Fig. 3
From: CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts
CoMetGeNe trail for E. coli in the peptidoglycan biosynthesis pathway. a Partial view of the peptidoglycan biosynthesis pathway, adapted from KEGG PATHWAY, map eco00550 (August 3, 2018 version). Green reaction nodes designate reactions present in E. coli. The gap parameter δG was set to one (thus allowing to skip one gene). Reactions in the trail (red contours) are labeled with the corresponding KEGG reaction identifiers (R numbers) and with the Blattner identifiers and gene names of genes coding for the respective enzymes. The genes involved in this trail are neighbors on the positive strand of the E. coli chromosome (see b). Dashed arrows from a metabolite m to another metabolite m′ signify that a chain of reactions, omitted in this figure for clarity, leads from m to m′. b Genomic context for genes involved in the trail in a. The gene in gray is not involved in the trail. c Group of homologous genes involved in the trail in a, present in various species. See Trail grouping by genes for details. d Group of reactions defining the trail in a. eco_gene designates the gene in E. coli whose product catalyzes the corresponding reaction. See Trail grouping by reactions for details. In this figure, all reactions that are absent from certain species (blanks) are highlighted in gray