Models

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn and NAD rec will be reproduced.

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts

Model for the Caulobacter crescentus α-ketoglutarate semialdehyde dehydrogenase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KGSADH will be reproduced.

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.

Model for the Caulobacter crescentus xylose dehydrogenase, describing the initial rate kinetics including substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XDH kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XDH will be reproduced.

Model for the Caulobacter crescentus xylonolactonase, describing the initial rate kinetics and substrate dependence. If the Mathematica notebook is downloaded and the data file for the XLA kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XLA will be reproduced.

Model for the Caulobacter crescentus xylonate dehydratase, describing the initial rate kinetics for substrate dependence. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XAD will be reproduced.

Model for the Caulobacter crescentus 2-keto-3-deoxy-D-xylonate dehydratase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KDXD will be reproduced.

Glycolytic model for Plasmodium falciparum; open system

Mathematica notebook for the parameterisation of the glucose transport rate equation based on SEEK linked experimental data.

Glycolytic model for Plasmodium falciparum; closed system

Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the ALD rate equation based on SEEK linked experimental data.

Mathematica notebook for the ATPase reaction.

Mathematica notebook for the parameterisation of the ENO rate equation based on SEEK linked experimental data.

Mathematica notebook for the lactate transport rate equation, based on literature data.

Mathematica notebook for the glycerol transport rate equation.

Mathematica notebook for the parameterisation of the GAPDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the LDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the TPI rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.

Mathematica notebook for the pyruvate transport rate equation, based on literature data.

Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set