Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-06 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 (TMP) Degradation Below is a CellML description of a general model of pyrimidine nucleotide (TMP) degradation. 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 $\frac{d \mathrm{dTMP}}{d \mathrm{time}}=\mathrm{delta\_dTMP\_rxn3}$ $\frac{d \mathrm{Thymidine}}{d \mathrm{time}}=\mathrm{delta\_Thymidine\_rxn3}+\mathrm{delta\_Thymidine\_rxn4}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn3}+\mathrm{delta\_H2O\_rxn6}+\mathrm{delta\_H2O\_rxn7}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn3}+\mathrm{delta\_Pi\_rxn4}$ $\frac{d \mathrm{Thymine}}{d \mathrm{time}}=\mathrm{delta\_Thymine\_rxn4}+\mathrm{delta\_Thymine\_rxn5}$ $\frac{d \mathrm{Deoxyribose\_2\_1\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Deoxyribose\_2\_1\_phosphate\_rxn4}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn9}+\mathrm{delta\_NADH\_rxn5}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn9}+\mathrm{delta\_H\_rxn5}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn5}+\mathrm{delta\_NAD\_rxn9}$ $\frac{d \mathrm{Dihydrothymine}}{d \mathrm{time}}=\mathrm{delta\_Dihydrothymine\_rxn5}+\mathrm{delta\_Dihydrothymine\_rxn6}$ $\frac{d \mathrm{beta\_Ureidoisobutyrate}}{d \mathrm{time}}=\mathrm{delta\_beta\_Ureidoisobutyrate\_rxn6}+\mathrm{delta\_beta\_Ureidoisobutyrate\_rxn7}$ $\frac{d \mathrm{beta\_Aminoisobutyrate}}{d \mathrm{time}}=\mathrm{delta\_beta\_Aminoisobutyrate\_rxn7}+\mathrm{delta\_beta\_Aminoisobutyrate\_rxn8}$ $\frac{d \mathrm{Glutamate}}{d \mathrm{time}}=\mathrm{delta\_Glutamate\_rxn8}$ $\frac{d \mathrm{Oxoglutarate\_2}}{d \mathrm{time}}=\mathrm{delta\_Oxoglutarate\_2\_rxn8}$ $\frac{d \mathrm{Methylmalonate\_semialdehyde}}{d \mathrm{time}}=\mathrm{delta\_Methylmalonate\_semialdehyde\_rxn8}+\mathrm{delta\_Methylmalonate\_semialdehyde\_rxn9}$ $\frac{d \mathrm{Methylmalonyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Methylmalonyl\_CoA\_rxn9}+\mathrm{delta\_Methylmalonyl\_CoA\_rxn0}$ $\frac{d \mathrm{CoA\_SH}}{d \mathrm{time}}=\mathrm{delta\_CoA\_SH\_rxn9}$ $\frac{d \mathrm{Succinyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Succinyl\_CoA\_rxn2}$ $\frac{d \mathrm{Deoxyadenosyl\_5\_B12}}{d \mathrm{time}}=\mathrm{delta\_Deoxyadenosyl\_5\_B12\_rxn2}+\mathrm{delta\_Deoxyadenosyl\_5\_B12\_rxn0}$ $\frac{d \mathrm{Methylmalonyl\_B12}}{d \mathrm{time}}=\mathrm{delta\_Methylmalonyl\_B12\_rxn0}+\mathrm{delta\_Methylmalonyl\_B12\_rxn1}$ $\frac{d \mathrm{Deoxyadenosine\_5}}{d \mathrm{time}}=\mathrm{delta\_Deoxyadenosine\_5\_rxn0}+\mathrm{delta\_Deoxyadenosine\_5\_rxn2}$ $\frac{d \mathrm{Succinyl\_B12}}{d \mathrm{time}}=\mathrm{delta\_Succinyl\_B12\_rxn1}+\mathrm{delta\_Succinyl\_B12\_rxn2}$ $\frac{d \mathrm{CO2}}{d \mathrm{time}}=\mathrm{delta\_CO2\_rxn7}$ $\frac{d \mathrm{NH4}}{d \mathrm{time}}=\mathrm{delta\_NH4\_rxn7}$ $\mathrm{rate}=\frac{\mathrm{dTMP}\mathrm{H2O}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{dTMP}+\mathrm{H2O}}$ $\mathrm{rate}=\frac{\mathrm{Thymidine}\mathrm{Pi}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{Thymidine}+\mathrm{Pi}}$ $\mathrm{rate}=\frac{\mathrm{Thymine}H\mathrm{NADH}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{Thymine}+H+\mathrm{NADH}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Dihydrothymine}\mathrm{vmax6}}{\mathrm{km6}+\mathrm{H2O}+\mathrm{Dihydrothymine}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{beta\_Ureidoisobutyrate}\mathrm{vmax7}}{\mathrm{km7}+\mathrm{H2O}+\mathrm{beta\_Ureidoisobutyrate}}$ $\mathrm{rate}=\frac{\mathrm{beta\_Aminoisobutyrate}\mathrm{Oxoglutarate\_2}\mathrm{vmax8}}{\mathrm{km8}+\mathrm{beta\_Aminoisobutyrate}+\mathrm{Oxoglutarate\_2}}$ $\mathrm{rate}=\frac{\mathrm{NAD}\mathrm{CoA\_SH}\mathrm{Methylmalonate\_semialdehyde}\mathrm{vmax9}}{\mathrm{km9}+\mathrm{NAD}+\mathrm{CoA\_SH}+\mathrm{Methylmalonate\_semialdehyde}}$