Table 3.

List of estimated complete KEGG modules.

Modulea	Module Nameb	% genomes with complete module
		Cpr	Cps	Cac	Ctu	Dpi
M00015	Proline biosynthesis, glutamate => proline	100	100	100	100	0
M00028	Ornithine biosynthesis, glutamate => ornithine	100	100	100	50	0
M00844	Arginine biosynthesis, ornithine => arginine	100	100	100	100	0
M00970	Proline degradation, proline => glutamate	100	100	100	100	0
M00022	Shikimate pathway, phosphoenolpyruvate + erythrose-4P => chorismate	100	100	100	100	0
M00023	Tryptophan biosynthesis, chorismate => tryptophan	100	100	100	100	0
M00019	Valine/isoleucine biosynthesis, pyruvate => valine / 2-oxobutanoate => isoleucine	100	100	100	100	0
M00432	Leucine biosynthesis, 2-oxoisovalerate => 2-oxoisocaproate	100	100	100	100	0
M00570	Isoleucine biosynthesis, threonine => 2-oxobutanoate => isoleucine	100	100	100	100	0
M00017	Methionine biosynthesis, aspartate => homoserine => methionine	100	100	100	100	0
M00021	Cysteine biosynthesis, serine => cysteine	100	100	100	100	0
M00026	Histidine biosynthesis, PRPP => histidine	100	100	90.9	0	0
M00045	Histidine degradation, histidine => N-formiminoglutamate => glutamate	100	100	100	100	0
M00016	Lysine biosynthesis, succinyl-DAP pathway, aspartate => lysine	100	100	100	50	0
M00018	Threonine biosynthesis, aspartate => homoserine => threonine	100	100	100	100	81.5
M00020	Serine biosynthesis, glycerate-3P => serine	100	100	100	87.5	0
M00621	Glycine cleavage system	0	0	100	100	100
M00793	dTDP-L-rhamnose biosynthesis	100	100	100	100	0
M00096	C5 isoprenoid biosynthesis, non-mevalonate pathway	0	0	100	100	0
M00364	C10-C20 isoprenoid biosynthesis, bacteria	0	0	100	100	0
M00365	C10-C20 isoprenoid biosynthesis, archaea	0	0	100	100	0
M00001	Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate	100	100	100	100	100
M00002	Glycolysis, core module involving three-carbon compounds	100	100	100	100	100
M00003	Gluconeogenesis, oxaloacetate => fructose-6P	100	100	100	100	0
M00004	Pentose phosphate pathway (Pentose phosphate cycle)	100	100	100	100	77.8
M00005	PRPP biosynthesis, ribose 5P => PRPP	100	100	100	100	100
M00006	Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P	100	100	100	100	100
M00007	Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P	100	100	100	100	77.8
M00009	Citrate cycle (TCA cycle, Krebs cycle)	100	100	100	100	0
M00010	Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate	100	100	100	100	0
M00011	Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate	100	100	100	100	0
M00307	Pyruvate oxidation, pyruvate => acetyl-CoA	100	69	100	100	0
M00549	Nucleotide sugar biosynthesis, glucose => UDP-glucose	0	0	0	100	0
M00550	Ascorbate degradation, ascorbate => D-xylulose-5P	0	0	0	0	37
M00554	Nucleotide sugar biosynthesis, galactose => UDP-galactose	100	100	100	100	0
M00632	Galactose degradation, Leloir pathway, galactose => alpha-D-glucose-1P	100	100	100	100	0
M00854	Glycogen biosynthesis, glucose-1P => glycogen/starch	0	0	0	0	96.3
M00909	UDP-N-acetyl-D-glucosamine biosynthesis, prokaryotes, glucose => UDP-GlcNAc	100	100	100	100	100
M00151	Cytochrome bc1 complex respiratory unit	100	100	100	100	0
M00155	Cytochrome c oxidase, prokaryotes	100	100	100	100	0
M00157	F-type ATPase, prokaryotes and chloroplasts	100	100	100	100	0
M00579	Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate	0	0	100	100	100
M00083	Fatty acid biosynthesis, elongation	100	100	0	0	96.3
M00086	beta-Oxidation, acyl-CoA synthesis	100	100	100	100	0
M00120	Coenzyme A biosynthesis, pantothenate => CoA	100	100	100	100	100
M00121	Heme biosynthesis, plants and bacteria, glutamate => heme	100	100	100	100	0
M00123	Biotin biosynthesis, pimeloyl-ACP/CoA => biotin	21.1	92.9	100	0	0
M00125	Riboflavin biosynthesis, plants and bacteria, GTP => riboflavin/FMN/FAD	100	100	100	100	14.8
M00126	Tetrahydrofolate biosynthesis, GTP => THF	0	0	100	100	0
M00140	C1-unit interconversion, prokaryotes	100	97.6	100	100	100
M00577	Biotin biosynthesis, BioW pathway, pimelate => pimeloyl-CoA => biotin	21.1	92.9	100	0	0
M00881	Lipoic acid biosynthesis, plants and bacteria, octanoyl-ACP => dihydrolipoyl-E2/H	100	100	100	100	0
M00899	Thiamine salvage pathway, HMP/HET => TMP	0	0	100	100	100
M00916	Pyridoxal-P biosynthesis, R5P + glyceraldehyde-3P + glutamine => pyridoxal-P	0	0	100	100	0
M00926	Heme biosynthesis, bacteria, glutamyl-tRNA => coproporphyrin III => heme	100	100	100	100	0
M00048	De novo purine biosynthesis, PRPP + glutamine => IMP	100	100	100	100	0
M00049	Adenine ribonucleotide biosynthesis, IMP => ADP,ATP	100	100	100	100	0
M00050	Guanine ribonucleotide biosynthesis, IMP => GDP,GTP	100	100	100	100	0
M00053	Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP	100	100	100	100	0
M00938	Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP	100	100	100	100	0

^aModules are colored based on their KEGG module subcategory; red: “amino acid metabolism”, dark teal: “biosynthesis of terpenoids and polyketides”, green: “carbohydrate metabolism”, grey: “energy metabolism”, dark orange: “lipid metabolism”, orange: “metabolism of cofactors and vitamins”, yellow: “nucleotide metabolism”.

^bPRPP is 5-phosphoribosyl diphosphate, DAP is diaminopimelate, FMN is flavin mononucleotide, FAD is flavin adenine dinucleotide, ACP is acyl-carrier protein, HMP is 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET is 5-(2-hydroxyethyl)-4-methylthiazole and TMP is thiamine monophosphate.