E.coli core DFBA model

Model version: 5

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: 2017-04-03 17:09
Modified: 2017-04-03 17:09

SBML model


idecoli_top
nameecoli (TOP)
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
UnitDefinitions [12] 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_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 unit derived unit sbo cvterm
bioreactor bioreactor 1.0 3 l litre

Species [21] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
pi_e Phosphate
bioreactor 0.0 mmol 10 3 mole litre
for_e Formate
bioreactor 0.0 mmol 10 3 mole litre
h_e H+
bioreactor 0.0 mmol 10 3 mole litre
o2_e O2
bioreactor 0.21 mmol 10 3 mole litre
lac__D_e D-Lactate
bioreactor 0.0 mmol 10 3 mole litre
pyr_e Pyruvate
bioreactor 0.0 mmol 10 3 mole litre
etoh_e Ethanol
bioreactor 0.0 mmol 10 3 mole litre
gln__L_e L-Glutamine
bioreactor 0.0 mmol 10 3 mole litre
akg_e 2-Oxoglutarate
bioreactor 0.0 mmol 10 3 mole litre
co2_e CO2
bioreactor 0.04 mmol 10 3 mole litre
acald_e Acetaldehyde
bioreactor 0.0 mmol 10 3 mole litre
glu__L_e L-Glutamate
bioreactor 0.0 mmol 10 3 mole litre
mal__L_e L-Malate
bioreactor 0.0 mmol 10 3 mole litre
fum_e Fumarate
bioreactor 0.0 mmol 10 3 mole litre
fru_e D-Fructose
bioreactor 0.0 mmol 10 3 mole litre
succ_e Succinate
bioreactor 1.0 mmol 10 3 mole litre
h2o_e H2O
bioreactor 0.0 mmol 10 3 mole litre
nh4_e Ammonium
bioreactor 0.0 mmol 10 3 mole litre
ac_e Acetate
bioreactor 0.0 mmol 10 3 mole litre
glc__D_e D-Glucose
bioreactor 20.0 mmol 10 3 mole litre
dummy_S dummy_S
bioreactor 0.0 mmol 10 3 mole litre

Parameters [61] name value unit derived unit constant sbo cvterm
dt 0.1 h 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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
EX_pi_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_for_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_h_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_o2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_lac__D_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pyr_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_etoh_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gln__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_akg_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_co2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_acald_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_glu__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_mal__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_fum_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_fru_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_succ_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_h2o_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_nh4_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ac_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_glc__D_e 1.0 mmol_per_h 10 3 mole 3600 s

Rules [20]   assignment derived units sbo cvterm
EX_pi_e = dummy_EX_pi_e 10 3 mole 3600 s
EX_for_e = dummy_EX_for_e 10 3 mole 3600 s
EX_h_e = dummy_EX_h_e 10 3 mole 3600 s
EX_o2_e = dummy_EX_o2_e 10 3 mole 3600 s
EX_lac__D_e = dummy_EX_lac__D_e 10 3 mole 3600 s
EX_pyr_e = dummy_EX_pyr_e 10 3 mole 3600 s
EX_etoh_e = dummy_EX_etoh_e 10 3 mole 3600 s
EX_gln__L_e = dummy_EX_gln__L_e 10 3 mole 3600 s
EX_akg_e = dummy_EX_akg_e 10 3 mole 3600 s
EX_co2_e = dummy_EX_co2_e 10 3 mole 3600 s
EX_acald_e = dummy_EX_acald_e 10 3 mole 3600 s
EX_glu__L_e = dummy_EX_glu__L_e 10 3 mole 3600 s
EX_mal__L_e = dummy_EX_mal__L_e 10 3 mole 3600 s
EX_fum_e = dummy_EX_fum_e 10 3 mole 3600 s
EX_fru_e = dummy_EX_fru_e 10 3 mole 3600 s
EX_succ_e = dummy_EX_succ_e 10 3 mole 3600 s
EX_h2o_e = dummy_EX_h2o_e 10 3 mole 3600 s
EX_nh4_e = dummy_EX_nh4_e 10 3 mole 3600 s
EX_ac_e = dummy_EX_ac_e 10 3 mole 3600 s
EX_glc__D_e = dummy_EX_glc__D_e 10 3 mole 3600 s

Reactions [20] name equation modifiers formula derived units sbo cvterm
dummy_EX_pi_e ➞ dummy_S
dummy_EX_for_e ➞ dummy_S
dummy_EX_h_e ➞ dummy_S
dummy_EX_o2_e ➞ dummy_S
dummy_EX_lac__D_e ➞ dummy_S
dummy_EX_pyr_e ➞ dummy_S
dummy_EX_etoh_e ➞ dummy_S
dummy_EX_gln__L_e ➞ dummy_S
dummy_EX_akg_e ➞ dummy_S
dummy_EX_co2_e ➞ dummy_S
dummy_EX_acald_e ➞ dummy_S
dummy_EX_glu__L_e ➞ dummy_S
dummy_EX_mal__L_e ➞ dummy_S
dummy_EX_fum_e ➞ dummy_S
dummy_EX_fru_e ➞ dummy_S
dummy_EX_succ_e ➞ dummy_S
dummy_EX_h2o_e ➞ dummy_S
dummy_EX_nh4_e ➞ dummy_S
dummy_EX_ac_e ➞ dummy_S
dummy_EX_glc__D_e ➞ dummy_S