E.coli core DFBA model

Model version: 10

UPDATE submodel

Submodel for dynamically updating the metabolite count. This updates the ode model based on the FBA fluxes.

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_update

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-11-11 19:47
Modified: 2017-11-11 19:47

id ecoli_update meta_ecoli_update
nameecoli (UPDATE)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
Access SBML model  L3V1 comp-V1

Ports [43] name referenced element port ref id ref unit ref metaid ref sbo cvterm
bioreactor_port port bioreactor Compartment: bioreactor bioreactor
for_e_port port for_e Species: for_e for_e
fru_e_port port fru_e Species: fru_e fru_e
h2o_e_port port h2o_e Species: h2o_e h2o_e
akg_e_port port akg_e Species: akg_e akg_e
pyr_e_port port pyr_e Species: pyr_e pyr_e
glc__D_e_port port glc__D_e Species: glc__D_e glc__D_e
fum_e_port port fum_e Species: fum_e fum_e
X_port port X Species: X X
pi_e_port port pi_e Species: pi_e pi_e
lac__D_e_port port lac__D_e Species: lac__D_e lac__D_e
gln__L_e_port port gln__L_e Species: gln__L_e gln__L_e
acald_e_port port acald_e Species: acald_e acald_e
etoh_e_port port etoh_e Species: etoh_e etoh_e
ac_e_port port ac_e Species: ac_e ac_e
succ_e_port port succ_e Species: succ_e succ_e
o2_e_port port o2_e Species: o2_e o2_e
mal__L_e_port port mal__L_e Species: mal__L_e mal__L_e
h_e_port port h_e Species: h_e h_e
co2_e_port port co2_e Species: co2_e co2_e
nh4_e_port port nh4_e Species: nh4_e nh4_e
glu__L_e_port port glu__L_e Species: glu__L_e glu__L_e
pEX_for_e_port port pEX_for_e Parameter: pEX_for_e pEX_for_e
pEX_fru_e_port port pEX_fru_e Parameter: pEX_fru_e pEX_fru_e
pEX_h2o_e_port port pEX_h2o_e Parameter: pEX_h2o_e pEX_h2o_e
pEX_akg_e_port port pEX_akg_e Parameter: pEX_akg_e pEX_akg_e
pEX_pyr_e_port port pEX_pyr_e Parameter: pEX_pyr_e pEX_pyr_e
pEX_glc__D_e_port port pEX_glc__D_e Parameter: pEX_glc__D_e pEX_glc__D_e
pEX_fum_e_port port pEX_fum_e Parameter: pEX_fum_e pEX_fum_e
pEX_X_port port pEX_X Parameter: pEX_X pEX_X
pEX_pi_e_port port pEX_pi_e Parameter: pEX_pi_e pEX_pi_e
pEX_lac__D_e_port port pEX_lac__D_e Parameter: pEX_lac__D_e pEX_lac__D_e
pEX_gln__L_e_port port pEX_gln__L_e Parameter: pEX_gln__L_e pEX_gln__L_e
pEX_acald_e_port port pEX_acald_e Parameter: pEX_acald_e pEX_acald_e
pEX_etoh_e_port port pEX_etoh_e Parameter: pEX_etoh_e pEX_etoh_e
pEX_ac_e_port port pEX_ac_e Parameter: pEX_ac_e pEX_ac_e
pEX_succ_e_port port pEX_succ_e Parameter: pEX_succ_e pEX_succ_e
pEX_o2_e_port port pEX_o2_e Parameter: pEX_o2_e pEX_o2_e
pEX_mal__L_e_port port pEX_mal__L_e Parameter: pEX_mal__L_e pEX_mal__L_e
pEX_h_e_port port pEX_h_e Parameter: pEX_h_e pEX_h_e
pEX_co2_e_port port pEX_co2_e Parameter: pEX_co2_e pEX_co2_e
pEX_nh4_e_port port pEX_nh4_e Parameter: pEX_nh4_e pEX_nh4_e
pEX_glu__L_e_port port pEX_glu__L_e Parameter: pEX_glu__L_e pEX_glu__L_e

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 conversion factor units substance units derived units sbo cvterm
for_e Formate bioreactor 1.0 mmol mmol 10 3 mole litre
fru_e D-Fructose bioreactor 1.0 mmol mmol 10 3 mole litre
h2o_e H2O bioreactor 1.0 mmol mmol 10 3 mole litre
akg_e 2-Oxoglutarate bioreactor 1.0 mmol mmol 10 3 mole litre
pyr_e Pyruvate bioreactor 1.0 mmol mmol 10 3 mole litre
glc__D_e D-Glucose bioreactor 1.0 mmol mmol 10 3 mole litre
fum_e Fumarate bioreactor 1.0 mmol mmol 10 3 mole litre
X biomass bioreactor 1.0 mmol mmol 10 3 mole litre
pi_e Phosphate bioreactor 1.0 mmol mmol 10 3 mole litre
lac__D_e D-Lactate bioreactor 1.0 mmol mmol 10 3 mole litre
gln__L_e L-Glutamine bioreactor 1.0 mmol mmol 10 3 mole litre
acald_e Acetaldehyde bioreactor 1.0 mmol mmol 10 3 mole litre
etoh_e Ethanol bioreactor 1.0 mmol mmol 10 3 mole litre
ac_e Acetate bioreactor 1.0 mmol mmol 10 3 mole litre
succ_e Succinate bioreactor 1.0 mmol mmol 10 3 mole litre
o2_e O2 bioreactor 1.0 mmol mmol 10 3 mole litre
mal__L_e L-Malate bioreactor 1.0 mmol mmol 10 3 mole litre
h_e H+ bioreactor 1.0 mmol mmol 10 3 mole litre
co2_e CO2 bioreactor 1.0 mmol mmol 10 3 mole litre
nh4_e Ammonium bioreactor 1.0 mmol mmol 10 3 mole litre
glu__L_e L-Glutamate bioreactor 1.0 mmol mmol 10 3 mole litre
X biomass c 0.001 cf_biomass=1.0 [g_per_mmol] g g 10 3 mole litre

Parameters [22] name constant value unit derived unit sbo cvterm
cf_biomass biomass conversion factor 1.0 g_per_mmol g 10 3 mole
pEX_for_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_akg_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_fum_e 1.0 mmol_per_h 10 3 mole 3600 s
pEX_X 1.0 mmol_per_h 10 3 mole 3600 s
pEX_pi_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_gln__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_etoh_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_succ_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_mal__L_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_co2_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_glu__L_e 1.0 mmol_per_h 10 3 mole 3600 s

Reactions [21] name equation modifiers kinetic law derived units sbo cvterm
update_for_e
for_e ⇆ pEX_for_e 10 3 mole 3600 s
update_fru_e
fru_e ⇆ pEX_fru_e 10 3 mole 3600 s
update_h2o_e
h2o_e ⇆ pEX_h2o_e 10 3 mole 3600 s
update_akg_e
akg_e ⇆ pEX_akg_e 10 3 mole 3600 s
update_pyr_e
pyr_e ⇆ pEX_pyr_e 10 3 mole 3600 s
update_glc__D_e
glc__D_e ⇆ pEX_glc__D_e 10 3 mole 3600 s
update_fum_e
fum_e ⇆ pEX_fum_e 10 3 mole 3600 s
update_X
X ⇆ pEX_X 10 3 mole 3600 s
update_pi_e
pi_e ⇆ pEX_pi_e 10 3 mole 3600 s
update_lac__D_e
lac__D_e ⇆ pEX_lac__D_e 10 3 mole 3600 s
update_gln__L_e
gln__L_e ⇆ pEX_gln__L_e 10 3 mole 3600 s
update_acald_e
acald_e ⇆ pEX_acald_e 10 3 mole 3600 s
update_etoh_e
etoh_e ⇆ pEX_etoh_e 10 3 mole 3600 s
update_ac_e
ac_e ⇆ pEX_ac_e 10 3 mole 3600 s
update_succ_e
succ_e ⇆ pEX_succ_e 10 3 mole 3600 s
update_o2_e
o2_e ⇆ pEX_o2_e 10 3 mole 3600 s
update_mal__L_e
mal__L_e ⇆ pEX_mal__L_e 10 3 mole 3600 s
update_h_e
h_e ⇆ pEX_h_e 10 3 mole 3600 s
update_co2_e
co2_e ⇆ pEX_co2_e 10 3 mole 3600 s
update_nh4_e
nh4_e ⇆ pEX_nh4_e 10 3 mole 3600 s
update_glu__L_e
glu__L_e ⇆ pEX_glu__L_e 10 3 mole 3600 s