E.coli core DFBA model

Model version: 1

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 Homo sapiens 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: iAB_RBC_283.

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 : rbc_update

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-31 17:30
Modified: 2017-03-31 17:30

SBML model


idrbc_update
namerbc (UPDATE)
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
UnitDefinitions [12] name units sbo cvterm
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_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 [1] name size constant spatial dimensions unit derived unit sbo cvterm
blood blood 1.0 3 l litre

Species [76] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
ins_e Inosine
blood 1.0 mmol 10 3 mole litre
gln__L_e L-Glutamine
blood 1.0 mmol 10 3 mole litre
lnlc_e Lnlc c
blood 1.0 mmol 10 3 mole litre
thm_e Thiamin
blood 1.0 mmol 10 3 mole litre
ncam_e Nicotinamide
blood 1.0 mmol 10 3 mole litre
nac_e Nicotinate
blood 1.0 mmol 10 3 mole litre
urea_e Urea
blood 1.0 mmol 10 3 mole litre
hco3_e Bicarbonate
blood 1.0 mmol 10 3 mole litre
fum_e Fumarate
blood 1.0 mmol 10 3 mole litre
pydxn_e Pyridoxine
blood 1.0 mmol 10 3 mole litre
M_4pyrdx_e 4pyrdx c
blood 1.0 mmol 10 3 mole litre
normete__L_e Normete L c
blood 1.0 mmol 10 3 mole litre
bilglcur_e Bilglcur c
blood 1.0 mmol 10 3 mole litre
glyc_e Glycerol
blood 1.0 mmol 10 3 mole litre
h2o_e H2O
blood 1.0 mmol 10 3 mole litre
h_e H+
blood 1.0 mmol 10 3 mole litre
lac__L_e L-Lactate
blood 1.0 mmol 10 3 mole litre
sprm_e Spermine C10H30N4
blood 1.0 mmol 10 3 mole litre
M_3moxtyr_e 3moxtyr c
blood 1.0 mmol 10 3 mole litre
nrpphr_e Nrpphr c
blood 1.0 mmol 10 3 mole litre
acnam_e N-Acetylneuraminate
blood 1.0 mmol 10 3 mole litre
thmmp_e Thiamin monophosphate
blood 1.0 mmol 10 3 mole litre
co2_e CO2
blood 1.0 mmol 10 3 mole litre
lac__D_e D-Lactate
blood 1.0 mmol 10 3 mole litre
mal__L_e L-Malate
blood 1.0 mmol 10 3 mole litre
ocdcea_e Octadecenoate (n-C18:1)
blood 1.0 mmol 10 3 mole litre
k_e Potassium
blood 1.0 mmol 10 3 mole litre
na1_e Sodium
blood 1.0 mmol 10 3 mole litre
dhdascb_e Dhdascb c
blood 1.0 mmol 10 3 mole litre
cl_e Chloride
blood 1.0 mmol 10 3 mole litre
arg__L_e L-Arginine
blood 1.0 mmol 10 3 mole litre
nh4_e Ammonium
blood 1.0 mmol 10 3 mole litre
adrnl_e Adrnl c
blood 1.0 mmol 10 3 mole litre
ala__L_e L-Alanine
blood 1.0 mmol 10 3 mole litre
ptrc_e Putrescine
blood 1.0 mmol 10 3 mole litre
gal_e D-Galactose
blood 1.0 mmol 10 3 mole litre
ascb__L_e L-Ascorbate
blood 1.0 mmol 10 3 mole litre
h2o2_e Hydrogen peroxide
blood 1.0 mmol 10 3 mole litre
mepi_e Mepi c
blood 1.0 mmol 10 3 mole litre
acald_e Acetaldehyde
blood 1.0 mmol 10 3 mole litre
leuktrB4_e LeuktrB4 c
blood 1.0 mmol 10 3 mole litre
adn_e Adenosine
blood 1.0 mmol 10 3 mole litre
pi_e Phosphate
blood 1.0 mmol 10 3 mole litre
orot_e Orotate
blood 1.0 mmol 10 3 mole litre
M_5aop_e 5-Amino-4-oxopentanoate
blood 1.0 mmol 10 3 mole litre
phe__L_e L-Phenylalanine
blood 1.0 mmol 10 3 mole litre
etha_e Ethanolamine
blood 1.0 mmol 10 3 mole litre
co_e Carbon monoxide
blood 1.0 mmol 10 3 mole litre
dopa_e Dopamine
blood 1.0 mmol 10 3 mole litre
man_e D-Mannose
blood 1.0 mmol 10 3 mole litre
gam_e D-Glucosamine
blood 1.0 mmol 10 3 mole litre
pydx_e Pyridoxal
blood 1.0 mmol 10 3 mole litre
ac_e Acetate
blood 1.0 mmol 10 3 mole litre
hxan_e Hypoxanthine
blood 1.0 mmol 10 3 mole litre
glc__D_e D-Glucose
blood 1.0 mmol 10 3 mole litre
uri_e Uridine
blood 1.0 mmol 10 3 mole litre
ade_e Adenine
blood 1.0 mmol 10 3 mole litre
camp_e CAMP
blood 1.0 mmol 10 3 mole litre
hcys__L_e L-Homocysteine
blood 1.0 mmol 10 3 mole litre
o2_e O2
blood 1.0 mmol 10 3 mole litre
hdca_e Hexadecanoate (n-C16:0)
blood 1.0 mmol 10 3 mole litre
pydam_e Pyridoxamine
blood 1.0 mmol 10 3 mole litre
M_35cgmp_e 3',5'-Cyclic GMP
blood 1.0 mmol 10 3 mole litre
met__L_e L-Methionine
blood 1.0 mmol 10 3 mole litre
gly_e Glycine
blood 1.0 mmol 10 3 mole litre
cys__L_e L-Cysteine
blood 1.0 mmol 10 3 mole litre
chol_e Choline
blood 1.0 mmol 10 3 mole litre
ca2_e Calcium
blood 1.0 mmol 10 3 mole litre
gluala_e 5 L Glutamyl L alanine C8H13N2O5
blood 1.0 mmol 10 3 mole litre
ribflv_e Riboflavin
blood 1.0 mmol 10 3 mole litre
fru_e D-Fructose
blood 1.0 mmol 10 3 mole litre
spmd_e Spermidine
blood 1.0 mmol 10 3 mole litre
fe2_e Fe2+
blood 1.0 mmol 10 3 mole litre
leuktrA4_e LeuktrA4 c
blood 1.0 mmol 10 3 mole litre
pyr_e Pyruvate
blood 1.0 mmol 10 3 mole litre
gthox_e Oxidized glutathione
blood 1.0 mmol 10 3 mole litre

Parameters [76] name value unit derived unit constant sbo cvterm
EX_ins_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gln__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_lnlc_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_thm_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ncam_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_nac_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_urea_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_hco3_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_fum_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pydxn_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_M_4pyrdx_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_normete__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_bilglcur_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_glyc_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_h2o_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_h_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_lac__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_sprm_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_M_3moxtyr_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_nrpphr_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_acnam_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_thmmp_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_co2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_lac__D_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_mal__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ocdcea_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_k_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_na1_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_dhdascb_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_cl_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_arg__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_nh4_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_adrnl_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ala__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ptrc_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gal_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ascb__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_h2o2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_mepi_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_acald_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_leuktrB4_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_adn_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pi_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_orot_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_M_5aop_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_phe__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_etha_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_co_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_dopa_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_man_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gam_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pydx_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ac_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_hxan_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_glc__D_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_uri_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ade_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_camp_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_hcys__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_o2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_hdca_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pydam_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_M_35cgmp_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_met__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gly_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_cys__L_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_chol_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ca2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gluala_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_ribflv_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_fru_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_spmd_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_fe2_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_leuktrA4_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_pyr_e 1.0 mmol_per_h 10 3 mole 3600 s
EX_gthox_e 1.0 mmol_per_h 10 3 mole 3600 s

Reactions [76] name equation modifiers formula derived units sbo cvterm
update_ins_e ins_e ⇆ EX_ins_e 10 3 mole 3600 s
update_gln__L_e gln__L_e ⇆ EX_gln__L_e 10 3 mole 3600 s
update_lnlc_e lnlc_e ⇆ EX_lnlc_e 10 3 mole 3600 s
update_thm_e thm_e ⇆ EX_thm_e 10 3 mole 3600 s
update_ncam_e ncam_e ⇆ EX_ncam_e 10 3 mole 3600 s
update_nac_e nac_e ⇆ EX_nac_e 10 3 mole 3600 s
update_urea_e urea_e ⇆ EX_urea_e 10 3 mole 3600 s
update_hco3_e hco3_e ⇆ EX_hco3_e 10 3 mole 3600 s
update_fum_e fum_e ⇆ EX_fum_e 10 3 mole 3600 s
update_pydxn_e pydxn_e ⇆ EX_pydxn_e 10 3 mole 3600 s
update_M_4pyrdx_e M_4pyrdx_e ⇆ EX_M_4pyrdx_e 10 3 mole 3600 s
update_normete__L_e normete__L_e ⇆ EX_normete__L_e 10 3 mole 3600 s
update_bilglcur_e bilglcur_e ⇆ EX_bilglcur_e 10 3 mole 3600 s
update_glyc_e glyc_e ⇆ EX_glyc_e 10 3 mole 3600 s
update_h2o_e h2o_e ⇆ EX_h2o_e 10 3 mole 3600 s
update_h_e h_e ⇆ EX_h_e 10 3 mole 3600 s
update_lac__L_e lac__L_e ⇆ EX_lac__L_e 10 3 mole 3600 s
update_sprm_e sprm_e ⇆ EX_sprm_e 10 3 mole 3600 s
update_M_3moxtyr_e M_3moxtyr_e ⇆ EX_M_3moxtyr_e 10 3 mole 3600 s
update_nrpphr_e nrpphr_e ⇆ EX_nrpphr_e 10 3 mole 3600 s
update_acnam_e acnam_e ⇆ EX_acnam_e 10 3 mole 3600 s
update_thmmp_e thmmp_e ⇆ EX_thmmp_e 10 3 mole 3600 s
update_co2_e co2_e ⇆ EX_co2_e 10 3 mole 3600 s
update_lac__D_e lac__D_e ⇆ EX_lac__D_e 10 3 mole 3600 s
update_mal__L_e mal__L_e ⇆ EX_mal__L_e 10 3 mole 3600 s
update_ocdcea_e ocdcea_e ⇆ EX_ocdcea_e 10 3 mole 3600 s
update_k_e k_e ⇆ EX_k_e 10 3 mole 3600 s
update_na1_e na1_e ⇆ EX_na1_e 10 3 mole 3600 s
update_dhdascb_e dhdascb_e ⇆ EX_dhdascb_e 10 3 mole 3600 s
update_cl_e cl_e ⇆ EX_cl_e 10 3 mole 3600 s
update_arg__L_e arg__L_e ⇆ EX_arg__L_e 10 3 mole 3600 s
update_nh4_e nh4_e ⇆ EX_nh4_e 10 3 mole 3600 s
update_adrnl_e adrnl_e ⇆ EX_adrnl_e 10 3 mole 3600 s
update_ala__L_e ala__L_e ⇆ EX_ala__L_e 10 3 mole 3600 s
update_ptrc_e ptrc_e ⇆ EX_ptrc_e 10 3 mole 3600 s
update_gal_e gal_e ⇆ EX_gal_e 10 3 mole 3600 s
update_ascb__L_e ascb__L_e ⇆ EX_ascb__L_e 10 3 mole 3600 s
update_h2o2_e h2o2_e ⇆ EX_h2o2_e 10 3 mole 3600 s
update_mepi_e mepi_e ⇆ EX_mepi_e 10 3 mole 3600 s
update_acald_e acald_e ⇆ EX_acald_e 10 3 mole 3600 s
update_leuktrB4_e leuktrB4_e ⇆ EX_leuktrB4_e 10 3 mole 3600 s
update_adn_e adn_e ⇆ EX_adn_e 10 3 mole 3600 s
update_pi_e pi_e ⇆ EX_pi_e 10 3 mole 3600 s
update_orot_e orot_e ⇆ EX_orot_e 10 3 mole 3600 s
update_M_5aop_e M_5aop_e ⇆ EX_M_5aop_e 10 3 mole 3600 s
update_phe__L_e phe__L_e ⇆ EX_phe__L_e 10 3 mole 3600 s
update_etha_e etha_e ⇆ EX_etha_e 10 3 mole 3600 s
update_co_e co_e ⇆ EX_co_e 10 3 mole 3600 s
update_dopa_e dopa_e ⇆ EX_dopa_e 10 3 mole 3600 s
update_man_e man_e ⇆ EX_man_e 10 3 mole 3600 s
update_gam_e gam_e ⇆ EX_gam_e 10 3 mole 3600 s
update_pydx_e pydx_e ⇆ EX_pydx_e 10 3 mole 3600 s
update_ac_e ac_e ⇆ EX_ac_e 10 3 mole 3600 s
update_hxan_e hxan_e ⇆ EX_hxan_e 10 3 mole 3600 s
update_glc__D_e glc__D_e ⇆ EX_glc__D_e 10 3 mole 3600 s
update_uri_e uri_e ⇆ EX_uri_e 10 3 mole 3600 s
update_ade_e ade_e ⇆ EX_ade_e 10 3 mole 3600 s
update_camp_e camp_e ⇆ EX_camp_e 10 3 mole 3600 s
update_hcys__L_e hcys__L_e ⇆ EX_hcys__L_e 10 3 mole 3600 s
update_o2_e o2_e ⇆ EX_o2_e 10 3 mole 3600 s
update_hdca_e hdca_e ⇆ EX_hdca_e 10 3 mole 3600 s
update_pydam_e pydam_e ⇆ EX_pydam_e 10 3 mole 3600 s
update_M_35cgmp_e M_35cgmp_e ⇆ EX_M_35cgmp_e 10 3 mole 3600 s
update_met__L_e met__L_e ⇆ EX_met__L_e 10 3 mole 3600 s
update_gly_e gly_e ⇆ EX_gly_e 10 3 mole 3600 s
update_cys__L_e cys__L_e ⇆ EX_cys__L_e 10 3 mole 3600 s
update_chol_e chol_e ⇆ EX_chol_e 10 3 mole 3600 s
update_ca2_e ca2_e ⇆ EX_ca2_e 10 3 mole 3600 s
update_gluala_e gluala_e ⇆ EX_gluala_e 10 3 mole 3600 s
update_ribflv_e ribflv_e ⇆ EX_ribflv_e 10 3 mole 3600 s
update_fru_e fru_e ⇆ EX_fru_e 10 3 mole 3600 s
update_spmd_e spmd_e ⇆ EX_spmd_e 10 3 mole 3600 s
update_fe2_e fe2_e ⇆ EX_fe2_e 10 3 mole 3600 s
update_leuktrA4_e leuktrA4_e ⇆ EX_leuktrA4_e 10 3 mole 3600 s
update_pyr_e pyr_e ⇆ EX_pyr_e 10 3 mole 3600 s
update_gthox_e gthox_e ⇆ EX_gthox_e 10 3 mole 3600 s