Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-05 Changed the model name so the model loads in the database easier. Cuellar Autumn A 2003-04-05 Added more metadata. Lloyd Catherine May 2002-07-22 The University of Auckland, Bioengineering Institute A Generic Model Of Pyrimidine Nucleotide Synthesis Below is a CellML description of a general model of pyrimidine nucleotide synthesis. It is not based on a specific published mathematical model, but instead it is based on a textbook defined pathway. The general sequential structure and all the reactant, product and enzyme components are included. Michaelis-Menten enzyme kinetics are assumed. The purpose of this description is to illustrate how CellML can be used to model a general metabolic pathway. Catherine Lloyd Homo sapiens keyword metabolism Bronk J Ramsey Human Metabolism 1999 Addison Wesley Longman Limited location England $\frac{d \mathrm{Glutamate}}{d \mathrm{time}}=\mathrm{delta\_Glutamate\_rxn7}$ $\frac{d \mathrm{Glutamine}}{d \mathrm{time}}=\mathrm{delta\_Glutamine\_rxn7}+\mathrm{delta\_Glutamine\_rxn8}$ $\frac{d \mathrm{Carbamoyl\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Carbamoyl\_phosphate\_rxn8}+\mathrm{delta\_Carbamoyl\_phosphate\_rxn0}$ $\frac{d \mathrm{Aspartate}}{d \mathrm{time}}=\mathrm{delta\_Aspartate\_rxn0}$ $\frac{d \mathrm{N\_Carbamoyl\_aspartate}}{d \mathrm{time}}=\mathrm{delta\_N\_Carbamoyl\_aspartate\_rxn0}+\mathrm{delta\_N\_Carbamoyl\_aspartate\_rxn1}$ $\frac{d \mathrm{Dihydroorotate}}{d \mathrm{time}}=\mathrm{delta\_Dihydroorotate\_rxn1}+\mathrm{delta\_Dihydroorotate\_rxn2}$ $\frac{d \mathrm{Orotate}}{d \mathrm{time}}=\mathrm{delta\_Orotate\_rxn2}+\mathrm{delta\_Orotate\_rxn3}$ $\frac{d \mathrm{Orotidine\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Orotidine\_5\_phosphate\_rxn3}+\mathrm{delta\_Orotidine\_5\_phosphate\_rxn4}$ $\frac{d \mathrm{Phosphoribosyl\_5\_1\_pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Phosphoribosyl\_5\_1\_pyrophosphate\_rxn3}$ $\frac{d \mathrm{Uridine\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Uridine\_5\_phosphate\_rxn4}+\mathrm{delta\_Uridine\_5\_phosphate\_rxn5}$ $\frac{d \mathrm{UDP}}{d \mathrm{time}}=\mathrm{delta\_UDP\_rxn5}+\mathrm{delta\_UDP\_rxn6}$ $\frac{d \mathrm{UTP}}{d \mathrm{time}}=\mathrm{delta\_UTP\_rxn6}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn5}+\mathrm{delta\_ATP\_rxn6}+\mathrm{delta\_ATP\_rxn7}+\mathrm{delta\_ATP\_rxn8}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn5}+\mathrm{delta\_ADP\_rxn6}+\mathrm{delta\_ADP\_rxn7}+\mathrm{delta\_ADP\_rxn8}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn1}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn0}+\mathrm{delta\_Pi\_rxn3}+\mathrm{delta\_Pi\_rxn7}+\mathrm{delta\_Pi\_rxn8}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn2}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn2}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn2}+\mathrm{delta\_H\_rxn7}$ $\frac{d \mathrm{CO2}}{d \mathrm{time}}=\mathrm{delta\_CO2\_rxn4}$ $\frac{d \mathrm{NH4}}{d \mathrm{time}}=\mathrm{delta\_NH4\_rxn7}$ $\frac{d \mathrm{HCO3}}{d \mathrm{time}}=\mathrm{delta\_HCO3\_rxn8}$ $\mathrm{rate}=\frac{\mathrm{vmax0}\mathrm{Aspartate}\mathrm{Carbamoyl\_phosphate}}{\mathrm{km0}+\mathrm{Aspartate}+\mathrm{Carbamoyl\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{N\_Carbamoyl\_aspartate}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{N\_Carbamoyl\_aspartate}}$ $\mathrm{rate}=\frac{\mathrm{Dihydroorotate}\mathrm{NAD}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{Dihydroorotate}+\mathrm{NAD}}$ $\mathrm{rate}=\frac{\mathrm{Orotate}\mathrm{Phosphoribosyl\_5\_1\_pyrophosphate}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{Orotate}+\mathrm{Phosphoribosyl\_5\_1\_pyrophosphate}}$ $\mathrm{rate}=\frac{\mathrm{Orotidine\_5\_phosphate}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{Orotidine\_5\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{Uridine\_5\_phosphate}\mathrm{ATP}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{Uridine\_5\_phosphate}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{UDP}\mathrm{ATP}\mathrm{vmax6}}{\mathrm{km6}+\mathrm{UDP}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{Glutamate}\mathrm{ATP}\mathrm{NH4}\mathrm{vmax7}}{\mathrm{km7}+\mathrm{Glutamate}+\mathrm{ATP}+\mathrm{NH4}}$