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Amino Acids and Derivatives L-2-amino-thiazoline-4-carboxylic acid-Lcysteine conversion Alanine, serine, and glycine Alanine biosynthesis Glycine Biosynthesis Glycine and Serine Utilization Glycine cleavage system Serine Biosynthesis Arginine; urea cycle, polyamines Arginine Biosynthesis Arginine Biosynthesis extended Arginine Deiminase Pathway Arginine and Ornithine Degradation Cyanophycin Metabolism Polyamine Metabolism Urea decomposition Aromatic amino acids and derivatives Aminotransferases:Aromatic Pathway and More, A work in progress Aromatic amino acid degradation Aromatic amino acid interconversions with aryl acids Bacilysin biosynthesis Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. Chorismate Synthesis Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) Phenylalanine and Tyrosine Branches from Chorismate Phenylalanine synthesis Tryptophan synthesis Branched-chain amino acids Branched-Chain Amino Acid Biosynthesis HMG CoA Synthesis Isoleucine degradation Ketoisovalerate oxidoreductase Leucine Biosynthesis Leucine Degradation and HMG-CoA Metabolism Valine degradation Glutamine, glutamate, aspartate, asparagine; ammonia assimilation Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis Glutamine synthetases Histidine Metabolism Histidine Biosynthesis Histidine Degradation Lysine, threonine, methionine, and cysteine Cysteine Biosynthesis Lysine Biosynthesis DAP Pathway Lysine degradation Methionine Biosynthesis Methionine Degradation Methionine Salvage Threonine anaerobic catabolism gene cluster Threonine and Homoserine Biosynthesis Threonine degradation Osmotic stress Choline and Betaine Uptake and Betaine Biosynthesis Proline and 4-hydroxyproline Proline, 4-hydroxyproline uptake and utilization Proline Synthesis Carbohydrates Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway beta-glucuronide utilization Aminosugars (GlcNAc)2 Catabolic Operon Chitin and N-acetylglucosamine utilization N-Acetyl-Galactosamine and Galactosamine Utilization Neotrehalosadiamine (NTD) Biosynthesis Operon CO2 fixation CO2 uptake, carboxysome Calvin-Benson cycle Photorespiration (oxidative C2 cycle) Central carbohydrate metabolism Dihydroxyacetone kinases Entner-Doudoroff Pathway Glycogen metabolism Glycolate, glyoxylate interconversions Glycolysis and Gluconeogenesis Glycolysis and Gluconeogenesis, including Archaeal enzymes Glyoxylate bypass Methylglyoxal Metabolism Pentose phosphate pathway Pyruvate:ferredoxin oxidoreductase Pyruvate Alanine Serine Interconversions Pyruvate metabolism I: anaplerotic reactions, PEP Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate TCA Cycle Clustering-based subsystems Unknown sugar utilization (cluster ydeVWYZ) Unknown sugar utilization (cluster yphABCDEFG) Di- and oligosaccharides Beta-Glucoside Metabolism Fructooligosaccharides(FOS) and Raffinose Utilization Lactose and Galactose Uptake and Utilization Maltose and Maltodextrin Utilization Melibiose Utilization Sucrose Metabolism Sucrose utilization Sucrose utilization Shewanella Trehalose Biosynthesis Trehalose Uptake and Utilization Fermentation Acetoin, butanediol metabolism Acetyl-CoA fermentation to Butyrate Butanol Biosynthesis Fermentations: Lactate Fermentations: Mixed acid Methanogenesis Methanogenesis from methylated compounds Monosaccharides 2-Ketogluconate Utilization D-Galacturonate Utilization D-Sorbitol(D-Glucitol) and L-Sorbose Utilization D-Tagatose and Galactitol Utilization D-allose utilization D-galactarate, D-glucarate and D-glycerate catabolism D-galactonate catabolism D-gluconate and ketogluconates metabolism D-ribose utilization Deoxyribose and Deoxynucleoside Catabolism Fructose utilization L-Arabinose utilization L-ascorbate utilization (and related gene clusters) L-fucose utilization L-fucose utilization temp L-rhamnose utilization Lactose utilization Mannitol Utilization Mannose Metabolism Xylose utilization One-carbon Metabolism Formaldehyde assimilation: Ribulose monophosphate pathway Methanogenesis One-carbon metabolism by tetrahydropterines Serine-glyoxylate cycle Organic acids 2-methylcitrate to 2-methylaconitate metabolism cluster Alpha-acetolactate operon Glyoxylate Synthesis Isobutyryl-CoA to Propionyl-CoA Module Lactate utilization Malonate decarboxylase Methylcitrate cycle Propanediol utilization Propionate-CoA to Succinate Module Propionyl-CoA to Succinyl-CoA Module Tricarballylate Utilization Quorum sensing and biofilm formation Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon) Biofilm Adhesin Biosynthesis Sugar alcohols Di-Inositol-Phosphate biosynthesis Erythritol utilization Ethanolamine utilization Glycerol and Glycerol-3-phosphate Uptake and Utilization Hexitol degradation Inositol catabolism Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization Uptake system Hexose Phosphate Uptake System Catabolism of an unknown compound CBSS-262316.1.peg.2929 Cell Division and Cell Cycle YgjD and YeaZ Cell cycle in Prokaryota Bacterial Cell Division Bacterial Cytoskeleton Cyanobacterial Circadian Clock MukBEF Chromosome Condensation Murein hydrolase regulation and cell death Two cell division clusters relating to chromosome partitioning Cell Wall and Capsule Murein Hydrolases Peptidoglycan Biosynthesis 2 UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis YjeE Capsular and extracellular polysacchrides Alginate metabolism CMP-N-acetylneuraminate Biosynthesis Capsular Polysaccharide (CPS) of Campylobacter Capsular Polysaccharide Biosynthesis in Vibrio Colanic acid biosynthesis Extracellular Polysaccharide Biosynthesis of Streptococci Lipid A modifications O-Methyl Phosphoramidate Capsule Modification in Campylobacter Phosphorylcholine incorporation in LPS Rhamnose containing glycans Serotype determining Capsular polysaccharide biosynthesis in Staphylococcus Sialic Acid Metabolism Xanthan Exopolysaccharide Biosynthesis and Export YjbEFGH Locus Involved in Exopolysaccharide Production dTDP-rhamnose synthesis Gram-Negative cell wall components Capsular heptose biosynthesis Capsular surface virulence antigen loci Core Oligosaccharide Glycosylation in Pseudomonas KDO2-Lipid A biosynthesis LOS core oligosaccharide biosynthesis Lipid A-Ara4N pathway ( Polymyxin resistance ) Major Outer Membrane Proteins Vibrio Core Oligosaccharide Biosynthesis Gram-Positive cell wall components Anthrose Biosynthesis D-Alanyl Lipoteichoic Acid Biosynthesis Teichoic and lipoteichoic acids biosynthesis Teichuronic acid biosynthesis Clustering-based subsystems Bacterial RNA-metabolizing Zn-dependent hydrolases CBSS-214092.1.peg.3450 Competence or DNA damage-inducible protein CinA and related protein families Conserved gene cluster associated with Met-tRNA formyltransferase Conserved gene cluster possibly involved in RNA metabolism LMPTP YfkJ cluster LMPTP YwlE cluster NusA-TFII Cluster PA0057 cluster Putative hemin transporter Putative sulfate assimilation cluster Staphylococcus aureus hypothetical repetitive gene loci Clustering-based subsystems CBSS-262719.3.peg.410 Conenzyme B12 related Hypothetical: Clusters with cobST Lysine, threonine, methionine, and cysteine YeiH Type III secretion system, extended CBSS-243265.1.peg.3592 proteosome related Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related Cofactors, Vitamins, Prosthetic Groups, Pigments Biotin Biotin biosynthesis Coenzyme A Coenzyme A Biosynthesis Coenzyme B Coenzyme B synthesis Coenzyme F420 Coenzyme F420 synthesis Fe-S clusters Fe-S cluster assembly Folate and pterines Folate Biosynthesis Molybdopterin biosynthesis Pterin biosynthesis p-Aminobenzoyl-Glutamate Utilization Isoprenoids Carotenoids Isoprenoid Biosynthesis Lipoic acid Lipoic acid metabolism NAD and NADP NAD and NADP cofactor biosynthesis global NAD regulation PnuC-like transporters Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis Quinone cofactors Coenzyme PQQ synthesis Menaquinone and Phylloquinone Biosynthesis Plastoquinone Biosynthesis Pyrroloquinoline Quinone biosynthesis Ubiquinone Biosynthesis Riboflavin, FMN, FAD Flavodoxin Riboflavin, FMN and FAD metabolism Tetrapyrroles Chlorophyll Biosynthesis Chlorophyll Degradation Cobalamin synthesis Coenzyme B12 biosynthesis Heme and Siroheme Biosynthesis Heme biosynthesis orphans Thiamine and thiamine pyrophosphate Thiamin biosynthesis DNA Metabolism CRISPRs DNA structural proteins, bacterial Restriction-Modification System YcfH DNA repair 2-phosphoglycolate salvage ATP-dependent Nuclease DNA repair, UvrABC system DNA repair, bacterial DNA repair, bacterial DinG and relatives DNA repair, bacterial MutL-MutS system DNA repair, bacterial RecFOR pathway DNA repair, bacterial UvrD and related helicases DNA repair and recombination eukaryotic Nonhomologous End-Joining in Bacteria DNA replication DNA-replication DNA Helicase of Unknown Function DNA replication, archaeal DNA topoisomerases, Type I, ATP-independent DNA topoisomerases, Type II, ATP-dependent Plasmid replication Dormancy and Sporulation Bacillus Sporulation Killing Factor A Biosynthetic Cluster Bacillus biofilm matrix protein component TasA and homologs Persister Cells Spore Coat Sporulation Cluster III A Sporulation gene orphans Spore DNA protection Dipicolinate Synthesis Small acid-soluble spore proteins Experimental Subsystems Accessory Gene Regulator CobW Experimental tye Fructose-bisphosphate aldolase protein family Hypothetical DUF454 Phosphoglycerate mutase protein family Synechocystis experimental rRNA methylation in clusters tRNA aminoacylase paralogs Clustering-based subsystems Lipopolysaccharide biosynthesis 2 RNA processing and modification Exosome Resistance to antibiotics and toxic compounds Acriflavin resistance cluster Fatty Acids and Lipids Polyhydroxybutyrate metabolism Fatty acids Fatty Acid Biosynthesis FASII carnitine metabolism Isoprenoids Archaeal lipids Phospholipids Glycerolipid and Glycerophospholipid Metabolism in Bacteria Triacylglycerols Glycerol fermenation to 1,3-propanediol Triacylglycerol metabolism Macromolecular Synthesis Control of Macromolecuar Synthesis CBSS-243277.1.peg.511 Membrane Transport Agrobacterium opine tran