Enzyme-constrained B. subtilis model (based on iYO844)

• Brief Repository Description:
  This repository contains the current enzyme-constrained metabolic model of Bacillus subtilis (<ec_iYO844.mat>).

• Model KeyWords:
  GEM Category: Species; Utilisation: predictive simulation, in silico strain design; Field: metabolic-network reconstruction; Type of Model: curated, reconstruction; Model Source: iYO844; Taxonomy: Bacillus subtilis; Metabolic System: General Metabolism; Condition: aerobic, glucose minimal medium.

• Last update: 2018-10-10

• The model contains:

• This repository is administered by Ilaria Massaiu, @IMassaiu, BMS Lab, University of Pavia, via Ferrata 5 (Italy), Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby (Denmark).

Recommended Software:

• A functional Matlab installation (MATLAB 2010a or higher).
• COBRA Toolbox for MATLAB.
• Gurobi Optimizer for MATLAB.

Complementary Scripts

• <analysis.m>: Example in which the model is analysed by pFBA, FVA and MOMA.

Complementary Data

• <EnzymaticData.xls>: The abbreviation name, locus name, protein, kcat [h^-1] value, 95% confidence interval of protein abundance value [mmol/g_dw] and molecular weights [kDa] are reported for each enzyme-constrained reaction.
• <Dataset.xls>: The experimental [Chubukov et al. 2013, Fischer and Sauer 2005 and Kobayashi K et al. 2003] and predicted (with iYO844 and ec_iYO844) data of B. subtilis wild-type and single-gene deletion strains are reported.

Contributors

• Ilaria Massaiu, @IMassaiu, BMS Lab, University of Pavia, via Ferrata 5 (Italy).
• Markus J. Herrgård, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby (Denmark).
• Nikolaus Sonnenschein, @phantomas1234, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.