Curated model mapping - Basic mapping


The template based model mapping of CARMEN can be used to perform a comparative metabolic reconstruction of two organisms.

This procedure was applied to Corynebacterium kroppenstedtii and Corynebacterium aurimucosum. A manually drawn template-model of C. kroppenstedtii stored in SBML was used as a reference containing a network of the central carbohydrate metabolism (Tauch et al.). Hence, the results of reciprocal best-BLAST hits between all genes of both species were employed. A detailed analysis of this network showed that the majority of genes involved in glycolysis, pentose phoshate pathway and TCA cycle are conserved. On the other hand several differences concerning their metabolic repertoire were identified (Figure 5).

Ckrop_central Carmen logo Cauri_central

Figure 5: Curated model mapping. Left: The manual reconstruction of the central carbohydrate metabolism of C. kroppenstedtii stored in SBML which was generated using the CellDesigner software. Proteins given by gene names are coloured yellow and simple molecules are coloured green. Right: Curated model mapping of C. aurimucosum on the draft template by CARMEN are orthologous genes. Missing genes and associated simple molecules are coloured grey.

Download Ckrop_centralDownload SBML file of C. kroppenstedtii
Download Cauri_centralDownload SBML file of C. aurimucosum