Figure 2

Genome and phenotype microarray comparison of three strains. (A) Number of genes shared among the three organisms—S. griseofuscus (sgri), S. coelicolor (scoe), S. venezuelae (sven). (B) Phenotype microarray data represented by activity index rings generated using DuctApe across 4 biolog plates consisting of 379 carbon, nitrogen, phosphate and sulphate nutrient sources across the three organisms. (C) Distribution of the number of genes per KEGG subsystem across the three organisms calculated using KEGG Automatic Annotation Server³⁵. 1—Protein families: signalling and cellular processes; 2—Protein families: genetic information processing; 3—Protein families: metabolism; 4—Carbohydrate metabolism; 5—Amino acid metabolism; 6—Metabolism of cofactors and vitamins; 7—Unclassified: metabolism; 8—Energy metabolism; 9—Poorly characterized; 10—Membrane transport; 11—Lipid metabolism; 12—Signal transduction; 13—Metabolism of terpenoids and polyketides; 14—Biosynthesis of other secondary metabolites, 15—Nucleotide metabolism; 16—Xenobiotics biodegradation and metabolism; 17—Translation; 18—Cellular community—prokaryotes; 19—Metabolism of other amino acids; 20—Replication and repair; 21—Folding, sorting and degradation; 22—Glycan biosynthesis and metabolism; 23—Unclassified: signalling and cellular processes; 24—Unclassified: genetic information processing; 25—Cell growth and death; 26—Transport and catabolism; 27—Drug resistance: antimicrobial; 28—Environmental adaptation; 29—Transcription. For further details on this dataset, please see Supplementary Data 1. (D) Distribution of the number of reactions per KEGG metabolic pathway across the three organisms. (a) Carbohydrate metabolism; (b) Amino acid metabolism; (c) Metabolism of cofactors and vitamins, (d) Lipid metabolism, (e) Nucleotide metabolism, (f) Metabolism of terpenoids and polyketides, (g) Energy metabolism, (h) Biosynthesis of other secondary metabolites, (i) Xenobiotics biodegradation and metabolism, (j) Metabolism of other amino acids, (k) Glycan biosynthesis and metabolism, (l) Translation, (m) Not included in regular maps, (n) Signal transduction. (E) Heatmap with activity index of different KEGG nutrients (y-axis) against the KEGG pathway maps (x-axis). (F) Confusion matrix representing a genome-scale model based prediction and the observed growth phenotypes of three organisms. (B) was generated using DuctApe³⁶, whereas the remaining figures were generated in this study using Python scripts and assembled using Adobe Illustrator 23 https://www.adobe.com/products/illustrator.html.