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.

The content of this model has been carefully created in a manual research effort. This file has been exported from the software COBRApy and further processed with the JSBML-based ModelPolisher application.
This file has been produced by the Systems Biology Research Group using BiGG Models knowledge-base version of Nov 21, 2016, where it is currently hosted and identified by: e_coli_core.

Terms of use

Copyright © 2016 The Regents of the University of California.

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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. 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.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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

id ecoli_fba e_coli_core
nameecoli (FBA)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
SBML model L3V1 fbc-V2 groups-V1 comp-V1

SBO:0000624
BQB_HAS_TAXON
511145
BQM_IS
e_coli_core
BQM_IS_DESCRIBED_BY
ecosalplus.10.2.1
Ports [63] name port ref id ref unit ref metaid ref sbo cvterm
EX_mal__L_e_port EX_mal__L_e
lb_EX_mal__L_e_port lb_EX_mal__L_e
ub_EX_mal__L_e_port ub_EX_mal__L_e
EX_acald_e_port EX_acald_e
lb_EX_acald_e_port lb_EX_acald_e
ub_EX_acald_e_port ub_EX_acald_e
EX_pyr_e_port EX_pyr_e
lb_EX_pyr_e_port lb_EX_pyr_e
ub_EX_pyr_e_port ub_EX_pyr_e
EX_glc__D_e_port EX_glc__D_e
lb_EX_glc__D_e_port lb_EX_glc__D_e
ub_EX_glc__D_e_port ub_EX_glc__D_e
EX_etoh_e_port EX_etoh_e
lb_EX_etoh_e_port lb_EX_etoh_e
ub_EX_etoh_e_port ub_EX_etoh_e
EX_nh4_e_port EX_nh4_e
lb_EX_nh4_e_port lb_EX_nh4_e
ub_EX_nh4_e_port ub_EX_nh4_e
EX_h2o_e_port EX_h2o_e
lb_EX_h2o_e_port lb_EX_h2o_e
ub_EX_h2o_e_port ub_EX_h2o_e
EX_ac_e_port EX_ac_e
lb_EX_ac_e_port lb_EX_ac_e
ub_EX_ac_e_port ub_EX_ac_e
EX_akg_e_port EX_akg_e
lb_EX_akg_e_port lb_EX_akg_e
ub_EX_akg_e_port ub_EX_akg_e
EX_co2_e_port EX_co2_e
lb_EX_co2_e_port lb_EX_co2_e
ub_EX_co2_e_port ub_EX_co2_e
EX_lac__D_e_port EX_lac__D_e
lb_EX_lac__D_e_port lb_EX_lac__D_e
ub_EX_lac__D_e_port ub_EX_lac__D_e
EX_fum_e_port EX_fum_e
lb_EX_fum_e_port lb_EX_fum_e
ub_EX_fum_e_port ub_EX_fum_e
EX_fru_e_port EX_fru_e
lb_EX_fru_e_port lb_EX_fru_e
ub_EX_fru_e_port ub_EX_fru_e
EX_for_e_port EX_for_e
lb_EX_for_e_port lb_EX_for_e
ub_EX_for_e_port ub_EX_for_e
EX_gln__L_e_port EX_gln__L_e
lb_EX_gln__L_e_port lb_EX_gln__L_e
ub_EX_gln__L_e_port ub_EX_gln__L_e
EX_succ_e_port EX_succ_e
lb_EX_succ_e_port lb_EX_succ_e
ub_EX_succ_e_port ub_EX_succ_e
EX_h_e_port EX_h_e
lb_EX_h_e_port lb_EX_h_e
ub_EX_h_e_port ub_EX_h_e
EX_pi_e_port EX_pi_e
lb_EX_pi_e_port lb_EX_pi_e
ub_EX_pi_e_port ub_EX_pi_e
EX_glu__L_e_port EX_glu__L_e
lb_EX_glu__L_e_port lb_EX_glu__L_e
ub_EX_glu__L_e_port ub_EX_glu__L_e
EX_o2_e_port EX_o2_e
lb_EX_o2_e_port lb_EX_o2_e
ub_EX_o2_e_port ub_EX_o2_e
EX_X_port EX_X
lb_EX_X_port lb_EX_X
ub_EX_X_port ub_EX_X

UnitDefinitions [14] name units sbo cvterm
mmol_per_gDW_per_hr 10 3 mole g 3600 s
h 3600 s
g g
m m
m2 m 2
l litre
mmol 10 3 mole
per_h 1 3600 s
mmol_per_h 10 3 mole 3600 s
mmol_per_hg 10 3 mole g 3600 s
mmol_per_l 10 3 mole litre
l_per_mmol litre 10 3 mole
g_per_l g litre
g_per_mmol g 10 3 mole

Compartments [2] name size constant spatial dimensions units derived units sbo cvterm
c _4b1e4f0f-bcca-42b1-b7d0-484ec9bbf3b6 cytosol l litre
BQB_IS
c
e cb207f38-8131-42d4-a528-217b1863e93a extracellular space l litre
BQB_IS
e

Species [73] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
M_13dpg_c M_13dpg_c 3-Phospho-D-glyceroyl phosphate
C3H4O10P2
c 0.0 mmol 10 3 mole litre
M_2pg_c M_2pg_c D-Glycerate 2-phosphate
C3H4O7P
c 0.0 mmol 10 3 mole litre
M_3pg_c M_3pg_c 3-Phospho-D-glycerate
C3H4O7P
c 0.0 mmol 10 3 mole litre
M_6pgc_c M_6pgc_c 6-Phospho-D-gluconate
C6H10O10P
c 0.0 mmol 10 3 mole litre
M_6pgl_c M_6pgl_c 6-phospho-D-glucono-1,5-lactone
C6H9O9P
c 0.0 mmol 10 3 mole litre
ac_c M_ac_c Acetate
C2H3O2
c 0.0 mmol 10 3 mole litre
ac_e M_ac_e Acetate
C2H3O2
e 0.0 mmol 10 3 mole litre
acald_c M_acald_c Acetaldehyde
C2H4O
c 0.0 mmol 10 3 mole litre
acald_e M_acald_e Acetaldehyde
C2H4O
e 0.0 mmol 10 3 mole litre
accoa_c M_accoa_c Acetyl-CoA
C23H34N7O17P3S
c 0.0 mmol 10 3 mole litre
acon_C_c M_acon_C_c Cis-Aconitate
C6H3O6
c 0.0 mmol 10 3 mole litre
actp_c M_actp_c Acetyl phosphate
C2H3O5P
c 0.0 mmol 10 3 mole litre
adp_c M_adp_c ADP
C10H12N5O10P2
c 0.0 mmol 10 3 mole litre
akg_c M_akg_c 2-Oxoglutarate
C5H4O5
c 0.0 mmol 10 3 mole litre
akg_e M_akg_e 2-Oxoglutarate
C5H4O5
e 0.0 mmol 10 3 mole litre
amp_c M_amp_c AMP
C10H12N5O7P
c 0.0 mmol 10 3 mole litre
atp_c M_atp_c ATP
C10H12N5O13P3
c 0.0 mmol 10 3 mole litre
cit_c M_cit_c Citrate
C6H5O7
c 0.0 mmol 10 3 mole litre
co2_c M_co2_c CO2
CO2
c 0.0 mmol 10 3 mole litre
co2_e M_co2_e CO2
CO2
e 0.0 mmol 10 3 mole litre
coa_c M_coa_c Coenzyme A
C21H32N7O16P3S
c 0.0 mmol 10 3 mole litre
dhap_c M_dhap_c Dihydroxyacetone phosphate
C3H5O6P
c 0.0 mmol 10 3 mole litre
e4p_c M_e4p_c D-Erythrose 4-phosphate
C4H7O7P
c 0.0 mmol 10 3 mole litre
etoh_c M_etoh_c Ethanol
C2H6O
c 0.0 mmol 10 3 mole litre
etoh_e M_etoh_e Ethanol
C2H6O
e 0.0 mmol 10 3 mole litre
f6p_c M_f6p_c D-Fructose 6-phosphate
C6H11O9P
c 0.0 mmol 10 3 mole litre
fdp_c M_fdp_c D-Fructose 1,6-bisphosphate
C6H10O12P2
c 0.0 mmol 10 3 mole litre
for_c M_for_c Formate
CH1O2
c 0.0 mmol 10 3 mole litre
for_e M_for_e Formate
CH1O2
e 0.0 mmol 10 3 mole litre
fru_e M_fru_e D-Fructose
C6H12O6
e 0.0 mmol 10 3 mole litre
fum_c M_fum_c Fumarate
C4H2O4
c 0.0 mmol 10 3 mole litre
fum_e M_fum_e Fumarate
C4H2O4
e 0.0 mmol 10 3 mole litre
g3p_c M_g3p_c Glyceraldehyde 3-phosphate
C3H5O6P
c 0.0 mmol 10 3 mole litre
g6p_c M_g6p_c D-Glucose 6-phosphate
C6H11O9P
c 0.0 mmol 10 3 mole litre
glc__D_e M_glc__D_e D-Glucose
C6H12O6
e 0.0 mmol 10 3 mole litre
gln__L_c M_gln__L_c L-Glutamine
C5H10N2O3
c 0.0 mmol 10 3 mole litre
gln__L_e M_gln__L_e L-Glutamine
C5H10N2O3
e 0.0 mmol 10 3 mole litre
glu__L_c M_glu__L_c L-Glutamate
C5H8NO4
c 0.0 mmol 10 3 mole litre
glu__L_e M_glu__L_e L-Glutamate
C5H8NO4
e 0.0 mmol 10 3 mole litre
glx_c M_glx_c Glyoxylate
C2H1O3
c 0.0 mmol 10 3 mole litre
h2o_c M_h2o_c H2O
H2O
c 0.0 mmol 10 3 mole litre
h2o_e M_h2o_e H2O
H2O
e 0.0 mmol 10 3 mole litre
h_c M_h_c H+
H
c 0.0 mmol 10 3 mole litre
h_e M_h_e H+
H
e 0.0 mmol 10 3 mole litre
icit_c M_icit_c Isocitrate
C6H5O7
c 0.0 mmol 10 3 mole litre
lac__D_c M_lac__D_c D-Lactate
C3H5O3
c 0.0 mmol 10 3 mole litre
lac__D_e M_lac__D_e D-Lactate
C3H5O3
e 0.0 mmol 10 3 mole litre
mal__L_c M_mal__L_c L-Malate
C4H4O5
c 0.0 mmol 10 3 mole litre
mal__L_e M_mal__L_e L-Malate
C4H4O5
e 0.0 mmol 10 3 mole litre
nad_c M_nad_c Nicotinamide adenine dinucleotide
C21H26N7O14P2
c 0.0 mmol 10 3 mole litre
nadh_c M_nadh_c Nicotinamide adenine dinucleotide - reduced
C21H27N7O14P2
c 0.0 mmol 10 3 mole litre
nadp_c M_nadp_c Nicotinamide adenine dinucleotide phosphate
C21H25N7O17P3
c 0.0 mmol 10 3 mole litre
nadph_c M_nadph_c Nicotinamide adenine dinucleotide phosphate - reduced
C21H26N7O17P3
c 0.0 mmol 10 3 mole litre
nh4_c M_nh4_c Ammonium
H4N
c 0.0 mmol 10 3 mole litre
nh4_e M_nh4_e Ammonium
H4N
e 0.0 mmol 10 3 mole litre
o2_c M_o2_c O2
O2
c 0.0 mmol 10 3 mole litre
o2_e M_o2_e O2
O2
e 0.0 mmol 10 3 mole litre
oaa_c M_oaa_c Oxaloacetate
C4H2O5
c 0.0 mmol 10 3 mole litre
pep_c M_pep_c Phosphoenolpyruvate
C3H2O6P
c 0.0 mmol 10 3 mole litre
pi_c M_pi_c Phosphate
HO4P
c 0.0 mmol 10 3 mole litre
pi_e M_pi_e Phosphate
HO4P
e 0.0 mmol 10 3 mole litre
pyr_c M_pyr_c Pyruvate
C3H3O3
c 0.0 mmol 10 3 mole litre
pyr_e M_pyr_e Pyruvate
C3H3O3
e 0.0 mmol 10 3 mole litre
q8_c M_q8_c Ubiquinone-8
C49H74O4
c 0.0 mmol 10 3 mole litre
q8h2_c M_q8h2_c Ubiquinol-8
C49H76O4
c 0.0 mmol 10 3 mole litre
r5p_c M_r5p_c Alpha-D-Ribose 5-phosphate
C5H9O8P
c 0.0 mmol 10 3 mole litre
ru5p__D_c M_ru5p__D_c D-Ribulose 5-phosphate
C5H9O8P
c 0.0 mmol 10 3 mole litre
s7p_c M_s7p_c Sedoheptulose 7-phosphate
C7H13O10P
c 0.0 mmol 10 3 mole litre
succ_c M_succ_c Succinate
C4H4O4
c 0.0 mmol 10 3 mole litre
succ_e M_succ_e Succinate
C4H4O4
e 0.0 mmol 10 3 mole litre
succoa_c M_succoa_c Succinyl-CoA
C25H35N7O19P3S
c 0.0 mmol 10 3 mole litre
xu5p__D_c M_xu5p__D_c D-Xylulose 5-phosphate
C5H9O8P
c 0.0 mmol 10 3 mole litre
X biomass c 0.001 mmol 10 3 mole

GeneProducts [137] name label associated species sbo cvterm
b0351 G_b0351 mhpF b0351
BQB_IS
P77580
BQB_IS_ENCODED_BY
GI:16128336; 945008; ABE-0001207; EG13625
b1241 G_b1241 adhE b1241
BQB_IS
P0A9Q7
BQB_IS_ENCODED_BY
GI:16129202; 945837; ABE-0004164; EG10031
s0001 s0001
b3115 G_b3115 tdcD b3115
BQB_IS
P11868
BQB_IS_ENCODED_BY
GI:145698313; 947635; ABE-0010245; EG11172
b1849 G_b1849 purT b1849
BQB_IS
P33221
BQB_IS_ENCODED_BY
GI:16129802; 946368; ABE-0006162; EG11809
b2296 G_b2296 ackA b2296
BQB_IS
P0A6A3
BQB_IS_ENCODED_BY
GI:16130231; 946775; ABE-0007579; EG10027
b0118 G_b0118 acnB b0118
BQB_IS
P36683
BQB_IS_ENCODED_BY
GI:16128111; 944864; ABE-0000411; EG12316
b1276 G_b1276 acnA b1276
BQB_IS
P25516
BQB_IS_ENCODED_BY
GI:16129237; 946724; ABE-0004283; EG11325
b0474 G_b0474 adk b0474
BQB_IS
P69441
BQB_IS_ENCODED_BY
GI:16128458; 945097; ABE-0001645; EG10032
b0116 G_b0116 lpd b0116
BQB_IS
P0A9P0
BQB_IS_ENCODED_BY
GI:16128109; 944854; ABE-0000404; EG10543
b0727 G_b0727 sucB b0727
BQB_IS
P0AFG6
BQB_IS_ENCODED_BY
GI:16128702; 945307; ABE-0002480; EG10980
b0726 G_b0726 sucA b0726
BQB_IS
P0AFG3
BQB_IS_ENCODED_BY
GI:16128701; 945303; ABE-0002478; EG10979
b2587 G_b2587 kgtP b2587
BQB_IS
P0AEX3
BQB_IS_ENCODED_BY
GI:16130512; 947069; ABE-0008515; EG10522
b0356 G_b0356 frmA b0356
BQB_IS
P25437
BQB_IS_ENCODED_BY
GI:16128341; 944988; ABE-0001221; EG50010
b1478 G_b1478 adhP b1478
BQB_IS
P39451
BQB_IS_ENCODED_BY
GI:90111280; 946036; ABE-0004928; EG12622
b3733 G_b3733 atpG b3733
BQB_IS
P0ABA6
BQB_IS_ENCODED_BY
GI:16131601; 948243; ABE-0012211; EG10104
b3739 G_b3739 atpI b3739
BQB_IS
P0ABC0
BQB_IS_ENCODED_BY
GI:90111645; 948251; ABE-0012224; EG10106
b3735 G_b3735 atpH b3735
BQB_IS
P0ABA4
BQB_IS_ENCODED_BY
GI:16131603; 948254; ABE-0012215; EG10105
b3734 G_b3734 atpA b3734
BQB_IS
P0ABB0
BQB_IS_ENCODED_BY
GI:16131602; 948242; ABE-0012213; EG10098
b3738 G_b3738 atpB b3738
BQB_IS
P0AB98
BQB_IS_ENCODED_BY
GI:16131606; 948252; ABE-0012222; EG10099
b3736 G_b3736 atpF b3736
BQB_IS
P0ABA0
BQB_IS_ENCODED_BY
GI:16131604; 948247; ABE-0012217; EG10103
b3732 G_b3732 atpD b3732
BQB_IS
P0ABB4
BQB_IS_ENCODED_BY
GI:16131600; 948244; ABE-0012208; EG10101
b3737 G_b3737 atpE b3737
BQB_IS
P68699
BQB_IS_ENCODED_BY
GI:16131605; 948253; ABE-0012220; EG10102
b3731 G_b3731 atpC b3731
BQB_IS
P0A6E6
BQB_IS_ENCODED_BY
GI:16131599; 948245; ABE-0012206; EG10100
b0720 G_b0720 gltA b0720
BQB_IS
P0ABH7
BQB_IS_ENCODED_BY
GI:16128695; 945323; ABE-0002451; EG10402
b0734 G_b0734 cydB b0734
BQB_IS
P0ABK2
BQB_IS_ENCODED_BY
GI:16128709; 945347; ABE-0002501; EG10174
b0978 G_b0978 cbdA b0978
BQB_IS
P26459
BQB_IS_ENCODED_BY
GI:16128944; 945585; ABE-0003300; EG11380
b0733 G_b0733 cydA b0733
BQB_IS
P0ABJ9
BQB_IS_ENCODED_BY
GI:90111166; 945341; ABE-0002499; EG10173
b0979 G_b0979 cbdB b0979
BQB_IS
P26458
BQB_IS_ENCODED_BY
GI:16128945; 947547; ABE-0003302; EG11379
b2975 G_b2975 glcA b2975
BQB_IS
Q46839
BQB_IS_ENCODED_BY
GI:16130875; 947259; ABE-0009763; EG12995
b3603 G_b3603 lldP b3603
BQB_IS
P33231
BQB_IS_ENCODED_BY
GI:16131474; 948114; ABE-0011777; EG11961
b2779 G_b2779 eno b2779
BQB_IS
P0A6P9
BQB_IS_ENCODED_BY
GI:16130686; 945032; ABE-0009110; EG10258
b2097 G_b2097 fbaB b2097
BQB_IS
P0A991
BQB_IS_ENCODED_BY
GI:90111385; 946632; ABE-0006941; EG14062
b2925 G_b2925 fbaA b2925
BQB_IS
P0AB71
BQB_IS_ENCODED_BY
GI:16130826; 947415; ABE-0009600; EG10282
b1773 G_b1773 ydjI b1773
BQB_IS
P77704
BQB_IS_ENCODED_BY
GI:16129727; 946291; ABE-0005906; EG13485
b3925 G_b3925 glpX b3925
BQB_IS
P0A9C9
BQB_IS_ENCODED_BY
GI:16131763; 948424; ABE-0012821; EG11517
b4232 G_b4232 fbp b4232
BQB_IS
P0A993
BQB_IS_ENCODED_BY
GI:16132054; 948753; ABE-0013842; EG10283
b2492 G_b2492 focB b2492
BQB_IS
P77733
BQB_IS_ENCODED_BY
GI:16130417; 949032; ABE-0008206; EG14220
b0904 G_b0904 focA b0904
BQB_IS
P0AC23
BQB_IS_ENCODED_BY
GI:16128871; 945513; ABE-0003073; EG11258
b4151 G_b4151 frdD b4151
BQB_IS
P0A8Q3
BQB_IS_ENCODED_BY
GI:16131976; 948668; ABE-0013595; EG10333
b4152 G_b4152 frdC b4152
BQB_IS
P0A8Q0
BQB_IS_ENCODED_BY
GI:16131977; 948680; ABE-0013598; EG10332
b4154 G_b4154 frdA b4154
BQB_IS
P00363
BQB_IS_ENCODED_BY
GI:16131979; 948667; ABE-0013604; EG10330
b4153 G_b4153 frdB b4153
BQB_IS
P0AC47
BQB_IS_ENCODED_BY
GI:16131978; 948666; ABE-0013602; EG10331
b2416 G_b2416 ptsI b2416
BQB_IS
P08839
BQB_IS_ENCODED_BY
GI:16130342; 946879; ABE-0007967; EG10789
b1818 G_b1818 manY b1818
BQB_IS
P69801
BQB_IS_ENCODED_BY
GI:16129772; 946332; ABE-0006056; EG10568
b1817 G_b1817 manX b1817
BQB_IS
P69797
BQB_IS_ENCODED_BY
GI:16129771; 946334; ABE-0006054; EG10567
b1819 G_b1819 manZ b1819
BQB_IS
P69805
BQB_IS_ENCODED_BY
GI:345452720; 946342; ABE-0006058; EG10569
b2415 G_b2415 ptsH b2415
BQB_IS
P0AA04
BQB_IS_ENCODED_BY
GI:16130341; 946886; ABE-0007962; EG10788
b1611 G_b1611 fumC b1611
BQB_IS
P05042
BQB_IS_ENCODED_BY
GI:16129569; 946147; ABE-0005380; EG10358
b4122 G_b4122 fumB b4122
BQB_IS
P14407
BQB_IS_ENCODED_BY
GI:16131948; 948642; ABE-0013501; EG10357
b1612 G_b1612 fumA b1612
BQB_IS
P0AC33
BQB_IS_ENCODED_BY
GI:16129570; 946826; ABE-0005392; EG10356
b3528 G_b3528 dctA b3528
BQB_IS
P0A830
BQB_IS_ENCODED_BY
GI:16131400; 948039; ABE-0011527; EG20044
b1852 G_b1852 zwf b1852
BQB_IS
P0AC53
BQB_IS_ENCODED_BY
GI:16129805; 946370; ABE-0006171; EG11221
b1779 G_b1779 gapA b1779
BQB_IS
P0A9B2
BQB_IS_ENCODED_BY
GI:16129733; 947679; ABE-0005920; EG10367
b1621 G_b1621 malX b1621
BQB_IS
P19642
BQB_IS_ENCODED_BY
GI:16129579; 946009; ABE-0005429; EG10563
b2417 G_b2417 crr b2417
BQB_IS
P69783
BQB_IS_ENCODED_BY
GI:16130343; 946880; ABE-0007971; EG10165
b1101 G_b1101 ptsG b1101
BQB_IS
P69786
BQB_IS_ENCODED_BY
GI:16129064; 945651; ABE-0003722; EG10787
b1297 G_b1297 puuA b1297
BQB_IS
P78061
BQB_IS_ENCODED_BY
GI:90111244; 946202; ABE-0004365; EG13908
b3870 G_b3870 glnA b3870
BQB_IS
P0A9C5
BQB_IS_ENCODED_BY
GI:16131710; 948370; ABE-0012640; EG10383
b0810 G_b0810 glnP b0810
BQB_IS
P0AEQ6
BQB_IS_ENCODED_BY
GI:16128778; 945621; ABE-0002766; EG10388
b0811 G_b0811 glnH b0811
BQB_IS
P0AEQ3
BQB_IS_ENCODED_BY
GI:16128779; 944872; ABE-0002771; EG10386
b0809 G_b0809 glnQ b0809
BQB_IS
P10346
BQB_IS_ENCODED_BY
GI:16128777; 945435; ABE-0002764; EG10389
b1761 G_b1761 gdhA b1761
BQB_IS
P00370
BQB_IS_ENCODED_BY
GI:16129715; 946802; ABE-0005865; EG10372
b0485 G_b0485 glsA b0485
BQB_IS
P77454
BQB_IS_ENCODED_BY
GI:16128469; 946187; ABE-0001688; EG13247
b1812 G_b1812 pabB b1812
BQB_IS
P05041
BQB_IS_ENCODED_BY
GI:16129766; 946337; ABE-0006031; EG10683
b1524 G_b1524 glsB b1524
BQB_IS
P0A6W0
BQB_IS_ENCODED_BY
GI:16129483; 944973; ABE-0005086; EG13816
b3213 G_b3213 gltD b3213
BQB_IS
P09832
BQB_IS_ENCODED_BY
GI:16131103; 947723; ABE-0010547; EG10404
b3212 G_b3212 gltB b3212
BQB_IS
P09831
BQB_IS_ENCODED_BY
GI:308209621; 947724; ABE-0010545; EG10403
b4077 G_b4077 gltP b4077
BQB_IS
P21345
BQB_IS_ENCODED_BY
GI:16131903; 948591; ABE-0013357; EG10405
b2029 G_b2029 gnd b2029
BQB_IS
P00350
BQB_IS_ENCODED_BY
GI:16129970; 946554; ABE-0006737; EG10411
b0875 G_b0875 aqpZ b0875
BQB_IS
P60844
BQB_IS_ENCODED_BY
GI:16128843; 945497; ABE-0002976; EG13270
b1136 G_b1136 icd b1136
BQB_IS
P08200
BQB_IS_ENCODED_BY
GI:16129099; 945702; ABE-0003823; EG10489
b4015 G_b4015 aceA b4015
BQB_IS
P0A9G6
BQB_IS_ENCODED_BY
GI:16131841; 948517; ABE-0013128; EG10022
b2133 G_b2133 dld b2133
BQB_IS
P06149
BQB_IS_ENCODED_BY
GI:16130071; 946653; ABE-0007048; EG10231
b1380 G_b1380 ldhA b1380
BQB_IS
P52643
BQB_IS_ENCODED_BY
GI:16129341; 946315; ABE-0004619; EG13186
b4014 G_b4014 aceB b4014
BQB_IS
P08997
BQB_IS_ENCODED_BY
GI:16131840; 948512; ABE-0013125; EG10023
b2976 G_b2976 glcB b2976
BQB_IS
P37330
BQB_IS_ENCODED_BY
GI:16130876; 948857; ABE-0009767; EG20080
b3236 G_b3236 mdh b3236
BQB_IS
P61889
BQB_IS_ENCODED_BY
GI:16131126; 947854; ABE-0010613; EG10576
b1479 G_b1479 maeA b1479
BQB_IS
P26616
BQB_IS_ENCODED_BY
GI:90111281; 946031; ABE-0004931; EG10948
b2463 G_b2463 maeB b2463
BQB_IS
P76558
BQB_IS_ENCODED_BY
GI:16130388; 946947; ABE-0008111; EG14193
b2280 G_b2280 nuoJ b2280
BQB_IS
P0AFE0
BQB_IS_ENCODED_BY
GI:16130215; 946756; ABE-0007536; EG12090
b2278 G_b2278 nuoL b2278
BQB_IS
P33607
BQB_IS_ENCODED_BY
GI:16130213; 945540; ABE-0007532; EG12092
b2281 G_b2281 nuoI b2281
BQB_IS
P0AFD6
BQB_IS_ENCODED_BY
GI:16130216; 946757; ABE-0007539; EG12089
b2288 G_b2288 nuoA b2288
BQB_IS
P0AFC3
BQB_IS_ENCODED_BY
GI:49176207; 946764; ABE-0007553; EG12082
b2282 G_b2282 nuoH b2282
BQB_IS
P0AFD4
BQB_IS_ENCODED_BY
GI:16130217; 946761; ABE-0007541; EG12088
b2286 G_b2286 nuoC b2286
BQB_IS
P33599
BQB_IS_ENCODED_BY
GI:145698291; 946759; ABE-0007549; EG12084
b2283 G_b2283 nuoG b2283
BQB_IS
P33602
BQB_IS_ENCODED_BY
GI:145698290; 946762; ABE-0007543; EG12087
b2277 G_b2277 nuoM b2277
BQB_IS
P0AFE8
BQB_IS_ENCODED_BY
GI:16130212; 947731; ABE-0007529; EG11773
b2287 G_b2287 nuoB b2287
BQB_IS
P0AFC7
BQB_IS_ENCODED_BY
GI:16130222; 946738; ABE-0007551; EG12083
b2284 G_b2284 nuoF b2284
BQB_IS
P31979
BQB_IS_ENCODED_BY
GI:16130219; 946753; ABE-0007545; EG11774
b2279 G_b2279 nuoK b2279
BQB_IS
P0AFE4
BQB_IS_ENCODED_BY
GI:16130214; 947580; ABE-0007534; EG12091
b2276 G_b2276 nuoN b2276
BQB_IS
P0AFF0
BQB_IS_ENCODED_BY
GI:145698289; 945136; ABE-0007526; EG12093
b2285 G_b2285 nuoE b2285
BQB_IS
P0AFD1
BQB_IS_ENCODED_BY
GI:16130220; 946746; ABE-0007547; EG12086
b3962 G_b3962 sthA b3962
BQB_IS
P27306
BQB_IS_ENCODED_BY
GI:90111670; 948461; ABE-0012975; EG11428
b1602 G_b1602 pntB b1602
BQB_IS
P0AB67
BQB_IS_ENCODED_BY
GI:16129560; 946144; ABE-0005352; EG10745
b1603 G_b1603 pntA b1603
BQB_IS
P07001
BQB_IS_ENCODED_BY
GI:16129561; 946628; ABE-0005354; EG10744
b0451 G_b0451 amtB b0451
BQB_IS
P69681
BQB_IS_ENCODED_BY
GI:16128436; 945084; ABE-0001564; EG11821
b0115 G_b0115 aceF b0115
BQB_IS
P06959
BQB_IS_ENCODED_BY
GI:16128108; 944794; ABE-0000400; EG10025
b0114 G_b0114 aceE b0114
BQB_IS
P0AFG8
BQB_IS_ENCODED_BY
GI:16128107; 944834; ABE-0000397; EG10024
b3916 G_b3916 pfkA b3916
BQB_IS
P0A796
BQB_IS_ENCODED_BY
GI:16131754; 948412; ABE-0012789; EG10699
b1723 G_b1723 pfkB b1723
BQB_IS
P06999
BQB_IS_ENCODED_BY
GI:49176138; 946230; ABE-0005748; EG10700
b0903 G_b0903 pflB b0903
BQB_IS
P09373
BQB_IS_ENCODED_BY
GI:16128870; 945514; ABE-0003071; EG10701
b3952 G_b3952 pflC b3952
BQB_IS
P32675
BQB_IS_ENCODED_BY
GI:49176447; 948453; ABE-0012937; EG11911
b3114 G_b3114 tdcE b3114
BQB_IS
P42632
BQB_IS_ENCODED_BY
GI:49176316; 947623; ABE-0010242; EG12758
b0902 G_b0902 pflA b0902
BQB_IS
P0A9N4
BQB_IS_ENCODED_BY
GI:16128869; 945517; ABE-0003068; EG10028
b2579 G_b2579 grcA b2579
BQB_IS
P68066
BQB_IS_ENCODED_BY
GI:16130504; 947068; ABE-0008489; EG11784
b3951 G_b3951 pflD b3951
BQB_IS
P32674
BQB_IS_ENCODED_BY
GI:16131789; 948454; ABE-0012934; EG11910
b4025 G_b4025 pgi b4025
BQB_IS
P0A6T1
BQB_IS_ENCODED_BY
GI:16131851; 948535; ABE-0013163; EG10702
b2926 G_b2926 pgk b2926
BQB_IS
P0A799
BQB_IS_ENCODED_BY
GI:16130827; 947414; ABE-0009605; EG10703
b0767 G_b0767 pgl b0767
BQB_IS
P52697
BQB_IS_ENCODED_BY
GI:16128735; 946398; ABE-0002611; EG13231
b0755 G_b0755 gpmA b0755
BQB_IS
P62707
BQB_IS_ENCODED_BY
GI:16128723; 945068; ABE-0002563; EG11699
b3612 G_b3612 gpmM b3612
BQB_IS
P37689
BQB_IS_ENCODED_BY
GI:16131483; 948130; ABE-0011818; EG12296
b4395 G_b4395 ytjC b4395
BQB_IS
P0A7A2
BQB_IS_ENCODED_BY
GI:16132212; 948918; ABE-0014416; EG12164
b2987 G_b2987 pitB b2987
BQB_IS
P43676
BQB_IS_ENCODED_BY
GI:16130887; 947475; ABE-0009800; EG12883
b3493 G_b3493 pitA b3493
BQB_IS
P0AFJ7
BQB_IS_ENCODED_BY
GI:16131365; 948009; ABE-0011407; EG12230
b3956 G_b3956 ppc b3956
BQB_IS
P00864
BQB_IS_ENCODED_BY
GI:16131794; 948457; ABE-0012950; EG10756
b3403 G_b3403 pck b3403
BQB_IS
P22259
BQB_IS_ENCODED_BY
GI:16131280; 945667; ABE-0011106; EG10688
b1702 G_b1702 ppsA b1702
BQB_IS
P23538
BQB_IS_ENCODED_BY
GI:16129658; 946209; ABE-0005678; EG10759
b2297 G_b2297 pta b2297
BQB_IS
P0A9M8
BQB_IS_ENCODED_BY
GI:16130232; 946778; ABE-0007582; EG20173
b2458 G_b2458 eutD b2458
BQB_IS
P77218
BQB_IS_ENCODED_BY
GI:16130383; 946940; ABE-0008097; EG14188
b1676 G_b1676 pykF b1676
BQB_IS
P0AD61
BQB_IS_ENCODED_BY
GI:16129632; 946179; ABE-0005600; EG10804
b1854 G_b1854 pykA b1854
BQB_IS
P21599
BQB_IS_ENCODED_BY
GI:16129807; 946527; ABE-0006182; EG10803
b4301 G_b4301 sgcE b4301
BQB_IS
P39362
BQB_IS_ENCODED_BY
GI:16132122; 948829; ABE-0014097; EG12553
b3386 G_b3386 rpe b3386
BQB_IS
P0AG07
BQB_IS_ENCODED_BY
GI:16131264; 947896; ABE-0011061; EG11960
b2914 G_b2914 rpiA b2914
BQB_IS
P0A7Z0
BQB_IS_ENCODED_BY
GI:16130815; 947407; ABE-0009567; EG11443
b4090 G_b4090 rpiB b4090
BQB_IS
P37351
BQB_IS_ENCODED_BY
GI:16131916; 948602; ABE-0013405; EG11827
b0723 G_b0723 sdhA b0723
BQB_IS
P0AC41
BQB_IS_ENCODED_BY
GI:16128698; 945402; ABE-0002466; EG10931
b0724 G_b0724 sdhB b0724
BQB_IS
P07014
BQB_IS_ENCODED_BY
GI:16128699; 945300; ABE-0002468; EG10932
b0722 G_b0722 sdhD b0722
BQB_IS
P0AC44
BQB_IS_ENCODED_BY
GI:16128697; 945322; ABE-0002464; EG10934
b0721 G_b0721 sdhC b0721
BQB_IS
P69054
BQB_IS_ENCODED_BY
GI:16128696; 945316; ABE-0002460; EG10933
b0728 G_b0728 sucC b0728
BQB_IS
P0A836
BQB_IS_ENCODED_BY
GI:16128703; 945312; ABE-0002483; EG10981
b0729 G_b0729 sucD b0729
BQB_IS
P0AGE9
BQB_IS_ENCODED_BY
GI:16128704; 945314; ABE-0002485; EG10982
b2464 G_b2464 talA b2464
BQB_IS
P0A867
BQB_IS_ENCODED_BY
GI:16130389; 947006; ABE-0008115; EG11797
b0008 G_b0008 talB b0008
BQB_IS
P0A870
BQB_IS_ENCODED_BY
GI:16128002; 944748; ABE-0000027; EG11556
b2465 G_b2465 tktB b2465
BQB_IS
P33570
BQB_IS_ENCODED_BY
GI:16130390; 945865; ABE-0008117; EG12100
b2935 G_b2935 tktA b2935
BQB_IS
P27302
BQB_IS_ENCODED_BY
GI:49176286; 947420; ABE-0009625; EG11427
b3919 G_b3919 tpiA b3919
BQB_IS
P0A858
BQB_IS_ENCODED_BY
GI:16131757; 948409; ABE-0012799; EG11015

Parameters [47] name constant value unit derived unit sbo cvterm
cobra_default_lb cobra default - lb -1000.0 mmol_per_gDW_per_hr 10 3 mole g 3600 s
cobra_default_ub cobra default - ub 1000.0 mmol_per_gDW_per_hr 10 3 mole g 3600 s
cobra_0_bound cobra 0 - bound 0.0 mmol_per_gDW_per_hr 10 3 mole g 3600 s
R_ATPM_lower_bound R ATPM lower - bound 0.0 mmol_per_gDW_per_hr 10 3 mole g 3600 s
R_EX_glc__D_e_lower_bound R EX glc-D e lower - bound -10.0 mmol_per_gDW_per_hr 10 3 mole g 3600 s
lb_EX_mal__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_mal__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_acald_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_acald_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_pyr_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_pyr_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_glc__D_e -10.0 mmol_per_h 10 3 mole 3600 s
ub_EX_glc__D_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_etoh_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_etoh_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_nh4_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_nh4_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_h2o_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_h2o_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_ac_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_ac_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_akg_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_akg_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_co2_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_co2_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_lac__D_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_lac__D_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_fum_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_fum_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_fru_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_fru_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_for_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_for_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_gln__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_gln__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_succ_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_succ_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_h_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_h_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_pi_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_pi_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_glu__L_e 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_glu__L_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_o2_e -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_o2_e 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_X 0.0 mmol_per_h 10 3 mole 3600 s
ub_EX_X 1000.0 mmol_per_h 10 3 mole 3600 s

Reactions [96] id name equation modifiers kinetic law derived units sbo cvterm
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
BQB_IS
ACALD
ACALDt R_ACALDt Acetaldehyde reversible transport
[-1000.0 1000.0]
s0001
acald_e ⇆ acald_c
BQB_IS
ACALDt
ACKr R_ACKr Acetate kinase
[-1000.0 1000.0]
(b2296 or b3115 or b1849)
ac_c + atp_c ⇆ actp_c + adp_c
BQB_IS
ACKr
ACONTa R_ACONTa Aconitase (half-reaction A, Citrate hydro-lyase)
[-1000.0 1000.0]
(b0118 or b1276)
cit_c ⇆ acon_C_c + h2o_c
BQB_IS
ACONTa
ACONTb R_ACONTb Aconitase (half-reaction B, Isocitrate hydro-lyase)
[-1000.0 1000.0]
(b0118 or b1276)
acon_C_c + h2o_c ⇆ icit_c
BQB_IS
ACONTb
ACt2r R_ACt2r Acetate reversible transport via proton symport
[-1000.0 1000.0]
ac_e + h_e ⇆ ac_c + h_c
BQB_IS
ACt2r
ADK1 R_ADK1 Adenylate kinase
[-1000.0 1000.0]
b0474
amp_c + atp_c ⇆ 2.0 adp_c
BQB_IS
ADK1
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
BQB_IS
AKGDH
AKGt2r R_AKGt2r 2 oxoglutarate reversible transport via symport
[-1000.0 1000.0]
b2587
akg_e + h_e ⇆ akg_c + h_c
BQB_IS
AKGt2r
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
BQB_IS
ALCD2x
ATPM R_ATPM ATP maintenance requirement
[0.0 1000.0]
atp_c + h2o_c ➞ adp_c + h_c + pi_c
BQB_IS
ATPM
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
BQB_IS
ATPS4r
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
CO2t R_CO2t CO2 transporter via diffusion
[-1000.0 1000.0]
s0001
co2_e ⇆ co2_c
BQB_IS
CO2t
CS R_CS Citrate synthase
[0.0 1000.0]
b0720
accoa_c + h2o_c + oaa_c ➞ cit_c + coa_c + h_c
BQB_IS
CS
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
BQB_IS
CYTBD
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
BQB_IS
D_LACt2
ENO R_ENO Enolase
[-1000.0 1000.0]
b2779
M_2pg_c ⇆ h2o_c + pep_c
BQB_IS
ENO
ETOHt2r R_ETOHt2r ETOHt2r
[-1000.0 1000.0]
etoh_e + h_e ⇆ etoh_c + h_c
BQB_IS
ETOHt2r
EX_ac_e R_EX_ac_e Acetate exchange
[0.0 1000.0]
ac_e ⇆
BQB_IS
ac
EX_acald_e R_EX_acald_e Acetaldehyde exchange
[0.0 1000.0]
acald_e ⇆
BQB_IS
acald
EX_akg_e R_EX_akg_e 2-Oxoglutarate exchange
[0.0 1000.0]
akg_e ⇆
BQB_IS
akg
EX_co2_e R_EX_co2_e CO2 exchange
[-1000.0 1000.0]
co2_e ⇆
BQB_IS
co2
EX_etoh_e R_EX_etoh_e Ethanol exchange
[0.0 1000.0]
etoh_e ⇆
BQB_IS
etoh
EX_for_e R_EX_for_e Formate exchange
[0.0 1000.0]
for_e ⇆
BQB_IS
for
EX_fru_e R_EX_fru_e D-Fructose exchange
[0.0 1000.0]
fru_e ⇆
BQB_IS
fru
EX_fum_e R_EX_fum_e Fumarate exchange
[0.0 1000.0]
fum_e ⇆
BQB_IS
fum
EX_glc__D_e R_EX_glc__D_e D-Glucose exchange
[-10.0 1000.0]
glc__D_e ⇆
BQB_IS
glc__D
EX_gln__L_e R_EX_gln__L_e L-Glutamine exchange
[0.0 1000.0]
gln__L_e ⇆
BQB_IS
gln__L
EX_glu__L_e R_EX_glu__L_e L-Glutamate exchange
[0.0 1000.0]
glu__L_e ⇆
BQB_IS
glu__L
EX_h_e R_EX_h_e H+ exchange
[-1000.0 1000.0]
h_e ⇆
BQB_IS
h
EX_h2o_e R_EX_h2o_e H2O exchange
[-1000.0 1000.0]
h2o_e ⇆
BQB_IS
h2o
EX_lac__D_e R_EX_lac__D_e D-lactate exchange
[0.0 1000.0]
lac__D_e ⇆
BQB_IS
lac__D
EX_mal__L_e R_EX_mal__L_e L-Malate exchange
[0.0 1000.0]
mal__L_e ⇆
BQB_IS
mal__L
EX_nh4_e R_EX_nh4_e Ammonia exchange
[-1000.0 1000.0]
nh4_e ⇆
BQB_IS
nh4
EX_o2_e R_EX_o2_e O2 exchange
[-1000.0 1000.0]
o2_e ⇆
BQB_IS
o2
EX_pi_e R_EX_pi_e Phosphate exchange
[-1000.0 1000.0]
pi_e ⇆
BQB_IS
pi
EX_pyr_e R_EX_pyr_e Pyruvate exchange
[0.0 1000.0]
pyr_e ⇆
BQB_IS
pyr
EX_succ_e R_EX_succ_e Succinate exchange
[0.0 1000.0]
succ_e ⇆
BQB_IS
succ
FBA R_FBA Fructose-bisphosphate aldolase
[-1000.0 1000.0]
(b1773 or b2097 or b2925)
fdp_c ⇆ dhap_c + g3p_c
BQB_IS
FBA
FBP R_FBP Fructose-bisphosphatase
[0.0 1000.0]
(b3925 or b4232)
fdp_c + h2o_c ➞ f6p_c + pi_c
BQB_IS
FBP
FORt2 R_FORt2 Formate transport in via proton symport
[0.0 1000.0]
(b0904 or b2492)
for_e + h_e ➞ for_c + h_c
BQB_IS
FORt2
FORti R_FORti Formate transport via diffusion
[0.0 1000.0]
(b0904 or b2492)
for_c ➞ for_e
BQB_IS
FORti
FRD7 R_FRD7 Fumarate reductase
[0.0 1000.0]
(b4153 and b4151 and b4152 and b4154)
fum_c + q8h2_c ➞ q8_c + succ_c
BQB_IS
FRD7
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
BQB_IS
FRUpts2
FUM R_FUM Fumarase
[-1000.0 1000.0]
(b4122 or b1612 or b1611)
fum_c + h2o_c ⇆ mal__L_c
BQB_IS
FUM
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
BQB_IS
FUMt2_2
G6PDH2r R_G6PDH2r Glucose 6-phosphate dehydrogenase
[-1000.0 1000.0]
b1852
g6p_c + nadp_c ⇆ M_6pgl_c + h_c + nadph_c
BQB_IS
G6PDH2r
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
BQB_IS
GAPD
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
BQB_IS
GLCpts
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
BQB_IS
GLNS
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
BQB_IS
GLNabc
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
BQB_IS
GLUDy
GLUN R_GLUN Glutaminase
[0.0 1000.0]
(b0485 or b1812 or b1524)
gln__L_c + h2o_c ➞ glu__L_c + nh4_c
BQB_IS
GLUN
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
BQB_IS
GLUSy
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
BQB_IS
GLUt2r
GND R_GND Phosphogluconate dehydrogenase
[0.0 1000.0]
b2029
M_6pgc_c + nadp_c ➞ co2_c + nadph_c + ru5p__D_c
BQB_IS
GND
H2Ot R_H2Ot H2O transport via diffusion
[-1000.0 1000.0]
(b0875 or s0001)
h2o_e ⇆ h2o_c
BQB_IS
H2Ot
ICDHyr R_ICDHyr Isocitrate dehydrogenase (NADP)
[-1000.0 1000.0]
b1136
icit_c + nadp_c ⇆ akg_c + co2_c + nadph_c
BQB_IS
ICDHyr
ICL R_ICL Isocitrate lyase
[0.0 1000.0]
b4015
icit_c ➞ glx_c + succ_c
BQB_IS
ICL
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
BQB_IS
LDH_D
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
BQB_IS
MALS
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
BQB_IS
MALt2_2
MDH R_MDH Malate dehydrogenase
[-1000.0 1000.0]
b3236
mal__L_c + nad_c ⇆ h_c + nadh_c + oaa_c
BQB_IS
MDH
ME1 R_ME1 Malic enzyme (NAD)
[0.0 1000.0]
b1479
mal__L_c + nad_c ➞ co2_c + nadh_c + pyr_c
BQB_IS
ME1
ME2 R_ME2 Malic enzyme (NADP)
[0.0 1000.0]
b2463
mal__L_c + nadp_c ➞ co2_c + nadph_c + pyr_c
BQB_IS
ME2
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
BQB_IS
NADH16
NADTRHD R_NADTRHD NAD transhydrogenase
[0.0 1000.0]
(b3962 or (b1602 and b1603))
nad_c + nadph_c ➞ nadh_c + nadp_c
BQB_IS
NADTRHD
NH4t R_NH4t Ammonia reversible transport
[-1000.0 1000.0]
(s0001 or b0451)
nh4_e ⇆ nh4_c
BQB_IS
NH4t
O2t R_O2t O2 transport diffusion
[-1000.0 1000.0]
s0001
o2_e ⇆ o2_c
BQB_IS
O2t
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
BQB_IS
PDH
PFK R_PFK Phosphofructokinase
[0.0 1000.0]
(b3916 or b1723)
atp_c + f6p_c ➞ adp_c + fdp_c + h_c
BQB_IS
PFK
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
BQB_IS
PFL
PGI R_PGI Glucose-6-phosphate isomerase
[-1000.0 1000.0]
b4025
g6p_c ⇆ f6p_c
BQB_IS
PGI
PGK R_PGK Phosphoglycerate kinase
[-1000.0 1000.0]
b2926
M_3pg_c + atp_c ⇆ M_13dpg_c + adp_c
BQB_IS
PGK
PGL R_PGL 6-phosphogluconolactonase
[0.0 1000.0]
b0767
M_6pgl_c + h2o_c ➞ M_6pgc_c + h_c
BQB_IS
PGL
PGM R_PGM Phosphoglycerate mutase
[-1000.0 1000.0]
(b4395 or b3612 or b0755)
M_2pg_c ⇆ M_3pg_c
BQB_IS
PGM
PIt2r R_PIt2r Phosphate reversible transport via symport
[-1000.0 1000.0]
(b2987 or b3493)
h_e + pi_e ⇆ h_c + pi_c
BQB_IS
PIt2r
PPC R_PPC Phosphoenolpyruvate carboxylase
[0.0 1000.0]
b3956
co2_c + h2o_c + pep_c ➞ h_c + oaa_c + pi_c
BQB_IS
PPC
PPCK R_PPCK Phosphoenolpyruvate carboxykinase
[0.0 1000.0]
b3403
atp_c + oaa_c ➞ adp_c + co2_c + pep_c
BQB_IS
PPCK
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
BQB_IS
PPS
PTAr R_PTAr Phosphotransacetylase
[-1000.0 1000.0]
(b2297 or b2458)
accoa_c + pi_c ⇆ actp_c + coa_c
BQB_IS
PTAr
PYK R_PYK Pyruvate kinase
[0.0 1000.0]
(b1854 or b1676)
adp_c + h_c + pep_c ➞ atp_c + pyr_c
BQB_IS
PYK
PYRt2 R_PYRt2 Pyruvate transport in via proton symport
[-1000.0 1000.0]
h_e + pyr_e ⇆ h_c + pyr_c
BQB_IS
PYRt2
RPE R_RPE Ribulose 5-phosphate 3-epimerase
[-1000.0 1000.0]
(b3386 or b4301)
ru5p__D_c ⇆ xu5p__D_c
BQB_IS
RPE
RPI R_RPI Ribose-5-phosphate isomerase
[-1000.0 1000.0]
(b2914 or b4090)
r5p_c ⇆ ru5p__D_c
BQB_IS
RPI
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
BQB_IS
SUCCt2_2
SUCCt3 R_SUCCt3 Succinate transport out via proton antiport
[0.0 1000.0]
h_e + succ_c ➞ h_c + succ_e
BQB_IS
SUCCt3
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
BQB_IS
SUCDi
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
BQB_IS
SUCOAS
TALA R_TALA Transaldolase
[-1000.0 1000.0]
(b2464 or b0008)
g3p_c + s7p_c ⇆ e4p_c + f6p_c
BQB_IS
TALA
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
BQB_IS
THD2
TKT1 R_TKT1 Transketolase
[-1000.0 1000.0]
(b2935 or b2465)
r5p_c + xu5p__D_c ⇆ g3p_c + s7p_c
BQB_IS
TKT1
TKT2 R_TKT2 Transketolase
[-1000.0 1000.0]
(b2935 or b2465)
e4p_c + xu5p__D_c ⇆ f6p_c + g3p_c
BQB_IS
TKT2
TPI R_TPI Triose-phosphate isomerase
[-1000.0 1000.0]
b3919
dhap_c ⇆ g3p_c
BQB_IS
TPI
EX_X
[0.0 1000.0]
X ⇆

Objectives [1] name type flux objectives sbo cvterm
obj maximize +1.0*BIOMASS_Ecoli_core_w_GAM