# Mario Latendresse, May-30-2013 # ml: This fba uses fast development mode. # This fba was derived from example-ecocyc.fba. pgdb: ecoli # ====================================================================== # Reactions # ====================================================================== # The fixed set of reactions for the model -- may be empty. # The word 'metab-all' can be used to specify all metabolic reactions # of the pgdb. Additional reactions can be specified by their unique # identifiers (frame-ids) or through a reaction equation. # 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) TRANS-RXN-157 ## latendre:Apr-23-2012. transporter of beta-D-glucose (GLC) from periplasmic space to cytosol # The reactions specified here will not be include in the generated model -- may be empty. # These reactions are removed from the fixed reactions set. # Remove-reactions is useful if 'metab-all' contains some reactions # you do not want to include in the FBA model. remove-reactions: # The following reactions are removed to demonstrate the fast development mode. # Reactions producing tetrahydrofolate (THF). DIHYDROFOLATEREDUCT-RXN GLYOHMETRANS-RXN HOMOCYSMETB12-RXN RXN0-1862 # Standard removal of reactions from ecocyc. CATAL-RXN # 2 hydrogen peroxide -> 2 H2O + oxygen SUPEROX-DISMUT-RXN PEROXID-RXN ##kr:Jun-1-2011 glyoxalate bypass: ISOCIT-CLEAV-RXN # D-threo-isocitrate <-> glyoxylate + succinate MALSYN-RXN # acetyl-CoA + glyoxylate + H2O -> (S)-malate + coenzyme A + H+ ###kr:Jun-2-2011 CITLY-RXN was run in the wrong direction, synth. citrate ! it was reversible. ### it is just used anaerobically, and furthermore usually is claimed to be inactive ! CITLY-RXN # citrate <-> acetate + oxaloacetate ###kr:Jun-2-2011 iAF1260 flux1.xml has rxn "FHL" constrained to zero. why ?? RXN0-3281 # formate + an oxidized electron acceptor + H+ -> CO2 + a reduced electron acceptor FHLMULTI-RXN # formate + H+ -> CO2 + H2 ###kr:Jun-2-2011 fructose-6-phosphate aldolase seems to be a new enzymatic activity. ### the physiol. role of FSA is not yet known. ==> so, better try to leave it out. ### Flux: 10.25746 (RXN0-313) RXN0-313 # D-fructose-6-phosphate -> dihydroxyacetone + D-glyceraldehyde-3-phosphate # The try-reactions section describes the reactions to try to add to # the FBA model to increase its objective function -- may be empty. Use # the word 'metacyc-metab-all' to include all MetaCyc metabolic reactions. # You can also add specific reactions using reaction IDs or reaction equations. try-reactions: metacyc-metab-all # ====================================================================== # Biomass Metabolites # ====================================================================== # The fixed set of biomass metabolites -- may be empty. # Optional coefficients may be specified to indicate mass ratios of these # compounds in the biomass, e.g., # TRP 1.0 try-biomass: # Protein building blocks VAL 0.411900 # L-valine TYR 0.134000 # L-tyrosine TRP 0.055230 # L-tryptophan THR 0.246500 # L-threonine SER 0.209700 # L-serine PRO 0.214800 # L-proline PHE 0.180000 # L-phenylalanine MET 0.149300 # L-methionine LYS 0.333400 # L-lysine LEU 0.437800 # L-leucine ILE 0.282300 # L-isoleucine HIS 0.092100 # L-histidine GLY 0.595300 # glycine GLT 0.255700 # L-glutamate GLN 0.255700 # L-glutamine CYS 0.088990 # L-cysteine L-ASPARTATE 0.234200 # L-aspartate ASN 0.234200 # L-asparagine ARG 0.287400 # L-arginine L-ALPHA-ALANINE 0.499100 # L-alanine # Nucleic acid building blocks UTP 0.140100 # UTP GTP 0.209100 # GTP TTP 0.024810 # dTTP DGTP 0.025610 # dGTP DCTP 0.025610 # dCTP DATP 0.024810 # dATP CTP 0.129800 # CTP ATP 59.980000 # ATP # Lipids and cell wall constituents UNDECAPRENYL-DIPHOSPHATE 0.000055 # di-trans,octa-cis-undecaprenyl diphosphate #L-1-PHOSPHATIDYL-GLYCEROL 0.001963 # an L-1-phosphatidyl-glycerol ;; pg181[p] ### we have wrong chain-length... #L-1-PHOSPHATIDYL-GLYCEROL 0.002286 # an L-1-phosphatidyl-glycerol ;; pg181[c] ### we have wrong chain-length... #CPD0-2330 0.003809 # phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1) ;; pg161[p] #CPD0-2330 0.004435 # phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1) ;; pg161[c] #CPD-8260 0.004897 # 1,2-dipalmitoyl-phosphatidylglycerol ;; pg160[p] #CPD-8260 0.005702 # 1,2-dipalmitoyl-phosphatidylglycerol ;; pg160[c] CPD-8260 0.023092 # 1,2-dipalmitoyl-phosphatidylglycerol ;; summed up all 6 above... #L-1-PHOSPHATIDYL-ETHANOLAMINE 0.012750 # an L-1-phosphatidyl-ethanolamine ;; pe181[p] ### we have wrong chain-length... #L-1-PHOSPHATIDYL-ETHANOLAMINE 0.004957 # an L-1-phosphatidyl-ethanolamine ;; pe181[c] ### we have wrong chain-length... #L-1-PHOSPHATIDYL-ETHANOLAMINE 0.024730 # an L-1-phosphatidyl-ethanolamine ;; pe161[p] #L-1-PHOSPHATIDYL-ETHANOLAMINE 0.009618 # an L-1-phosphatidyl-ethanolamine ;; pe161[c] #CPD-12819 0.031800 # 1,2-dipalmitoyl-phosphatidyl-ethanolamine ;; pe160[p] #CPD-12819 0.012370 # 1,2-dipalmitoyl-phosphatidyl-ethanolamine ;; pe160[c] CPD-12819 0.096225 # 1,2-dipalmitoyl-phosphatidyl-ethanolamine ;; summed up all 6 above... #CARDIOLIPIN 0.001180 # a cardiolipin ;; clpn181[p] #CARDIOLIPIN 0.002290 # a cardiolipin ;; clpn161[p] CPD-12824 0.002944 # cardiolipin (tetrahexadecanoyl, n-C16:0) ;; clpn160[p] #CPD0-2271 0.008151 # core oligosaccharide lipid A CPD0-939 0.008151 # "Lipid A-core" iAF1260 has CPD0-2271 "core oligosaccharide lipid A" and i don't know whether this is the same ??? # Ions #ZN+2 0.003008 # Zn2+ SULFATE 0.003760 # sulfate AMMONIUM 0.011280 # ammonium #CPD-3 0.003008 # molybdate #MN+2 0.003008 # Mn2+ #MG+2 0.007519 # Mg2+ #K+ 0.169200 # K+ #FE+3 0.006767 # Fe3+ FE+2 0.006767 # Fe2+ #CU+2 0.003008 # Cu2+ #CO+2 0.003008 # Co2+ #CL- 0.004512 # chloride #CA+2 0.004512 # Ca2+ # Cofactors SIROHEME 0.000223 # siroheme PYRIDOXAL_PHOSPHATE 0.000223 # pyridoxal 5'-phosphate PROTOHEME 0.000223 # protoheme IX NADPH 0.000335 # NADPH NADP 0.000112 # NADP+ NADH 0.000045 # NADH NAD 0.001787 # NAD+ FAD 0.000223 # FAD CO-A 0.000168 # coenzyme A S-ADENOSYLMETHIONINE 0.000223 # S-adenosyl-L-methionine ###kr:Jun-10-2011 Can't currentl be produced: #THIAMINE-PYROPHOSPHATE 0.000223 # thiamin diphosphate #ADENOSYLCOBALAMIN 0.000223 # coenzyme B12 # Other THF 0.000223 # tetrahydrofolate SUC-COA 0.000098 # succinyl-CoA SPERMIDINE 0.006744 # spermidine RIBOFLAVIN 0.000223 # riboflavin CPD-9956 0.000223 # ubiquinol-8 PUTRESCINE 0.033270 # putrescine ###kr:Jun-10-2011 These are not connected to anything in EcoCyc: ###CPD0-2288 0.000673 # three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) & tetrapeptide crosslinked tetrapeptide (A2pm->D-ala)) (middle of chain) ###CPD0-2270 0.005448 # two disacharide linked murein units, tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain) ###CPD0-2269 0.005381 # two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain) ###CPD0-2273 0.000605 # two disacharide linked murein units, tripeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain) ###CPD0-2272 0.001345 # two linked disacharide tripeptide murein units (uncrosslinked, middle of chain) ###kr:Jun-10-2011 Instead of the fragments above, I'll add this one: # CPD-12231 0.013452 # a peptidoglycan dimer (meso-diaminopimelate containing) ;; summes up REDUCED-MENAQUINONE 0.000223 # menaquinol-8 METHYLENE-THF 0.000223 # 5,10-methylenetetrahydrofolate MALONYL-COA 0.000031 # malonyl-CoA HEME_O 0.000223 # heme o GLUTATHIONE 0.000223 # glutathione #6-alpha-D--1-4-alpha-D-Glucano--Glucan 0.154200 # glycogen ENTEROBACTIN 0.000223 # enterobactin CHORISMATE 0.000223 # chorismate ACETYL-COA 0.000279 # acetyl-CoA 5-METHYL-THF 0.000223 # 5-methyl-tetrahydrofolate CPD-12115 0.000223 # demethylmenaquinol-8 10-FORMYL-THF 0.000223 # 10-formyl-tetrahydrofolate WATER 54.613000 # H2O # GAM #ADP -59.810000 # ADP #PROTON -59.810000 # H+ #Pi -58.806200 # phosphate #PPI -0.749800 # diphosphate ### biomass: # ====================================================================== # Nutrients # ====================================================================== # # The fixed nutrients (metabolites) to use -- may be empty. # Optional coefficients may be specified, which are treated as multiplicative # factors applied to the fluxes. # Optionally, lower and/or upper bounds may be specified for nutrient # fluxes, with examples below. The default lower bound is 0; the default # upper bound is 1000. A coefficient is supplied in the first example; # no coefficient is supplied in the second example. # ammonium 2 :lower-bound 5.0 # ammonium :lower-bound 5.0 :upper-bound 100.0 nutrients: GLC[cco-peri-bac] :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[cytosol] Pi[CCO-CYTOSOL] SULFATE[CCO-CYTOSOL] FE+2 #kr:May-12-2011 For SIROHEME # The nutrients (metabolites) to try to add to the model -- may be empty. try-nutrients: # ====================================================================== # Secretions # ====================================================================== # The fixed secretions (metabolites) to use -- may be empty. 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 -- may be empty. try-secretions: ## DIMETHYLBENZIMIDAZOLE 0.00556904183921177 # Dimethylbenzimidazole ## COBINAMIDE 0.00556904183921177 # cobinamide ###apo-ACP 0.00556904183921177 # apo-[acyl carrier protein] # ====================================================================== # Try-Set Weights # ====================================================================== # If all try-sets are empty, these weights are not used. # A weight is only meaningful if a corresponding try set is specified for it. # The cost for adding one nutrient. This value is typically a small negative value (cost). try-nutrients-weight: -20 # The weight for adding the reverse of a irreversible reaction from # the PGDB to the model. This value is typically negative (cost). try-reactions-reverse-weight: -40 # The weight for adding one reaction within the taxonomic range of the PGDB from MetaCyc to the model. # This value is typically negative (cost). try-reactions-in-taxa-weight: -5 # The weight for adding one reaction from MetaCyc with an unknown taxonomic range. # This value is typically negative (cost). try-reactions-unknown-taxa-weight: -80 # The cost for adding one reaction outside the taxonomic range of the PGDB from MetaCyc to the model. # This value is typically negative (cost). try-reactions-weight: -250 # The weight for adding the reverse of an irreversible reaction from # MetaCyc to the model. This value is typically negative (cost). try-reactions-reverse-try-weight: -250 # The weight for adding a secretion to the model. This value is typically negative. try-secretions-weight: -2 # The weight of adding one metabolite to the biomass. # Typically, this value is positive and at least ten times larger, # in absolute value, than all the other weights. try-biomass-weight: 5000 # Add, to the try-reactions set, the reverse of irreversible reactions # provided by the reactions section? try-add-reverse-rxns: no # Add, to the try-reactions set, the reverse of irreversible reactions # provided by section try-reactions? try-add-reverse-try-rxns: no # Other parameters. fast-development-mode: yes # 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: 40 minimize-fluxes: no # End of File