E coli SBML

E. coli SBML files

SBML files contain reconstruction (see sbml.org for documentation)

  • reactions (format: ‘R_< reaction abbreviation >’)
    • reaction name, reversibility, reaction stoichiometry, gene-protein-reaction (GPR) association, subsystem, E.C. number
  • metabolites (format: ‘M_< metabolite abbreviation >_< compartment abbreviation >’)
    • metabolite name, compartment, charge, formula (appended to the end of the name, < metabolite name >_FORMULA)
  • Optional (files noted with a 'flux'): a flux distribution associated with a steady-state modeling simulation
    • lower bound, upper bound, objective coefficient, flux value, reduced cost

Reconstructions

core - E. coli core model - Ec_core_flux1.xml This is a condensed version of the genome-scale E. coli reconstruction and contains central metabolism reactions. The network contains 62 internal reactions, 14 exchange reactions and a biomass objective function. It is utilized extensively in Systems Biology: Properties of Reconstructed Networks by Bernhard O. Palsson as a teaching device.

File info: This flux distribution was generated using FBA optimizing for the flux through the 'Biomass_Ecoli_core_N (w/GAM)' reaction in the network. The constraining exchange reaction flux in the simulation is the 'Ex_glc(e)' reaction (glucose uptake of 10 mmol gDW-1 hr-1). Aerobic minimal media conditions. Also, a set non-growth associated maintenance of 7.6 mmol ATP gDW-1 hr-1 is constrained in the file using the 'ATPM' reaction. See file for all system constraints.

iJE660a (Formerly Version 1.01) (739 Reactions) - removed, use more recent

iJR904 Published in Genome Biology (2003) (931 Reactions)

SBML (level 2, version 1): Ec_iJR904.xml

SBML (level 2, version 1) w/ a flux distribution: Ec_iJR904_flux1.xml File info: This flux distribution was generated using FBA optimizing for the flux through the 'BiomassEcoli' reaction in the network. The constraining exchange reaction flux in the simulation is the 'Ex_glc(e)' reaction (glucose uptake of 10 mmol gDW-1 hr-1). Aerobic minimal media conditions. See file for all system constraints.

iAF1260 Published in Molecular Systems Biology (2007)

(2077 Reactions)

SBML (level 2, version 1) w/ a flux distribution: Ec_iAF1260_flux1.xml & flux.xml

(Supplementary Information 4 from MSB publication)

File info for iAF1260:

SBML File Properties  
file name Ec_iAF1260_flux1.xml
organism E. coli K-12 MG1655
model iAF1260
Biomass Objective Function (BOF) Ec_biomass_iAF1260_core_59p81M (E. coli biomass objective function (iAF1260) - core - with 59.81 GAM estimate)
flux balance analysis objective maximize BOF
Growth Associated Maintenance (GAM) 59.81 mmol ATP gDW-1
Non-Growth Associated Maintenance (NGAM) 8.39 mmol ATP gDW-1 hr-1
media conditions computational minimal media
carbon source 8 mmol glucose gDw-1 hr-1
aerobic or anaerobic 18.5 mmol O2 gDw-1 hr-1
additional constraints  
reactions constrained to zero CAT, SPODM, SPODMpp, FHL
flux split between reaction pairs  
SBML File Properties  
file name Ec_iAF1260_flux2.xml
organism E. coli K-12 MG1655
model iAF1260
Biomass Objective Function (BOF) Ec_biomass_iAF1260_core_59p81M (E. coli biomass objective function (iAF1260) - core - with 59.81 GAM estimate)
flux balance analysis objective maximize BOF
Growth Associated Maintenance (GAM) 59.81 mmol ATP gDW-1
Non-Growth Associated Maintenance (NGAM) 8.39 mmol ATP gDW-1 hr-1
media conditions computational minimal media
carbon source 11.0 mmol glucose gDw-1 hr-1
aerobic or anaerobic 18.2 mmol O2 gDw-1 hr-1
additional constraints  
reactions constrained to zero 152 reactions identified to be unavailable to the cell under glucose aerobic conditions
flux split between reaction pairs NDH-1:NDH-2 is 1:1 (3 pairs of reactions - different quinone usage) NADH10:NADH17pp, NADH5:NADH16pp, NADH9:NADH18pp

SBML files are periodically updated. For changes, see change log.

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