E.coli core DFBA model
Model version: 7
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: 2017-06-12 17:02
Modified: 2017-06-12 17:02
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type | Submodels [3] | name | model ref | deletions | time conversion | extent conversion | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Submodel | fba
|
ecoli_fba | ||||||
Submodel | bounds
|
ecoli_bounds | ||||||
Submodel | update
|
ecoli_update |
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 [22] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | mal__L_e
|
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
|
Pyruvate | bioreactor | F | F | 1.0 | mmol | ||||
Species | glc__D_e
|
D-Glucose | bioreactor | F | F | 20.0 | mmol | ||||
Species | etoh_e
|
Ethanol | bioreactor | F | F | 1.0 | mmol | ||||
Species | nh4_e
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Ammonium | bioreactor | F | F | 1.0 | mmol | ||||
Species | h2o_e
|
H2O | bioreactor | F | F | 20.0 | mmol | ||||
Species | ac_e
|
Acetate | bioreactor | F | F | 1.0 | mmol | ||||
Species | akg_e
|
2-Oxoglutarate | bioreactor | F | F | 1.0 | mmol | ||||
Species | co2_e
|
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
|
Formate | bioreactor | F | F | 1.0 | mmol | ||||
Species | gln__L_e
|
L-Glutamine | bioreactor | F | F | 10.0 | mmol | ||||
Species | succ_e
|
Succinate | bioreactor | F | F | 1.0 | mmol | ||||
Species | h_e
|
H+ | bioreactor | F | F | 1.0 | mmol | ||||
Species | pi_e
|
Phosphate | bioreactor | F | F | 1.0 | mmol | ||||
Species | X
|
biomass | bioreactor | F | F | 0.001 | 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 | ||||
Species | dummy_S
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dummy_S | bioreactor | F | F | 0.0 | mmol |
type | Parameters [64] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt
|
T | 0.1 | h | ||||
Parameter | lb_EX_mal__L_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_mal__L_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_acald_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_acald_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_pyr_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_pyr_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_glc__D_e
|
F | -10.0 | mmol_per_h | ||||
Parameter | ub_EX_glc__D_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_etoh_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_etoh_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_nh4_e
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F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_nh4_e
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F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_h2o_e
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F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_h2o_e
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F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_ac_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_ac_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_akg_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_akg_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_co2_e
|
F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_co2_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_lac__D_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_lac__D_e
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F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_fum_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_fum_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_fru_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_fru_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_for_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_for_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_gln__L_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_gln__L_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_succ_e
|
F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_succ_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_h_e
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F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_h_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_pi_e
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F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_pi_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_X
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_X
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F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_glu__L_e
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F | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_glu__L_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_o2_e
|
F | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_o2_e
|
F | 1000.0 | mmol_per_h | ||||
Parameter | pEX_mal__L_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_acald_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_pyr_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_glc__D_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_etoh_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_nh4_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_h2o_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_ac_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_akg_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_co2_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_lac__D_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_fum_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_fru_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_for_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_gln__L_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_succ_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_h_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_pi_e
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_X
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F | 1.0 | mmol_per_h | ||||
Parameter | pEX_glu__L_e
|
F | 1.0 | mmol_per_h | ||||
Parameter | pEX_o2_e
|
F | 1.0 | mmol_per_h |
type | Rules [21] | assignment | name | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|
Rule | pEX_mal__L_e
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= | |||||
Rule | pEX_acald_e
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= | |||||
Rule | pEX_pyr_e
|
= | |||||
Rule | pEX_glc__D_e
|
= | |||||
Rule | pEX_etoh_e
|
= | |||||
Rule | pEX_nh4_e
|
= | |||||
Rule | pEX_h2o_e
|
= | |||||
Rule | pEX_ac_e
|
= | |||||
Rule | pEX_akg_e
|
= | |||||
Rule | pEX_co2_e
|
= | |||||
Rule | pEX_lac__D_e
|
= | |||||
Rule | pEX_fum_e
|
= | |||||
Rule | pEX_fru_e
|
= | |||||
Rule | pEX_for_e
|
= | |||||
Rule | pEX_gln__L_e
|
= | |||||
Rule | pEX_succ_e
|
= | |||||
Rule | pEX_h_e
|
= | |||||
Rule | pEX_pi_e
|
= | |||||
Rule | pEX_X
|
= | |||||
Rule | pEX_glu__L_e
|
= | |||||
Rule | pEX_o2_e
|
= |
type | Reactions [21] | id | name | equation | modifiers | kinetic law | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|---|
Reaction | fba:portRef=EX_mal__L_e_port |
EX_mal__L_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_acald_e_port |
EX_acald_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_pyr_e_port |
EX_pyr_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_glc__D_e_port |
EX_glc__D_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_etoh_e_port |
EX_etoh_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_nh4_e_port |
EX_nh4_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_h2o_e_port |
EX_h2o_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_ac_e_port |
EX_ac_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_akg_e_port |
EX_akg_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_co2_e_port |
EX_co2_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_lac__D_e_port |
EX_lac__D_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_fum_e_port |
EX_fum_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_fru_e_port |
EX_fru_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_for_e_port |
EX_for_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_gln__L_e_port |
EX_gln__L_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_succ_e_port |
EX_succ_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_h_e_port |
EX_h_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_pi_e_port |
EX_pi_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_X_port |
EX_X
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_glu__L_e_port |
EX_glu__L_e
|
➞ | ➞ dummy_S | ||||||
Reaction | fba:portRef=EX_o2_e_port |
EX_o2_e
|
➞ | ➞ dummy_S |