Figure 4.

CoA Biosynthesis Subsystem. Functional roles, abbreviations, key intermediates and reactions in the pathway diagram are presented using the same conventions as in Figure 2. Background colors in the diagram illustrate the comparison of subsystem variants by highlighting functional roles asserted in two organisms: E.coli (yellow) and H.sapiens (blue). Shared functional roles are highlighted green. The lower panel is a modification of the subsystem spreadsheet. It shows a classification of major subsystem variants representing a substantially different reaction topology revealed by semi-automated graph analysis as described in (21). Selected genomes unambiguously associated with each variant are shown after variant description (e.g. De novo, complete/100). Patterns of functional roles which constitute each functional variant are generalized by: ‘+’, presence of a gene (for a given role) is required; ‘±’, optional; ‘?’, function is inferred by pathway analysis but a gene is unknown or ‘missing’ (i.e. can not be located by similarity). Typical sub-variants characterized by the same topology but relying on alternative (non-orthologous) forms of specific enzymes (e.g. PANK) are illustrated by the following genomes: E.coli K12 [NCBI taxonomy ID 83333.1], D.radiodurans R1 [243230.1], S.aureus subsp. aureus N315 [158879.1], S.oneidensis MR-1 [211586.1], G.metallireducens [28232.1], Saccharomyces cerevisiae [4932.1], P.aerophilum str. IM2 [178306.1], Streptococcus pneumoniae R6 [171101.1], Thermoanaerobacter tengcongensis [119072.1], H.sapiens [9606.2], B.aphidicola str. APS (Acyrthosiphon pisum) [107806.1], Treponema pallidum subsp. pallidum str. Nichols [243276.1] and Chlamydia trachomatis D/UW-3/CX [272561.1]. Genes assigned with respective functional roles are shown by SEED unique IDs for all illustrated genomes (except E.coli where common gene names are used). Matching background colors highlight genes that occur close to each other on the chromosome.