### 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