Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-04 Updated syntax to conform with cellml1.1 specs Villiger Peter J 2005-04-20 Added more metadata. Lloyd Catherine May 2002-07-22 The University of Auckland, Bioengineering Institute A Generic Model Of Transamination Below is a CellML description of a general model of transamination. 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 $\frac{d \mathrm{Oxaloacetate}}{d \mathrm{time}}=\mathrm{delta\_Oxaloacetate\_rxn0}$ $\frac{d \mathrm{Aspartate}}{d \mathrm{time}}=\mathrm{delta\_Aspartate\_rxn0}+\mathrm{delta\_Aspartate\_rxn5}$ $\frac{d \mathrm{alpha\_amino\_acid}}{d \mathrm{time}}=\mathrm{delta\_alpha\_amino\_acid\_rxn0}+\mathrm{delta\_alpha\_amino\_acid\_rxn1}$ $\frac{d \mathrm{Oxo\_2\_acid}}{d \mathrm{time}}=\mathrm{delta\_Oxo\_2\_acid\_rxn0}+\mathrm{delta\_Oxo\_2\_acid\_rxn1}$ $\frac{d \mathrm{Oxoglutarate\_2}}{d \mathrm{time}}=\mathrm{delta\_Oxoglutarate\_2\_rxn2}+\mathrm{delta\_Oxoglutarate\_2\_rxn1}$ $\frac{d \mathrm{Glutamate}}{d \mathrm{time}}=\mathrm{delta\_Glutamate\_rxn1}+\mathrm{delta\_Glutamate\_rxn4}+\mathrm{delta\_Glutamate\_rxn2}+\mathrm{delta\_Glutamate\_rxn3}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn2}$ $\frac{d \mathrm{NH4}}{d \mathrm{time}}=\mathrm{delta\_NH4\_rxn2}+\mathrm{delta\_NH4\_rxn4}+\mathrm{delta\_NH4\_rxn3}+\mathrm{delta\_NH4\_rxn8}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn2}+\mathrm{delta\_H\_rxn3}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn2}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn2}+\mathrm{delta\_H2O\_rxn4}+\mathrm{delta\_H2O\_rxn6}$ $\frac{d \mathrm{Glutamine}}{d \mathrm{time}}=\mathrm{delta\_Glutamine\_rxn3}+\mathrm{delta\_Glutamine\_rxn4}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn3}+\mathrm{delta\_ATP\_rxn5}+\mathrm{delta\_ATP\_rxn8}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn3}+\mathrm{delta\_ADP\_rxn8}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn3}+\mathrm{delta\_Pi\_rxn5}+\mathrm{delta\_Pi\_rxn7}+\mathrm{delta\_Pi\_rxn8}$ $\frac{d \mathrm{Fumarate}}{d \mathrm{time}}=\mathrm{delta\_Fumarate\_rxn5b}$ $\frac{d \mathrm{AMP}}{d \mathrm{time}}=\mathrm{delta\_AMP\_rxn5}$ $\frac{d \mathrm{Arginine}}{d \mathrm{time}}=\mathrm{delta\_Arginine\_rxn5b}+\mathrm{delta\_Arginine\_rxn6}$ $\frac{d \mathrm{Argininosuccinate}}{d \mathrm{time}}=\mathrm{delta\_Argininosuccinate\_rxn5}+\mathrm{delta\_Argininosuccinate\_rxn5b}$ $\frac{d \mathrm{Citrulline}}{d \mathrm{time}}=\mathrm{delta\_Citrulline\_rxn7}+\mathrm{delta\_Citrulline\_rxn5}$ $\frac{d \mathrm{Ornithine}}{d \mathrm{time}}=\mathrm{delta\_Ornithine\_rxn6}+\mathrm{delta\_Ornithine\_rxn7}$ $\frac{d \mathrm{Urea}}{d \mathrm{time}}=\mathrm{delta\_Urea\_rxn6}$ $\frac{d \mathrm{Carbamoyl\_Pi}}{d \mathrm{time}}=\mathrm{delta\_Carbamoyl\_Pi\_rxn8}+\mathrm{delta\_Carbamoyl\_Pi\_rxn7}$ $\frac{d \mathrm{CO2}}{d \mathrm{time}}=\mathrm{delta\_CO2\_rxn8}$ $\mathrm{rate}=\frac{\mathrm{vmax0}\mathrm{alpha\_amino\_acid}\mathrm{Oxaloacetate}}{\mathrm{km0}+\mathrm{alpha\_amino\_acid}+\mathrm{Oxaloacetate}}$ $\mathrm{rate}=\frac{\mathrm{alpha\_amino\_acid}\mathrm{Oxoglutarate\_2}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{alpha\_amino\_acid}+\mathrm{Oxoglutarate\_2}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{NAD}\mathrm{Glutamate}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{H2O}+\mathrm{NAD}+\mathrm{Glutamate}}$ $\mathrm{rate}=\frac{\mathrm{Glutamate}\mathrm{ATP}\mathrm{NH4}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{ATP}+\mathrm{NH4}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Glutamine}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{H2O}+\mathrm{Glutamine}}$ $\mathrm{rate}=\frac{\mathrm{Aspartate}\mathrm{ATP}\mathrm{Citrulline}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{Aspartate}+\mathrm{ATP}+\mathrm{Citrulline}}$ $\mathrm{rate}=\frac{\mathrm{Argininosuccinate}\mathrm{vmax5b}}{\mathrm{km5b}+\mathrm{Argininosuccinate}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Arginine}\mathrm{vmax6}}{\mathrm{km6}+\mathrm{H2O}+\mathrm{Arginine}}$ $\mathrm{rate}=\frac{\mathrm{Carbamoyl\_Pi}\mathrm{Ornithine}\mathrm{vmax7}}{\mathrm{km7}+\mathrm{Carbamoyl\_Pi}+\mathrm{Ornithine}}$