Classification I	Classification II	Subsystem	Preference	Comparison
Amino Acids and Derivatives	Alanine, serine, and glycine	Alanine Biosynthesis	AMD	black vs. amd
Amino Acids and Derivatives	Alanine, serine, and glycine	Glycine cleavage system	AMD	black vs. amd
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	AMD	black vs. amd
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Phenylalanine synthesis	AMD	black vs. amd
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Asp-Glu-tRNA(Asn-Gln) transamidation	AMD	black vs. amd
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	AMD	black vs. amd
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	AMD	black vs. amd
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	AMD	black vs. amd
Carbohydrates	CO2 fixation	Carboxysome	AMD	black vs. amd
Carbohydrates	CO2 fixation	Cyanobacterial CO2 uptake	AMD	black vs. amd
Carbohydrates	Di- and oligosaccharides	Trehalose biosynthesis	AMD	black vs. amd
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	AMD	black vs. amd
Carbohydrates	Monosaccharides	Ketogluconate metabolism	AMD	black vs. amd
Clustering-based Subsystems		LMPTP YwlE cluster	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups,	Pigments	Cobalamin synthesis	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Folate Biosynthesis	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP tutorial 10	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Biosynthesis	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis in pathogens	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	Riboflavin metabolism	AMD	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Chlorophyll Biosynthesis	AMD	black vs. amd
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	AMD	black vs. amd
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	AMD	black vs. amd
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	AMD	black vs. amd
Fatty Acids and Lipids	Phospholipids	Betaine biosynthesis	AMD	black vs. amd
Membrane Transport	ABC transporters	ABC transporter dipeptide (TC 3.A.1.5.2)	AMD	black vs. amd
Membrane Transport	ABC transporters	ABC transporter glycerol (TC 3.A.1.1.3)	AMD	black vs. amd
Membrane Transport	ABC transporters	ABC transporter maltose	AMD	black vs. amd
Membrane Transport	ABC transporters	P-type ATPase transporter potassium (TC 3.A.3.7.1)	AMD	black vs. amd
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	AMD	black vs. amd
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate degradation	AMD	black vs. amd
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	p-Hydroxybenzoate degradation	AMD	black vs. amd
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	AMD	black vs. amd
Motility and Chemotaxis	Flagellar motility in Prokaryota	Flagellum	AMD	black vs. amd
Nitrogen Metabolism		Allantoin degradation	AMD	black vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome LSU eukaryotic and archaeal	AMD	black vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome SSU eukaryotic and archaeal	AMD	black vs. amd
Protein Metabolism	Protein Biosynthesis	Translation initiation factors eukaryotic and archaeal	AMD	black vs. amd
Protein Metabolism	Protein Degradation	Proteasome archaeal	AMD	black vs. amd
Protein Metabolism	Protein Degradation	Protein degradation	AMD	black vs. amd
Protein Metabolism	Selenoproteins	Glycine reductase, sarcosine reductase and betaine reductase	AMD	black vs. amd
Protein Metabolism	Selenoproteins	Selenocysteine metabolism	AMD	black vs. amd
Respiration	ATP synthases	V-Type ATP synthase	AMD	black vs. amd
Respiration	Electron donating reactions	Formate hydrogenase	AMD	black vs. amd
Respiration	Electron donating reactions	Hydrogenases	AMD	black vs. amd
Respiration	Electron donating reactions	Respiratory Complex I	AMD	black vs. amd
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	AMD	black vs. amd
Respiration	Soluble electron carries	Soluble cytochromes and functionally related electron carriers	AMD	black vs. amd
Virulence	Adhesion and colonization factors	Mannose-sensitive hemagglutinin type 4 pilus	AMD	black vs. amd
Virulence	Detection	MLST	AMD	black vs. amd
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	black	black vs. amd
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Chorismate Synthesis	black	black vs. amd
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	black	black vs. amd
Amino Acids and Derivatives	Branched-chain amino acids	Isoleucine degradation	black	black vs. amd
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	black	black vs. amd
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Degradation and HMG-CoA Metabolism	black	black vs. amd
Amino Acids and Derivatives	Branched-chain amino acids	Valine degradation	black	black vs. amd
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Salvage	black	black vs. amd
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	black	black vs. amd
Carbohydrates	Monosaccharides	Mannose and fructose metabolism	black	black vs. amd
Carbohydrates	Sugar alcohols	Hexitol degradation	black	black vs. amd
Cell Wall and Capsule	Glycosylation	N-linked Glycosylation in Bacteria	black	black vs. amd
Cell Wall and Capsule	Gram-Negative cell wall components	dTDP-rhamnose synthesis	black	black vs. amd
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	black	black vs. amd
Cell Wall and Capsule	Peptidoglycan biosynthesis	Peptidoglycan Biosynthesis	black	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	Carotenoids	black	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyisoprenoid biosynthesis	black	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP cofactor biosynthesis global	black	black vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Siderophores	Siderophore enterobactin biosynthesis and ferric enterbactin transport	black	black vs. amd
DNA metabolism	DNA Replication	DNA-replication	black	black vs. amd
Experimental Subsystems	Auxiliary Subsystems	Fructose-bisphosphate aldolase protein family	black	black vs. amd
Experimental Subsystems	Temporary subsystems	Test ADP-ribose	black	black vs. amd
Membrane Transport	ABC transporters	ABC transporter alkylphosphonate (TC 3.A.1.9.1)	black	black vs. amd
Membrane Transport	ABC transporters	ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	black	black vs. amd
Membrane Transport	ABC transporters	ABC transporter heme (TC3.A.1.107.1)	black	black vs. amd
Membrane Transport	ABC transporters	ABC transporter ribose (TC 3.A.1.2.1)	black	black vs. amd
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Homogentisate pathway of aromatic compound degradation	black	black vs. amd
Motility and Chemotaxis	Social motility and nonflagellar swimming in bacteria	Bacterial motility:Gliding 	black	black vs. amd
Nitrogen Metabolism		Denitrification	black	black vs. amd
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	black	black vs. amd
Protein Metabolism	Protein Folding	GroEL GroES	black	black vs. amd
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	black	black vs. amd
Respiration	Electron donating reactions	NiFe hydrogenase maturation	black	black vs. amd
RNA metabolism		RNA polymerase bacterial	black	black vs. amd
RNA metabolism		Transcription factors bacterial	black	black vs. amd
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	black	black vs. farm
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Chorismate Synthesis	black	black vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	black	black vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Isoleucine degradation	black	black vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	black	black vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Valine degradation	black	black vs. farm
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Salvage	black	black vs. farm
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	black	black vs. farm
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	black	black vs. farm
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyisoprenoid biosynthesis	black	black vs. farm
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP cofactor biosynthesis global	black	black vs. farm
Experimental Subsystems	Temporary subsystems	Test ADP-ribose	black	black vs. farm
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Homogentisate pathway of aromatic compound degradation	black	black vs. farm
Nitrogen Metabolism		Denitrification	black	black vs. farm
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	black	black vs. farm
Respiration	Electron donating reactions	NiFe hydrogenase maturation	black	black vs. farm
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	farm	black vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	HMG CoA Synthesis	farm	black vs. farm
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	farm	black vs. farm
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	farm	black vs. farm
Carbohydrates	Sugar alcohols	Ethanolamine utilization	farm	black vs. farm
Cell Division and Cell Cycle	Cell cycle in Prokaryota	Cyanobacterial Circadian Clock	farm	black vs. farm
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	farm	black vs. farm
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	farm	black vs. farm
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	farm	black vs. farm
Membrane Transport	ABC transporters	ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	farm	black vs. farm
Membrane Transport	ABC transporters	ABC transporter macrolide	farm	black vs. farm
Membrane Transport	ABC transporters	ABC transporter ribose (TC 3.A.1.2.1)	farm	black vs. farm
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	farm	black vs. farm
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	farm	black vs. farm
Motility and Chemotaxis	Flagellar motility in Prokaryota	Flagellum	farm	black vs. farm
Nitrogen Metabolism		Nitrate and nitrite ammonification	farm	black vs. farm
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	farm	black vs. farm
Membrane Transport	ABC transporters	ABC transporter ferrichrome (TC 3.A.1.14.3)	black	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Valine degradation	black	black vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter heme (TC3.A.1.107.1)	black	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	black	black vs. Sargasso
DNA metabolism	DNA Replication	DNA-replication	black	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis	black	black vs. Sargasso
Experimental Subsystems	Temporary subsystems	Test ADP-ribose	black	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Entner-Doudoroff Pathway	black	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	black	black vs. Sargasso
Nitrogen Metabolism		Denitrification	black	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	black	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	black	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Degradation and HMG-CoA Metabolism	black	black vs. Sargasso
Carbohydrates	Organic acids	Methylcitrate cycle	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP cofactor biosynthesis global	black	black vs. Sargasso
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Salvage	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyisoprenoid biosynthesis	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Porphyrin, Heme, and Siroheme Biosynthesis	black	black vs. Sargasso
RNA metabolism		tRNA aminoacylation	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Pyrroloquinoline Quinone biosynthesis	black	black vs. Sargasso
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Homogentisate pathway of aromatic compound degradation	black	black vs. Sargasso
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	black	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Isoleucine degradation	black	black vs. Sargasso
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	black	black vs. Sargasso
Respiration	Electron accepting reactions	Terminal cytochrome oxidases	black	black vs. Sargasso
Stress response	Oxidative stress	Protection from Reactive Oxygen Species	black	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	black	black vs. Sargasso
Respiration	Electron donating reactions	NiFe hydrogenase maturation	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Coenzyme PQQ synthesis	black	black vs. Sargasso
Membrane Transport	Uni-, Sym- and Antiporters	Sodium Hydrogen Antiporter	black	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	black	black vs. Sargasso
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	black	black vs. Sargasso
Respiration	Electron donating reactions	Hydrogenases	Sargasso	black vs. Sargasso
RNA metabolism		Transcription factors cyanobacterial RpoD-like sigma factors	Sargasso	black vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter maltose	Sargasso	black vs. Sargasso
Carbohydrates	CO2 fixation	Cyanobacterial CO2 uptake	Sargasso	black vs. Sargasso
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	Sargasso	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	Sargasso	black vs. Sargasso
Nitrogen Metabolism		Allantoin degradation	Sargasso	black vs. Sargasso
Nitrogen Metabolism		Ammonia assimilation	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	Sargasso	black vs. Sargasso
Respiration	Electron donating reactions	Respiratory Complex I	Sargasso	black vs. Sargasso
Fatty Acids and Lipids	Phospholipids	Betaine biosynthesis	Sargasso	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	Sargasso	black vs. Sargasso
Fatty Acids and Lipids	Fatty acids	carnitine metabolism	Sargasso	black vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome LSU chloroplast	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	cysteine biosynthesis	Sargasso	black vs. Sargasso
Carbohydrates	Monosaccharides	D-galacturonate degradation	Sargasso	black vs. Sargasso
Fatty Acids and Lipids	Fatty acids	Fatty Acid Biosynthesis FASII	Sargasso	black vs. Sargasso
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	Sargasso	black vs. Sargasso
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	Sargasso	black vs. Sargasso
Motility and Chemotaxis	Flagellar motility in Prokaryota	Flagellum	Sargasso	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Folate Biosynthesis	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Tryptophan synthesis	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Histidine	Histidine Biosynthesis	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	HMG CoA Synthesis	Sargasso	black vs. Sargasso
Carbohydrates	Fermentation	Homofermentative lactate fermentation	Sargasso	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Pterin biosynthesis	Sargasso	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	Sargasso	black vs. Sargasso
Membrane Transport	ABC transporters	Choline Transport	Sargasso	black vs. Sargasso
Carbohydrates	Monosaccharides	Ketogluconate metabolism	Sargasso	black vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter glutamate aspartate (TC 3.A.1.3.4)	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Lysine Biosynthesis DAP Pathway	Sargasso	black vs. Sargasso
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	Sargasso	black vs. Sargasso
Carbohydrates	Sugar alcohols	Inositol catabolism	Sargasso	black vs. Sargasso
Phosphorus Metabolism		P uptake (cyanobacteria)	Sargasso	black vs. Sargasso
Stress response	Starvation response	ppGpp biosynthesis	Sargasso	black vs. Sargasso
Respiration	ATP synthases	F0F1-type ATP synthase	Sargasso	black vs. Sargasso
Carbohydrates	Fermentation	Fermentations: Homofermentative lactate fermentation	Sargasso	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Pyruvate Alanine Serine Interconversions	Sargasso	black vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	Sargasso	black vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome SSU chloroplast	Sargasso	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	Riboflavin metabolism	Sargasso	black vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome LSU bacterial	Sargasso	black vs. Sargasso
Clustering-based Subsystems		LMPTP YwlE cluster	Sargasso	black vs. Sargasso
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Quinate degradation	Sargasso	black vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter glutamine (TC 3.A.1.3.2)	Sargasso	black vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	Sargasso	black vs. Sargasso
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	n-Phenylalkanoic acid degradation	Sargasso	black vs. Sargasso
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	Sargasso	black vs. Sargasso
RNA metabolism		RNA polymerase chloroplast	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Aromatic amino acid degradation	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Central meta-cleavage pathway of aromatic compound degradation	Sargasso	black vs. Sargasso
Experimental Subsystems	Temporary subsystems	NAD and NADP tutorial 10	Sargasso	black vs. Sargasso
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	Sargasso	black vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome LSU mitochondrial	Sargasso	black vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome SSU mitochondrial	Sargasso	black vs. Sargasso
RNA metabolism		tRNA aminoacylation, mitochondrial	Sargasso	black vs. Sargasso
Sulfur Metabolism	Inorganic sulfur assimilation	Inorganic Sulfur Assimilation	Sargasso	black vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1)	Sargasso	black vs. Sargasso
Cell Wall and Capsule	Capsular and extracellular polysacchrides	Capsular polysaccharide biosynthesis	Sargasso	black vs. Sargasso
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	Sargasso	black vs. Sargasso
Respiration	Electron donating reactions	Coenzyme F420-H2 dehydrogenase (methanophenazine)	Sargasso	black vs. Sargasso
Clustering-based Subsystems		EC699-706	Sargasso	black vs. Sargasso
Respiration	Electron donating reactions	Formate dehydrogenase	Sargasso	black vs. Sargasso
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	black	black vs. seed
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Chorismate Synthesis	black	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	black	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Isoleucine degradation	black	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	black	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Degradation and HMG-CoA Metabolism	black	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Valine degradation	black	black vs. seed
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Glutamate biosynthesis	black	black vs. seed
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Glutamate, aspartate and asparagine biosynthisis	black	black vs. seed
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Salvage	black	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis	black	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	black	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	black	black vs. seed
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	black	black vs. seed
Carbohydrates	Organic acids	Methylcitrate cycle	black	black vs. seed
Cell Wall and Capsule	Gram-Negative cell wall components	dTDP-rhamnose synthesis	black	black vs. seed
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	black	black vs. seed
Cell Wall and Capsule	Peptidoglycan biosynthesis	Peptidoglycan Biosynthesis	black	black vs. seed
Clustering-based Subsystems		NusA-TFII Cluster	black	black vs. seed
Clustering-based Subsystems		SA:14-24	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyisoprenoid biosynthesis	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP cofactor biosynthesis global	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Coenzyme PQQ synthesis	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Pyrroloquinoline Quinone biosynthesis	black	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Porphyrin, Heme, and Siroheme Biosynthesis	black	black vs. seed
DNA metabolism	DNA Replication	DNA-replication	black	black vs. seed
Experimental Subsystems	Temporary subsystems	Test ADP-ribose	black	black vs. seed
Membrane Transport	Uni-, Sym- and Antiporters	Sodium Hydrogen Antiporter	black	black vs. seed
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Homogentisate pathway of aromatic compound degradation	black	black vs. seed
Nitrogen Metabolism		Denitrification	black	black vs. seed
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	black	black vs. seed
Nucleosides and Nucleotides	Purines	Purine conversions	black	black vs. seed
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	black	black vs. seed
Protein Metabolism	Protein Biosynthesis	Universal GTPases	black	black vs. seed
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	black	black vs. seed
Respiration	Electron donating reactions	NiFe hydrogenase maturation	black	black vs. seed
RNA metabolism		tRNA aminoacylation	black	black vs. seed
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	black	black vs. seed
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	SEED	black vs. seed
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Central meta-cleavage pathway of aromatic compound degradation	SEED	black vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	HMG CoA Synthesis	SEED	black vs. seed
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	cysteine biosynthesis	SEED	black vs. seed
Carbohydrates	Aminosugars	N-Acetyl-D-Glucosamine Utilization	SEED	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	SEED	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	SEED	black vs. seed
Carbohydrates	Central carbohydrate metabolism	Pyruvate Alanine Serine Interconversions	SEED	black vs. seed
Carbohydrates	CO2 fixation	Carboxysome	SEED	black vs. seed
Carbohydrates	CO2 fixation	Cyanobacterial CO2 uptake	SEED	black vs. seed
Carbohydrates	Methanogenesis	Methanogenesis	SEED	black vs. seed
Carbohydrates	Monosaccharides	D-galacturonate degradation	SEED	black vs. seed
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	SEED	black vs. seed
Carbohydrates	Organic acids	Citrate Metabolism, Transport, and Regulation	SEED	black vs. seed
Carbohydrates	Organic acids	Propanediol utilization	SEED	black vs. seed
Carbohydrates	Sugar alcohols	Inositol catabolism	SEED	black vs. seed
Cell signaling	Signal transduction in prokaryota	Phytochromes	SEED	black vs. seed
Cell signaling	Signal transduction in Prokaryota	Rrf2 family transcriptional regulators	SEED	black vs. seed
Cell Wall and Capsule	Capsular and extracellular polysacchrides	Capsular polysaccharide biosynthesis	SEED	black vs. seed
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	SEED	black vs. seed
Cell Wall and Capsule	Gram-Negative cell wall components	Capsular surface virulence antigen loci	SEED	black vs. seed
Clustering-based Subsystems		LMPTP YwlE cluster	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups,	Pigments	Cobalamin synthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Folate Biosynthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Pterin biosynthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyprenyl synthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP tutorial 10	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Biosynthesis	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	SEED	black vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Chlorophyll Biosynthesis	SEED	black vs. seed
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	SEED	black vs. seed
Experimental Subsystems	Temporary subsystems	Vibrio Experimental Type III secretion system 	SEED	black vs. seed
Fatty Acids and Lipids	Fatty acids	carnitine metabolism	SEED	black vs. seed
Fatty Acids and Lipids	Fatty acids	Fatty Acid Biosynthesis FASII	SEED	black vs. seed
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	SEED	black vs. seed
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter glutamate aspartate (TC 3.A.1.3.4)	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter histidine lysine arginine ornithine (TC 3.A.1.3.1)	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter iron(III) dicitrate (TC 3.A.1.14.1)	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter maltose	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter molybdenum (TC 3.A.1.8.1)	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter nickel (TC 3.A.1.5.3)	SEED	black vs. seed
Membrane Transport	ABC transporters	ABC transporter peptide (TC 3.A.1.5.5)	SEED	black vs. seed
Membrane Transport	ABC transporters	CbiQO-type ABC transporter systems	SEED	black vs. seed
Membrane Transport	ABC transporters	Transport of Nickel and Cobalt	SEED	black vs. seed
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	SEED	black vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate catabolism	SEED	black vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate degradation	SEED	black vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	n-Phenylalkanoic acid degradation	SEED	black vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Phenylpropanoid compound degradation	SEED	black vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Quinate degradation	SEED	black vs. seed
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	SEED	black vs. seed
Motility and Chemotaxis	Flagellar motility in Prokaryota	Flagellum	SEED	black vs. seed
Nitrogen Metabolism		Nitrosative stress	SEED	black vs. seed
Phosphorus Metabolism		P uptake (cyanobacteria)	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome biogenesis bacterial	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU chloroplast	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU eukaryotic and archaeal	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU mitochondrial	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU chloroplast	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU eukaryotic and archaeal	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU mitochondrial	SEED	black vs. seed
Protein Metabolism	Protein Biosynthesis	Translation initiation factors eukaryotic and archaeal	SEED	black vs. seed
Protein Metabolism	Protein Degradation	Proteasome eukaryotic	SEED	black vs. seed
Protein Metabolism	Protein Degradation	Protein degradation	SEED	black vs. seed
Protein Metabolism	Selenoproteins	Selenocysteine metabolism	SEED	black vs. seed
Respiration	Electron donating reactions	Coenzyme F420-H2 dehydrogenase (methanophenazine)	SEED	black vs. seed
Respiration	Electron donating reactions	Hydrogenases	SEED	black vs. seed
Respiration	Electron donating reactions	Membrane-bound Ni, Fe-hydrogenase	SEED	black vs. seed
Respiration	Electron donating reactions	Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	SEED	black vs. seed
Respiration	Electron donating reactions	Respiratory Complex I	SEED	black vs. seed
Respiration	Soluble electron carries	Soluble cytochromes and functionally related electron carriers	SEED	black vs. seed
RNA metabolism		RNA polymerase chloroplast	SEED	black vs. seed
RNA metabolism		RNA polymerase II initiation factors	SEED	black vs. seed
RNA metabolism		Transcription factors cyanobacterial RpoD-like sigma factors	SEED	black vs. seed
RNA metabolism		tRNA aminoacylation, mitochondrial	SEED	black vs. seed
Sulfur Metabolism	Inorganic sulfur assimilation	Inorganic Sulfur Assimilation	SEED	black vs. seed
Sulfur Metabolism	Organic sulfur assimilation	Alkanesulfonates Utilization	SEED	black vs. seed
Virulence	Invasion and intracellular resistance	Listeria surface proteins: Internalin-like proteins	SEED	black vs. seed
Virulence	Invasion and intracellular resistance	Listeria surface proteins: LPXTG motif	SEED	black vs. seed
Virulence	Toxins, Superantigens	Cholera toxin	SEED	black vs. seed
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	black	black vs. whale
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Chorismate Synthesis	black	black vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	black	black vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	black	black vs. whale
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Salvage	black	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis	black	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	black	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	black	black vs. whale
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	black	black vs. whale
Carbohydrates	Organic acids	Methylcitrate cycle	black	black vs. whale
Cell Wall and Capsule	Gram-Negative cell wall components	dTDP-rhamnose synthesis	black	black vs. whale
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	Carotenoids	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	polyisoprenoid biosynthesis	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP cofactor biosynthesis global	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Coenzyme PQQ synthesis	black	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Pyrroloquinoline Quinone biosynthesis	black	black vs. whale
Experimental Subsystems	Auxiliary Subsystems	Fructose-bisphosphate aldolase protein family	black	black vs. whale
Experimental Subsystems	Temporary subsystems	Test ADP-ribose	black	black vs. whale
Membrane Transport	ABC transporters	ABC transporter heme (TC3.A.1.107.1)	black	black vs. whale
Membrane Transport	ABC transporters	CbiQO-type ABC transporter systems	black	black vs. whale
Membrane Transport	Uni-, Sym- and Antiporters	Sodium Hydrogen Antiporter	black	black vs. whale
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Homogentisate pathway of aromatic compound degradation	black	black vs. whale
Nitrogen Metabolism		Denitrification	black	black vs. whale
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	black	black vs. whale
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	black	black vs. whale
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	black	black vs. whale
Respiration	Electron donating reactions	NiFe hydrogenase maturation	black	black vs. whale
RNA metabolism		tRNA aminoacylation	black	black vs. whale
Amino Acids and Derivatives	Alanine, serine, and glycine	Alanine Biosynthesis	whale	black vs. whale
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	whale	black vs. whale
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Central meta-cleavage pathway of aromatic compound degradation	whale	black vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	HMG CoA Synthesis	whale	black vs. whale
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Lysine Biosynthesis DAP Pathway	whale	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	whale	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	whale	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	whale	black vs. whale
Carbohydrates	Central carbohydrate metabolism	Pyruvate metabolism I: anaplerotic reactions, PEP	whale	black vs. whale
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	whale	black vs. whale
Carbohydrates	Sugar alcohols	Inositol catabolism	whale	black vs. whale
Cell Wall and Capsule	Capsular and extracellular polysacchrides	Capsular polysaccharide biosynthesis	whale	black vs. whale
Cell Wall and Capsule	Capsular and extracellular polysacchrides	Colanic acid biosynthesis	whale	black vs. whale
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	whale	black vs. whale
Clustering-based Subsystems		EC699-706	whale	black vs. whale
Clustering-based Subsystems		LMPTP YwlE cluster	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Folate Biosynthesis	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	NAD and NADP	NAD and NADP tutorial 10	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Biosynthesis	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis in pathogens	whale	black vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	Riboflavin metabolism	whale	black vs. whale
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	whale	black vs. whale
Fatty Acids and Lipids	Fatty acids	carnitine metabolism	whale	black vs. whale
Fatty Acids and Lipids	Fatty acids	Fatty Acid Biosynthesis FASII	whale	black vs. whale
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	whale	black vs. whale
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	whale	black vs. whale
Fatty Acids and Lipids	Phospholipids	Betaine biosynthesis	whale	black vs. whale
Membrane Transport	ABC transporters	ABC transporter iron(III) dicitrate (TC 3.A.1.14.1)	whale	black vs. whale
Membrane Transport	ABC transporters	ABC transporter macrolide	whale	black vs. whale
Membrane Transport	ABC transporters	ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1)	whale	black vs. whale
Membrane Transport	ABC transporters	ABC transporter putrescine (TC 3.A.1.11.2)	whale	black vs. whale
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	whale	black vs. whale
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Protocatechuate branch of beta-ketoadipate pathway	whale	black vs. whale
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate catabolism	whale	black vs. whale
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	n-Phenylalkanoic acid degradation	whale	black vs. whale
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	whale	black vs. whale
Motility and Chemotaxis	Flagellar motility in Prokaryota	Flagellum	whale	black vs. whale
Nitrogen Metabolism		Nitrosative stress	whale	black vs. whale
Protein Metabolism	Protein Biosynthesis	Ribosome biogenesis bacterial	whale	black vs. whale
Protein Metabolism	Protein Degradation	Protein degradation	whale	black vs. whale
Respiration	Electron accepting reactions	Anaerobic respiratory reductases	whale	black vs. whale
Respiration	Electron donating reactions	Hydrogenases	whale	black vs. whale
Respiration	Electron donating reactions	Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	whale	black vs. whale
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	whale	black vs. whale
Stress response	Oxidative stress	Glutathione Redox Metabolism	whale	black vs. whale
Stress response	Starvation response	ppGpp biosynthesis	whale	black vs. whale
Virulence	Adhesion and colonization factors	Mannose-sensitive hemagglutinin type 4 pilus	whale	black vs. whale
Amino Acids and Derivatives	Alanine, serine, and glycine	Alanine Biosynthesis	AMD	red vs. amd
Amino Acids and Derivatives	Alanine, serine, and glycine	Glycine cleavage system	AMD	red vs. amd
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Arginine Biosynthesis	AMD	red vs. amd
Amino Acids and Derivatives	Proline and 4-hydroxyproline	Proline Catabolism	AMD	red vs. amd
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	AMD	red vs. amd
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	AMD	red vs. amd
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	AMD	red vs. amd
Carbohydrates	CO2 fixation	Cyanobacterial CO2 uptake	AMD	red vs. amd
Carbohydrates	Di- and oligosaccharides	Trehalose biosynthesis	AMD	red vs. amd
Carbohydrates	Fermentation	Heterofermentative lactate fermentation	AMD	red vs. amd
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	AMD	red vs. amd
Carbohydrates	Monosaccharides	Ketogluconate metabolism	AMD	red vs. amd
Clustering-based Subsystems		EC49-61	AMD	red vs. amd
Clustering-based Subsystems		SA:14-24	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups,	Pigments	Cobalamin synthesis	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Pyrroloquinoline Quinone biosynthesis	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis in pathogens	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	Riboflavin metabolism	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Chlorophyll Biosynthesis	AMD	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Porphyrin, Heme, and Siroheme Biosynthesis	AMD	red vs. amd
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	AMD	red vs. amd
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	AMD	red vs. amd
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	AMD	red vs. amd
Fatty Acids and Lipids	Glycerolipids	Glycerolipid and glycerphospholipid metabolism	AMD	red vs. amd
Membrane Transport	ABC transporters	ABC transporter dipeptide (TC 3.A.1.5.2)	AMD	red vs. amd
Membrane Transport	Uni-, Sym- and Antiporters	Sodium Hydrogen Antiporter	AMD	red vs. amd
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate degradation	AMD	red vs. amd
Nitrogen Metabolism		Allantoin degradation	AMD	red vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome LSU eukaryotic and archaeal	AMD	red vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome SSU eukaryotic and archaeal	AMD	red vs. amd
Protein Metabolism	Protein Biosynthesis	Translation initiation factors eukaryotic and archaeal	AMD	red vs. amd
Protein Metabolism	Protein Degradation	Proteasome archaeal	AMD	red vs. amd
Respiration	ATP synthases	V-Type ATP synthase	AMD	red vs. amd
Respiration	Electron donating reactions	Formate hydrogenase	AMD	red vs. amd
Respiration	Soluble electron carries	Soluble cytochromes and functionally related electron carriers	AMD	red vs. amd
Virulence	Detection	MLST	AMD	red vs. amd
Amino Acids and Derivatives	Arginine; urea cycle, polyamines	Urea decomposition	red	red vs. amd
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Tryptophan synthesis	red	red vs. amd
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Biosynthesis	red	red vs. amd
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	red	red vs. amd
Carbohydrates	Central carbohydrate metabolism	Pyruvate metabolism I: anaplerotic reactions, PEP	red	red vs. amd
Cell Wall and Capsule	Capsular and extracellular polysacchrides	Capsular polysaccharide biosynthesis	red	red vs. amd
Cell Wall and Capsule	Peptidoglycan biosynthesis	Peptidoglycan Biosynthesis	red	red vs. amd
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	red	red vs. amd
DNA metabolism	DNA Replication	DNA-replication	red	red vs. amd
Membrane Transport	ABC transporters	ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	red	red vs. amd
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	red	red vs. amd
Nucleosides and Nucleotides		Ribonucleotide reduction	red	red vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome biogenesis bacterial	red	red vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome LSU bacterial	red	red vs. amd
Protein Metabolism	Protein Biosynthesis	Ribosome SSU bacterial	red	red vs. amd
Protein Metabolism	Protein Biosynthesis	Translation factors bacterial	red	red vs. amd
Protein Metabolism	Protein Biosynthesis	Universal GTPases	red	red vs. amd
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	red	red vs. amd
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	red	red vs. amd
Protein Metabolism	Protein Folding	GroEL GroES	red	red vs. amd
Respiration	ATP synthases	F0F1-type ATP synthase	red	red vs. amd
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	red	red vs. amd
Respiration	Electron donating reactions	Membrane-bound Ni, Fe-hydrogenase	red	red vs. amd
RNA metabolism	RNA processing and modification	Polyadenylation bacterial	red	red vs. amd
RNA metabolism		RNA polymerase bacterial	red	red vs. amd
RNA metabolism		Transcription factors bacterial	red	red vs. amd
RNA metabolism		tRNA aminoacylation	red	red vs. amd
Stress response	Oxidative stress	Protection from Reactive Oxygen Species	red	red vs. amd
Stress response	Starvation response	ppGpp biosynthesis	red	red vs. amd
Sulfur Metabolism	Inorganic sulfur assimilation	Inorganic Sulfur Assimilation	red	red vs. amd
Sulfur Metabolism	Inorganic sulfur assimilation	Sulfate assimilation	red	red vs. amd
Sulfur Metabolism	Inorganic sulfur assimilation	Sulfate to Sulfide	red	red vs. amd
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	red	red vs. amd
Amino Acids and Derivatives	Proline and 4-hydroxyproline	Proline Catabolism	farm	red vs. farm
Carbohydrates	Aminosugars	N-Acetyl-D-Glucosamine Utilization	farm	red vs. farm
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	farm	red vs. farm
Carbohydrates	Monosaccharides	Ketogluconate metabolism	farm	red vs. farm
Carbohydrates	Sugar alcohols	Ethanolamine utilization	farm	red vs. farm
Cell Division and Cell Cycle	Cell cycle in Prokaryota	Cyanobacterial Circadian Clock	farm	red vs. farm
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	farm	red vs. farm
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	farm	red vs. farm
Clustering-based Subsystems		EC49-61	farm	red vs. farm
Clustering-based Subsystems		SA:14-24	farm	red vs. farm
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	farm	red vs. farm
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	farm	red vs. farm
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	farm	red vs. farm
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	farm	red vs. farm
Membrane Transport	ABC transporters	ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	farm	red vs. farm
Membrane Transport	ABC transporters	ABC transporter macrolide	farm	red vs. farm
Membrane Transport	ABC transporters	ABC transporter nickel (TC 3.A.1.5.3)	farm	red vs. farm
Membrane Transport	ABC transporters	ABC transporter ribose (TC 3.A.1.2.1)	farm	red vs. farm
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	farm	red vs. farm
Nitrogen Metabolism		Nitrate and nitrite ammonification	farm	red vs. farm
Respiration	Electron accepting reactions	Anaerobic respiratory reductases	farm	red vs. farm
Respiration	Electron donating reactions	Formate dehydrogenase	farm	red vs. farm
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	farm	red vs. farm
Respiration	Soluble electron carries	Soluble cytochromes and functionally related electron carriers	farm	red vs. farm
RNA metabolism	RNA processing and modification	tRNA processing	farm	red vs. farm
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Tryptophan synthesis	red	red vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	red	red vs. farm
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	red	red vs. farm
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Asp-Glu-tRNA(Asn-Gln) transamidation	red	red vs. farm
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Glutamate biosynthesis	red	red vs. farm
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Biosynthesis	red	red vs. farm
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	red	red vs. farm
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	red	red vs. farm
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	red	red vs. farm
Carbohydrates	Organic acids	Methylcitrate cycle	red	red vs. farm
Cell Division and Cell Cycle	Structural elements	Cytoskeleton	red	red vs. farm
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	red	red vs. farm
DNA metabolism	DNA Repair	DNA repair, bacterial	red	red vs. farm
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	red	red vs. farm
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	red	red vs. farm
Nucleosides and Nucleotides		Ribonucleotide reduction	red	red vs. farm
Protein Metabolism	Protein Biosynthesis	Ribosome LSU bacterial	red	red vs. farm
Protein Metabolism	Protein Biosynthesis	Ribosome SSU bacterial	red	red vs. farm
Protein Metabolism	Protein Biosynthesis	Translation factors bacterial	red	red vs. farm
Protein Metabolism	Protein Biosynthesis	Universal GTPases	red	red vs. farm
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	red	red vs. farm
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	red	red vs. farm
Protein Metabolism	Protein Folding	GroEL GroES	red	red vs. farm
Respiration	ATP synthases	F0F1-type ATP synthase	red	red vs. farm
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	red	red vs. farm
Respiration	Electron donating reactions	Respiratory Complex I	red	red vs. farm
RNA metabolism	RNA processing and modification	Polyadenylation bacterial	red	red vs. farm
RNA metabolism		RNA polymerase bacterial	red	red vs. farm
RNA metabolism		tRNA aminoacylation	red	red vs. farm
Stress response	Starvation response	ppGpp biosynthesis	red	red vs. farm
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	red	red vs. farm
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	red	red vs. Sargasso
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	red	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis	red	red vs. Sargasso
Respiration	Electron donating reactions	Respiratory Complex I	red	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	red	red vs. Sargasso
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	red	red vs. Sargasso
Nitrogen Metabolism		Denitrification	red	red vs. Sargasso
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	red	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	red	red vs. Sargasso
Protein Metabolism	Protein Folding	GroEL GroES	red	red vs. Sargasso
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	red	red vs. Sargasso
Carbohydrates	Organic acids	Methylcitrate cycle	red	red vs. Sargasso
Stress response	Starvation response	ppGpp biosynthesis	red	red vs. Sargasso
Respiration	ATP synthases	F0F1-type ATP synthase	red	red vs. Sargasso
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	red	red vs. Sargasso
Nucleosides and Nucleotides		Ribonucleotide reduction	red	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome SSU bacterial	red	red vs. Sargasso
RNA metabolism		tRNA aminoacylation	red	red vs. Sargasso
RNA metabolism		Transcription factors bacterial	red	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Translation factors bacterial	red	red vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	red	red vs. Sargasso
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Asp-Glu-tRNA(Asn-Gln) transamidation	red	red vs. Sargasso
Respiration	Electron donating reactions	Membrane-bound Ni, Fe-hydrogenase	red	red vs. Sargasso
Stress response	Oxidative stress	Protection from Reactive Oxygen Species	red	red vs. Sargasso
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	red	red vs. Sargasso
RNA metabolism	RNA processing and modification	Queuosine-Archaeosine Biosynthesis	red	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Universal GTPases	red	red vs. Sargasso
DNA metabolism	DNA Repair	DNA repair, bacterial	red	red vs. Sargasso
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	red	red vs. Sargasso
RNA metabolism		Transcription factors cyanobacterial RpoD-like sigma factors	Sargasso	red vs. Sargasso
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	Sargasso	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	Sargasso	red vs. Sargasso
Nitrogen Metabolism		Allantoin degradation	Sargasso	red vs. Sargasso
Nitrogen Metabolism		Ammonia assimilation	Sargasso	red vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	Carotenoids	Sargasso	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	Sargasso	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome LSU chloroplast	Sargasso	red vs. Sargasso
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Chorismate Synthesis	Sargasso	red vs. Sargasso
Fatty Acids and Lipids	Fatty acids	Fatty Acid Biosynthesis FASII	Sargasso	red vs. Sargasso
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	Sargasso	red vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	Sargasso	red vs. Sargasso
Carbohydrates	Monosaccharides	Ketogluconate metabolism	Sargasso	red vs. Sargasso
Cell Wall and Capsule	Gram-Negative cell wall components	Lipid A biosynthesis	Sargasso	red vs. Sargasso
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	Sargasso	red vs. Sargasso
Carbohydrates	Aminosugars	N-Acetyl-D-Glucosamine Utilization	Sargasso	red vs. Sargasso
Cell Wall and Capsule	Glycosylation	N-linked Glycosylation in Bacteria	Sargasso	red vs. Sargasso
Phosphorus Metabolism		P uptake (cyanobacteria)	Sargasso	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis Archaeal	Sargasso	red vs. Sargasso
Carbohydrates	Central carbohydrate metabolism	Pyruvate Alanine Serine Interconversions	Sargasso	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome SSU chloroplast	Sargasso	red vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Thiamine and thiamine pyrophosphate	Thiamin biosynthesis	Sargasso	red vs. Sargasso
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Quinate degradation	Sargasso	red vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter glutamine (TC 3.A.1.3.2)	Sargasso	red vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter L-proline glycine betaine (TC 3.A.1.12.1)	Sargasso	red vs. Sargasso
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	Sargasso	red vs. Sargasso
RNA metabolism		RNA polymerase chloroplast	Sargasso	red vs. Sargasso
Clustering-based Subsystems		SA:14-24	Sargasso	red vs. Sargasso
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Central meta-cleavage pathway of aromatic compound degradation	Sargasso	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome LSU mitochondrial	Sargasso	red vs. Sargasso
Protein Metabolism	Protein Biosynthesis	Ribosome SSU mitochondrial	Sargasso	red vs. Sargasso
RNA metabolism		tRNA aminoacylation, mitochondrial	Sargasso	red vs. Sargasso
Membrane Transport	ABC transporters	ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1)	Sargasso	red vs. Sargasso
Fatty Acids and Lipids	Glycerolipids	Glycerolipid and glycerphospholipid metabolism	Sargasso	red vs. Sargasso
Respiration	Electron donating reactions	Coenzyme F420-H2 dehydrogenase (methanophenazine)	Sargasso	red vs. Sargasso
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	Sargasso	red vs. Sargasso
Virulence	Detection	MLST	Sargasso	red vs. Sargasso
Amino Acids and Derivatives	Alanine, serine, and glycine	Glycine cleavage system	red	red vs. seed
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Tryptophan synthesis	red	red vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	red	red vs. seed
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Biosynthesis v2	red	red vs. seed
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Asp-Glu-tRNA(Asn-Gln) transamidation	red	red vs. seed
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Glutamate biosynthesis	red	red vs. seed
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Glutamate, aspartate and asparagine biosynthisis	red	red vs. seed
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Biosynthesis	red	red vs. seed
Carbohydrates	Central carbohydrate metabolism	Embden-Meyerhof and Gluconeogenesis	red	red vs. seed
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	red	red vs. seed
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	red	red vs. seed
Carbohydrates	Central carbohydrate metabolism	Pyruvate metabolism I: anaplerotic reactions, PEP	red	red vs. seed
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	red	red vs. seed
Carbohydrates	Organic acids	Methylcitrate cycle	red	red vs. seed
Cell Division and Cell Cycle	Structural elements	Cytoskeleton	red	red vs. seed
Cell Wall and Capsule	Gram-Negative cell wall components	dTDP-rhamnose synthesis	red	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	red	red vs. seed
DNA metabolism	DNA Repair	DNA Repair Base Excision	red	red vs. seed
DNA metabolism	DNA Repair	DNA repair, bacterial	red	red vs. seed
DNA metabolism	DNA Replication	DNA-replication	red	red vs. seed
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	red	red vs. seed
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	red	red vs. seed
Nucleosides and Nucleotides		Ribonucleotide reduction	red	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU bacterial	red	red vs. seed
Protein Metabolism	Protein Biosynthesis	Translation factors bacterial	red	red vs. seed
Protein Metabolism	Protein Biosynthesis	Universal GTPases	red	red vs. seed
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	red	red vs. seed
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	red	red vs. seed
Protein Metabolism	Protein Folding	GroEL GroES	red	red vs. seed
Respiration	ATP synthases	F0F1-type ATP synthase	red	red vs. seed
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	red	red vs. seed
Respiration	Electron donating reactions	Respiratory Complex I	red	red vs. seed
Respiration	Electron donating reactions	Respiratory dehydrogenases 1	red	red vs. seed
RNA metabolism	RNA processing and modification	Polyadenylation bacterial	red	red vs. seed
RNA metabolism		RNA polymerase bacterial	red	red vs. seed
RNA metabolism		Transcription factors bacterial	red	red vs. seed
RNA metabolism		tRNA aminoacylation	red	red vs. seed
Stress response	Starvation response	ppGpp biosynthesis	red	red vs. seed
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	red	red vs. seed
Carbohydrates	Aminosugars	N-Acetyl-D-Glucosamine Utilization	SEED	red vs. seed
Carbohydrates	Central carbohydrate metabolism	Pyruvate Alanine Serine Interconversions	SEED	red vs. seed
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	SEED	red vs. seed
Carbohydrates	Monosaccharides	Ketogluconate metabolism	SEED	red vs. seed
Carbohydrates	Monosaccharides	L-ascorbate degradation	SEED	red vs. seed
Carbohydrates	Monosaccharides	The Tartronate Semialdehyde Hub	SEED	red vs. seed
Carbohydrates	Organic acids	Propanediol utilization	SEED	red vs. seed
Carbohydrates	Sugar alcohols	Ethanolamine utilization	SEED	red vs. seed
Carbohydrates	Sugar alcohols	Galactitol degradation	SEED	red vs. seed
Cell Division and Cell Cycle	Cell cycle in Prokaryota	Cyanobacterial Circadian Clock	SEED	red vs. seed
Cell signaling	Signal transduction in prokaryota	Phytochromes	SEED	red vs. seed
Cell signaling	Signal transduction in Prokaryota	Rrf2 family transcriptional regulators	SEED	red vs. seed
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	SEED	red vs. seed
Cell Wall and Capsule	Glycosylation	N-linked Glycosylation in Bacteria	SEED	red vs. seed
Cell Wall and Capsule	Gram-Negative cell wall components	Capsular surface virulence antigen loci	SEED	red vs. seed
Clustering-based Subsystems		EC49-61	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups,	Pigments	Cobalamin synthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Biotin	Biotin biosynthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Folate and pterines	Molybdopterin biosynthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Isoprenoids	Carotenoids	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Menaquinone and Phylloquinone Biosynthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Siderophores	Siderophore enterobactin biosynthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Siderophores	Siderophore enterobactin biosynthesis and ferric enterbactin transport	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Tetrapyrroles	Chlorophyll Biosynthesis	SEED	red vs. seed
Cofactors, Vitamins, Prosthetic Groups, Pigments	Thiamine and thiamine pyrophosphate	Thiamin biosynthesis	SEED	red vs. seed
DNA metabolism	DNA uptake, competence	gram plus late competence	SEED	red vs. seed
Experimental Subsystems	Auxiliary Subsystems	Phosphoglycerate mutase protein family	SEED	red vs. seed
Experimental Subsystems	Temporary subsystems	Vibrio Experimental Type III secretion system 	SEED	red vs. seed
Fatty Acids and Lipids	Glycerolipids	Glycerolipid and glycerphospholipid metabolism	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter alkylphosphonate (TC 3.A.1.9.1)	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter ferrichrome (TC 3.A.1.14.3)	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter iron(III) dicitrate (TC 3.A.1.14.1)	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter molybdenum (TC 3.A.1.8.1)	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter nickel (TC 3.A.1.5.3)	SEED	red vs. seed
Membrane Transport	ABC transporters	ABC transporter peptide (TC 3.A.1.5.5)	SEED	red vs. seed
Membrane Transport	ABC transporters	CbiQO-type ABC transporter systems	SEED	red vs. seed
Membrane Transport	ABC transporters	Transport of Nickel and Cobalt	SEED	red vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate degradation	SEED	red vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Biphenyl Degradation	SEED	red vs. seed
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Phenylpropanoid compound degradation	SEED	red vs. seed
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	SEED	red vs. seed
Phosphorus Metabolism		P uptake (cyanobacteria)	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU chloroplast	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU eukaryotic and archaeal	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome LSU mitochondrial	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU chloroplast	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU eukaryotic and archaeal	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Ribosome SSU mitochondrial	SEED	red vs. seed
Protein Metabolism	Protein Biosynthesis	Translation initiation factors eukaryotic and archaeal	SEED	red vs. seed
Protein Metabolism	Protein Degradation	Phenylpropionate Degradation	SEED	red vs. seed
Protein Metabolism	Protein Degradation	Proteasome eukaryotic	SEED	red vs. seed
Respiration	Electron accepting reactions	Anaerobic respiratory reductases	SEED	red vs. seed
Respiration	Electron donating reactions	Coenzyme F420-H2 dehydrogenase (methanophenazine)	SEED	red vs. seed
Respiration	Electron donating reactions	Formate dehydrogenase	SEED	red vs. seed
Respiration	Soluble electron carries	Soluble cytochromes and functionally related electron carriers	SEED	red vs. seed
RNA metabolism		RNA polymerase chloroplast	SEED	red vs. seed
RNA metabolism		RNA polymerase II initiation factors	SEED	red vs. seed
RNA metabolism		Transcription factors cyanobacterial RpoD-like sigma factors	SEED	red vs. seed
RNA metabolism		tRNA aminoacylation, mitochondrial	SEED	red vs. seed
Sulfur Metabolism	Inorganic sulfur assimilation	Inorganic Sulfur Assimilation	SEED	red vs. seed
Sulfur Metabolism	Organic sulfur assimilation	Alkanesulfonates Utilization	SEED	red vs. seed
Virulence	Invasion and intracellular resistance	Listeria surface proteins: Internalin-like proteins	SEED	red vs. seed
Virulence	Invasion and intracellular resistance	Listeria surface proteins: LPXTG motif	SEED	red vs. seed
Virulence	Toxins, Superantigens	Cholera toxin	SEED	red vs. seed
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Tryptophan synthesis	red	red vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Branched-Chain Amino Acid Biosynthesis	red	red vs. whale
Amino Acids and Derivatives	Glutamine, glutamate, aspartate, asparagine; ammonia assimilation	Asp-Glu-tRNA(Asn-Gln) transamidation	red	red vs. whale
Amino Acids and Derivatives	Lysine, threonine, methionine, and cysteine	Methionine Biosynthesis	red	red vs. whale
Carbohydrates	Central carbohydrate metabolism	Glyoxylate Synthesis	red	red vs. whale
Carbohydrates	Central carbohydrate metabolism	Pentose phosphate pathway	red	red vs. whale
Carbohydrates	Central carbohydrate metabolism	TCA Cycle	red	red vs. whale
Carbohydrates	Organic acids	Methylcitrate cycle	red	red vs. whale
Cell Division and Cell Cycle	Structural elements	Cytoskeleton	red	red vs. whale
Cell Wall and Capsule	Gram-Negative cell wall components	dTDP-rhamnose synthesis	red	red vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Quinone cofactors	Ubiquinone Menaquinone-cytochrome c reductase complexes	red	red vs. whale
DNA metabolism	DNA Repair	DNA repair, bacterial	red	red vs. whale
Nucleosides and Nucleotides	Purines	De Novo Purine Biosynthesis	red	red vs. whale
Nucleosides and Nucleotides	Pyrimidines	De Novo Pyrimidine Synthesis	red	red vs. whale
Nucleosides and Nucleotides		Ribonucleotide reduction	red	red vs. whale
Protein Metabolism	Protein Biosynthesis	Ribosome LSU bacterial	red	red vs. whale
Protein Metabolism	Protein Biosynthesis	Ribosome SSU bacterial	red	red vs. whale
Protein Metabolism	Protein Biosynthesis	Translation factors bacterial	red	red vs. whale
Protein Metabolism	Protein Biosynthesis	Universal GTPases	red	red vs. whale
Protein Metabolism	Protein Degradation	Proteolysis in bacteria, ATP-dependent	red	red vs. whale
Protein Metabolism	Protein Export and Secretion	General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1)	red	red vs. whale
Protein Metabolism	Protein Folding	GroEL GroES	red	red vs. whale
Respiration	ATP synthases	F0F1-type ATP synthase	red	red vs. whale
Respiration	Electron accepting reactions	Terminal cytochrome C oxidases	red	red vs. whale
Respiration	Electron donating reactions	Respiratory Complex I	red	red vs. whale
RNA metabolism	RNA processing and modification	Polyadenylation bacterial	red	red vs. whale
RNA metabolism		RNA polymerase bacterial	red	red vs. whale
RNA metabolism		Transcription factors bacterial	red	red vs. whale
RNA metabolism		tRNA aminoacylation	red	red vs. whale
Virulence	Resistance to Antibiotics	Resistance to fluoroquinolones	red	red vs. whale
Amino Acids and Derivatives	Alanine, serine, and glycine	Alanine Biosynthesis	whale	red vs. whale
Amino Acids and Derivatives	Aromatic amino acids and derivatives	Central meta-cleavage pathway of aromatic compound degradation	whale	red vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	HMG CoA Synthesis	whale	red vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Isoleucine degradation	whale	red vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Leucine Degradation and HMG-CoA Metabolism	whale	red vs. whale
Amino Acids and Derivatives	Branched-chain amino acids	Valine degradation	whale	red vs. whale
Carbohydrates	Aminosugars	N-Acetyl-D-Glucosamine Utilization	whale	red vs. whale
Carbohydrates	Central carbohydrate metabolism	Acetogenesis from Pyruvate	whale	red vs. whale
Carbohydrates	Central carbohydrate metabolism	Butyrate and Butanol Acetone fermentation	whale	red vs. whale
Carbohydrates	Central carbohydrate metabolism	Methylglyoxal Metabolism	whale	red vs. whale
Carbohydrates	Monosaccharides	Fucose and rhamnose degradation	whale	red vs. whale
Carbohydrates	Monosaccharides	Ketogluconate metabolism	whale	red vs. whale
Cell Division and Cell Cycle	Cell cycle in Prokaryota	Cyanobacterial Circadian Clock	whale	red vs. whale
Cell Wall and Capsule	Cell wall of Mycobacteria	mycolic acid synthesis	whale	red vs. whale
Cell Wall and Capsule	Gram-Positive cell wall components	Teichoic acid Biosynthesis	whale	red vs. whale
Clustering-based Subsystems		EC49-61	whale	red vs. whale
Clustering-based Subsystems		SA:14-24	whale	red vs. whale
Cofactors, Vitamins, Prosthetic Groups,	Pigments	Cobalamin synthesis	whale	red vs. whale
Cofactors, Vitamins, Prosthetic Groups, Pigments	Riboflavin, FMN, FAD	FMN and FAD biosynthesis in pathogens	whale	red vs. whale
Degradation of Xenobiotics	Anaerobic degradation of aromatic compounds	Anaerobic benzoate metabolism	whale	red vs. whale
Fatty Acids and Lipids	Fatty acids	fatty acid metabolism	whale	red vs. whale
Fatty Acids and Lipids	Fatty acids	fatty acid oxidation pathway	whale	red vs. whale
Fatty Acids and Lipids	Glycerolipids	Glycerolipid and glycerphospholipid metabolism	whale	red vs. whale
Membrane Transport	ABC transporters	ABC transporter ferrichrome (TC 3.A.1.14.3)	whale	red vs. whale
Membrane Transport	ABC transporters	ABC transporter iron(III) dicitrate (TC 3.A.1.14.1)	whale	red vs. whale
Membrane Transport	ABC transporters	ABC transporter macrolide	whale	red vs. whale
Membrane Transport	ABC transporters	ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1)	whale	red vs. whale
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Phenylacetate pathway of aromatic compound degradation	whale	red vs. whale
Metabolism of aromatic compounds	Metabolism of central aromatic intermediates	Protocatechuate branch of beta-ketoadipate pathway	whale	red vs. whale
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	Benzoate degradation	whale	red vs. whale
Metabolism of aromatic compounds	Peripheral pathways for catabolism of aromatic compounds	n-Phenylalkanoic acid degradation	whale	red vs. whale
Motility and Chemotaxis	Chemotaxis in Prokaryota	Bacterial Chemotaxis	whale	red vs. whale
Respiration	Electron accepting reactions	Anaerobic respiratory reductases	whale	red vs. whale
Virulence	Detection	MLST	whale	red vs. whale