PHOSGLYPHOS-RXN# --- Automatically generated FBA file --- pgdb: current-pgdb reactions: metab-all transport-all remove-reactions: AKBLIG-RXN GLYOHMETRANS-RXN THREONINE-ALDOLASE-RXN NQOR-RXN # still broken for menaquinone/menaquinol RXN0-6359 # HCN cycle R15-RXN # strange transamination MCPMETEST-RXN # methanol production RXN0-6945 # mercaptopyruvate cycle FHLMULTI-RXN # off for comparison with Varma data try-reactions: metacyc-metab-all try-biomass: ## Protein building blocks VAL # 0.411184 TYR # 0.133993 TRP # 0.055234 THR # 0.246506 SER # 0.209684 PRO # 0.214798 PHE # 0.180021 MET # 0.149336 LYS # 0.333448 LEU # 0.437778 ILE # 0.282306 HIS # 0.092056 GLY # 0.595297 GLT # 0.255712 GLN # 0.255712 CYS # 0.088988 L-ASPARTATE # 0.234232 ASN # 0.234232 ARG # 0.287420 L-ALPHA-ALANINE # 0.499149 ## Nucleic acid building blocks UTP # 0.140101 GTP # 0.209121 TTP # 0.024805 ## represents dTTP DGTP # 0.025612 DCTP # 0.025612 DATP # 0.024805 CTP # 0.129799 ## GAM (+ RNA ATP requirement) ATP # 54.119975 WATER # 48.752916 ADP # -53.950000 PROTON # -53.950000 Pi # -53.945874 PPI # -0.749831 ## Lipids and cell wall constituents UNDECAPRENYL-DIPHOSPHATE # 0.000055 CPD-8260 # 0.023092 CPD-12819 # 0.096225 CPD-12824 # 0.006414 CPD0-939 # 0.008151 ## Ions # AMMONIUM # 0.012379 FE+2 # 0.013816 ## Cofactors # SIROHEME # 0.000223 PYRIDOXAL_PHOSPHATE # 0.000223 PROTOHEME # 0.000223 NADPH # 0.000335 NADP # 0.000112 NADH # 0.000045 NAD # 0.001787 FAD # 0.000223 CO-A # 0.000168 S-ADENOSYLMETHIONINE # 0.000223 ## Other # THF # 0.000223 SUC-COA # 0.000098 SPERMIDINE # 0.006744 RIBOFLAVIN # 0.000223 CPD-9956 # 0.000223 #weaver:Jul-16-2013 breaks if oxygen is not available PUTRESCINE # 0.033270 CPD-12231[CCO-PERI-BAC] # 0.013452 REDUCED-MENAQUINONE # 0.000223 METHYLENE-THF # 0.000223 MALONYL-COA # 0.000031 HEME_O # 0.000223 GLUTATHIONE # 0.000223 ENTEROBACTIN # 0.000223 CHORISMATE # 0.000223 ACETYL-COA # 0.000279 5-METHYL-THF # 0.000223 CPD-12115 # 0.000223 10-FORMYL-THF # 0.000223 BIOTIN # 0.000010 GLUTATHIONE[CCO-PERI-BAC]# 0.000010 nutrients: GLC[CCO-PERI-BAC] # :upper-bound 10. OXYGEN-MOLECULE[CCO-PERI-BAC] AMMONIUM[CCO-PERI-BAC] Pi[CCO-PERI-BAC] SULFATE[CCO-PERI-BAC] FE+2[CCO-PERI-BAC] WATER[CCO-PERI-BAC] CARBON-DIOXIDE[CCO-PERI-BAC] PROTON[CCO-PERI-BAC] try-secretions: ## General secretions CARBON-DIOXIDE[CCO-PERI-BAC] OXYGEN-MOLECULE[CCO-PERI-BAC] WATER[CCO-PERI-BAC] PROTON[CCO-PERI-BAC] Pi[CCO-PERI-BAC] FORMATE[CCO-PERI-BAC] ACET[CCO-PERI-BAC] SUC ETOH[CCO-PERI-BAC] D-LACTATE GLYCEROL[CCO-PERI-BAC] UREA[CCO-PERI-BAC] CIT[CCO-PERI-BAC] PYRUVATE[CCO-PERI-BAC] ## Hydrogen (anaerobically relevant) HYDROGEN-MOLECULE ## Amino acids VAL[CCO-PERI-BAC] TYR[CCO-PERI-BAC] TRP[CCO-PERI-BAC] THR[CCO-PERI-BAC] SER[CCO-PERI-BAC] PRO[CCO-PERI-BAC] PHE[CCO-PERI-BAC] MET[CCO-PERI-BAC] LYS[CCO-PERI-BAC] LEU[CCO-PERI-BAC] ILE[CCO-PERI-BAC] HIS[CCO-PERI-BAC] GLY[CCO-PERI-BAC] GLT[CCO-PERI-BAC] GLN[CCO-PERI-BAC] CYS[CCO-PERI-BAC] L-ASPARTATE[CCO-PERI-BAC] ASN[CCO-PERI-BAC] ARG[CCO-PERI-BAC] L-ALPHA-ALANINE[CCO-PERI-BAC] URACIL[CCO-PERI-BAC] XANTHINE[CCO-PERI-BAC] HYPOXANTHINE[CCO-PERI-BAC] INDOLE[CCO-PERI-BAC] ### uncertain about export in K-12 MG1655 OROTATE[CCO-PERI-BAC] URATE[CCO-PERI-BAC] THYMINE[CCO-PERI-BAC] ### dead end metabolites CPD-560 CPD-108 CPD0-2167 CPD-1772 S-ADENOSYL-4-METHYLTHIO-2-OXOBUTANOATE CPD-10774 UNDECAPRENYL-DIPHOSPHATE[CCO-PERI-BAC] BUTANAL MI-PENTAKISPHOSPHATE[CCO-PERI-BAC] CPD-534[CCO-PERI-BAC] METOH[CCO-PERI-BAC] # knockout-genes: try-nutrients-weight: -20 try-reactions-reverse-weight: -40 try-reactions-in-taxa-weight: -40 try-reactions-unknown-taxa-weight: -80 try-reactions-weight: -200 try-reactions-reverse-try-weight: -250 try-secretions-weight: -2 try-biomass-weight: 10000 try-add-reverse-rxns: no try-add-reverse-try-rxns: no minimize-fluxes: no # fast-development-mode: yes max-time-solver: 3600