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.