e_coli_core - [organism]
E.coli core DFBA model
Model version: 7
DFBA FBA submodel.
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_fba
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type | Ports [63] | name | port ref | id ref | unit ref | metaid ref | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
FunctionDefinition | EX_mal__L_e_port
|
EX_mal__L_e | ||||||
FunctionDefinition | lb_EX_mal__L_e_port
|
lb_EX_mal__L_e | ||||||
FunctionDefinition | ub_EX_mal__L_e_port
|
ub_EX_mal__L_e | ||||||
FunctionDefinition | EX_acald_e_port
|
EX_acald_e | ||||||
FunctionDefinition | lb_EX_acald_e_port
|
lb_EX_acald_e | ||||||
FunctionDefinition | ub_EX_acald_e_port
|
ub_EX_acald_e | ||||||
FunctionDefinition | EX_pyr_e_port
|
EX_pyr_e | ||||||
FunctionDefinition | lb_EX_pyr_e_port
|
lb_EX_pyr_e | ||||||
FunctionDefinition | ub_EX_pyr_e_port
|
ub_EX_pyr_e | ||||||
FunctionDefinition | EX_glc__D_e_port
|
EX_glc__D_e | ||||||
FunctionDefinition | lb_EX_glc__D_e_port
|
lb_EX_glc__D_e | ||||||
FunctionDefinition | ub_EX_glc__D_e_port
|
ub_EX_glc__D_e | ||||||
FunctionDefinition | EX_etoh_e_port
|
EX_etoh_e | ||||||
FunctionDefinition | lb_EX_etoh_e_port
|
lb_EX_etoh_e | ||||||
FunctionDefinition | ub_EX_etoh_e_port
|
ub_EX_etoh_e | ||||||
FunctionDefinition | EX_nh4_e_port
|
EX_nh4_e | ||||||
FunctionDefinition | lb_EX_nh4_e_port
|
lb_EX_nh4_e | ||||||
FunctionDefinition | ub_EX_nh4_e_port
|
ub_EX_nh4_e | ||||||
FunctionDefinition | EX_h2o_e_port
|
EX_h2o_e | ||||||
FunctionDefinition | lb_EX_h2o_e_port
|
lb_EX_h2o_e | ||||||
FunctionDefinition | ub_EX_h2o_e_port
|
ub_EX_h2o_e | ||||||
FunctionDefinition | EX_ac_e_port
|
EX_ac_e | ||||||
FunctionDefinition | lb_EX_ac_e_port
|
lb_EX_ac_e | ||||||
FunctionDefinition | ub_EX_ac_e_port
|
ub_EX_ac_e | ||||||
FunctionDefinition | EX_akg_e_port
|
EX_akg_e | ||||||
FunctionDefinition | lb_EX_akg_e_port
|
lb_EX_akg_e | ||||||
FunctionDefinition | ub_EX_akg_e_port
|
ub_EX_akg_e | ||||||
FunctionDefinition | EX_co2_e_port
|
EX_co2_e | ||||||
FunctionDefinition | lb_EX_co2_e_port
|
lb_EX_co2_e | ||||||
FunctionDefinition | ub_EX_co2_e_port
|
ub_EX_co2_e | ||||||
FunctionDefinition | EX_lac__D_e_port
|
EX_lac__D_e | ||||||
FunctionDefinition | lb_EX_lac__D_e_port
|
lb_EX_lac__D_e | ||||||
FunctionDefinition | ub_EX_lac__D_e_port
|
ub_EX_lac__D_e | ||||||
FunctionDefinition | EX_fum_e_port
|
EX_fum_e | ||||||
FunctionDefinition | lb_EX_fum_e_port
|
lb_EX_fum_e | ||||||
FunctionDefinition | ub_EX_fum_e_port
|
ub_EX_fum_e | ||||||
FunctionDefinition | EX_fru_e_port
|
EX_fru_e | ||||||
FunctionDefinition | lb_EX_fru_e_port
|
lb_EX_fru_e | ||||||
FunctionDefinition | ub_EX_fru_e_port
|
ub_EX_fru_e | ||||||
FunctionDefinition | EX_for_e_port
|
EX_for_e | ||||||
FunctionDefinition | lb_EX_for_e_port
|
lb_EX_for_e | ||||||
FunctionDefinition | ub_EX_for_e_port
|
ub_EX_for_e | ||||||
FunctionDefinition | EX_gln__L_e_port
|
EX_gln__L_e | ||||||
FunctionDefinition | lb_EX_gln__L_e_port
|
lb_EX_gln__L_e | ||||||
FunctionDefinition | ub_EX_gln__L_e_port
|
ub_EX_gln__L_e | ||||||
FunctionDefinition | EX_succ_e_port
|
EX_succ_e | ||||||
FunctionDefinition | lb_EX_succ_e_port
|
lb_EX_succ_e | ||||||
FunctionDefinition | ub_EX_succ_e_port
|
ub_EX_succ_e | ||||||
FunctionDefinition | EX_h_e_port
|
EX_h_e | ||||||
FunctionDefinition | lb_EX_h_e_port
|
lb_EX_h_e | ||||||
FunctionDefinition | ub_EX_h_e_port
|
ub_EX_h_e | ||||||
FunctionDefinition | EX_pi_e_port
|
EX_pi_e | ||||||
FunctionDefinition | lb_EX_pi_e_port
|
lb_EX_pi_e | ||||||
FunctionDefinition | ub_EX_pi_e_port
|
ub_EX_pi_e | ||||||
FunctionDefinition | EX_glu__L_e_port
|
EX_glu__L_e | ||||||
FunctionDefinition | lb_EX_glu__L_e_port
|
lb_EX_glu__L_e | ||||||
FunctionDefinition | ub_EX_glu__L_e_port
|
ub_EX_glu__L_e | ||||||
FunctionDefinition | EX_o2_e_port
|
EX_o2_e | ||||||
FunctionDefinition | lb_EX_o2_e_port
|
lb_EX_o2_e | ||||||
FunctionDefinition | ub_EX_o2_e_port
|
ub_EX_o2_e | ||||||
FunctionDefinition | EX_X_port
|
EX_X | ||||||
FunctionDefinition | lb_EX_X_port
|
lb_EX_X | ||||||
FunctionDefinition | ub_EX_X_port
|
ub_EX_X |
type | UnitDefinitions [14] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | mmol_per_gDW_per_hr
|
||||
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 [2] | name | size | constant | spatial dimensions | units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | c _4b1e4f0f-bcca-42b1-b7d0-484ec9bbf3b6
|
cytosol | T | l | |||||
Compartment | e cb207f38-8131-42d4-a528-217b1863e93a
|
extracellular space | T | l |
type | GeneProducts [137] | name | label | associated species | sbo | cvterm |
---|---|---|---|---|---|---|
GeneProduct | b0351 G_b0351
|
mhpF | b0351 | |||
GeneProduct | b1241 G_b1241
|
adhE | b1241 | |||
GeneProduct | s0001
|
s0001 | ||||
GeneProduct | b3115 G_b3115
|
tdcD | b3115 | |||
GeneProduct | b1849 G_b1849
|
purT | b1849 | |||
GeneProduct | b2296 G_b2296
|
ackA | b2296 | |||
GeneProduct | b0118 G_b0118
|
acnB | b0118 | |||
GeneProduct | b1276 G_b1276
|
acnA | b1276 | |||
GeneProduct | b0474 G_b0474
|
adk | b0474 | |||
GeneProduct | b0116 G_b0116
|
lpd | b0116 | |||
GeneProduct | b0727 G_b0727
|
sucB | b0727 | |||
GeneProduct | b0726 G_b0726
|
sucA | b0726 | |||
GeneProduct | b2587 G_b2587
|
kgtP | b2587 | |||
GeneProduct | b0356 G_b0356
|
frmA | b0356 | |||
GeneProduct | b1478 G_b1478
|
adhP | b1478 | |||
GeneProduct | b3733 G_b3733
|
atpG | b3733 | |||
GeneProduct | b3739 G_b3739
|
atpI | b3739 | |||
GeneProduct | b3735 G_b3735
|
atpH | b3735 | |||
GeneProduct | b3734 G_b3734
|
atpA | b3734 | |||
GeneProduct | b3738 G_b3738
|
atpB | b3738 | |||
GeneProduct | b3736 G_b3736
|
atpF | b3736 | |||
GeneProduct | b3732 G_b3732
|
atpD | b3732 | |||
GeneProduct | b3737 G_b3737
|
atpE | b3737 | |||
GeneProduct | b3731 G_b3731
|
atpC | b3731 | |||
GeneProduct | b0720 G_b0720
|
gltA | b0720 | |||
GeneProduct | b0734 G_b0734
|
cydB | b0734 | |||
GeneProduct | b0978 G_b0978
|
cbdA | b0978 | |||
GeneProduct | b0733 G_b0733
|
cydA | b0733 | |||
GeneProduct | b0979 G_b0979
|
cbdB | b0979 | |||
GeneProduct | b2975 G_b2975
|
glcA | b2975 | |||
GeneProduct | b3603 G_b3603
|
lldP | b3603 | |||
GeneProduct | b2779 G_b2779
|
eno | b2779 | |||
GeneProduct | b2097 G_b2097
|
fbaB | b2097 | |||
GeneProduct | b2925 G_b2925
|
fbaA | b2925 | |||
GeneProduct | b1773 G_b1773
|
ydjI | b1773 | |||
GeneProduct | b3925 G_b3925
|
glpX | b3925 | |||
GeneProduct | b4232 G_b4232
|
fbp | b4232 | |||
GeneProduct | b2492 G_b2492
|
focB | b2492 | |||
GeneProduct | b0904 G_b0904
|
focA | b0904 | |||
GeneProduct | b4151 G_b4151
|
frdD | b4151 | |||
GeneProduct | b4152 G_b4152
|
frdC | b4152 | |||
GeneProduct | b4154 G_b4154
|
frdA | b4154 | |||
GeneProduct | b4153 G_b4153
|
frdB | b4153 | |||
GeneProduct | b2416 G_b2416
|
ptsI | b2416 | |||
GeneProduct | b1818 G_b1818
|
manY | b1818 | |||
GeneProduct | b1817 G_b1817
|
manX | b1817 | |||
GeneProduct | b1819 G_b1819
|
manZ | b1819 | |||
GeneProduct | b2415 G_b2415
|
ptsH | b2415 | |||
GeneProduct | b1611 G_b1611
|
fumC | b1611 | |||
GeneProduct | b4122 G_b4122
|
fumB | b4122 | |||
GeneProduct | b1612 G_b1612
|
fumA | b1612 | |||
GeneProduct | b3528 G_b3528
|
dctA | b3528 | |||
GeneProduct | b1852 G_b1852
|
zwf | b1852 | |||
GeneProduct | b1779 G_b1779
|
gapA | b1779 | |||
GeneProduct | b1621 G_b1621
|
malX | b1621 | |||
GeneProduct | b2417 G_b2417
|
crr | b2417 | |||
GeneProduct | b1101 G_b1101
|
ptsG | b1101 | |||
GeneProduct | b1297 G_b1297
|
puuA | b1297 | |||
GeneProduct | b3870 G_b3870
|
glnA | b3870 | |||
GeneProduct | b0810 G_b0810
|
glnP | b0810 | |||
GeneProduct | b0811 G_b0811
|
glnH | b0811 | |||
GeneProduct | b0809 G_b0809
|
glnQ | b0809 | |||
GeneProduct | b1761 G_b1761
|
gdhA | b1761 | |||
GeneProduct | b0485 G_b0485
|
glsA | b0485 | |||
GeneProduct | b1812 G_b1812
|
pabB | b1812 | |||
GeneProduct | b1524 G_b1524
|
glsB | b1524 | |||
GeneProduct | b3213 G_b3213
|
gltD | b3213 | |||
GeneProduct | b3212 G_b3212
|
gltB | b3212 | |||
GeneProduct | b4077 G_b4077
|
gltP | b4077 | |||
GeneProduct | b2029 G_b2029
|
gnd | b2029 | |||
GeneProduct | b0875 G_b0875
|
aqpZ | b0875 | |||
GeneProduct | b1136 G_b1136
|
icd | b1136 | |||
GeneProduct | b4015 G_b4015
|
aceA | b4015 | |||
GeneProduct | b2133 G_b2133
|
dld | b2133 | |||
GeneProduct | b1380 G_b1380
|
ldhA | b1380 | |||
GeneProduct | b4014 G_b4014
|
aceB | b4014 | |||
GeneProduct | b2976 G_b2976
|
glcB | b2976 | |||
GeneProduct | b3236 G_b3236
|
mdh | b3236 | |||
GeneProduct | b1479 G_b1479
|
maeA | b1479 | |||
GeneProduct | b2463 G_b2463
|
maeB | b2463 | |||
GeneProduct | b2280 G_b2280
|
nuoJ | b2280 | |||
GeneProduct | b2278 G_b2278
|
nuoL | b2278 | |||
GeneProduct | b2281 G_b2281
|
nuoI | b2281 | |||
GeneProduct | b2288 G_b2288
|
nuoA | b2288 | |||
GeneProduct | b2282 G_b2282
|
nuoH | b2282 | |||
GeneProduct | b2286 G_b2286
|
nuoC | b2286 | |||
GeneProduct | b2283 G_b2283
|
nuoG | b2283 | |||
GeneProduct | b2277 G_b2277
|
nuoM | b2277 | |||
GeneProduct | b2287 G_b2287
|
nuoB | b2287 | |||
GeneProduct | b2284 G_b2284
|
nuoF | b2284 | |||
GeneProduct | b2279 G_b2279
|
nuoK | b2279 | |||
GeneProduct | b2276 G_b2276
|
nuoN | b2276 | |||
GeneProduct | b2285 G_b2285
|
nuoE | b2285 | |||
GeneProduct | b3962 G_b3962
|
sthA | b3962 | |||
GeneProduct | b1602 G_b1602
|
pntB | b1602 | |||
GeneProduct | b1603 G_b1603
|
pntA | b1603 | |||
GeneProduct | b0451 G_b0451
|
amtB | b0451 | |||
GeneProduct | b0115 G_b0115
|
aceF | b0115 | |||
GeneProduct | b0114 G_b0114
|
aceE | b0114 | |||
GeneProduct | b3916 G_b3916
|
pfkA | b3916 | |||
GeneProduct | b1723 G_b1723
|
pfkB | b1723 | |||
GeneProduct | b0903 G_b0903
|
pflB | b0903 | |||
GeneProduct | b3952 G_b3952
|
pflC | b3952 | |||
GeneProduct | b3114 G_b3114
|
tdcE | b3114 | |||
GeneProduct | b0902 G_b0902
|
pflA | b0902 | |||
GeneProduct | b2579 G_b2579
|
grcA | b2579 | |||
GeneProduct | b3951 G_b3951
|
pflD | b3951 | |||
GeneProduct | b4025 G_b4025
|
pgi | b4025 | |||
GeneProduct | b2926 G_b2926
|
pgk | b2926 | |||
GeneProduct | b0767 G_b0767
|
pgl | b0767 | |||
GeneProduct | b0755 G_b0755
|
gpmA | b0755 | |||
GeneProduct | b3612 G_b3612
|
gpmM | b3612 | |||
GeneProduct | b4395 G_b4395
|
ytjC | b4395 | |||
GeneProduct | b2987 G_b2987
|
pitB | b2987 | |||
GeneProduct | b3493 G_b3493
|
pitA | b3493 | |||
GeneProduct | b3956 G_b3956
|
ppc | b3956 | |||
GeneProduct | b3403 G_b3403
|
pck | b3403 | |||
GeneProduct | b1702 G_b1702
|
ppsA | b1702 | |||
GeneProduct | b2297 G_b2297
|
pta | b2297 | |||
GeneProduct | b2458 G_b2458
|
eutD | b2458 | |||
GeneProduct | b1676 G_b1676
|
pykF | b1676 | |||
GeneProduct | b1854 G_b1854
|
pykA | b1854 | |||
GeneProduct | b4301 G_b4301
|
sgcE | b4301 | |||
GeneProduct | b3386 G_b3386
|
rpe | b3386 | |||
GeneProduct | b2914 G_b2914
|
rpiA | b2914 | |||
GeneProduct | b4090 G_b4090
|
rpiB | b4090 | |||
GeneProduct | b0723 G_b0723
|
sdhA | b0723 | |||
GeneProduct | b0724 G_b0724
|
sdhB | b0724 | |||
GeneProduct | b0722 G_b0722
|
sdhD | b0722 | |||
GeneProduct | b0721 G_b0721
|
sdhC | b0721 | |||
GeneProduct | b0728 G_b0728
|
sucC | b0728 | |||
GeneProduct | b0729 G_b0729
|
sucD | b0729 | |||
GeneProduct | b2464 G_b2464
|
talA | b2464 | |||
GeneProduct | b0008 G_b0008
|
talB | b0008 | |||
GeneProduct | b2465 G_b2465
|
tktB | b2465 | |||
GeneProduct | b2935 G_b2935
|
tktA | b2935 | |||
GeneProduct | b3919 G_b3919
|
tpiA | b3919 |
type | Parameters [47] | name | constant | value | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | cobra_default_lb
|
cobra default - lb | T | -1000.0 | mmol_per_gDW_per_hr | |||
Parameter | cobra_default_ub
|
cobra default - ub | T | 1000.0 | mmol_per_gDW_per_hr | |||
Parameter | cobra_0_bound
|
cobra 0 - bound | T | 0.0 | mmol_per_gDW_per_hr | |||
Parameter | R_ATPM_lower_bound
|
R ATPM lower - bound | T | 0.0 | mmol_per_gDW_per_hr | |||
Parameter | R_EX_glc__D_e_lower_bound
|
R EX glc-D e lower - bound | T | -10.0 | mmol_per_gDW_per_hr | |||
Parameter | lb_EX_mal__L_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_mal__L_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_acald_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_acald_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_pyr_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_pyr_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_glc__D_e
|
T | -10.0 | mmol_per_h | ||||
Parameter | ub_EX_glc__D_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_etoh_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_etoh_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_nh4_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_nh4_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_h2o_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_h2o_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_ac_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_ac_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_akg_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_akg_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_co2_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_co2_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_lac__D_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_lac__D_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_fum_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_fum_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_fru_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_fru_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_for_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_for_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_gln__L_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_gln__L_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_succ_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_succ_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_h_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_h_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_pi_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_pi_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_glu__L_e
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_glu__L_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_o2_e
|
T | -1000.0 | mmol_per_h | ||||
Parameter | ub_EX_o2_e
|
T | 1000.0 | mmol_per_h | ||||
Parameter | lb_EX_X
|
T | 0.0 | mmol_per_h | ||||
Parameter | ub_EX_X
|
T | 1000.0 | mmol_per_h |
type | Reactions [96] | id | name | equation | modifiers | kinetic law | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|---|
Reaction | ACALD R_ACALD
|
Acetaldehyde dehydrogenase (acetylating)[-1000.0 1000.0] (b0351 or b1241) |
⇆ | acald_c + coa_c + nad_c ⇆ accoa_c + h_c + nadh_c | ||||||
Reaction | ACALDt R_ACALDt
|
Acetaldehyde reversible transport[-1000.0 1000.0] s0001 |
⇆ | acald_e ⇆ acald_c | ||||||
Reaction | ACKr R_ACKr
|
Acetate kinase[-1000.0 1000.0] (b2296 or b3115 or b1849) |
⇆ | ac_c + atp_c ⇆ actp_c + adp_c | ||||||
Reaction | ACONTa R_ACONTa
|
Aconitase (half-reaction A, Citrate hydro-lyase)[-1000.0 1000.0] (b0118 or b1276) |
⇆ | cit_c ⇆ acon_C_c + h2o_c | ||||||
Reaction | ACONTb R_ACONTb
|
Aconitase (half-reaction B, Isocitrate hydro-lyase)[-1000.0 1000.0] (b0118 or b1276) |
⇆ | acon_C_c + h2o_c ⇆ icit_c | ||||||
Reaction | ACt2r R_ACt2r
|
Acetate reversible transport via proton symport[-1000.0 1000.0] |
⇆ | ac_e + h_e ⇆ ac_c + h_c | ||||||
Reaction | ADK1 R_ADK1
|
Adenylate kinase[-1000.0 1000.0] b0474 |
⇆ | amp_c + atp_c ⇆ 2.0 adp_c | ||||||
Reaction | AKGDH R_AKGDH
|
2-Oxogluterate dehydrogenase[0.0 1000.0] (b0726 and b0116 and b0727) |
➞ | akg_c + coa_c + nad_c ➞ co2_c + nadh_c + succoa_c | ||||||
Reaction | AKGt2r R_AKGt2r
|
2 oxoglutarate reversible transport via symport[-1000.0 1000.0] b2587 |
⇆ | akg_e + h_e ⇆ akg_c + h_c | ||||||
Reaction | ALCD2x R_ALCD2x
|
Alcohol dehydrogenase (ethanol)[-1000.0 1000.0] (b1478 or b0356 or b1241) |
⇆ | etoh_c + nad_c ⇆ acald_c + h_c + nadh_c | ||||||
Reaction | ATPM R_ATPM
|
ATP maintenance requirement[0.0 1000.0] |
➞ | atp_c + h2o_c ➞ adp_c + h_c + pi_c | ||||||
Reaction | ATPS4r R_ATPS4r
|
ATP synthase (four protons for one ATP)[-1000.0 1000.0] ((b3738 and b3736 and b3737 and b3735 and b3733 and b3731 and b3732 and b3734) or (b3734 and b3732 and b3731 and b3733 and b3735 and b3737 and b3736 and b3738 and b3739)) |
⇆ | adp_c + 4.0 h_e + pi_c ⇆ atp_c + h2o_c + 3.0 h_c | ||||||
Reaction | BIOMASS_Ecoli_core_w_GAM R_BIOMASS_Ecoli_core_w_GAM
|
Biomass Objective Function with GAM[0.0 1000.0] |
➞ | 1.496 M_3pg_c + 3.7478 accoa_c + 59.81 atp_c + 0.361 e4p_c + 0.0709 f6p_c + 0.129 g3p_c + 0.205 g6p_c + 0.2557 gln__L_c + 4.9414 glu__L_c + 59.81 h2o_c + 3.547 nad_c + 13.0279 nadph_c + 1.7867 oaa_c + 0.5191 pep_c + 2.8328 pyr_c + 0.8977 r5p_c ➞ 59.81 adp_c + 4.1182 akg_c + 3.7478 coa_c + 59.81 h_c + 3.547 nadh_c + 13.0279 nadp_c + 59.81 pi_c + X | ||||||
Reaction | CO2t R_CO2t
|
CO2 transporter via diffusion[-1000.0 1000.0] s0001 |
⇆ | co2_e ⇆ co2_c | ||||||
Reaction | CS R_CS
|
Citrate synthase[0.0 1000.0] b0720 |
➞ | accoa_c + h2o_c + oaa_c ➞ cit_c + coa_c + h_c | ||||||
Reaction | CYTBD R_CYTBD
|
Cytochrome oxidase bd (ubiquinol-8: 2 protons)[0.0 1000.0] ((b0978 and b0979) or (b0733 and b0734)) |
➞ | 2.0 h_c + 0.5 o2_c + q8h2_c ➞ h2o_c + 2.0 h_e + q8_c | ||||||
Reaction | D_LACt2 R_D_LACt2
|
D lactate transport via proton symport[-1000.0 1000.0] (b2975 or b3603) |
⇆ | h_e + lac__D_e ⇆ h_c + lac__D_c | ||||||
Reaction | ENO R_ENO
|
Enolase[-1000.0 1000.0] b2779 |
⇆ | M_2pg_c ⇆ h2o_c + pep_c | ||||||
Reaction | ETOHt2r R_ETOHt2r
|
ETOHt2r[-1000.0 1000.0] |
⇆ | etoh_e + h_e ⇆ etoh_c + h_c | ||||||
Reaction | EX_ac_e R_EX_ac_e
|
Acetate exchange[0.0 1000.0] |
⇆ | ac_e ⇆ | ||||||
Reaction | EX_acald_e R_EX_acald_e
|
Acetaldehyde exchange[0.0 1000.0] |
⇆ | acald_e ⇆ | ||||||
Reaction | EX_akg_e R_EX_akg_e
|
2-Oxoglutarate exchange[0.0 1000.0] |
⇆ | akg_e ⇆ | ||||||
Reaction | EX_co2_e R_EX_co2_e
|
CO2 exchange[-1000.0 1000.0] |
⇆ | co2_e ⇆ | ||||||
Reaction | EX_etoh_e R_EX_etoh_e
|
Ethanol exchange[0.0 1000.0] |
⇆ | etoh_e ⇆ | ||||||
Reaction | EX_for_e R_EX_for_e
|
Formate exchange[0.0 1000.0] |
⇆ | for_e ⇆ | ||||||
Reaction | EX_fru_e R_EX_fru_e
|
D-Fructose exchange[0.0 1000.0] |
⇆ | fru_e ⇆ | ||||||
Reaction | EX_fum_e R_EX_fum_e
|
Fumarate exchange[0.0 1000.0] |
⇆ | fum_e ⇆ | ||||||
Reaction | EX_glc__D_e R_EX_glc__D_e
|
D-Glucose exchange[-10.0 1000.0] |
⇆ | glc__D_e ⇆ | ||||||
Reaction | EX_gln__L_e R_EX_gln__L_e
|
L-Glutamine exchange[0.0 1000.0] |
⇆ | gln__L_e ⇆ | ||||||
Reaction | EX_glu__L_e R_EX_glu__L_e
|
L-Glutamate exchange[0.0 1000.0] |
⇆ | glu__L_e ⇆ | ||||||
Reaction | EX_h_e R_EX_h_e
|
H+ exchange[-1000.0 1000.0] |
⇆ | h_e ⇆ | ||||||
Reaction | EX_h2o_e R_EX_h2o_e
|
H2O exchange[-1000.0 1000.0] |
⇆ | h2o_e ⇆ | ||||||
Reaction | EX_lac__D_e R_EX_lac__D_e
|
D-lactate exchange[0.0 1000.0] |
⇆ | lac__D_e ⇆ | ||||||
Reaction | EX_mal__L_e R_EX_mal__L_e
|
L-Malate exchange[0.0 1000.0] |
⇆ | mal__L_e ⇆ | ||||||
Reaction | EX_nh4_e R_EX_nh4_e
|
Ammonia exchange[-1000.0 1000.0] |
⇆ | nh4_e ⇆ | ||||||
Reaction | EX_o2_e R_EX_o2_e
|
O2 exchange[-1000.0 1000.0] |
⇆ | o2_e ⇆ | ||||||
Reaction | EX_pi_e R_EX_pi_e
|
Phosphate exchange[-1000.0 1000.0] |
⇆ | pi_e ⇆ | ||||||
Reaction | EX_pyr_e R_EX_pyr_e
|
Pyruvate exchange[0.0 1000.0] |
⇆ | pyr_e ⇆ | ||||||
Reaction | EX_succ_e R_EX_succ_e
|
Succinate exchange[0.0 1000.0] |
⇆ | succ_e ⇆ | ||||||
Reaction | FBA R_FBA
|
Fructose-bisphosphate aldolase[-1000.0 1000.0] (b1773 or b2097 or b2925) |
⇆ | fdp_c ⇆ dhap_c + g3p_c | ||||||
Reaction | FBP R_FBP
|
Fructose-bisphosphatase[0.0 1000.0] (b3925 or b4232) |
➞ | fdp_c + h2o_c ➞ f6p_c + pi_c | ||||||
Reaction | FORt2 R_FORt2
|
Formate transport in via proton symport[0.0 1000.0] (b0904 or b2492) |
➞ | for_e + h_e ➞ for_c + h_c | ||||||
Reaction | FORti R_FORti
|
Formate transport via diffusion[0.0 1000.0] (b0904 or b2492) |
➞ | for_c ➞ for_e | ||||||
Reaction | FRD7 R_FRD7
|
Fumarate reductase[0.0 1000.0] (b4153 and b4151 and b4152 and b4154) |
➞ | fum_c + q8h2_c ➞ q8_c + succ_c | ||||||
Reaction | FRUpts2 R_FRUpts2
|
Fructose transport via PEP:Pyr PTS (f6p generating)[0.0 1000.0] (b2415 and b1818 and b1817 and b1819 and b2416) |
➞ | fru_e + pep_c ➞ f6p_c + pyr_c | ||||||
Reaction | FUM R_FUM
|
Fumarase[-1000.0 1000.0] (b4122 or b1612 or b1611) |
⇆ | fum_c + h2o_c ⇆ mal__L_c | ||||||
Reaction | FUMt2_2 R_FUMt2_2
|
Fumarate transport via proton symport (2 H)[0.0 1000.0] b3528 |
➞ | fum_e + 2.0 h_e ➞ fum_c + 2.0 h_c | ||||||
Reaction | G6PDH2r R_G6PDH2r
|
Glucose 6-phosphate dehydrogenase[-1000.0 1000.0] b1852 |
⇆ | g6p_c + nadp_c ⇆ M_6pgl_c + h_c + nadph_c | ||||||
Reaction | GAPD R_GAPD
|
Glyceraldehyde-3-phosphate dehydrogenase[-1000.0 1000.0] b1779 |
⇆ | g3p_c + nad_c + pi_c ⇆ M_13dpg_c + h_c + nadh_c | ||||||
Reaction | GLCpts R_GLCpts
|
D-glucose transport via PEP:Pyr PTS[0.0 1000.0] ((b2415 and b1818 and b1817 and b1819 and b2416) or (b2415 and b2417 and b1101 and b2416) or (b2415 and b2417 and b1621 and b2416)) |
➞ | glc__D_e + pep_c ➞ g6p_c + pyr_c | ||||||
Reaction | GLNS R_GLNS
|
Glutamine synthetase[0.0 1000.0] (b3870 or b1297) |
➞ | atp_c + glu__L_c + nh4_c ➞ adp_c + gln__L_c + h_c + pi_c | ||||||
Reaction | GLNabc R_GLNabc
|
GLNabc[0.0 1000.0] (b0810 and b0811 and b0809) |
➞ | atp_c + gln__L_e + h2o_c ➞ adp_c + gln__L_c + h_c + pi_c | ||||||
Reaction | GLUDy R_GLUDy
|
Glutamate dehydrogenase (NADP)[-1000.0 1000.0] b1761 |
⇆ | glu__L_c + h2o_c + nadp_c ⇆ akg_c + h_c + nadph_c + nh4_c | ||||||
Reaction | GLUN R_GLUN
|
Glutaminase[0.0 1000.0] (b0485 or b1812 or b1524) |
➞ | gln__L_c + h2o_c ➞ glu__L_c + nh4_c | ||||||
Reaction | GLUSy R_GLUSy
|
Glutamate synthase (NADPH)[0.0 1000.0] (b3212 and b3213) |
➞ | akg_c + gln__L_c + h_c + nadph_c ➞ 2.0 glu__L_c + nadp_c | ||||||
Reaction | GLUt2r R_GLUt2r
|
L glutamate transport via proton symport reversible[-1000.0 1000.0] b4077 |
⇆ | glu__L_e + h_e ⇆ glu__L_c + h_c | ||||||
Reaction | GND R_GND
|
Phosphogluconate dehydrogenase[0.0 1000.0] b2029 |
➞ | M_6pgc_c + nadp_c ➞ co2_c + nadph_c + ru5p__D_c | ||||||
Reaction | H2Ot R_H2Ot
|
H2O transport via diffusion[-1000.0 1000.0] (b0875 or s0001) |
⇆ | h2o_e ⇆ h2o_c | ||||||
Reaction | ICDHyr R_ICDHyr
|
Isocitrate dehydrogenase (NADP)[-1000.0 1000.0] b1136 |
⇆ | icit_c + nadp_c ⇆ akg_c + co2_c + nadph_c | ||||||
Reaction | ICL R_ICL
|
Isocitrate lyase[0.0 1000.0] b4015 |
➞ | icit_c ➞ glx_c + succ_c | ||||||
Reaction | LDH_D R_LDH_D
|
D-lactate dehydrogenase[-1000.0 1000.0] (b2133 or b1380) |
⇆ | lac__D_c + nad_c ⇆ h_c + nadh_c + pyr_c | ||||||
Reaction | MALS R_MALS
|
Malate synthase[0.0 1000.0] (b4014 or b2976) |
➞ | accoa_c + glx_c + h2o_c ➞ coa_c + h_c + mal__L_c | ||||||
Reaction | MALt2_2 R_MALt2_2
|
Malate transport via proton symport (2 H)[0.0 1000.0] b3528 |
➞ | 2.0 h_e + mal__L_e ➞ 2.0 h_c + mal__L_c | ||||||
Reaction | MDH R_MDH
|
Malate dehydrogenase[-1000.0 1000.0] b3236 |
⇆ | mal__L_c + nad_c ⇆ h_c + nadh_c + oaa_c | ||||||
Reaction | ME1 R_ME1
|
Malic enzyme (NAD)[0.0 1000.0] b1479 |
➞ | mal__L_c + nad_c ➞ co2_c + nadh_c + pyr_c | ||||||
Reaction | ME2 R_ME2
|
Malic enzyme (NADP)[0.0 1000.0] b2463 |
➞ | mal__L_c + nadp_c ➞ co2_c + nadph_c + pyr_c | ||||||
Reaction | NADH16 R_NADH16
|
NADH dehydrogenase (ubiquinone-8 & 3 protons)[0.0 1000.0] (b2287 and b2285 and b2283 and b2281 and b2279 and b2277 and b2276 and b2278 and b2280 and b2282 and b2284 and b2286 and b2288) |
➞ | 4.0 h_c + nadh_c + q8_c ➞ 3.0 h_e + nad_c + q8h2_c | ||||||
Reaction | NADTRHD R_NADTRHD
|
NAD transhydrogenase[0.0 1000.0] (b3962 or (b1602 and b1603)) |
➞ | nad_c + nadph_c ➞ nadh_c + nadp_c | ||||||
Reaction | NH4t R_NH4t
|
Ammonia reversible transport[-1000.0 1000.0] (s0001 or b0451) |
⇆ | nh4_e ⇆ nh4_c | ||||||
Reaction | O2t R_O2t
|
O2 transport diffusion [-1000.0 1000.0] s0001 |
⇆ | o2_e ⇆ o2_c | ||||||
Reaction | PDH R_PDH
|
Pyruvate dehydrogenase[0.0 1000.0] (b0115 and b0114 and b0116) |
➞ | coa_c + nad_c + pyr_c ➞ accoa_c + co2_c + nadh_c | ||||||
Reaction | PFK R_PFK
|
Phosphofructokinase[0.0 1000.0] (b3916 or b1723) |
➞ | atp_c + f6p_c ➞ adp_c + fdp_c + h_c | ||||||
Reaction | PFL R_PFL
|
Pyruvate formate lyase[0.0 1000.0] ((b0902 and b3114) or (b0903 and b0902 and b2579) or (b0902 and b0903) or (b3951 and b3952)) |
➞ | coa_c + pyr_c ➞ accoa_c + for_c | ||||||
Reaction | PGI R_PGI
|
Glucose-6-phosphate isomerase[-1000.0 1000.0] b4025 |
⇆ | g6p_c ⇆ f6p_c | ||||||
Reaction | PGK R_PGK
|
Phosphoglycerate kinase[-1000.0 1000.0] b2926 |
⇆ | M_3pg_c + atp_c ⇆ M_13dpg_c + adp_c | ||||||
Reaction | PGL R_PGL
|
6-phosphogluconolactonase[0.0 1000.0] b0767 |
➞ | M_6pgl_c + h2o_c ➞ M_6pgc_c + h_c | ||||||
Reaction | PGM R_PGM
|
Phosphoglycerate mutase[-1000.0 1000.0] (b4395 or b3612 or b0755) |
⇆ | M_2pg_c ⇆ M_3pg_c | ||||||
Reaction | PIt2r R_PIt2r
|
Phosphate reversible transport via symport[-1000.0 1000.0] (b2987 or b3493) |
⇆ | h_e + pi_e ⇆ h_c + pi_c | ||||||
Reaction | PPC R_PPC
|
Phosphoenolpyruvate carboxylase[0.0 1000.0] b3956 |
➞ | co2_c + h2o_c + pep_c ➞ h_c + oaa_c + pi_c | ||||||
Reaction | PPCK R_PPCK
|
Phosphoenolpyruvate carboxykinase[0.0 1000.0] b3403 |
➞ | atp_c + oaa_c ➞ adp_c + co2_c + pep_c | ||||||
Reaction | PPS R_PPS
|
Phosphoenolpyruvate synthase[0.0 1000.0] b1702 |
➞ | atp_c + h2o_c + pyr_c ➞ amp_c + 2.0 h_c + pep_c + pi_c | ||||||
Reaction | PTAr R_PTAr
|
Phosphotransacetylase[-1000.0 1000.0] (b2297 or b2458) |
⇆ | accoa_c + pi_c ⇆ actp_c + coa_c | ||||||
Reaction | PYK R_PYK
|
Pyruvate kinase[0.0 1000.0] (b1854 or b1676) |
➞ | adp_c + h_c + pep_c ➞ atp_c + pyr_c | ||||||
Reaction | PYRt2 R_PYRt2
|
Pyruvate transport in via proton symport[-1000.0 1000.0] |
⇆ | h_e + pyr_e ⇆ h_c + pyr_c | ||||||
Reaction | RPE R_RPE
|
Ribulose 5-phosphate 3-epimerase[-1000.0 1000.0] (b3386 or b4301) |
⇆ | ru5p__D_c ⇆ xu5p__D_c | ||||||
Reaction | RPI R_RPI
|
Ribose-5-phosphate isomerase[-1000.0 1000.0] (b2914 or b4090) |
⇆ | r5p_c ⇆ ru5p__D_c | ||||||
Reaction | SUCCt2_2 R_SUCCt2_2
|
Succinate transport via proton symport (2 H)[0.0 1000.0] b3528 |
➞ | 2.0 h_e + succ_e ➞ 2.0 h_c + succ_c | ||||||
Reaction | SUCCt3 R_SUCCt3
|
Succinate transport out via proton antiport[0.0 1000.0] |
➞ | h_e + succ_c ➞ h_c + succ_e | ||||||
Reaction | SUCDi R_SUCDi
|
Succinate dehydrogenase (irreversible)[0.0 1000.0] (b0723 and b0721 and b0722 and b0724) |
➞ | q8_c + succ_c ➞ fum_c + q8h2_c | ||||||
Reaction | SUCOAS R_SUCOAS
|
Succinyl-CoA synthetase (ADP-forming)[-1000.0 1000.0] (b0728 and b0729) |
⇆ | atp_c + coa_c + succ_c ⇆ adp_c + pi_c + succoa_c | ||||||
Reaction | TALA R_TALA
|
Transaldolase[-1000.0 1000.0] (b2464 or b0008) |
⇆ | g3p_c + s7p_c ⇆ e4p_c + f6p_c | ||||||
Reaction | THD2 R_THD2
|
NAD(P) transhydrogenase[0.0 1000.0] (b1602 and b1603) |
➞ | 2.0 h_e + nadh_c + nadp_c ➞ 2.0 h_c + nad_c + nadph_c | ||||||
Reaction | TKT1 R_TKT1
|
Transketolase[-1000.0 1000.0] (b2935 or b2465) |
⇆ | r5p_c + xu5p__D_c ⇆ g3p_c + s7p_c | ||||||
Reaction | TKT2 R_TKT2
|
Transketolase[-1000.0 1000.0] (b2935 or b2465) |
⇆ | e4p_c + xu5p__D_c ⇆ f6p_c + g3p_c | ||||||
Reaction | TPI R_TPI
|
Triose-phosphate isomerase[-1000.0 1000.0] b3919 |
⇆ | dhap_c ⇆ g3p_c | ||||||
Reaction | EX_X
|
[0.0 1000.0] |
⇆ | X ⇆ |
type | Objectives [1] | name | type | flux objectives | sbo | cvterm |
---|---|---|---|---|---|---|
Reaction | obj
|
maximize | +1.0*BIOMASS_Ecoli_core_w_GAM |