E.coli core DFBA model
Model version: 7
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: 2017-06-12 17:02
Modified: 2017-06-12 17:02
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type | Ports [43] | name | port ref | id ref | unit ref | metaid ref | sbo | cvterm |
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FunctionDefinition | bioreactor_port
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bioreactor | ||||||
FunctionDefinition | mal__L_e_port
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mal__L_e | ||||||
FunctionDefinition | acald_e_port
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acald_e | ||||||
FunctionDefinition | pyr_e_port
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pyr_e | ||||||
FunctionDefinition | glc__D_e_port
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glc__D_e | ||||||
FunctionDefinition | etoh_e_port
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etoh_e | ||||||
FunctionDefinition | nh4_e_port
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nh4_e | ||||||
FunctionDefinition | h2o_e_port
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h2o_e | ||||||
FunctionDefinition | ac_e_port
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ac_e | ||||||
FunctionDefinition | akg_e_port
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akg_e | ||||||
FunctionDefinition | co2_e_port
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co2_e | ||||||
FunctionDefinition | lac__D_e_port
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lac__D_e | ||||||
FunctionDefinition | fum_e_port
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fum_e | ||||||
FunctionDefinition | fru_e_port
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fru_e | ||||||
FunctionDefinition | for_e_port
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for_e | ||||||
FunctionDefinition | gln__L_e_port
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gln__L_e | ||||||
FunctionDefinition | succ_e_port
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succ_e | ||||||
FunctionDefinition | h_e_port
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h_e | ||||||
FunctionDefinition | pi_e_port
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pi_e | ||||||
FunctionDefinition | X_port
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X | ||||||
FunctionDefinition | glu__L_e_port
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glu__L_e | ||||||
FunctionDefinition | o2_e_port
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o2_e | ||||||
FunctionDefinition | pEX_mal__L_e_port
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pEX_mal__L_e | ||||||
FunctionDefinition | pEX_acald_e_port
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pEX_acald_e | ||||||
FunctionDefinition | pEX_pyr_e_port
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pEX_pyr_e | ||||||
FunctionDefinition | pEX_glc__D_e_port
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pEX_glc__D_e | ||||||
FunctionDefinition | pEX_etoh_e_port
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pEX_etoh_e | ||||||
FunctionDefinition | pEX_nh4_e_port
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pEX_nh4_e | ||||||
FunctionDefinition | pEX_h2o_e_port
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pEX_h2o_e | ||||||
FunctionDefinition | pEX_ac_e_port
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pEX_ac_e | ||||||
FunctionDefinition | pEX_akg_e_port
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pEX_akg_e | ||||||
FunctionDefinition | pEX_co2_e_port
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pEX_co2_e | ||||||
FunctionDefinition | pEX_lac__D_e_port
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pEX_lac__D_e | ||||||
FunctionDefinition | pEX_fum_e_port
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pEX_fum_e | ||||||
FunctionDefinition | pEX_fru_e_port
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pEX_fru_e | ||||||
FunctionDefinition | pEX_for_e_port
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pEX_for_e | ||||||
FunctionDefinition | pEX_gln__L_e_port
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pEX_gln__L_e | ||||||
FunctionDefinition | pEX_succ_e_port
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pEX_succ_e | ||||||
FunctionDefinition | pEX_h_e_port
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pEX_h_e | ||||||
FunctionDefinition | pEX_pi_e_port
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pEX_pi_e | ||||||
FunctionDefinition | pEX_X_port
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pEX_X | ||||||
FunctionDefinition | pEX_glu__L_e_port
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pEX_glu__L_e | ||||||
FunctionDefinition | pEX_o2_e_port
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pEX_o2_e |
type | UnitDefinitions [13] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | h
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UnitDefinition | g
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UnitDefinition | m
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UnitDefinition | m2
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UnitDefinition | l
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UnitDefinition | mmol
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UnitDefinition | per_h
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UnitDefinition | mmol_per_h
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UnitDefinition | mmol_per_hg
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UnitDefinition | mmol_per_l
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UnitDefinition | l_per_mmol
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UnitDefinition | g_per_l
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UnitDefinition | g_per_mmol
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type | Compartments [1] | name | size | constant | spatial dimensions | units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor
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bioreactor | 1.0 | T | 3 | l |
type | Species [21] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | mal__L_e
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L-Malate | bioreactor | F | F | 1.0 | mmol | ||||
Species | acald_e
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Acetaldehyde | bioreactor | F | F | 1.0 | mmol | ||||
Species | pyr_e
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Pyruvate | bioreactor | F | F | 1.0 | mmol | ||||
Species | glc__D_e
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D-Glucose | bioreactor | F | F | 1.0 | mmol | ||||
Species | etoh_e
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Ethanol | bioreactor | F | F | 1.0 | mmol | ||||
Species | nh4_e
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Ammonium | bioreactor | F | F | 1.0 | mmol | ||||
Species | h2o_e
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H2O | bioreactor | F | F | 1.0 | mmol | ||||
Species | ac_e
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Acetate | bioreactor | F | F | 1.0 | mmol | ||||
Species | akg_e
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2-Oxoglutarate | bioreactor | F | F | 1.0 | mmol | ||||
Species | co2_e
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CO2 | bioreactor | F | F | 1.0 | mmol | ||||
Species | lac__D_e
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D-Lactate | bioreactor | F | F | 1.0 | mmol | ||||
Species | fum_e
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Fumarate | bioreactor | F | F | 1.0 | mmol | ||||
Species | fru_e
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D-Fructose | bioreactor | F | F | 1.0 | mmol | ||||
Species | for_e
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Formate | bioreactor | F | F | 1.0 | mmol | ||||
Species | gln__L_e
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L-Glutamine | bioreactor | F | F | 1.0 | mmol | ||||
Species | succ_e
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Succinate | bioreactor | F | F | 1.0 | mmol | ||||
Species | h_e
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H+ | bioreactor | F | F | 1.0 | mmol | ||||
Species | pi_e
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Phosphate | bioreactor | F | F | 1.0 | mmol | ||||
Species | X
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biomass | bioreactor | F | F | 1.0 | mmol | ||||
Species | glu__L_e
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L-Glutamate | bioreactor | F | F | 1.0 | mmol | ||||
Species | o2_e
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O2 | bioreactor | F | F | 1.0 | mmol |
type | Parameters [21] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | pEX_mal__L_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_acald_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_pyr_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_glc__D_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_etoh_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_nh4_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_h2o_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_ac_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_akg_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_co2_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_lac__D_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_fum_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_fru_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_for_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_gln__L_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_succ_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_h_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_pi_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_X
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_glu__L_e
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T | 1.0 | mmol_per_h | ||||
Parameter | pEX_o2_e
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T | 1.0 | mmol_per_h |
type | Reactions [21] | id | name | equation | modifiers | kinetic law | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|---|
Reaction | update_mal__L_e
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⇆ | mal__L_e ⇆ | |||||||
Reaction | update_acald_e
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⇆ | acald_e ⇆ | |||||||
Reaction | update_pyr_e
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⇆ | pyr_e ⇆ | |||||||
Reaction | update_glc__D_e
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⇆ | glc__D_e ⇆ | |||||||
Reaction | update_etoh_e
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⇆ | etoh_e ⇆ | |||||||
Reaction | update_nh4_e
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⇆ | nh4_e ⇆ | |||||||
Reaction | update_h2o_e
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⇆ | h2o_e ⇆ | |||||||
Reaction | update_ac_e
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⇆ | ac_e ⇆ | |||||||
Reaction | update_akg_e
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⇆ | akg_e ⇆ | |||||||
Reaction | update_co2_e
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⇆ | co2_e ⇆ | |||||||
Reaction | update_lac__D_e
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⇆ | lac__D_e ⇆ | |||||||
Reaction | update_fum_e
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⇆ | fum_e ⇆ | |||||||
Reaction | update_fru_e
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⇆ | fru_e ⇆ | |||||||
Reaction | update_for_e
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⇆ | for_e ⇆ | |||||||
Reaction | update_gln__L_e
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⇆ | gln__L_e ⇆ | |||||||
Reaction | update_succ_e
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⇆ | succ_e ⇆ | |||||||
Reaction | update_h_e
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⇆ | h_e ⇆ | |||||||
Reaction | update_pi_e
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⇆ | pi_e ⇆ | |||||||
Reaction | update_X
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⇆ | X ⇆ | |||||||
Reaction | update_glu__L_e
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⇆ | glu__L_e ⇆ | |||||||
Reaction | update_o2_e
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⇆ | o2_e ⇆ |