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:
| Taxonomy | Template Model | Reaction | Metabolites | Genes |
|---|---|---|---|---|
| Bacillus subtilis | iYO844 | 1250 | 990 | 844 |
- 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/gdw] 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.