Figure 6
Hierarchical levels of E. coli CAF network using a “real”? Food set. Top- Hierarchical clustering dendrogram of E. coli metabolic pathways (leafs) according to the hierarchical levels defined in the text. Bottom- Heatmap representing the occurrence of reactions from each one of metabolic pathways (columns) and the 53 hierarchical levels of the CAF network (rows). Blue squares represent the occurrence of at least one reaction from that pathway in a given level. Numbers represent grouped pathways. 1- Nucleotide-excision-, mismatch-, and base-excision- repair; DNA-replication. 2- Glycolysis/gluconeogenesis; methane-, carbon-, amino acids biosynthesis, glycine, serine and threonine- metabolism. 3- Fatty acid biosynthesis and metabolism; valine, leucine and isoleucine-, geraniol- and fatty-acid- degradation. 4 - Lysine degradation; tryptophan metabolism; limonene-, caprolactam- degradation; beta-alanine metabolism. 5- Unsaturated fatty-acids biosynthesis, biotin-, propanoate- and butanoate- metabolism. 6– Glycerophospholipid- and alpha-linolenic acid metabolism; ethylbenzene degradation; pantothenate and CoA biosynthesis. 7- Purine-, pyrimidine- and porphyrin- metabolism; Valine, leucine and isoleucine biosynthesis. 8- Oxocarboxylic acid metabolism; phenylalanine, tyrosine and tryptophan biosynthesis. 9- Lipopolysaccharide biosynthesis. 10- Arginine and proline-, amino sugar and nucleotide sugar-, glycerolipid-, histidine-, glyoxylate- and dicarboxylate metabolism; benzoate degradation; nicotinate-, starch and sucrose metabolism. 11- Quinone biosynthesis; pyruvate-, galactose- metabolism; lysine biosynthesis; PLP metabolism; aminoacyl-tRNA biosynthesis. 12- Cysteine and methionine metabolism; siderophore-group nonribosomal-peptides biosynthesis; glutathione-, citrate-cycle, sulfur- metabolism. 13- Pentose phosphate pathway; fructose-, mannose metabolism; pentose and glucuronate interconversions; peptidoglycan- and folate- biosynthesis. 14- Phenylalanine metabolism; novobiocin biosynthesis. 15– Tyrosine-, riboflavin and cyanoamino-acid metabolism; terpenoid-backbone biosynthesis; Selenocompound metabolism. 16– Thiamine-, Sulfur-relay system, D-Alanine metabolism. 17– Dioxin-, Xylene-, Chloroalkane-, naphthalene-, aromatic- degradation. 18- C5-Branched dibasic acid-, inositolphosphate-, oxidative phosphorylation, nitrogen-, two-component system, taurine- metabolism. 19- lipoic acid-, alanine, aspartate, glutamate-, D-glutamine and D-glutamate- metabolism; nitrotoluene degradation; folate one-carbon pool; ascorbate metabolism. 20- Aminobenzoate degradation; streptomycin-, polyketide-sugar biosynthesis; RNA-, toluene- degradation. 21- Arachidonic acid metabolism. 22- phosphotransferase system.