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.
Terms of use
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:
- Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
- 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.
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
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-11-11 19:47
Modified: 2017-11-11 19:47
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type | Ports [43] | name | referenced element | port ref | id ref | unit ref | metaid ref | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Port | bioreactor_port
|
port bioreactor | Compartment: bioreactor |
bioreactor | |||||
Port | for_e_port
|
port for_e | Species: for_e |
for_e | |||||
Port | fru_e_port
|
port fru_e | Species: fru_e |
fru_e | |||||
Port | h2o_e_port
|
port h2o_e | Species: h2o_e |
h2o_e | |||||
Port | akg_e_port
|
port akg_e | Species: akg_e |
akg_e | |||||
Port | pyr_e_port
|
port pyr_e | Species: pyr_e |
pyr_e | |||||
Port | glc__D_e_port
|
port glc__D_e | Species: glc__D_e |
glc__D_e | |||||
Port | fum_e_port
|
port fum_e | Species: fum_e |
fum_e | |||||
Port | X_port
|
port X | Species: X |
X | |||||
Port | pi_e_port
|
port pi_e | Species: pi_e |
pi_e | |||||
Port | lac__D_e_port
|
port lac__D_e | Species: lac__D_e |
lac__D_e | |||||
Port | gln__L_e_port
|
port gln__L_e | Species: gln__L_e |
gln__L_e | |||||
Port | acald_e_port
|
port acald_e | Species: acald_e |
acald_e | |||||
Port | etoh_e_port
|
port etoh_e | Species: etoh_e |
etoh_e | |||||
Port | ac_e_port
|
port ac_e | Species: ac_e |
ac_e | |||||
Port | succ_e_port
|
port succ_e | Species: succ_e |
succ_e | |||||
Port | o2_e_port
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port o2_e | Species: o2_e |
o2_e | |||||
Port | mal__L_e_port
|
port mal__L_e | Species: mal__L_e |
mal__L_e | |||||
Port | h_e_port
|
port h_e | Species: h_e |
h_e | |||||
Port | co2_e_port
|
port co2_e | Species: co2_e |
co2_e | |||||
Port | nh4_e_port
|
port nh4_e | Species: nh4_e |
nh4_e | |||||
Port | glu__L_e_port
|
port glu__L_e | Species: glu__L_e |
glu__L_e | |||||
Port | pEX_for_e_port
|
port pEX_for_e | Parameter: pEX_for_e |
pEX_for_e | |||||
Port | pEX_fru_e_port
|
port pEX_fru_e | Parameter: pEX_fru_e |
pEX_fru_e | |||||
Port | pEX_h2o_e_port
|
port pEX_h2o_e | Parameter: pEX_h2o_e |
pEX_h2o_e | |||||
Port | pEX_akg_e_port
|
port pEX_akg_e | Parameter: pEX_akg_e |
pEX_akg_e | |||||
Port | pEX_pyr_e_port
|
port pEX_pyr_e | Parameter: pEX_pyr_e |
pEX_pyr_e | |||||
Port | pEX_glc__D_e_port
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port pEX_glc__D_e | Parameter: pEX_glc__D_e |
pEX_glc__D_e | |||||
Port | pEX_fum_e_port
|
port pEX_fum_e | Parameter: pEX_fum_e |
pEX_fum_e | |||||
Port | pEX_X_port
|
port pEX_X | Parameter: pEX_X |
pEX_X | |||||
Port | pEX_pi_e_port
|
port pEX_pi_e | Parameter: pEX_pi_e |
pEX_pi_e | |||||
Port | pEX_lac__D_e_port
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port pEX_lac__D_e | Parameter: pEX_lac__D_e |
pEX_lac__D_e | |||||
Port | pEX_gln__L_e_port
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port pEX_gln__L_e | Parameter: pEX_gln__L_e |
pEX_gln__L_e | |||||
Port | pEX_acald_e_port
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port pEX_acald_e | Parameter: pEX_acald_e |
pEX_acald_e | |||||
Port | pEX_etoh_e_port
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port pEX_etoh_e | Parameter: pEX_etoh_e |
pEX_etoh_e | |||||
Port | pEX_ac_e_port
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port pEX_ac_e | Parameter: pEX_ac_e |
pEX_ac_e | |||||
Port | pEX_succ_e_port
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port pEX_succ_e | Parameter: pEX_succ_e |
pEX_succ_e | |||||
Port | pEX_o2_e_port
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port pEX_o2_e | Parameter: pEX_o2_e |
pEX_o2_e | |||||
Port | pEX_mal__L_e_port
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port pEX_mal__L_e | Parameter: pEX_mal__L_e |
pEX_mal__L_e | |||||
Port | pEX_h_e_port
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port pEX_h_e | Parameter: pEX_h_e |
pEX_h_e | |||||
Port | pEX_co2_e_port
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port pEX_co2_e | Parameter: pEX_co2_e |
pEX_co2_e | |||||
Port | pEX_nh4_e_port
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port pEX_nh4_e | Parameter: pEX_nh4_e |
pEX_nh4_e | |||||
Port | pEX_glu__L_e_port
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port pEX_glu__L_e | Parameter: pEX_glu__L_e |
pEX_glu__L_e |
type | UnitDefinitions [13] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | h
|
||||
UnitDefinition | g
|
||||
UnitDefinition | m
|
||||
UnitDefinition | m2
|
||||
UnitDefinition | l
|
||||
UnitDefinition | mmol
|
||||
UnitDefinition | per_h
|
||||
UnitDefinition | mmol_per_h
|
||||
UnitDefinition | mmol_per_hg
|
||||
UnitDefinition | mmol_per_l
|
||||
UnitDefinition | l_per_mmol
|
||||
UnitDefinition | g_per_l
|
||||
UnitDefinition | g_per_mmol
|
type | Compartments [1] | name | size | constant | spatial dimensions | units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor
|
bioreactor | 1.0 | T | 3 | l |
type | Species [22] | name | compartment | boundary condition | constant | initial amount | initial concentration | conversion factor | units | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Species | for_e
|
Formate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | fru_e
|
D-Fructose | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | h2o_e
|
H2O | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | akg_e
|
2-Oxoglutarate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | pyr_e
|
Pyruvate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | glc__D_e
|
D-Glucose | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | fum_e
|
Fumarate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | X
|
biomass | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | pi_e
|
Phosphate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | lac__D_e
|
D-Lactate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | gln__L_e
|
L-Glutamine | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | acald_e
|
Acetaldehyde | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | etoh_e
|
Ethanol | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | ac_e
|
Acetate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | succ_e
|
Succinate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | o2_e
|
O2 | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | mal__L_e
|
L-Malate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | h_e
|
H+ | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | co2_e
|
CO2 | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | nh4_e
|
Ammonium | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | glu__L_e
|
L-Glutamate | bioreactor | F | F | 1.0 | mmol | mmol | |||||
Species | X
|
biomass | c | F | F | 0.001 | cf_biomass=1.0 [g_per_mmol] | g | g |
type | Parameters [22] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | cf_biomass
|
biomass conversion factor | T | 1.0 | g_per_mmol | |||
Parameter | pEX_for_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_fru_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_h2o_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_akg_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_pyr_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_glc__D_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_fum_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_X
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_pi_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_lac__D_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_gln__L_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_acald_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_etoh_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_ac_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_succ_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_o2_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_mal__L_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_h_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_co2_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_nh4_e
|
T | 1.0 | mmol_per_h | ||||
Parameter | pEX_glu__L_e
|
T | 1.0 | mmol_per_h |
type | Reactions [21] | name | equation | modifiers | kinetic law | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | update_for_e
|
⇆ | for_e ⇆ | ||||||
Reaction | update_fru_e
|
⇆ | fru_e ⇆ | ||||||
Reaction | update_h2o_e
|
⇆ | h2o_e ⇆ | ||||||
Reaction | update_akg_e
|
⇆ | akg_e ⇆ | ||||||
Reaction | update_pyr_e
|
⇆ | pyr_e ⇆ | ||||||
Reaction | update_glc__D_e
|
⇆ | glc__D_e ⇆ | ||||||
Reaction | update_fum_e
|
⇆ | fum_e ⇆ | ||||||
Reaction | update_X
|
⇆ | X ⇆ | ||||||
Reaction | update_pi_e
|
⇆ | pi_e ⇆ | ||||||
Reaction | update_lac__D_e
|
⇆ | lac__D_e ⇆ | ||||||
Reaction | update_gln__L_e
|
⇆ | gln__L_e ⇆ | ||||||
Reaction | update_acald_e
|
⇆ | acald_e ⇆ | ||||||
Reaction | update_etoh_e
|
⇆ | etoh_e ⇆ | ||||||
Reaction | update_ac_e
|
⇆ | ac_e ⇆ | ||||||
Reaction | update_succ_e
|
⇆ | succ_e ⇆ | ||||||
Reaction | update_o2_e
|
⇆ | o2_e ⇆ | ||||||
Reaction | update_mal__L_e
|
⇆ | mal__L_e ⇆ | ||||||
Reaction | update_h_e
|
⇆ | h_e ⇆ | ||||||
Reaction | update_co2_e
|
⇆ | co2_e ⇆ | ||||||
Reaction | update_nh4_e
|
⇆ | nh4_e ⇆ | ||||||
Reaction | update_glu__L_e
|
⇆ | glu__L_e ⇆ |