Curated model mapping - Additional reactions
Another option of the template-based reconstruction supports the acquisition of reaction information expanding the metabolic network of the SBML template. These affiliated reactions are reconstructed based on KEGG files for compounds, enzymes and reactions and they have to satisfy two criteria. First, the reactions are adjacent to reactions of the SBML template. Second, genes encoding for proteins catalyzing a certain reaction are annotated in the newly sequenced and annotated genome. Thus, it is possible to identify direct connections of related pathways, which will be stored in a newly generated SBML file. This analysis allows a more precise view on genome data by finding alternative or continuative pathways extending the chosen reference model.
Figure 7: The template-based reconstruction of the central carbohydrate metabolism of C. aurimucosum was performed by CARMEN using the SBML template of C. kroppenstedtii with the option to create further adjacent reactions. A subset of ten reactions is displayed on the figure.
Download SBML file containing additional reactions.