E.coli core DFBA model
Model version: 4
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.
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_top
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-31 15:20
Modified: 2017-03-31 15:20
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type | UnitDefinitions [12] | 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_l | ||||
UnitDefinition | l_per_mmol | ||||
UnitDefinition | g_per_l | ||||
UnitDefinition | g_per_mmol |
type | Compartments [1] | name | size | constant | spatial dimensions | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor | 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 | pi_e | Phosphate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | for_e | Formate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | h_e | H+ |
bioreactor | F | F | 0.0 | mmol | ||||
Species | o2_e | O2 |
bioreactor | F | F | 0.21 | mmol | ||||
Species | lac__D_e | D-Lactate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | pyr_e | Pyruvate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | etoh_e | Ethanol |
bioreactor | F | F | 0.0 | mmol | ||||
Species | gln__L_e | L-Glutamine |
bioreactor | F | F | 0.0 | mmol | ||||
Species | akg_e | 2-Oxoglutarate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | co2_e | CO2 |
bioreactor | F | F | 0.04 | mmol | ||||
Species | acald_e | Acetaldehyde |
bioreactor | F | F | 0.0 | mmol | ||||
Species | glu__L_e | L-Glutamate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | mal__L_e | L-Malate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | fum_e | Fumarate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | fru_e | D-Fructose |
bioreactor | F | F | 0.0 | mmol | ||||
Species | succ_e | Succinate |
bioreactor | F | F | 1.0 | mmol | ||||
Species | h2o_e | H2O |
bioreactor | F | F | 0.0 | mmol | ||||
Species | nh4_e | Ammonium |
bioreactor | F | F | 0.0 | mmol | ||||
Species | ac_e | Acetate |
bioreactor | F | F | 0.0 | mmol | ||||
Species | glc__D_e | D-Glucose |
bioreactor | F | F | 20.0 | mmol | ||||
Species | dummy_S | dummy_S |
bioreactor | F | F | 0.0 | mmol |
type | Parameters [61] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt | 0.1 | h | T | ||||
Parameter | lb_EX_pi_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_pi_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_for_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_for_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_h_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_h_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_o2_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_o2_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_lac__D_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_lac__D_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_pyr_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_pyr_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_etoh_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_etoh_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_gln__L_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_gln__L_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_akg_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_akg_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_co2_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_co2_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_acald_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_acald_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_glu__L_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_glu__L_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_mal__L_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_mal__L_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_fum_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_fum_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_fru_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_fru_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_succ_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_succ_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_h2o_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_h2o_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_nh4_e | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_nh4_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_ac_e | 0.0 | mmol_per_h | F | ||||
Parameter | ub_EX_ac_e | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_glc__D_e | -10.0 | mmol_per_h | F | ||||
Parameter | ub_EX_glc__D_e | 1000.0 | mmol_per_h | F | ||||
Parameter | EX_pi_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_for_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_h_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_o2_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_lac__D_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_pyr_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_etoh_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_gln__L_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_akg_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_co2_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_acald_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_glu__L_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_mal__L_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_fum_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_fru_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_succ_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_h2o_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_nh4_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_ac_e | 1.0 | mmol_per_h | F | ||||
Parameter | EX_glc__D_e | 1.0 | mmol_per_h | F |
type | Rules [20] | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|
Rule | EX_pi_e | = | ||||
Rule | EX_for_e | = | ||||
Rule | EX_h_e | = | ||||
Rule | EX_o2_e | = | ||||
Rule | EX_lac__D_e | = | ||||
Rule | EX_pyr_e | = | ||||
Rule | EX_etoh_e | = | ||||
Rule | EX_gln__L_e | = | ||||
Rule | EX_akg_e | = | ||||
Rule | EX_co2_e | = | ||||
Rule | EX_acald_e | = | ||||
Rule | EX_glu__L_e | = | ||||
Rule | EX_mal__L_e | = | ||||
Rule | EX_fum_e | = | ||||
Rule | EX_fru_e | = | ||||
Rule | EX_succ_e | = | ||||
Rule | EX_h2o_e | = | ||||
Rule | EX_nh4_e | = | ||||
Rule | EX_ac_e | = | ||||
Rule | EX_glc__D_e | = |
type | Reactions [20] | name | equation | modifiers | formula | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | dummy_EX_pi_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_for_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_h_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_o2_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_lac__D_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_pyr_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_etoh_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_gln__L_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_akg_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_co2_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_acald_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_glu__L_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_mal__L_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_fum_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_fru_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_succ_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_h2o_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_nh4_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_ac_e | ➞ | ➞ dummy_S | ||||||
Reaction | dummy_EX_glc__D_e | ➞ | ➞ dummy_S |