Curated model mapping - Core mapping


CARMEN can be used to perform an integration of core genome data of a choosen group of organisms. An application case of this feature is the visualisation of the central carbohydrate metabolism of different Corynebacteria. The reference template was the SBML file of C. kroppenstedtii that was used as before for the template-based model reconstruction of C. aurimucosum. In addition to the SBML template, the core genome of C. kroppenstedtii, C. glutamicum and C. jeikeium was computed by EDGAR and stored in a tab-separated file. Afterwards, this information was used by CARMEN for mapping related information onto the SBML template. As expected, the reconstructed network showed that genes coding for the glycolysis, the pentose phosphate pathway and the complete TCA cycle were conserved. This analysis points out the existence of various import mechanisms of C. kroppenstedtii, which are not encoded by genes of the core genome (Figure 6).

Ckrop_central Carmen logo Core_central

Figure 6: Curated model mapping. Left: The manual reconstruction of the central carbohydrate metabolism of C. kroppenstedtii stored in a SBML which was generated using the CellDesigner software. Proteins given by gene names are coloured yellow and simple molecules are coloured green. Right: Mapping of core genome genes of C. kroppenstedtii, C.jeikeium and C. glutamicum computed by EDGAR. Core genome genes are coloured red.

Download Ckrop_centralDownload SBML file of C. kroppenstedtii
Download Core_centralDownload SBML file of the core genome