# 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