E.coli core DFBA model

Model version: 7

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

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-06-12 17:02
Modified: 2017-06-12 17:02

id ecoli_top meta_ecoli_top
nameecoli (TOP)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
SBML model L3V1 comp-V1

Submodels [3] name model ref deletions time conversion extent conversion sbo cvterm
fba ecoli_fba
bounds ecoli_bounds
update ecoli_update

UnitDefinitions [13] 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

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
bioreactor bioreactor 1.0 3 l litre

Species [22] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
mal__L_e L-Malate bioreactor 1.0 mmol 10 3 mole litre
acald_e Acetaldehyde bioreactor 1.0 mmol 10 3 mole litre
pyr_e Pyruvate bioreactor 1.0 mmol 10 3 mole litre
glc__D_e D-Glucose bioreactor 20.0 mmol 10 3 mole litre
etoh_e Ethanol bioreactor 1.0 mmol 10 3 mole litre
nh4_e Ammonium bioreactor 1.0 mmol 10 3 mole litre
h2o_e H2O bioreactor 20.0 mmol 10 3 mole litre
ac_e Acetate bioreactor 1.0 mmol 10 3 mole litre
akg_e 2-Oxoglutarate bioreactor 1.0 mmol 10 3 mole litre
co2_e CO2 bioreactor 1.0 mmol 10 3 mole litre
lac__D_e D-Lactate bioreactor 1.0 mmol 10 3 mole litre
fum_e Fumarate bioreactor 1.0 mmol 10 3 mole litre
fru_e D-Fructose bioreactor 1.0 mmol 10 3 mole litre
for_e Formate bioreactor 1.0 mmol 10 3 mole litre
gln__L_e L-Glutamine bioreactor 10.0 mmol 10 3 mole litre
succ_e Succinate bioreactor 1.0 mmol 10 3 mole litre
h_e H+ bioreactor 1.0 mmol 10 3 mole litre
pi_e Phosphate bioreactor 1.0 mmol 10 3 mole litre
X biomass bioreactor 0.001 mmol 10 3 mole litre
glu__L_e L-Glutamate bioreactor 1.0 mmol 10 3 mole litre
o2_e O2 bioreactor 1.0 mmol 10 3 mole litre
dummy_S dummy_S bioreactor 0.0 mmol 10 3 mole litre

Parameters [64] name constant value unit derived unit sbo cvterm
dt 0.1 h 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_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_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_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_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_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_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_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_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_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_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_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_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_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
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_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_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_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_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_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_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
pEX_mal__L_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_acald_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_glc__D_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_nh4_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_ac_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_co2_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_fum_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_for_e 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_succ_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_pi_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_X 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_o2_e 1.0 mmol_per_h 10 3 mole 3600 s

Rules [21]   assignment name derived units sbo cvterm
pEX_mal__L_e = EX_mal__L_e 10 3 mole 3600 s
pEX_acald_e = EX_acald_e 10 3 mole 3600 s
pEX_pyr_e = EX_pyr_e 10 3 mole 3600 s
pEX_glc__D_e = EX_glc__D_e 10 3 mole 3600 s
pEX_etoh_e = EX_etoh_e 10 3 mole 3600 s
pEX_nh4_e = EX_nh4_e 10 3 mole 3600 s
pEX_h2o_e = EX_h2o_e 10 3 mole 3600 s
pEX_ac_e = EX_ac_e 10 3 mole 3600 s
pEX_akg_e = EX_akg_e 10 3 mole 3600 s
pEX_co2_e = EX_co2_e 10 3 mole 3600 s
pEX_lac__D_e = EX_lac__D_e 10 3 mole 3600 s
pEX_fum_e = EX_fum_e 10 3 mole 3600 s
pEX_fru_e = EX_fru_e 10 3 mole 3600 s
pEX_for_e = EX_for_e 10 3 mole 3600 s
pEX_gln__L_e = EX_gln__L_e 10 3 mole 3600 s
pEX_succ_e = EX_succ_e 10 3 mole 3600 s
pEX_h_e = EX_h_e 10 3 mole 3600 s
pEX_pi_e = EX_pi_e 10 3 mole 3600 s
pEX_X = EX_X 10 3 mole 3600 s
pEX_glu__L_e = EX_glu__L_e 10 3 mole 3600 s
pEX_o2_e = EX_o2_e 10 3 mole 3600 s

Reactions [21] id name equation modifiers kinetic law derived units sbo cvterm
fba:portRef=EX_mal__L_e_port EX_mal__L_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_acald_e_port EX_acald_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_pyr_e_port EX_pyr_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_glc__D_e_port EX_glc__D_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_etoh_e_port EX_etoh_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_nh4_e_port EX_nh4_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_h2o_e_port EX_h2o_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_ac_e_port EX_ac_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_akg_e_port EX_akg_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_co2_e_port EX_co2_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_lac__D_e_port EX_lac__D_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_fum_e_port EX_fum_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_fru_e_port EX_fru_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_for_e_port EX_for_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_gln__L_e_port EX_gln__L_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_succ_e_port EX_succ_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_h_e_port EX_h_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_pi_e_port EX_pi_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_X_port EX_X
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_glu__L_e_port EX_glu__L_e
➞ dummy_S 0 10 3 mole 3600 s
fba:portRef=EX_o2_e_port EX_o2_e
➞ dummy_S 0 10 3 mole 3600 s