E.coli core DFBA model

Model version: 6

TOP model

Main comp DFBA model by combining fba, update and bounds model with additional kinetics in the top model.

Description

This is a metabolism model of Escherichia coli str. K-12 substr. MG1655 in SBML format.

The content of this model has been carefully created in a manual research effort. This file has been exported from the software COBRApy and further processed with the JSBML-based ModelPolisher application.
This file has been produced by the Systems Biology Research Group using BiGG Models knowledge-base version of Nov 21, 2016, where it is currently hosted and identified by: e_coli_core.

Terms of use

Copyright © 2016 The Regents of the University of California.

Redistribution and use of any part of this model from BiGG Models knowledge-base, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For specific licensing terms about this particular model and regulations of commercial use, see this model in BiGG Models knowledge-base.

References

When using content from BiGG Models knowledge-base in your research works, please cite
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015).
BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucl Acids Res. doi:10.1093/nar/gkv1049

Model : ecoli_top_flat

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-04-26 19:26
Modified: 2017-04-26 19:26

SBML model


idecoli_top_flat
nameecoli (TOP)_flat
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
bounds__max min x y x x y y
bounds__min max x y x x y y

UnitDefinitions [14] name units sbo cvterm
h 3600 s
g g
m m
m2 m 2
l litre
mmol 10 3 mole
per_h 1 3600 s
mmol_per_h 10 3 mole 3600 s
mmol_per_hg 10 3 mole g 3600 s
mmol_per_l 10 3 mole litre
l_per_mmol litre 10 3 mole
g_per_l g litre
g_per_mmol g 10 3 mole
fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s

Compartments [3] name size constant spatial dimensions unit derived unit sbo cvterm
bioreactor bioreactor 1.0 3 l litre
fba__c cytosol 0 l litre
BQB_IS
c
fba__e extracellular space 0 l litre
BQB_IS
e

Species [95] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
acald_e Acetaldehyde
bioreactor 1.0 mmol 10 3 mole litre
succ_e Succinate
bioreactor 1.0 mmol 10 3 mole litre
etoh_e Ethanol
bioreactor 1.0 mmol 10 3 mole litre
o2_e O2
bioreactor 1.0 mmol 10 3 mole litre
glc__D_e D-Glucose
bioreactor 20.0 mmol 10 3 mole litre
fru_e D-Fructose
bioreactor 1.0 mmol 10 3 mole litre
h2o_e H2O
bioreactor 20.0 mmol 10 3 mole litre
X biomass
bioreactor 0.001 mmol 10 3 mole litre
gln__L_e L-Glutamine
bioreactor 10.0 mmol 10 3 mole litre
glu__L_e L-Glutamate
bioreactor 1.0 mmol 10 3 mole litre
co2_e CO2
bioreactor 1.0 mmol 10 3 mole litre
h_e H+
bioreactor 1.0 mmol 10 3 mole litre
mal__L_e L-Malate
bioreactor 1.0 mmol 10 3 mole litre
ac_e Acetate
bioreactor 1.0 mmol 10 3 mole litre
nh4_e Ammonium
bioreactor 1.0 mmol 10 3 mole litre
pi_e Phosphate
bioreactor 1.0 mmol 10 3 mole litre
fum_e Fumarate
bioreactor 1.0 mmol 10 3 mole litre
pyr_e Pyruvate
bioreactor 1.0 mmol 10 3 mole litre
akg_e 2-Oxoglutarate
bioreactor 1.0 mmol 10 3 mole litre
lac__D_e D-Lactate
bioreactor 1.0 mmol 10 3 mole litre
for_e Formate
bioreactor 1.0 mmol 10 3 mole litre
dummy_S dummy_S
bioreactor 0.0 mmol 10 3 mole litre
fba__M_13dpg_c 3-Phospho-D-glyceroyl phosphate
C3H4O10P2
fba__c 0.0 mmol 10 3 mole litre
fba__M_2pg_c D-Glycerate 2-phosphate
C3H4O7P
fba__c 0.0 mmol 10 3 mole litre
fba__M_3pg_c 3-Phospho-D-glycerate
C3H4O7P
fba__c 0.0 mmol 10 3 mole litre
fba__M_6pgc_c 6-Phospho-D-gluconate
C6H10O10P
fba__c 0.0 mmol 10 3 mole litre
fba__M_6pgl_c 6-phospho-D-glucono-1,5-lactone
C6H9O9P
fba__c 0.0 mmol 10 3 mole litre
fba__ac_c Acetate
C2H3O2
fba__c 0.0 mmol 10 3 mole litre
fba__ac_e Acetate
C2H3O2
fba__e 0.0 mmol 10 3 mole litre
fba__acald_c Acetaldehyde
C2H4O
fba__c 0.0 mmol 10 3 mole litre
fba__acald_e Acetaldehyde
C2H4O
fba__e 0.0 mmol 10 3 mole litre
fba__accoa_c Acetyl-CoA
C23H34N7O17P3S
fba__c 0.0 mmol 10 3 mole litre
fba__acon_C_c Cis-Aconitate
C6H3O6
fba__c 0.0 mmol 10 3 mole litre
fba__actp_c Acetyl phosphate
C2H3O5P
fba__c 0.0 mmol 10 3 mole litre
fba__adp_c ADP
C10H12N5O10P2
fba__c 0.0 mmol 10 3 mole litre
fba__akg_c 2-Oxoglutarate
C5H4O5
fba__c 0.0 mmol 10 3 mole litre
fba__akg_e 2-Oxoglutarate
C5H4O5
fba__e 0.0 mmol 10 3 mole litre
fba__amp_c AMP
C10H12N5O7P
fba__c 0.0 mmol 10 3 mole litre
fba__atp_c ATP
C10H12N5O13P3
fba__c 0.0 mmol 10 3 mole litre
fba__cit_c Citrate
C6H5O7
fba__c 0.0 mmol 10 3 mole litre
fba__co2_c CO2
CO2
fba__c 0.0 mmol 10 3 mole litre
fba__co2_e CO2
CO2
fba__e 0.0 mmol 10 3 mole litre
fba__coa_c Coenzyme A
C21H32N7O16P3S
fba__c 0.0 mmol 10 3 mole litre
fba__dhap_c Dihydroxyacetone phosphate
C3H5O6P
fba__c 0.0 mmol 10 3 mole litre
fba__e4p_c D-Erythrose 4-phosphate
C4H7O7P
fba__c 0.0 mmol 10 3 mole litre
fba__etoh_c Ethanol
C2H6O
fba__c 0.0 mmol 10 3 mole litre
fba__etoh_e Ethanol
C2H6O
fba__e 0.0 mmol 10 3 mole litre
fba__f6p_c D-Fructose 6-phosphate
C6H11O9P
fba__c 0.0 mmol 10 3 mole litre
fba__fdp_c D-Fructose 1,6-bisphosphate
C6H10O12P2
fba__c 0.0 mmol 10 3 mole litre
fba__for_c Formate
CH1O2
fba__c 0.0 mmol 10 3 mole litre
fba__for_e Formate
CH1O2
fba__e 0.0 mmol 10 3 mole litre
fba__fru_e D-Fructose
C6H12O6
fba__e 0.0 mmol 10 3 mole litre
fba__fum_c Fumarate
C4H2O4
fba__c 0.0 mmol 10 3 mole litre
fba__fum_e Fumarate
C4H2O4
fba__e 0.0 mmol 10 3 mole litre
fba__g3p_c Glyceraldehyde 3-phosphate
C3H5O6P
fba__c 0.0 mmol 10 3 mole litre
fba__g6p_c D-Glucose 6-phosphate
C6H11O9P
fba__c 0.0 mmol 10 3 mole litre
fba__glc__D_e D-Glucose
C6H12O6
fba__e 0.0 mmol 10 3 mole litre
fba__gln__L_c L-Glutamine
C5H10N2O3
fba__c 0.0 mmol 10 3 mole litre
fba__gln__L_e L-Glutamine
C5H10N2O3
fba__e 0.0 mmol 10 3 mole litre
fba__glu__L_c L-Glutamate
C5H8NO4
fba__c 0.0 mmol 10 3 mole litre
fba__glu__L_e L-Glutamate
C5H8NO4
fba__e 0.0 mmol 10 3 mole litre
fba__glx_c Glyoxylate
C2H1O3
fba__c 0.0 mmol 10 3 mole litre
fba__h2o_c H2O
H2O
fba__c 0.0 mmol 10 3 mole litre
fba__h2o_e H2O
H2O
fba__e 0.0 mmol 10 3 mole litre
fba__h_c H+
H
fba__c 0.0 mmol 10 3 mole litre
fba__h_e H+
H
fba__e 0.0 mmol 10 3 mole litre
fba__icit_c Isocitrate
C6H5O7
fba__c 0.0 mmol 10 3 mole litre
fba__lac__D_c D-Lactate
C3H5O3
fba__c 0.0 mmol 10 3 mole litre
fba__lac__D_e D-Lactate
C3H5O3
fba__e 0.0 mmol 10 3 mole litre
fba__mal__L_c L-Malate
C4H4O5
fba__c 0.0 mmol 10 3 mole litre
fba__mal__L_e L-Malate
C4H4O5
fba__e 0.0 mmol 10 3 mole litre
fba__nad_c Nicotinamide adenine dinucleotide
C21H26N7O14P2
fba__c 0.0 mmol 10 3 mole litre
fba__nadh_c Nicotinamide adenine dinucleotide - reduced
C21H27N7O14P2
fba__c 0.0 mmol 10 3 mole litre
fba__nadp_c Nicotinamide adenine dinucleotide phosphate
C21H25N7O17P3
fba__c 0.0 mmol 10 3 mole litre
fba__nadph_c Nicotinamide adenine dinucleotide phosphate - reduced
C21H26N7O17P3
fba__c 0.0 mmol 10 3 mole litre
fba__nh4_c Ammonium
H4N
fba__c 0.0 mmol 10 3 mole litre
fba__nh4_e Ammonium
H4N
fba__e 0.0 mmol 10 3 mole litre
fba__o2_c O2
O2
fba__c 0.0 mmol 10 3 mole litre
fba__o2_e O2
O2
fba__e 0.0 mmol 10 3 mole litre
fba__oaa_c Oxaloacetate
C4H2O5
fba__c 0.0 mmol 10 3 mole litre
fba__pep_c Phosphoenolpyruvate
C3H2O6P
fba__c 0.0 mmol 10 3 mole litre
fba__pi_c Phosphate
HO4P
fba__c 0.0 mmol 10 3 mole litre
fba__pi_e Phosphate
HO4P
fba__e 0.0 mmol 10 3 mole litre
fba__pyr_c Pyruvate
C3H3O3
fba__c 0.0 mmol 10 3 mole litre
fba__pyr_e Pyruvate
C3H3O3
fba__e 0.0 mmol 10 3 mole litre
fba__q8_c Ubiquinone-8
C49H74O4
fba__c 0.0 mmol 10 3 mole litre
fba__q8h2_c Ubiquinol-8
C49H76O4
fba__c 0.0 mmol 10 3 mole litre
fba__r5p_c Alpha-D-Ribose 5-phosphate
C5H9O8P
fba__c 0.0 mmol 10 3 mole litre
fba__ru5p__D_c D-Ribulose 5-phosphate
C5H9O8P
fba__c 0.0 mmol 10 3 mole litre
fba__s7p_c Sedoheptulose 7-phosphate
C7H13O10P
fba__c 0.0 mmol 10 3 mole litre
fba__succ_c Succinate
C4H4O4
fba__c 0.0 mmol 10 3 mole litre
fba__succ_e Succinate
C4H4O4
fba__e 0.0 mmol 10 3 mole litre
fba__succoa_c Succinyl-CoA
C25H35N7O19P3S
fba__c 0.0 mmol 10 3 mole litre
fba__xu5p__D_c D-Xylulose 5-phosphate
C5H9O8P
fba__c 0.0 mmol 10 3 mole litre
fba__X biomass
fba__c 0.001 mmol 10 3 mole

Parameters [90] name value unit derived unit constant sbo cvterm
dt 0.1 h 3600 s
lb_EX_acald_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_acald_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_succ_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_succ_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_etoh_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_etoh_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_o2_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_o2_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_glc__D_e -10.0 mmol_per_h 10 3 mole 3600 s
ub_EX_glc__D_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_fru_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_fru_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_h2o_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_h2o_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_X 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_X 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_gln__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_gln__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_glu__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_glu__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_co2_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_co2_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_h_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_h_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_mal__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_mal__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_ac_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_ac_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_nh4_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_nh4_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_pi_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_pi_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_fum_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_fum_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_pyr_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_pyr_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_akg_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_akg_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_lac__D_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_lac__D_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_for_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_for_e 1000.0 mmol_per_h 10 3 mole 3600 s
pEX_acald_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_succ_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_etoh_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_o2_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_glc__D_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_fru_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_h2o_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_X 1.0 mmol_per_h 10 3 mole 3600 s
pEX_gln__L_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_glu__L_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_co2_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_h_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_mal__L_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_ac_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_nh4_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_pi_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_fum_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_pyr_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_akg_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_lac__D_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_for_e 1.0 mmol_per_h 10 3 mole 3600 s
fba__cobra_default_lb cobra default - lb -1000.0 fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s
fba__cobra_default_ub cobra default - ub 1000.0 fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s
fba__cobra_0_bound cobra 0 - bound 0.0 fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s
fba__R_ATPM_lower_bound R ATPM lower - bound 0.0 fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s
fba__R_EX_glc__D_e_lower_bound R EX glc-D e lower - bound -10.0 fba__mmol_per_gDW_per_hr 10 3 mole g 3600 s
bounds__fbalb_EX_acald_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_succ_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_etoh_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_o2_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_glc__D_e -10.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_fru_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_h2o_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_X 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_gln__L_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_glu__L_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_co2_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_h_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_mal__L_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_ac_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_nh4_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_pi_e -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_fum_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_pyr_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_akg_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_lac__D_e 0.0 mmol_per_h 10 3 mole 3600 s
bounds__fbalb_EX_for_e 0.0 mmol_per_h 10 3 mole 3600 s

Rules [42]   assignment derived units sbo cvterm
pEX_acald_e = EX_acald_e 10 3 mole 3600 s
pEX_succ_e = EX_succ_e 10 3 mole 3600 s
pEX_etoh_e = EX_etoh_e 10 3 mole 3600 s
pEX_o2_e = EX_o2_e 10 3 mole 3600 s
pEX_glc__D_e = EX_glc__D_e 10 3 mole 3600 s
pEX_fru_e = EX_fru_e 10 3 mole 3600 s
pEX_h2o_e = EX_h2o_e 10 3 mole 3600 s
pEX_X = EX_X 10 3 mole 3600 s
pEX_gln__L_e = EX_gln__L_e 10 3 mole 3600 s
pEX_glu__L_e = EX_glu__L_e 10 3 mole 3600 s
pEX_co2_e = EX_co2_e 10 3 mole 3600 s
pEX_h_e = EX_h_e 10 3 mole 3600 s
pEX_mal__L_e = EX_mal__L_e 10 3 mole 3600 s
pEX_ac_e = EX_ac_e 10 3 mole 3600 s
pEX_nh4_e = EX_nh4_e 10 3 mole 3600 s
pEX_pi_e = EX_pi_e 10 3 mole 3600 s
pEX_fum_e = EX_fum_e 10 3 mole 3600 s
pEX_pyr_e = EX_pyr_e 10 3 mole 3600 s
pEX_akg_e = EX_akg_e 10 3 mole 3600 s
pEX_lac__D_e = EX_lac__D_e 10 3 mole 3600 s
pEX_for_e = EX_for_e 10 3 mole 3600 s
lb_EX_acald_e = bounds__max bounds__fbalb_EX_acald_e acald_e bioreactor dt 10 3 mole 3600 s
lb_EX_succ_e = bounds__max bounds__fbalb_EX_succ_e succ_e bioreactor dt 10 3 mole 3600 s
lb_EX_etoh_e = bounds__max bounds__fbalb_EX_etoh_e etoh_e bioreactor dt 10 3 mole 3600 s
lb_EX_o2_e = bounds__max bounds__fbalb_EX_o2_e o2_e bioreactor dt 10 3 mole 3600 s
lb_EX_glc__D_e = bounds__max bounds__fbalb_EX_glc__D_e glc__D_e bioreactor dt 10 3 mole 3600 s
lb_EX_fru_e = bounds__max bounds__fbalb_EX_fru_e fru_e bioreactor dt 10 3 mole 3600 s
lb_EX_h2o_e = bounds__max bounds__fbalb_EX_h2o_e h2o_e bioreactor dt 10 3 mole 3600 s
lb_EX_X = bounds__max bounds__fbalb_EX_X X bioreactor dt 10 3 mole 3600 s
lb_EX_gln__L_e = bounds__max bounds__fbalb_EX_gln__L_e gln__L_e bioreactor dt 10 3 mole 3600 s
lb_EX_glu__L_e = bounds__max bounds__fbalb_EX_glu__L_e glu__L_e bioreactor dt 10 3 mole 3600 s
lb_EX_co2_e = bounds__max bounds__fbalb_EX_co2_e co2_e bioreactor dt 10 3 mole 3600 s
lb_EX_h_e = bounds__max bounds__fbalb_EX_h_e h_e bioreactor dt 10 3 mole 3600 s
lb_EX_mal__L_e = bounds__max bounds__fbalb_EX_mal__L_e mal__L_e bioreactor dt 10 3 mole 3600 s
lb_EX_ac_e = bounds__max bounds__fbalb_EX_ac_e ac_e bioreactor dt 10 3 mole 3600 s
lb_EX_nh4_e = bounds__max bounds__fbalb_EX_nh4_e nh4_e bioreactor dt 10 3 mole 3600 s
lb_EX_pi_e = bounds__max bounds__fbalb_EX_pi_e pi_e bioreactor dt 10 3 mole 3600 s
lb_EX_fum_e = bounds__max bounds__fbalb_EX_fum_e fum_e bioreactor dt 10 3 mole 3600 s
lb_EX_pyr_e = bounds__max bounds__fbalb_EX_pyr_e pyr_e bioreactor dt 10 3 mole 3600 s
lb_EX_akg_e = bounds__max bounds__fbalb_EX_akg_e akg_e bioreactor dt 10 3 mole 3600 s
lb_EX_lac__D_e = bounds__max bounds__fbalb_EX_lac__D_e lac__D_e bioreactor dt 10 3 mole 3600 s
lb_EX_for_e = bounds__max bounds__fbalb_EX_for_e for_e bioreactor dt 10 3 mole 3600 s

Reactions [117] name equation modifiers formula derived units sbo cvterm
fba__ACALD Acetaldehyde dehydrogenase (acetylating) fba__acald_c + fba__coa_c + fba__nad_c ⇆ fba__accoa_c + fba__h_c + fba__nadh_c
BQB_IS
ACALD
fba__ACALDt Acetaldehyde reversible transport fba__acald_e ⇆ fba__acald_c
BQB_IS
ACALDt
fba__ACKr Acetate kinase fba__ac_c + fba__atp_c ⇆ fba__actp_c + fba__adp_c
BQB_IS
ACKr
fba__ACONTa Aconitase (half-reaction A, Citrate hydro-lyase) fba__cit_c ⇆ fba__acon_C_c + fba__h2o_c
BQB_IS
ACONTa
fba__ACONTb Aconitase (half-reaction B, Isocitrate hydro-lyase) fba__acon_C_c + fba__h2o_c ⇆ fba__icit_c
BQB_IS
ACONTb
fba__ACt2r Acetate reversible transport via proton symport fba__ac_e + fba__h_e ⇆ fba__ac_c + fba__h_c
BQB_IS
ACt2r
fba__ADK1 Adenylate kinase fba__amp_c + fba__atp_c ⇆ 2.0 fba__adp_c
BQB_IS
ADK1
fba__AKGDH 2-Oxogluterate dehydrogenase fba__akg_c + fba__coa_c + fba__nad_c ➞ fba__co2_c + fba__nadh_c + fba__succoa_c
BQB_IS
AKGDH
fba__AKGt2r 2 oxoglutarate reversible transport via symport fba__akg_e + fba__h_e ⇆ fba__akg_c + fba__h_c
BQB_IS
AKGt2r
fba__ALCD2x Alcohol dehydrogenase (ethanol) fba__etoh_c + fba__nad_c ⇆ fba__acald_c + fba__h_c + fba__nadh_c
BQB_IS
ALCD2x
fba__ATPM ATP maintenance requirement fba__atp_c + fba__h2o_c ➞ fba__adp_c + fba__h_c + fba__pi_c
BQB_IS
ATPM
fba__ATPS4r ATP synthase (four protons for one ATP) fba__adp_c + 4.0 fba__h_e + fba__pi_c ⇆ fba__atp_c + fba__h2o_c + 3.0 fba__h_c
BQB_IS
ATPS4r
fba__BIOMASS_Ecoli_core_w_GAM Biomass Objective Function with GAM 1.496 fba__M_3pg_c + 3.7478 fba__accoa_c + 59.81 fba__atp_c + 0.361 fba__e4p_c + 0.0709 fba__f6p_c + 0.129 fba__g3p_c + 0.205 fba__g6p_c + 0.2557 fba__gln__L_c + 4.9414 fba__glu__L_c + 59.81 fba__h2o_c + 3.547 fba__nad_c + 13.0279 fba__nadph_c + 1.7867 fba__oaa_c + 0.5191 fba__pep_c + 2.8328 fba__pyr_c + 0.8977 fba__r5p_c ➞ 59.81 fba__adp_c + 4.1182 fba__akg_c + 3.7478 fba__coa_c + 59.81 fba__h_c + 3.547 fba__nadh_c + 13.0279 fba__nadp_c + 59.81 fba__pi_c + fba__X
fba__CO2t CO2 transporter via diffusion fba__co2_e ⇆ fba__co2_c
BQB_IS
CO2t
fba__CS Citrate synthase fba__accoa_c + fba__h2o_c + fba__oaa_c ➞ fba__cit_c + fba__coa_c + fba__h_c
BQB_IS
CS
fba__CYTBD Cytochrome oxidase bd (ubiquinol-8: 2 protons) 2.0 fba__h_c + 0.5 fba__o2_c + fba__q8h2_c ➞ fba__h2o_c + 2.0 fba__h_e + fba__q8_c
BQB_IS
CYTBD
fba__D_LACt2 D lactate transport via proton symport fba__h_e + fba__lac__D_e ⇆ fba__h_c + fba__lac__D_c
BQB_IS
D_LACt2
fba__ENO Enolase fba__M_2pg_c ⇆ fba__h2o_c + fba__pep_c
BQB_IS
ENO
fba__ETOHt2r ETOHt2r fba__etoh_e + fba__h_e ⇆ fba__etoh_c + fba__h_c
BQB_IS
ETOHt2r
EX_ac_e Acetate exchange fba__ac_e ⇆
BQB_IS
ac
EX_acald_e Acetaldehyde exchange fba__acald_e ⇆
BQB_IS
acald
EX_akg_e 2-Oxoglutarate exchange fba__akg_e ⇆
BQB_IS
akg
EX_co2_e CO2 exchange fba__co2_e ⇆
BQB_IS
co2
EX_etoh_e Ethanol exchange fba__etoh_e ⇆
BQB_IS
etoh
EX_for_e Formate exchange fba__for_e ⇆
BQB_IS
for
EX_fru_e D-Fructose exchange fba__fru_e ⇆
BQB_IS
fru
EX_fum_e Fumarate exchange fba__fum_e ⇆
BQB_IS
fum
EX_glc__D_e D-Glucose exchange fba__glc__D_e ⇆
BQB_IS
glc__D
EX_gln__L_e L-Glutamine exchange fba__gln__L_e ⇆
BQB_IS
gln__L
EX_glu__L_e L-Glutamate exchange fba__glu__L_e ⇆
BQB_IS
glu__L
EX_h_e H+ exchange fba__h_e ⇆
BQB_IS
h
EX_h2o_e H2O exchange fba__h2o_e ⇆
BQB_IS
h2o
EX_lac__D_e D-lactate exchange fba__lac__D_e ⇆
BQB_IS
lac__D
EX_mal__L_e L-Malate exchange fba__mal__L_e ⇆
BQB_IS
mal__L
EX_nh4_e Ammonia exchange fba__nh4_e ⇆
BQB_IS
nh4
EX_o2_e O2 exchange fba__o2_e ⇆
BQB_IS
o2
EX_pi_e Phosphate exchange fba__pi_e ⇆
BQB_IS
pi
EX_pyr_e Pyruvate exchange fba__pyr_e ⇆
BQB_IS
pyr
EX_succ_e Succinate exchange fba__succ_e ⇆
BQB_IS
succ
fba__FBA Fructose-bisphosphate aldolase fba__fdp_c ⇆ fba__dhap_c + fba__g3p_c
BQB_IS
FBA
fba__FBP Fructose-bisphosphatase fba__fdp_c + fba__h2o_c ➞ fba__f6p_c + fba__pi_c
BQB_IS
FBP
fba__FORt2 Formate transport in via proton symport fba__for_e + fba__h_e ➞ fba__for_c + fba__h_c
BQB_IS
FORt2
fba__FORti Formate transport via diffusion fba__for_c ➞ fba__for_e
BQB_IS
FORti
fba__FRD7 Fumarate reductase fba__fum_c + fba__q8h2_c ➞ fba__q8_c + fba__succ_c
BQB_IS
FRD7
fba__FRUpts2 Fructose transport via PEP:Pyr PTS (f6p generating) fba__fru_e + fba__pep_c ➞ fba__f6p_c + fba__pyr_c
BQB_IS
FRUpts2
fba__FUM Fumarase fba__fum_c + fba__h2o_c ⇆ fba__mal__L_c
BQB_IS
FUM
fba__FUMt2_2 Fumarate transport via proton symport (2 H) fba__fum_e + 2.0 fba__h_e ➞ fba__fum_c + 2.0 fba__h_c
BQB_IS
FUMt2_2
fba__G6PDH2r Glucose 6-phosphate dehydrogenase fba__g6p_c + fba__nadp_c ⇆ fba__M_6pgl_c + fba__h_c + fba__nadph_c
BQB_IS
G6PDH2r
fba__GAPD Glyceraldehyde-3-phosphate dehydrogenase fba__g3p_c + fba__nad_c + fba__pi_c ⇆ fba__M_13dpg_c + fba__h_c + fba__nadh_c
BQB_IS
GAPD
fba__GLCpts D-glucose transport via PEP:Pyr PTS fba__glc__D_e + fba__pep_c ➞ fba__g6p_c + fba__pyr_c
BQB_IS
GLCpts
fba__GLNS Glutamine synthetase fba__atp_c + fba__glu__L_c + fba__nh4_c ➞ fba__adp_c + fba__gln__L_c + fba__h_c + fba__pi_c
BQB_IS
GLNS
fba__GLNabc GLNabc fba__atp_c + fba__gln__L_e + fba__h2o_c ➞ fba__adp_c + fba__gln__L_c + fba__h_c + fba__pi_c
BQB_IS
GLNabc
fba__GLUDy Glutamate dehydrogenase (NADP) fba__glu__L_c + fba__h2o_c + fba__nadp_c ⇆ fba__akg_c + fba__h_c + fba__nadph_c + fba__nh4_c
BQB_IS
GLUDy
fba__GLUN Glutaminase fba__gln__L_c + fba__h2o_c ➞ fba__glu__L_c + fba__nh4_c
BQB_IS
GLUN
fba__GLUSy Glutamate synthase (NADPH) fba__akg_c + fba__gln__L_c + fba__h_c + fba__nadph_c ➞ 2.0 fba__glu__L_c + fba__nadp_c
BQB_IS
GLUSy
fba__GLUt2r L glutamate transport via proton symport reversible fba__glu__L_e + fba__h_e ⇆ fba__glu__L_c + fba__h_c
BQB_IS
GLUt2r
fba__GND Phosphogluconate dehydrogenase fba__M_6pgc_c + fba__nadp_c ➞ fba__co2_c + fba__nadph_c + fba__ru5p__D_c
BQB_IS
GND
fba__H2Ot H2O transport via diffusion fba__h2o_e ⇆ fba__h2o_c
BQB_IS
H2Ot
fba__ICDHyr Isocitrate dehydrogenase (NADP) fba__icit_c + fba__nadp_c ⇆ fba__akg_c + fba__co2_c + fba__nadph_c
BQB_IS
ICDHyr
fba__ICL Isocitrate lyase fba__icit_c ➞ fba__glx_c + fba__succ_c
BQB_IS
ICL
fba__LDH_D D-lactate dehydrogenase fba__lac__D_c + fba__nad_c ⇆ fba__h_c + fba__nadh_c + fba__pyr_c
BQB_IS
LDH_D
fba__MALS Malate synthase fba__accoa_c + fba__glx_c + fba__h2o_c ➞ fba__coa_c + fba__h_c + fba__mal__L_c
BQB_IS
MALS
fba__MALt2_2 Malate transport via proton symport (2 H) 2.0 fba__h_e + fba__mal__L_e ➞ 2.0 fba__h_c + fba__mal__L_c
BQB_IS
MALt2_2
fba__MDH Malate dehydrogenase fba__mal__L_c + fba__nad_c ⇆ fba__h_c + fba__nadh_c + fba__oaa_c
BQB_IS
MDH
fba__ME1 Malic enzyme (NAD) fba__mal__L_c + fba__nad_c ➞ fba__co2_c + fba__nadh_c + fba__pyr_c
BQB_IS
ME1
fba__ME2 Malic enzyme (NADP) fba__mal__L_c + fba__nadp_c ➞ fba__co2_c + fba__nadph_c + fba__pyr_c
BQB_IS
ME2
fba__NADH16 NADH dehydrogenase (ubiquinone-8 & 3 protons) 4.0 fba__h_c + fba__nadh_c + fba__q8_c ➞ 3.0 fba__h_e + fba__nad_c + fba__q8h2_c
BQB_IS
NADH16
fba__NADTRHD NAD transhydrogenase fba__nad_c + fba__nadph_c ➞ fba__nadh_c + fba__nadp_c
BQB_IS
NADTRHD
fba__NH4t Ammonia reversible transport fba__nh4_e ⇆ fba__nh4_c
BQB_IS
NH4t
fba__O2t O2 transport diffusion fba__o2_e ⇆ fba__o2_c
BQB_IS
O2t
fba__PDH Pyruvate dehydrogenase fba__coa_c + fba__nad_c + fba__pyr_c ➞ fba__accoa_c + fba__co2_c + fba__nadh_c
BQB_IS
PDH
fba__PFK Phosphofructokinase fba__atp_c + fba__f6p_c ➞ fba__adp_c + fba__fdp_c + fba__h_c
BQB_IS
PFK
fba__PFL Pyruvate formate lyase fba__coa_c + fba__pyr_c ➞ fba__accoa_c + fba__for_c
BQB_IS
PFL
fba__PGI Glucose-6-phosphate isomerase fba__g6p_c ⇆ fba__f6p_c
BQB_IS
PGI
fba__PGK Phosphoglycerate kinase fba__M_3pg_c + fba__atp_c ⇆ fba__M_13dpg_c + fba__adp_c
BQB_IS
PGK
fba__PGL 6-phosphogluconolactonase fba__M_6pgl_c + fba__h2o_c ➞ fba__M_6pgc_c + fba__h_c
BQB_IS
PGL
fba__PGM Phosphoglycerate mutase fba__M_2pg_c ⇆ fba__M_3pg_c
BQB_IS
PGM
fba__PIt2r Phosphate reversible transport via symport fba__h_e + fba__pi_e ⇆ fba__h_c + fba__pi_c
BQB_IS
PIt2r
fba__PPC Phosphoenolpyruvate carboxylase fba__co2_c + fba__h2o_c + fba__pep_c ➞ fba__h_c + fba__oaa_c + fba__pi_c
BQB_IS
PPC
fba__PPCK Phosphoenolpyruvate carboxykinase fba__atp_c + fba__oaa_c ➞ fba__adp_c + fba__co2_c + fba__pep_c
BQB_IS
PPCK
fba__PPS Phosphoenolpyruvate synthase fba__atp_c + fba__h2o_c + fba__pyr_c ➞ fba__amp_c + 2.0 fba__h_c + fba__pep_c + fba__pi_c
BQB_IS
PPS
fba__PTAr Phosphotransacetylase fba__accoa_c + fba__pi_c ⇆ fba__actp_c + fba__coa_c
BQB_IS
PTAr
fba__PYK Pyruvate kinase fba__adp_c + fba__h_c + fba__pep_c ➞ fba__atp_c + fba__pyr_c
BQB_IS
PYK
fba__PYRt2 Pyruvate transport in via proton symport fba__h_e + fba__pyr_e ⇆ fba__h_c + fba__pyr_c
BQB_IS
PYRt2
fba__RPE Ribulose 5-phosphate 3-epimerase fba__ru5p__D_c ⇆ fba__xu5p__D_c
BQB_IS
RPE
fba__RPI Ribose-5-phosphate isomerase fba__r5p_c ⇆ fba__ru5p__D_c
BQB_IS
RPI
fba__SUCCt2_2 Succinate transport via proton symport (2 H) 2.0 fba__h_e + fba__succ_e ➞ 2.0 fba__h_c + fba__succ_c
BQB_IS
SUCCt2_2
fba__SUCCt3 Succinate transport out via proton antiport fba__h_e + fba__succ_c ➞ fba__h_c + fba__succ_e
BQB_IS
SUCCt3
fba__SUCDi Succinate dehydrogenase (irreversible) fba__q8_c + fba__succ_c ➞ fba__fum_c + fba__q8h2_c
BQB_IS
SUCDi
fba__SUCOAS Succinyl-CoA synthetase (ADP-forming) fba__atp_c + fba__coa_c + fba__succ_c ⇆ fba__adp_c + fba__pi_c + fba__succoa_c
BQB_IS
SUCOAS
fba__TALA Transaldolase fba__g3p_c + fba__s7p_c ⇆ fba__e4p_c + fba__f6p_c
BQB_IS
TALA
fba__THD2 NAD(P) transhydrogenase 2.0 fba__h_e + fba__nadh_c + fba__nadp_c ➞ 2.0 fba__h_c + fba__nad_c + fba__nadph_c
BQB_IS
THD2
fba__TKT1 Transketolase fba__r5p_c + fba__xu5p__D_c ⇆ fba__g3p_c + fba__s7p_c
BQB_IS
TKT1
fba__TKT2 Transketolase fba__e4p_c + fba__xu5p__D_c ⇆ fba__f6p_c + fba__g3p_c
BQB_IS
TKT2
fba__TPI Triose-phosphate isomerase fba__dhap_c ⇆ fba__g3p_c
BQB_IS
TPI
EX_X fba__X ⇆
update__update_acald_e acald_e ⇆ pEX_acald_e 10 3 mole 3600 s
update__update_succ_e succ_e ⇆ pEX_succ_e 10 3 mole 3600 s
update__update_etoh_e etoh_e ⇆ pEX_etoh_e 10 3 mole 3600 s
update__update_o2_e o2_e ⇆ pEX_o2_e 10 3 mole 3600 s
update__update_glc__D_e glc__D_e ⇆ pEX_glc__D_e 10 3 mole 3600 s
update__update_fru_e fru_e ⇆ pEX_fru_e 10 3 mole 3600 s
update__update_h2o_e h2o_e ⇆ pEX_h2o_e 10 3 mole 3600 s
update__update_X X ⇆ pEX_X 10 3 mole 3600 s
update__update_gln__L_e gln__L_e ⇆ pEX_gln__L_e 10 3 mole 3600 s
update__update_glu__L_e glu__L_e ⇆ pEX_glu__L_e 10 3 mole 3600 s
update__update_co2_e co2_e ⇆ pEX_co2_e 10 3 mole 3600 s
update__update_h_e h_e ⇆ pEX_h_e 10 3 mole 3600 s
update__update_mal__L_e mal__L_e ⇆ pEX_mal__L_e 10 3 mole 3600 s
update__update_ac_e ac_e ⇆ pEX_ac_e 10 3 mole 3600 s
update__update_nh4_e nh4_e ⇆ pEX_nh4_e 10 3 mole 3600 s
update__update_pi_e pi_e ⇆ pEX_pi_e 10 3 mole 3600 s
update__update_fum_e fum_e ⇆ pEX_fum_e 10 3 mole 3600 s
update__update_pyr_e pyr_e ⇆ pEX_pyr_e 10 3 mole 3600 s
update__update_akg_e akg_e ⇆ pEX_akg_e 10 3 mole 3600 s
update__update_lac__D_e lac__D_e ⇆ pEX_lac__D_e 10 3 mole 3600 s
update__update_for_e for_e ⇆ pEX_for_e 10 3 mole 3600 s