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pathwayList.txt
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// List of metabolic pathways considered for the comparison
// NOTE 1: double slash means comment
// NOTE 2: after commenting/activating pathways you must force the organism's download from KEGG
// Carbohydrate metabolism
00010;Glycolysis / Gluconeogenesis
00020;Citrate cycle (TCA cycle)
00030;Pentose phosphate pathway
00040;Pentose and glucuronate interconversions
00051;Fructose and mannose metabolism
00052;Galactose metabolism
00053;Ascorbate and aldarate metabolism
00500;Starch and sucrose metabolism
00520;Amino sugar and nucleotide sugar metabolism
00620;Pyruvate metabolism
00630;Glyoxylate and dicarboxylate metabolism
00640;Propanoate metabolism
00650;Butanoate metabolism
00660;C5-Branched dibasic acid metabolism
00562;Inositol phosphate metabolism
// Energy metabolism
00190;Oxidative phosphorylation
00195;Photosynthesis
00196;Photosynthesis - antenna proteins
00710;Carbon fixation in photosynthetic organisms
00720;Carbon fixation pathways in prokaryotes
00680;Methane metabolism
00910;Nitrogen metabolism
00920;Sulfur metabolism
// Lipid metabolism
00061;Fatty acid biosynthesis
00062;Fatty acid elongation
00071;Fatty acid degradation
00073;Cutin, suberine and wax biosynthesis
00100;Steroid biosynthesis
00120;Primary bile acid biosynthesis
00121;Secondary bile acid biosynthesis
00140;Steroid hormone biosynthesis
00561;Glycerolipid metabolism
00564;Glycerophospholipid metabolism
00565;Ether lipid metabolism
00600;Sphingolipid metabolism
00590;Arachidonic acid metabolism
00591;Linoleic acid metabolism
00592;alpha-Linolenic acid metabolism
01040;Biosynthesis of unsaturated fatty acids
// Nucleotide metabolism
00230;Purine metabolism
00240;Pyrimidine metabolism
// Amino acid metabolism
00250;Alanine, aspartate and glutamate metabolism
00260;Glycine, serine and threonine metabolism
00270;Cysteine and methionine metabolism
00280;Valine, leucine and isoleucine degradation
00290;Valine, leucine and isoleucine biosynthesis
00300;Lysine biosynthesis
00310;Lysine degradation
00220;Arginine biosynthesis
00330;Arginine and proline metabolism
00340;Histidine metabolism
00350;Tyrosine metabolism
00360;Phenylalanine metabolism
00380;Tryptophan metabolism
00400;Phenylalanine, tyrosine and tryptophan biosynthesis
// Metabolism of other amino acids
00410;beta-Alanine metabolism
00430;Taurine and hypotaurine metabolism
00440;Phosphonate and phosphinate metabolism
00450;Selenocompound metabolism
00460;Cyanoamino acid metabolism
00470;D-Amino acid metabolism
00480;Glutathione metabolism
// Glycan biosynthesis and metabolism
00510;N-Glycan biosynthesis
00513;Various types of N-glycan biosynthesis
00512;Mucin type O-glycan biosynthesis
00515;Mannose type O-glycan biosynthesis
00514;Other types of O-glycan biosynthesis
00532;Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate
00534;Glycosaminoglycan biosynthesis - heparan sulfate / heparin
00533;Glycosaminoglycan biosynthesis - keratan sulfate
00531;Glycosaminoglycan degradation
00563;Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
00601;Glycosphingolipid biosynthesis - lacto and neolacto series
00603;Glycosphingolipid biosynthesis - globo and isoglobo series
00604;Glycosphingolipid biosynthesis - ganglio series
00540;Lipopolysaccharide biosynthesis
00542;O-Antigen repeat unit biosynthesis
00541;O-Antigen nucleotide sugar biosynthesis
00550;Peptidoglycan biosynthesis
00511;Other glycan degradation
00571;Lipoarabinomannan (LAM) biosynthesis
00572;Arabinogalactan biosynthesis - Mycobacterium
// Metabolism of cofactors and vitamins
00730;Thiamine metabolism
00740;Riboflavin metabolism
00750;Vitamin B6 metabolism
00760;Nicotinate and nicotinamide metabolism
00770;Pantothenate and CoA biosynthesis
00780;Biotin metabolism
00785;Lipoic acid metabolism
00790;Folate biosynthesis
00670;One carbon pool by folate
00830;Retinol metabolism
00860;Porphyrin metabolism
00130;Ubiquinone and other terpenoid-quinone biosynthesis
//Metabolism of terpenoids and polyketides
00900;Terpenoid backbone biosynthesis
00902;Monoterpenoid biosynthesis
00909;Sesquiterpenoid and triterpenoid biosynthesis
00904;Diterpenoid biosynthesis
00906;Carotenoid biosynthesis
00905;Brassinosteroid biosynthesis
00981;Insect hormone biosynthesis
00908;Zeatin biosynthesis
00903;Limonene and pinene degradation
00281;Geraniol degradation
01052;Type I polyketide structures
00522;Biosynthesis of 12-, 14- and 16-membered macrolides
01051;Biosynthesis of ansamycins
01059;Biosynthesis of enediyne antibiotics
01056;Biosynthesis of type II polyketide backbone
01057;Biosynthesis of type II polyketide products
00253;Tetracycline biosynthesis
00523;Polyketide sugar unit biosynthesis
01054;Nonribosomal peptide structures
01053;Biosynthesis of siderophore group nonribosomal peptides
01055;Biosynthesis of vancomycin group antibiotics
// Biosynthesis of other secondary metabolites
00940;Phenylpropanoid biosynthesis
00945;Stilbenoid, diarylheptanoid and gingerol biosynthesis
00941;Flavonoid biosynthesis
00944;Flavone and flavonol biosynthesis
00942;Anthocyanin biosynthesis
00943;Isoflavonoid biosynthesis
00901;Indole alkaloid biosynthesis
00403;Indole diterpene alkaloid biosynthesis
00950;Isoquinoline alkaloid biosynthesis
00960;Tropane, piperidine and pyridine alkaloid biosynthesis
00996;Biosynthesis of various alkaloids
00232;Caffeine metabolism
00965;Betalain biosynthesis
00966;Glucosinolate biosynthesis
00402;Benzoxazinoid biosynthesis
00311;Penicillin and cephalosporin biosynthesis
00332;Carbapenem biosynthesis
00261;Monobactam biosynthesis
00331;Clavulanic acid biosynthesis
00521;Streptomycin biosynthesis
00524;Neomycin, kanamycin and gentamicin biosynthesis
00525;Acarbose and validamycin biosynthesis
00401;Novobiocin biosynthesis
00404;Staurosporine biosynthesis
00405;Phenazine biosynthesis
00333;Prodigiosin biosynthesis
00254;Aflatoxin biosynthesis
00998;Biosynthesis of various antibiotics
00999;Biosynthesis of various plant secondary metabolites
00997;Biosynthesis of various other secondary metabolites
// Xenobiotics biodegradation and metabolism
00362;Benzoate degradation
00627;Aminobenzoate degradation
00364;Fluorobenzoate degradation
00625;Chloroalkane and chloroalkene degradation
00361;Chlorocyclohexane and chlorobenzene degradation
00623;Toluene degradation
00622;Xylene degradation
00633;Nitrotoluene degradation
00642;Ethylbenzene degradation
00643;Styrene degradation
00791;Atrazine degradation
00930;Caprolactam degradation
00363;Bisphenol degradation
00621;Dioxin degradation
00626;Naphthalene degradation
00624;Polycyclic aromatic hydrocarbon degradation
00365;Furfural degradation
00984;Steroid degradation
00980;Metabolism of xenobiotics by cytochrome P450
00982;Drug metabolism - cytochrome P450
00983;Drug metabolism - other enzymes