degradation_1.2.7.8_phenylpyruvate 0  # pathway uncertain, allows higher biomass
# Select correct fatty acid and phospholipid composition by commenting out the appropriate pair of constraints
#UB fatty-acid-composition_benzoate-anaerobic 0
#UB phospholipid-composition_benzoate-anaerobic 0
# UB fatty-acid-composition_succinate-anaerobic 0
# UB phospholipid-composition_succinate-anaerobic 0
# --- Terminal electron acceptor
# LB _boundary_nitrate_flux 0 # mFBA matrix
# LB _boundary_CO2_flux 0 # mFBA matrix
# LB _boundary_molybdate_flux 0 # in the medium
# LB _boundary_Ca2+_flux 0 # in the medium
# LB _boundary_ammonium_flux 0 # in the medium
# LB _boundary_Fe2+_flux 0 # in the medium
# LB _boundary_Mg2+_flux 0 # in the medium
# LB _boundary_Co2+_flux 0 # in the medium
# LB _boundary_Cl-_flux 0 # in the medium
# LB _boundary_Zn2+_flux 0 # in the medium
LB _boundary_nitrite_flux 0
# --- Nitrogen source
# LB _boundary_ammonia_flux 0
# --- Sulfur source
#LB _boundary_sulfate_flux 0 # in the medium
# --- trace elements --- #
# LB _boundary_phosphate_flux 0 # in the medium
# LB _boundary_potassium_flux 0
# LB _boundary_Cu+_flux 0
LB _boundary_Fe3+_flux 0
LB _boundary_F-_flux 0
# --- cofactors and other metabolites --- #
# LB _boundary_folate_flux 0 # in the medium
# LB _boundary_adenosylcobalamin_flux 0 # in the medium
LB _boundary_riboflavin_flux 0
LB _boundary_heme_flux 0
LB _boundary_glutathione_flux 0
LB _boundary_arsenate_flux 0
LB _boundary_taurine_flux 0
LB _boundary_tungstate_flux 0
LB _boundary_sn-glycerol-3-phosphate_flux 0
LB _boundary_S-adenosyl-L-methionine_flux 0
LB _boundary_S-adenosyl-L-homocysteine_flux 0
# --- Carbon source (aliphatic)
# LB _boundary_acetate_flux 0 # mFBA matrix
LB _boundary_L-alanine_flux 0
LB _boundary_L-proline_flux 0
LB _boundary_succinate_flux 0
LB _boundary_(S)-malate_flux 0
LB _boundary_fumarate_flux 0
LB _boundary_L-aspartate_flux 0
LB _boundary_2-oxoglutarate_flux 0
LB _boundary_pyruvate_flux 0
LB _boundary_D-mannose_flux 0
LB _boundary_D-fructose_flux 0
LB _boundary_L-glutamate_flux 0
# --- Carbon source (aromatic)
# LB _boundary_3-(4-hydroxyphenyl)propanoate_flux 0 # mFBA matrix
# LB _boundary_benzoate_flux 0 # mFBA matrix
# LB _boundary_L-phenylalanine_flux 0 # mFBA matrix
# LB _boundary_3-hydroxybenzoate_flux 0 # mFBA matrix
# LB _boundary_4-hydroxybenzoate_flux 0 # mFBA matrix
LB _boundary_4-ethylphenol_flux 0
LB _boundary_phenylacetate_flux 0
LB _boundary_phthalate_flux 0
LB _boundary_cyclohexanecarboxylate_flux 0
LB _boundary_benzylamine_flux 0
LB _boundary_indoleacetate_flux 0
LB _boundary_benzaldehyde_flux 0
LB _boundary_4-cresol_flux 0
LB _boundary_phenol_flux 0
LB _boundary_toluene_flux 0
LB _boundary_ethylbenzene_flux 0
LB _boundary_3-phenylpropanoate_flux 0
LB _boundary_2-phenylethylamine_flux 0
LB _boundary_Co2+_efflux 0
UB _boundary_Co2+_efflux 0
LB _boundary_Mg2+_efflux 0
UB _boundary_Mg2+_efflux 0
LB glycolysis_5.3.1.9_PGLUCISOM-RXN 0
UB glycolysis_5.3.1.9_PGLUCISOM-RXN 0
LB NGAM	3.150
LB _boundary_benzoate_flux	0.0
LB _boundary_3-(4-hydroxyphenyl)propanoate_flux	0.0
LB _boundary_L-phenylalanine_flux	0.0
LB _boundary_3-hydroxybenzoate_flux	-3.0
LB _boundary_acetate_flux	0.0
LB _boundary_oxygen_flux	0
LB _boundary_nitrate_flux	-30
LB _boundary_4-hydroxybenzoate_flux	0
UB cof_ubiquinol-8-syn-(anaerobic)_1.14.13.-_2-OCTAPRENYLPHENOL-HYDROX-RXN	1000
UB cof_ubiquinol-8-syn-(anaerobic)_1.14.13.-_2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN	1000
UB cof_ubiquinol-8-syn-(anaerobic)_1.14.99.60_OCTAPRENYL-METHYL-METHOXY-BENZOQ-OH-RXN	1000
LB Bz-degradation-(anaerobic)_BcrABCD_1.3.7.8	-1000
UB nitrate-reduction_1.7.5.1_RXN0-6369	1000
UB ethylbenzene-degradation-(anaerobic)_1.17.99.2_RXN-1301	1000