### imk:Jun-10-2011 modification of ecocyc-9g-fba-no-CITLY-RXN.fba ### # Beginning of the sections. # A pgdb is a unique symbol denoting a PGDB (e.g., ecoli). # You can write "current-pgdb", and the PGDB used will be the one # currently selected in the FBA tool when this file is read. # Notice that most of the metabolites and reactions described # in this file are assumed to come from the specified pgdb. pgdb: current-pgdb # ====================================================================== # Fixed sets. These sets could be empty. # ====================================================================== # # The fixed set of reactions for the model. The word 'metab-all' # can be used to specify all metabolic reactions of the # pgdb. More reactions can be specified by using their unique # identifiers (frame-ids). # reactions: metab-all ATPSYN-RXN ## ATP synthase, a transport rxn TRANS-RXN0-277 ## kr:May-9-2011 pyridine nucleotide transhydrogenase (can regenerate NADPH from NADH, with H+ flux into cytosol) # # Temporarily disregard the specified reactions # for the generation of the model. These reactions # are removed from the set of reactions just specified. # This is useful if 'metab-all' contains some reactions # you do not want to include in the FBA model. remove-reactions: ###kr:May-25-2011 fixes bicarbonate PROPIONYL-COA-CARBOXY-RXN CATAL-RXN # 2 hydrogen peroxide -> 2 H2O + oxygen SUPEROX-DISMUT-RXN PEROXID-RXN MALSYN-RXN # acetyl-CoA + glyoxylate + H2O -> (S)-malate + coenzyme A + H+ FHLMULTI-RXN # formate + H+ -> CO2 + H2 try-reactions: # metacyc-metab-all try-remove-reactions: # # The fixed set of biomass metabolites. # biomass: # ============================================================================== # Try sets. These sets could be empty. There can be several non-empty try sets. # If at least one try set is not empty, the FBA analysis is a gap filling FBA. # If there are no try sets, it is a standard FBA analysis. # =============================================================================== # # The biomass metabolites to try to add to the model. # try-biomass: # Protein building blocks - IMK: assuming the units are mmol/g DCW, transferring data from PMID 17573341, Table 2 GLT 0.2604 # L-glutamate GLY 0.4083 # glycine L-ALPHA-ALANINE 0.2669 # L-alanine LYS 0.3231 # L-lysine L-ASPARTATE 0.1480 # L-aspartate ARG 0.1930 # L-arginine GLN 0.2603 # L-glutamine SER 0.2162 # L-serine MET 0.1133 # L-methionine TRP 0.0543 # L-tryptophan PHE 0.1759 # L-phenylalanine TYR 0.1108 # L-tyrosine CYS 0.0567 # L-cysteine LEU 0.3464 # L-leucine HIS 0.0817 # L-histidine PRO 0.1606 # L-proline ASN 0.1480 # L-asparagine VAL 0.3067 # L-valine THR 0.1863 # L-threonine ILE 0.2699 # L-isoleucine # Nucleic acid building blocks - IMK: assuming the units are mmol/g DCW, transferring data from PMID 17573341, biomass assembly equation # strangely, ribonucleotides seem much lower - half or less than E. coli; deoxyribonucleotides slightly higher # added other nucleotides from biomass assembly equation, e.g. AMP ## ATP is in the GAM term below GTP 0.0631 # GTP CTP 0.0394 # CTP UTP 0.0415 # UTP DATP 0.0230 # dATP DGTP 0.0174 # dGTP DCTP 0.0174 # dCTP TTP 0.0229 # dTTP AMP 0.0047 # AMP ADP 0.0026 # ADP CMP 0.001 # CMP GMP 0.0005 # GMP CDP 0.0003 # CDP GDP 0.0002 # GDP # Lipids and cell wall constituents # neither Meta nor Bsub have pathways for teichoic/lipoteichoic acid biosynthesis; this is a major cell wall component and will have to be left out ### length 16 # CPD-12824 0.0106480421341882 # "cardiolipin (tetrahexadecanoyl, n-C16:0)" # CPD-8260 0.0106480421341882 # "phosphatidylglycerol (dihexadecanoyl, n-C16:0)" # CPD-12819 0.0106480421341882 # "phosphatidylethanolamine (dihexadecanoyl, n-C16:0)" ### length 18 : first will need more curation kr:May-12-2011 ###CPD-12822 0.0106480421341882 # "phosphatidylglycerol (dioctadecanoyl, n-C18:0)" # C6 0.0924764890282131 # "N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine" # CPD0-939 0.02 # "Lipid A-core" iAF1260 has CPD0-2271 "core oligosaccharide lipid A" and i don't know whether this is the same ??? # Cofactors - IMK: assuming the units are mmol/g DCW, transferring data from PMID 17573341, biomass assembly equation ##kr:May-25-2011 Play with these ratios: NAD 0.0162 # NAD+ done #NADH 0.00100 # NADH NADP 0.0009 # NADP+ done NADPH 0.0002 # NADPH done #CO-A 0.00556904183921177 # CoA #FAD 0.00556904183921177 # FAD #PYRIDOXAL_PHOSPHATE 0.00556904183921177 # pyridoxal 5'-phosphate #S-ADENOSYLMETHIONINE 0.00556904183921177 # S-adenosyl-L-methionine #RIBOFLAVIN 0.00556904183921177 # riboflavin CPD-12125 0.0003 # menaquinol-7 done #SIROHEME 0.00556904183921177 # siroheme iAF1260 has this #HEME_O 0.00556904183921177 # heme o iAF1260 has this ### ADENOSYLCOBALAMIN 0.00556904183921177 # coenzyme B12 # Other #SPERMIDINE 0.00556904183921177 # spermidine #PUTRESCINE 0.025 # putrescine iAF1260 has this, with a bigger coeff than spermidine #UNDECAPRENYL-DIPHOSPHATE 0.0924764890282131 # di-trans,poly-cis-undecaprenyl diphosphate #ENTEROBACTIN 0.00556904183921177 # enterobactin iAF1260 has this #GLUTATHIONE 0.00556904183921177 # glutathione iAF1260 has this 10-FORMYL-THF 0.0004 # 10-formyltetrahydrofolate done #5-METHYL-THF 0.00556904183921177 # 5-methyl-tetrahydrofolate iAF1260 has this - replacing with 10-formyl-thf #SULFATE 0.00556904183921177 # sulfate # GAM - IMK: assuming the units are mmol/g DCW, transferring data from PMID 17573341, biomass assembly equation # PMID 17573341 has an additional 1 mg biomass term that is produced - no idea how that is incorporated here??? WATER 105 # H2O done ATP 105.0535 # ATP done ADP -104.9974 Pi -104.9856 #PPI -0.602395563079457 # diphosphate - don't have that term in Bsub PROTON -105 ###kr:Apr-14-2011 The biomass eqn. I found on ModelSEED contained all the ions too, but we will ignore them for now. ## MN+2 0.00556904183921177 # Manganese ## ZN+2 0.00556904183921177 # Zn2+ ## CU+2 0.00556904183921177 # Copper2 ## CA+2 0.00556904183921177 # Calcium ## CL- 0.00556904183921177 # chloride ## CO+2 0.00556904183921177 # Cobalt ## K+ 0.00556904183921177 # K+ ## MG+2 0.00556904183921177 # Mg2+ # # The fixed nutrients (metabolites) to use. # nutrients: GLC # :lower-bound 10.9 :upper-bound 11.1 # from Fischer et al. 2004 Table 2 , Reactor OXYGEN-MOLECULE # :lower-bound 18.1 :upper-bound 18.3 # from Fischer et al. 2004 Table 2 , Reactor AMMONIUM Pi SULFATE FE+2 #kr:May-12-2011 For SIROHEME # # The nutrients (metabolites) to try to add to the model. # try-nutrients: # # The fixed secretions (metabolites) to use. # secretions: CARBON-DIOXIDE #ACET ## acetate WATER PROTON #CPD-560 ## "S-methyl-5-thio-D-ribose" A dead-end metabolite, that has to be secreted to produce spermidine # # The secretions (metabolites) to try to add to the model. # try-secretions: ## DIMETHYLBENZIMIDAZOLE 0.00556904183921177 # Dimethylbenzimidazole ## COBINAMIDE 0.00556904183921177 # cobinamide ###apo-ACP 0.00556904183921177 # apo-[acyl carrier protein] # The try-reactions section describe the reactions to try to add to # the FBA model to increase its objective function. You can use the word # 'metacyc-metab-all' which means all MetaCyc metabolic reactions. # You can also add specific reactions using reaction equations. try-reactions: # Weights for the try sets. # # Note: if no try-sets are given all these weights are not used. # A weight is only meaningful if a corresponding try set # is specified for it. # The weight for adding one nutrient. This value is typically a small negative value (cost). try-nutrients-weight: -20 # The weight for adding one reaction from MetaCyc. This value is typically negative (cost). try-reactions-weight: -200 # The weight for adding the reverse of a irreversible reaction from # the pgdb. This is typically negative (cost). try-reactions-reverse-weight: -40 # The weight for adding the reverse of a irreversible reaction from # the MetaCyc. This is typically negative (cost). try-reactions-reverse-try-weight: -250 # The weight for adding one reaction from MetaCyc in the taxonomic range of # the pgdb. This is typically negative (cost). try-reactions-in-taxa-weight: -40 # The weight for adding one reaction from MetaCyc in the taxonomic range of # the pgdb. This is typically negative (cost). try-reactions-unknown-taxa-weight: -80 # The weight for adding a secretion to the model. try-secretions-weight: 10 # The weight of adding one metabolite to the biomass. # Typically, this is positive and at least ten times larger, # in absolute value, than all the other weights. try-biomass-weight: 10000 try-reactions-spontaneous-weight: -1 # Add, to the try-reactions set, the reverse of irreversible reactions # provided by section reactions? try-add-reverse-rxns: yes # Add, to the try-reactions set, the reverse of irreversible reactions # provided by section try-reactions? try-add-reverse-try-rxns: yes # Other parameters. # The maximum number of seconds to let the solver run. If the solver # has not optimally solved the model after that time, a suboptimal solution # will be reported. max-time-solver: 300 # End of File