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 -0.83 LB _boundary_3-hydroxybenzoate_flux 0.0 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