PlantPathMarks Database

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PyrusXbretschneideri Maps overview

Pathway Name: Glycolysis / Gluconeogenesis
Pathway ID	ko00010
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P; glyceraldehyde-3P; glycerate-3P; phosphoenolpyruvate; and pyruvate [MD:M00001]. Acetyl-CoA; another important precursor metabolite; is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes; the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002]; which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003]. Source: KEGG Database

Pathway Name: Citrate cycle (TCA cycle)
Pathway ID	ko00020
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	The citrate cycle (TCA cycle; Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA; the activated form of acetate; derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data; many organisms seem to lack genes for the full cycle [MD:M00009]; but contain genes for specific segments [MD:M00010 M00011]. Source: KEGG Database

Pathway Name: Pentose phosphate pathway
Pathway ID	ko00030
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway. One is irreversible oxidative phase in which glucose-6P is converted to ribulose-5P by oxidative decarboxylation; and NADPH is generated [MD:M00006]. The other is reversible non-oxidative phase in which phosphorylated sugars are interconverted to generate xylulose-5P; ribulose-5P; and ribose-5P [MD:M00007]. Phosphoribosyl pyrophosphate (PRPP) formed from ribose-5P [MD:M00005] is an activated compound used in the biosynthesis of histidine and purine/pyrimidine nucleotides. This pathway map also shows the Entner-Doudoroff pathway where 6-P-gluconate is dehydrated and then cleaved into pyruvate and glyceraldehyde-3P [MD:M00008]. Source: KEGG Database

Pathway Name: Pentose and glucuronate interconversions
Pathway ID	ko00040
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Pentose and glucuronate interconversions Source: KEGG Database

Pathway Name: Fructose and mannose metabolism
Pathway ID	ko00051
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Fructose and mannose metabolism Source: KEGG Database

Pathway Name: Galactose metabolism
Pathway ID	ko00052
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Galactose metabolism Source: KEGG Database

Pathway Name: Ascorbate and aldarate metabolism
Pathway ID	ko00053
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Ascorbate and aldarate metabolism Source: KEGG Database

Pathway Name: Fatty acid biosynthesis
Pathway ID	ko00061
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Fatty acid biosynthesis Source: KEGG Database

Pathway Name: Fatty acid elongation
Pathway ID	ko00062
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Fatty acid elongation Source: KEGG Database

Pathway Name: Fatty acid degradation
Pathway ID	ko00071
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Fatty acid degradation Source: KEGG Database

Pathway Name: Synthesis and degradation of ketone bodies
Pathway ID	ko00072
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Synthesis and degradation of ketone bodies Source: KEGG Database

Pathway Name: Cutin, suberine and wax biosynthesis
Pathway ID	ko00073
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Cutin, suberine and wax biosynthesis Source: KEGG Database

Pathway Name: Steroid biosynthesis
Pathway ID	ko00100
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Steroid biosynthesis Source: KEGG Database

Pathway Name: Ubiquinone and other terpenoid-quinone biosynthesis
Pathway ID	ko00130
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Ubiquinone (UQ); also called coenzyme Q; and plastoquinone (PQ) are electron carriers in oxidative phosphorylation and photosynthesis; respectively. The quinoid nucleus of ubiquinone is derived from the shikimate pathway; 4-hydroxybenzoate is directly formed from chorismate in bacteria; while it can be formed from either chorismate or tyrosine in yeast. The following biosynthesis of terpenoid moiety involves reactions of prenylation; decarboxylation; and three hydroxylations alternating with three methylations. The order of these reactions are somewhat different between bacteria and yeast. Phylloquinone (vitamin K1); menaquinone (vitamin K2); and tocopherol (vitamin E) are fat-soluble vitamins. Phylloquinone is a compound present in all photosynthetic plants serving as a cofactor for photosystem I-mediated electron transport. Menaquinone is an obligatory component of the electron-transfer pathway in bacteria. Source: KEGG Database

Pathway Name: Oxidative phosphorylation
Pathway ID	ko00190
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	Oxidative phosphorylation Source: KEGG Database

Pathway Name: Photosynthesis
Pathway ID	ko00195
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	Photosynthesis in green plants and specialized bacteria is the process of utilizing light energy to synthesize organic compounds from carbon dioxide and water. It consists of the light dependent part (light reaction) and the light independent part (dark reaction; carbon fixation). The light reaction takes place in thylakoid; a membrane-bound compartment inside chloroplasts and cyanobacteria. The light energy is used by photosystems I and II to generate proton motive force and reducing power (NADPH or NADH). The proton motive force is used by ATP synthase to generate ATP; essentially in the same way as the mitochondrial respiratory chain. The supplies of ATP and NAD(P)H are then used to fix carbon dioxide. Source: KEGG Database

Pathway Name: Photosynthesis - antenna proteins
Pathway ID	ko00196
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	The chlorophyll-binding subunits of photosystems I and II are internal antenna light-harvesting proteins of oxygenic photosynthesis. The antenna proteins that exist in phycobilisomes in cyanobacteria and light-harvesting chlorophyll protein complexes in green plants act as peripheral antenna systems; enabling more efficient absorption of light energy. Source: KEGG Database

Pathway Name: Arginine biosynthesis
Pathway ID	ko00220
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Arginine biosynthesis Source: KEGG Database

Pathway Name: Purine metabolism
Pathway ID	ko00230
Class & Sub-Class	Class: Metabolism Sub-Class: Nucleotide metabolism
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Description	Purine metabolism Source: KEGG Database

Pathway Name: Caffeine metabolism
Pathway ID	ko00232
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Caffeine metabolism Source: KEGG Database

Pathway Name: Pyrimidine metabolism
Pathway ID	ko00240
Class & Sub-Class	Class: Metabolism Sub-Class: Nucleotide metabolism
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Description	Pyrimidine metabolism Source: KEGG Database

Pathway Name: Alanine, aspartate and glutamate metabolism
Pathway ID	ko00250
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Alanine, aspartate and glutamate metabolism Source: KEGG Database

Pathway Name: Glycine, serine and threonine metabolism
Pathway ID	ko00260
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Serine is derived from 3-phospho-D-glycerate; an intermediate of glycolysis [MD:M00020]; and glycine is derived from serine. Threonine is an essential amino acid; which animals cannot synthesize. In bacteria and plants; threonine is derived from aspartate [MD:M00018]. Source: KEGG Database

Pathway Name: Monobactam biosynthesis
Pathway ID	ko00261
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Monobactams are beta-lactam antibiotics containing a monocyclic beta-lactam nucleus; which is structurally different from penicillin and cephalosporin core structures with another fused ring. This diagram shows biosynthesis of nocardicin A; a naturally occurring monobactam; via the pentapeptide formed by condensation of L-4-hydroxyphenylglycine (L-pHPG); L-arginine and L-serine [MD:M00736]. Other naturally occurring monobactams are also shown but the biosynthetic pathway is not yet fully characterized. Sulfazecin and other 3-aminomonobactamic acid derivatives are derived from serine or threonine; and tabtoxinine-beta-lactam is a phytotoxin. Aztreonam; a synthetic monobactam originally isolated as SQ 26;180 from Chromobacterium violaceum; is the first clinically used monobactam. Source: KEGG Database

Pathway Name: Cysteine and methionine metabolism
Pathway ID	ko00270
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Cysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants; cysteine is converted from serine (via acetylserine) by transfer of hydrogen sulfide [MD:M00021]. In animals; methionine-derived homocysteine is used as sulfur source and its condensation product with serine (cystathionine) is converted to cysteine [MD:M00338]. Cysteine is metabolized to pyruvate in multiple routes. Methionine is an essential amino acid; which animals cannot synthesize. In bacteria and plants; methionine is synthesized from aspartate [MD:M00017]. S-Adenosylmethionine (SAM); synthesized from methionine and ATP; is a methyl group donor in many important transfer reactions including DNA methylation for regulation of gene expression. SAM may also be used to regenerate methionine in the methionine salvage pathway [MD:M00034]. Source: KEGG Database

Pathway Name: Valine, leucine and isoleucine degradation
Pathway ID	ko00280
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Valine, leucine and isoleucine degradation Source: KEGG Database

Pathway Name: Valine, leucine and isoleucine biosynthesis
Pathway ID	ko00290
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Valine, leucine and isoleucine biosynthesis Source: KEGG Database

Pathway Name: Lysine biosynthesis
Pathway ID	ko00300
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Lysine biosynthesis Source: KEGG Database

Pathway Name: Lysine degradation
Pathway ID	ko00310
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Lysine degradation Source: KEGG Database

Pathway Name: Arginine and proline metabolism
Pathway ID	ko00330
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Arginine and proline metabolism Source: KEGG Database

Pathway Name: Histidine metabolism
Pathway ID	ko00340
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Histidine metabolism Source: KEGG Database

Pathway Name: Tyrosine metabolism
Pathway ID	ko00350
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Tyrosine metabolism Source: KEGG Database

Pathway Name: Phenylalanine metabolism
Pathway ID	ko00360
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Phenylalanine metabolism Source: KEGG Database

Pathway Name: Tryptophan metabolism
Pathway ID	ko00380
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Tryptophan metabolism Source: KEGG Database

Pathway Name: Phenylalanine, tyrosine and tryptophan biosynthesis
Pathway ID	ko00400
Class & Sub-Class	Class: Metabolism Sub-Class: Amino acid metabolism
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Description	Phenylalanine, tyrosine and tryptophan biosynthesis Source: KEGG Database

Pathway Name: beta-Alanine metabolism
Pathway ID	ko00410
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	beta-Alanine metabolism Source: KEGG Database

Pathway Name: Taurine and hypotaurine metabolism
Pathway ID	ko00430
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	Taurine and hypotaurine metabolism Source: KEGG Database

Pathway Name: Phosphonate and phosphinate metabolism
Pathway ID	ko00440
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	Natural products containing carbon-phosphorous bonds; so-called C-P compounds; are derivatives of phosphonate and phosphinate with substitution of alkyl group for hydrogen of phosphorus-hydrogen bonds. C-P compounds have been found in many organisms; but only protists and bacteria; mostly Actinobacteria; have biosynthetic capacity. A common reaction in the biosynthetic pathway is C-P bond forming reaction from phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy) catalyzed by PEP phosphomutase. 2-Aminoethylphosphonate (AEP) is the most abundant C-P compound in the natural world. AEP derivatives include phosphonoprotein; phosphonoglycan; and phosphonolipid. Other known C-P compounds are bioactive substances used in medicine (antibiotics) and agriculture (herbicide) such as fosfomycin; FR-33289; rhizocticin; and bialaphos. Source: KEGG Database

Pathway Name: Selenocompound metabolism
Pathway ID	ko00450
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	Selenocompound metabolism Source: KEGG Database

Pathway Name: Cyanoamino acid metabolism
Pathway ID	ko00460
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	Cyanoamino acid metabolism Source: KEGG Database

Pathway Name: Glutathione metabolism
Pathway ID	ko00480
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of other amino acids
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Description	Glutathione metabolism Source: KEGG Database

Pathway Name: Starch and sucrose metabolism
Pathway ID	ko00500
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Starch and sucrose metabolism Source: KEGG Database

Pathway Name: N-Glycan biosynthesis
Pathway ID	ko00510
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	N-glycans or asparagine-linked glycans are major constituents of glycoproteins in eukaryotes. N-glycans are covalently attached to asparagine with the consensus sequence of Asn-X-Ser/Thr by an N-glycosidic bond; GlcNAc b1- Asn. Biosynthesis of N-glycans begins on the cytoplasmic face of the ER membrane with the transferase reaction of UDP-GlcNAc and the lipid-like precursor P-Dol (dolichol phosphate) to generate GlcNAc a1- PP-Dol. After sequential addition of monosaccharides by ALG glycosyltransferases [MD:M00055]; the N-glycan precursor is attached by the OST (oligosaccharyltransferase) complex to the polypeptide chain that is being synthesized and translocated through the ER membrane. The protein-bound N-glycan precursor is subsequently trimmed; extended; and modified in the ER and Golgi by a complex series of reactions catalyzed by membrane-bound glycosidases and glycosyltransferases. N-glycans thus synthesized are classified into three types: high-mannose type; complex type; and hybrid type. Defects in N-glycan biosynthesis lead to a variety of human diseases known as congenital disorders of glycosylation [DS:H00118 H00119]. Source: KEGG Database

Pathway Name: Various types of N-glycan biosynthesis
Pathway ID	ko00513
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Various types of N-glycan biosynthesis Source: KEGG Database

Pathway Name: Amino sugar and nucleotide sugar metabolism
Pathway ID	ko00520
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Amino sugar and nucleotide sugar metabolism Source: KEGG Database

Pathway Name: Glycosaminoglycan degradation
Pathway ID	ko00531
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Glycosaminoglycan degradation Source: KEGG Database

Pathway Name: Glycerolipid metabolism
Pathway ID	ko00561
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Glycerolipid metabolism Source: KEGG Database

Pathway Name: Inositol phosphate metabolism
Pathway ID	ko00562
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Inositol phosphate metabolism Source: KEGG Database

Pathway Name: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
Pathway ID	ko00563
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Cell surface proteins can be attached to the cell membrane via the glycolipid structure called glycosylphosphatidylinositol (GPI) anchor. Hundreds of GPI-anchored proteins have been identified in many eukaryotes ranging from protozoa and fungi to mammals. All protein-linked GPI anchors share a common core structure; characterized by the substructure Man (a1-4) GlcN (a1-6) myo-inositol-1P-lipid. Biosynthesis of GPI anchors proceeds in three stages: (i) preassembly of a GPI precursor in the ER membrane; (ii) attachment of the GPI to the C-terminus of a newly synthesized protein in the lumen of the ER; and (iii) lipid remodeling and/or carbohydrate side-chain modifications in the ER and the Golgi. Defects of GPI anchor biosynthesis gene result in a genetic disorder; paroxysmal nocturnal hemoglobinuria. Source: KEGG Database

Pathway Name: Glycerophospholipid metabolism
Pathway ID	ko00564
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Glycerophospholipid metabolism Source: KEGG Database

Pathway Name: Ether lipid metabolism
Pathway ID	ko00565
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Ether lipid metabolism Source: KEGG Database

Pathway Name: Arachidonic acid metabolism
Pathway ID	ko00590
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Arachidonic acid metabolism Source: KEGG Database

Pathway Name: Linoleic acid metabolism
Pathway ID	ko00591
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Linoleic acid metabolism Source: KEGG Database

Pathway Name: alpha-Linolenic acid metabolism
Pathway ID	ko00592
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	alpha-Linolenic acid metabolism Source: KEGG Database

Pathway Name: Sphingolipid metabolism
Pathway ID	ko00600
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Sphingolipid metabolism Source: KEGG Database

Pathway Name: Glycosphingolipid biosynthesis - lacto and neolacto series
Pathway ID	ko00601
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Glycosphingolipid biosynthesis - lacto and neolacto series Source: KEGG Database

Pathway Name: Glycosphingolipid biosynthesis - globo and isoglobo series
Pathway ID	ko00603
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Glycosphingolipid biosynthesis - globo and isoglobo series Source: KEGG Database

Pathway Name: Glycosphingolipid biosynthesis - ganglio series
Pathway ID	ko00604
Class & Sub-Class	Class: Metabolism Sub-Class: Glycan biosynthesis and metabolism
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Description	Glycosphingolipid biosynthesis - ganglio series Source: KEGG Database

Pathway Name: Pyruvate metabolism
Pathway ID	ko00620
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Pyruvate metabolism Source: KEGG Database

Pathway Name: Glyoxylate and dicarboxylate metabolism
Pathway ID	ko00630
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Glyoxylate and dicarboxylate metabolism Source: KEGG Database

Pathway Name: Propanoate metabolism
Pathway ID	ko00640
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Propanoate metabolism Source: KEGG Database

Pathway Name: Butanoate metabolism
Pathway ID	ko00650
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	Butanoate metabolism Source: KEGG Database

Pathway Name: C5-Branched dibasic acid metabolism
Pathway ID	ko00660
Class & Sub-Class	Class: Metabolism Sub-Class: Carbohydrate metabolism
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Description	C5-Branched dibasic acid metabolism Source: KEGG Database

Pathway Name: One carbon pool by folate
Pathway ID	ko00670
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	One carbon pool by folate Source: KEGG Database

Pathway Name: Carbon fixation in photosynthetic organisms
Pathway ID	ko00710
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	Carbon fixation in photosynthetic organisms Source: KEGG Database

Pathway Name: Thiamine metabolism
Pathway ID	ko00730
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Thiamine metabolism Source: KEGG Database

Pathway Name: Riboflavin metabolism
Pathway ID	ko00740
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Riboflavin metabolism Source: KEGG Database

Pathway Name: Vitamin B6 metabolism
Pathway ID	ko00750
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Vitamin B6 metabolism Source: KEGG Database

Pathway Name: Nicotinate and nicotinamide metabolism
Pathway ID	ko00760
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Nicotinate and nicotinamide metabolism Source: KEGG Database

Pathway Name: Pantothenate and CoA biosynthesis
Pathway ID	ko00770
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Pantothenate and CoA biosynthesis Source: KEGG Database

Pathway Name: Biotin metabolism
Pathway ID	ko00780
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Biotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases; such as pyruvate carboxylase and acetyl-CoA carboxylase. Mammals cannot synthesize biotin; while in bacteria; fungi; and plants it is synthesized from pimelate thioester through different pathways. In E. coli and many organisms; pimelate thioester is derived from malonyl-ACP. The pathway starts with the methylation to malonyl-ACP methyl ester; followed by the fatty acid chain elongation cycle to form pimeloyl-ACP methyl ester; which is then demethylated to form pimeloyl-ACP [MD:M00572]. Pimeloyl-ACP is converted to biotin through the final four steps in the biotin bicyclic ring assembly; which are conserved among biotin-producing organisms [MD:M00123]. In B. subtilis; biotin is derived from pimeloyl-ACP formed by oxidative cleavage of long-chain acyl-ACPs [MD:M00573]. Some bacteria synthesize biotin from pimeloyl-CoA derived from pimelate [MD:M00577]. Biotin is covalently attached to biotin-dependent carboxylase by biotin protein ligase; also known as holocarboxylase synthase in mammals; to form an active holocarboxylase. After degradation of the biotinylated carboxylase into biocytin; it is further degraded by biotinidase to release free biotin; which is recycled in holocarboxylase synthesis. Biotin is catabolized by beta-oxidation of the valeric acid side chain or oxidation of sulfur in the heterocyclic ring. Source: KEGG Database

Pathway Name: Lipoic acid metabolism
Pathway ID	ko00785
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Lipoic acid metabolism Source: KEGG Database

Pathway Name: Folate biosynthesis
Pathway ID	ko00790
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Folate biosynthesis Source: KEGG Database

Pathway Name: Porphyrin and chlorophyll metabolism
Pathway ID	ko00860
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of cofactors and vitamins
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Description	Porphyrin and chlorophyll metabolism Source: KEGG Database

Pathway Name: Terpenoid backbone biosynthesis
Pathway ID	ko00900
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Terpenoids; also known as isoprenoids; are a large class of natural products consisting of isoprene (C5) units. There are two biosynthetic pathways; the mevalonate pathway [MD:M00095] and the non-mevalonate pathway or the MEP/DOXP pathway [MD:M00096]; for the terpenoid building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). The action of prenyltransferases then generates higher-order building blocks: geranyl diphosphate (GPP); farsenyl diphosphate (FPP); and geranylgeranyl diphosphate (GGPP); which are the precursors of monoterpenoids (C10); sesquiterpenoids (C15); and diterpenoids (C20); respectively. Condensation of these building blocks gives rise to the precursors of sterols (C30) and carotenoids (C40). The MEP/DOXP pathway is absent in higher animals and fungi; but in green plants the MEP/DOXP and mevalonate pathways co-exist in separate cellular compartments. The MEP/DOXP pathway; operating in the plastids; is responsible for the formation of essential oil monoterpenes and linalyl acetate; some sesquiterpenes; diterpenes; and carotenoids and phytol. The mevalonate pathway; operating in the cytosol; gives rise to triterpenes; sterols; and most sesquiterpenes. Source: KEGG Database

Pathway Name: Limonene and pinene degradation
Pathway ID	ko00903
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Limonene and pinene degradation Source: KEGG Database

Pathway Name: Diterpenoid biosynthesis
Pathway ID	ko00904
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Diterpenoid biosynthesis Source: KEGG Database

Pathway Name: Brassinosteroid biosynthesis
Pathway ID	ko00905
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Brassinosteroids are a group of plant steroid hormones that regulate growth and development. More than fifty naturally occurring brassinosteroids have been identified in a wide range of plant species. The most abundant and widely occurring brassinosteroids are C28 steroids; and among them brassinolide (BL) is the most biologically active. Plants have multiple pathways for biosynthesis of BL; which are derived from the steroid biosynthetic pathway. Two pathways from campestanol to castasterone (CS); C6 oxidation and the late-C6 oxidation pathways; operate in many plants. Another branching pathway; the early-C22 oxidation pathway; was demonstrated using a brassinosteroid-deficient mutant of Arabidopsis thaliana. Recently; a new shortcut pathway from campesterol to 6-deoxotyphasterol was demonstrated by a functional analysis of cytochrome P450 monooxygenases responsible for brassinosteroid biosynthesis. Thus; at least four pathways are involved in the biosynthesis of CS; and CS is further metabolized to BL by lactonization of the B ring. Source: KEGG Database

Pathway Name: Carotenoid biosynthesis
Pathway ID	ko00906
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Carotenoid biosynthesis Source: KEGG Database

Pathway Name: Zeatin biosynthesis
Pathway ID	ko00908
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Zeatin is a member of the cytokinin family; a class of phytohormones involved in various processes of growth and development in plants. Most abundant cytokinins are adenine-type; where the N6 position of adenine is substituted with an isoprenoid; such as in zeatin; or an aromatic side chain; such as in kinetin. Zeatin can be synthesized in two different pathways: the tRNA pathway and the AMP pathway. In the tRNA pathway zeatin is a recycled product of isopentenylated tRNAs. In the AMP pathway zeatin is synthesized from an isopentenyl donor; dimethylallyl diphosphate (DMAPP); and AMP; ADP; or ATP by isopentenyltransferases. After synthesis cytokinins can be glucosylated. Source: KEGG Database

Pathway Name: Sesquiterpenoid and triterpenoid biosynthesis
Pathway ID	ko00909
Class & Sub-Class	Class: Metabolism Sub-Class: Metabolism of terpenoids and polyketides
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Description	Sesquiterpenoids (C15 terpenoids) are a group of terpenoids consisting of three isoprene units. They are derive from farnesyl diphosphate (FPP) and can be cyclized to produce various skeletal structures. Sesquiterpenoid biosynthesis begins with the loss of diphosphate from FPP under the action of sesquiterpene synthesis enzymes; generating an allylic cation that is highly susceptible to intramolecular attacks. Cyclization of the farnesyl cation may take place onto either of the remaining double bonds with the result that 6-; 10-; or 11-membered rings may be formed. Many sesquiterpenoids have been isolated from plants; fungi; marine organisms; and Streptomyces species. This map shows a few examples of acyclic and cyclic sesquiterpenoids. Source: KEGG Database

Pathway Name: Nitrogen metabolism
Pathway ID	ko00910
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions; where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:M00175] is the process of reducing atmospheric molecular nitrogen to ammonia; a biologically useful reduced form incorporated into amino acids and other vital compounds. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction [MD:M00531] and dissimilatory nitrate reduction [MD:M00530] both for conversion to ammonia; and denitrification [MD:M00529]. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions; producing gaseous nitrogen compounds (N2; NO and N2O) to the atmosphere. The two oxidation pathways are nitrification [MD:M00528] and anaerobic ammonium oxidation (anammox). Nitrification is the oxidation of ammonia (NH3) with oxygen into nitrite followed by the oxidation of nitrite into nitrate. The first step is performed by ammonia-oxidizing microorganisms (e.g.; Nitrosomonas and Nitrosococcus) and the second step by nitrite-oxidizing microorganisms (e.g.; Nitrobacter). Anammox is a biochemical process of oxidizing ammonium (NH4+) into dinitrogen gas (N2) using nitrite as an electron acceptor. It occurs in the anammoxosome; a membrane bound compartment inside the cytoplasm; of anammox bacteria (e.g.; Planctomycetes). Source: KEGG Database

Pathway Name: Sulfur metabolism
Pathway ID	ko00920
Class & Sub-Class	Class: Metabolism Sub-Class: Energy metabolism
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Description	Sulfur is an essential element for life and the metabolism of organic sulfur compounds plays an important role in the global sulfur cycle. Sulfur occurs in various oxidation states ranging from +6 in sulfate to -2 in sulfide (H2S). Sulfate reduction can occur in both an energy consuming assimilatory pathway and an energy producing dissimilatory pathway. The assimilatory pathway; which is found in a wide range of organisms; produces reduced sulfur compounds for the biosynthesis of S-containing amino acids and does not lead to direct excretion of sulfide. In the dissimilatory pathway; which is restricted to obligatory anaerobic bacterial and archaeal lineages; sulfate (or sulfur) is the terminal electron acceptor of the respiratory chain producing large quantities of inorganic sulfide. Both pathways start from the activation of sulfate by reaction with ATP to form adenylyl sulfate (APS). In the assimilatory pathway [MD:M00176] APS is converted to 3'-phosphoadenylyl sulfate (PAPS) and then reduced to sulfite; and sulfite is further reduced to sulfide by the assimilatory sulfite reductase. In the dissimilatory pathway [MD:M00596] APS is directly reduced to sulfite; and sulfite is further reduced to sulfide by the dissimilatory sulfite reductase. The capacity for oxidation of sulfur is quite widespread among bacteria and archaea; comprising phototrophs and chemolithoautotrophs. The SOX (sulfur-oxidation) system [MD:M00595] is a well-known sulfur oxidation pathway and is found in both photosynthetic and non-photosynthetic sulfur-oxidizing bacteria. Green sulfur bacteria and purple sulfur bacteria carry out anoxygenic photosynthesis with reduced sulfur compounds such as sulfide and elemental sulfur; as well as thiosulfate (in some species with the SOX system); as the electron donor for photoautotrophic growth. In some chemolithoautotrophic sulfur oxidizers (such as Thiobacillus denitrificans); it has been suggested that dissimilatory sulfur reduction enzymes operate in the reverse direction; forming a sulfur oxidation pathway from sulfite to APS and then to sulfate. Source: KEGG Database

Pathway Name: Phenylpropanoid biosynthesis
Pathway ID	ko00940
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Phenylpropanoids are a group of plant secondary metabolites derived from phenylalanine and having a wide variety of functions both as structural and signaling molecules. Phenylalanine is first converted to cinnamic acid by deamination. It is followed by hydroxylation and frequent methylation to generate coumaric acid and other acids with a phenylpropane (C6-C3) unit. Reduction of the CoA-activated carboxyl groups of these acids results in the corresponding aldehydes and alcohols. The alcohols are called monolignols; the starting compounds for biosynthesis of lignin. Source: KEGG Database

Pathway Name: Flavonoid biosynthesis
Pathway ID	ko00941
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Flavonoids are a major class of plant secondary metabolites that serves a multitude of functions including pigments and antioxidant activity. Flavonoids are synthesized from phenylpropanoid derivatives by condensation with malonyl-CoA. For example; condensation of p-coumaroyl-CoA (C6-C3) with three malonyl-CoA (C3) molecules results in naringenin chalcone with a diphenylpropane (C6-C3-C6) unit; which is converted to naringenin with the flavone (2-phenylchromen-4-one) backbone by conjugate ring closure. These and further modifications yield a variety of structural forms including chalcones; flavanones; dihyroflavonols; and flavans; anthocyanins; flavones and flavonols; and isoflavonoids. Source: KEGG Database

Pathway Name: Anthocyanin biosynthesis
Pathway ID	ko00942
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Anthocyanidins (aglycones) and anthocyanins (glycosides) are common plant pigments and belong to a structural subclass of flavonoids characterized by a 2-phenylbenzopyrylium unit. They are derived along the flavonoid modification pathways and further separated into three types; pelargonidin; cyanidin; and delphinidin; due to the different number of hydroxyl groups in the phenyl group. Source: KEGG Database

Pathway Name: Isoflavonoid biosynthesis
Pathway ID	ko00943
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Isoflavonoids are biologically active compounds; such as phytoestrogens; produced by pea family plants. While flavonoids (in the narrow sense) have the 2-phenylchromen-4-one backbone; isoflavonoids have the 3-phenylchromen-4-one backbone with no hydroxyl group substitution at position 2. Isoflavonoids are derived from the flavonoid biosynthesis pathway via liquiritigenin or naringenin. Source: KEGG Database

Pathway Name: Flavone and flavonol biosynthesis
Pathway ID	ko00944
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Flavones and flavonols (3-hydroxyflavones) are common flavonoids in the plant kingdom. They are synthesized as part of the flavonoid modification pathways in aglycone and glucoside forms. Source: KEGG Database

Pathway Name: Stilbenoid, diarylheptanoid and gingerol biosynthesis
Pathway ID	ko00945
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Stilbenoids are a group of phenolic compounds; biosynthetically interrelated through their common origin from a C6-C2-C6 intermediate; such as resveratol found in grapes. Stilbenoids can also exist as glycosides (e.g.; piceid). Combretastatins are potentially useful stilbenoid natural products with known antitumor activity. Diarylheptanoid is a compound group having phenyl rings at 1;7 positions of n-heptane (C6-C7-C6); such as curcumin found in the ginger family. [6]-Gingerol is a major active component of ginger and has diverse pharmacologic effects. Source: KEGG Database

Pathway Name: Isoquinoline alkaloid biosynthesis
Pathway ID	ko00950
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Isoquinoline alkaloids are tyrosine-derived plant alkaloids with an isoquinoline skeleton. Among them benzylisoquinoline alkaloids form an important group with potent pharmacological activity; including analgesic compounds of morphine and codeine; and anti-infective agents of berberine; palmatine; and magnoflorine. Biosynthesis of isoquinoline alkaloids proceeds via decarboxylation of tyrosine or DOPA to yield dopamine; which together with 4-hydroxyphenylacetaldehyde; an aldehyde derived from tyrosine; is converted to reticuline; an important precursor of various benzylisoquinoline alkaloids. Source: KEGG Database

Pathway Name: Tropane, piperidine and pyridine alkaloid biosynthesis
Pathway ID	ko00960
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Tropane, piperidine and pyridine alkaloid biosynthesis Source: KEGG Database

Pathway Name: Betalain biosynthesis
Pathway ID	ko00965
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Betalains are water-soluble nitrogen-containing pigments that are present in plants belonging to the order Caryophyllales (such as cactus and amaranth families) and in higher fungi. They contain betalamic acid as the chromophore and are classified into two types: betacyanins and betaxanthins. Betacyanins contain a cyclo-DOPA residue and exhibit red/violet coloration; while betaxanthins contain different amino acids or amino side chains and exhibit a yellow/orange coloration. The condensation of betalamic acid with amino acids (including cyclo-DOPA or amines) in plants is a spontaneous reaction; not an enzyme-catalyzed reaction. Source: KEGG Database

Pathway Name: Biosynthesis of various secondary metabolites - part 2
Pathway ID	ko00998
Class & Sub-Class	Class: Metabolism Sub-Class: Biosynthesis of other secondary metabolites
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Description	Biosynthesis of various secondary metabolites - part 2 Source: KEGG Database

Pathway Name: Biosynthesis of unsaturated fatty acids
Pathway ID	ko01040
Class & Sub-Class	Class: Metabolism Sub-Class: Lipid metabolism
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Description	Biosynthesis of unsaturated fatty acids Source: KEGG Database

Pathway Name: Aminoacyl-tRNA biosynthesis
Pathway ID	ko00970
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Translation
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Description	Aminoacyl-tRNA biosynthesis

Pathway Name: Ribosome biogenesis in eukaryotes
Pathway ID	ko03008
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Translation
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Description	Ribosomes are the cellular factories responsible for making proteins. In eukaryotes; ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It requires hundreds of factors not present in the mature particle. In the absence of these proteins; ribosome biogenesis is stalled and cell growth is terminated even under optimal growth conditions. The primary pre-rRNA transcript is assembled into the 90S pre-ribosome; which contains both 40S and 60S assembly factors. Within this complex; the pre-rRNA is cleaved. pre-60S ribosomes are subjected to several sequential processing steps in the nucleoplasm involving numerous assembly intermediates before it is exported to the cytoplasm and matured into the 60S ribosomal subunit. The pre-40S ribosome is matured to the small ribosomal subunit in the cytoplasm by cleavage.

Pathway Name: Ribosome
Pathway ID	ko03010
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Translation
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Description	Ribosome

Pathway Name: RNA transport
Pathway ID	ko03013
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Translation
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Description	RNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) via mobile export receptors. The majority of RNAs; such as tRNAs; rRNAs; and U snRNAs; are transported by specific export receptors; which belong to the karyopherin-beta family proteins. A feature of karyopherins is their regulation by the small GTPase Ran. However; general mRNA export is mechanistically different. Nuclear export of mRNAs is functionally coupled to different steps in gene expression processes; such as transcription; splicing; 3'-end formation and even translation.

Pathway Name: mRNA surveillance pathway
Pathway ID	ko03015
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Translation
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Description	The mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD); nonstop mRNA decay (NSD); and no-go decay (NGD). NMD is a mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In vertebrates; PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Upf3; together with Upf1 and Upf2; may signal the presence of the PTC to the 5'end of the transcript; resulting in decapping and rapid exonucleolytic digestion of the mRNA. In the NSD pathway; which targets mRNAs lacking termination codons; the ribosome is believed to translate through the 3' untranslated region and stall at the end of the poly(A) tail. NSD involves an eRF3-like protein; Ski7p; which is hypothesized to bind the empty A site of the ribosome and recruit the exosome to degrade the mRNA from the 3' end. NGD targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins.

Pathway Name: RNA degradation
Pathway ID	ko03018
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	The correct processing; quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes; two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway; this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway; the exosome; a large multisubunit complex; plays a key role. The exosome exists in archaeal cells; too. In bacteria; endoribonuclease E; a key enzyme involved in RNA decay and processing; organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase; DEAD-box helicases; and additional factors in the RNA-degrading complex.

Pathway Name: RNA polymerase
Pathway ID	ko03020
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Transcription
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Description	RNA polymerase

Pathway Name: Basal transcription factors
Pathway ID	ko03022
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Transcription
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Description	Basal transcription factors

Pathway Name: DNA replication
Pathway ID	ko03030
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	A complex network of interacting proteins and enzymes is required for DNA replication. Generally; DNA replication follows a multistep enzymatic pathway. At the DNA replication fork; a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. On the leading strand; replication occurs continuously in a 5 to 3 direction; whereas on the lagging strand; DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. In prokaryotes; the leading strand replication apparatus consists of a DNA polymerase (pol III core); a sliding clamp (beta); and a clamp loader (gamma delta complex). The DNA primase (DnaG) is needed to form RNA primers. Normally; during replication of the lagging-strand DNA template; an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I; and the DNA ligase joins the Okazaki fragments. In eukaryotes; three DNA polymerases (alpha; delta; and epsilon) have been identified. DNA primase forms a permanent complex with DNA polymerase alpha. PCNA and RFC function as a clamp and a clamp loader. FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA.

Pathway Name: Spliceosome
Pathway ID	ko03040
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Transcription
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Description	After transcription; eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing; introns are excised and exons are joined by a macromolecular complex; the spliceosome. The standard spliceosome is made up of five small nuclear ribonucleoproteins (snRNPs); U1; U2; U4; U5; and U6 snRNPs; and several spliceosome-associated proteins (SAPs). Spliceosomes are not a simple stable complex; but a dynamic family of particles that assemble on the mRNA precursor and help fold it into a conformation that allows transesterification to proceed. Various spliceosome forms (e.g. A-; B- and C-complexes) have been identified.

Pathway Name: Proteasome
Pathway ID	ko03050
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	The proteasome is a protein-destroying apparatus involved in many essential cellular functions; such as regulation of cell cycle; cell differentiation; signal transduction pathways; antigen processing for appropriate immune responses; stress signaling; inflammatory responses; and apoptosis. It is capable of degrading a variety of cellular proteins in a rapid and timely fashion and most substrate proteins are modified by ubiquitin before their degradation by the proteasome. The proteasome is a large protein complex consisting of a proteolytic core called the 20S particle and ancillary factors that regulate its activity in various ways. The most common form is the 26S proteasome containing one 20S core particle and two 19S regulatory particles that enable the proteasome to degrade ubiquitinated proteins by an ATP-dependent mechanism. Another form is the immunoproteasome containing two 11S regulatory particles; PA28 alpha and PA28 beta; which are induced by interferon gamma under the conditions of intensified immune response. Other regulatory particles include PA28 gamma and PA200. Although PA28 gamma also belongs to a family of activators of the 20S proteasome; it is localized within the nucleus and forms a homoheptamer. PA28 gamma has been implicated in the regulation of cell cycle progression and apoptosis. PA200 has been identified as a large nuclear protein that stimulates proteasomal hydrolysis of peptides.

Pathway Name: Protein export
Pathway ID	ko03060
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	The protein export is the active transport of proteins from the cytoplasm to the exterior of the cell; or to the periplasmic compartment in Gram-negative bacteria. The sec dependent pathway is the general protein export system that transports newly synthesized proteins into or across the cell membrane. The translocation channel is formed from a conserved trimeric membrane protein complex; called the Sec61/SecY complex. The twin-arginine translocation (Tat) pathway is another protein transport system that transports folded proteins in bacteria; archaea; and chloroplasts. Many Tat systems comprise three functionally different membrane proteins; TatA; TatB; and TatC; but TatA and TatE seem to have overlapping functions; with TatA having by far the more important role.

Pathway Name: Base excision repair
Pathway ID	ko03410
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions; derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway; thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates.

Pathway Name: Nucleotide excision repair
Pathway ID	ko03420
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds; environmental carcinogens; and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP); Cockayne syndrome (CS); and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes; uvrAB complex). The following steps of GGR-NER and TCR-NER are similar.

Pathway Name: Mismatch repair
Pathway ID	ko03430
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	DNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication; thereby preventing mutations from becoming permanent in dividing cells. MMR also suppresses homologous recombination and was recently shown to play a role in DNA damage signaling. Defects in MMR are associated with genome-wide instability; predisposition to certain types of cancer including HNPCC; resistance to certain chemotherapeutic agents; and abnormalities in meiosis and sterility in mammalian systems. The Escherichia coli MMR pathway has been extensively studied and is well characterized. In E. coli; the mismatch-activated MutS-MutL-ATP complex licenses MutH to incise the nearest unmethylated GATC sequence. UvrD and an exonuclease generate a gap. This gap is filled by pol III and DNA ligase. The GATC sites are then methylated by Dam. Several human MMR proteins have been identified based on their homology to E. coli MMR proteins. These include human homologs of MutS and MutL. Although E. coli MutS and MutL proteins are homodimers; human MutS and MutL homologs are heterodimers. The role of hemimethylated dGATC sites as a signal for strand discrimination is not conserved from E. coli to human. Human MMR is presumed to be nick-directed in vivo; and is thought to discriminate daughter and template strands using a strand-specific nick.

Pathway Name: Homologous recombination
Pathway ID	ko03440
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	Homologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs); potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves the generation of a single-stranded region of DNA; followed by strand invasion; formation of a Holliday junction; DNA synthesis using the intact strand as a template; branch migration and resolution. It is investigated that RecA/Rad51 family proteins play a central role. The breast cancer susceptibility protein Brca2 and the RecQ helicase BLM (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity; at least in part; through HR.

Pathway Name: Non-homologous end-joining
Pathway ID	ko03450
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Replication and repair
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Description	Nonhomologous end joining (NHEJ) eliminates DNA double-strand breaks (DSBs) by direct ligation. NHEJ involves binding of the KU heterodimer to double-stranded DNA ends; recruitment of DNA-PKcs (MRX complex in yeast); processing of ends; and recruitment of the DNA ligase IV (LIG4)-XRCC4 complex; which brings about ligation. A recent study shows that bacteria accomplish NHEJ using just two proteins (Ku and DNA ligase); whereas eukaryotes require many factors. NHEJ repairs DSBs at all stages of the cell cycle; bringing about the ligation of two DNA DSBs without the need for sequence homology; and so is error-prone.

Pathway Name: Ubiquitin mediated proteolysis
Pathway ID	ko04120
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	Protein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to proteins being degraded is performed by a reaction cascade consisting of three enzymes; named E1 (ubiquitin activating enzyme); E2 (ubiquitin conjugating enzyme); and E3 (ubiquitin ligase). Each E3 has specificity to its substrate; or proteins to be targeted by ubiquitination. Many E3s are discovered in eukaryotes and they are classified into four types: HECT type; U-box type; single RING-finger type; and multi-subunit RING-finger type. Multi-subunit RING-finger E3s are exemplified by cullin-Rbx E3s and APC/C. They consist of a RING-finger-containing subunit (RBX1 or RBX2) that functions to bind E2s; a scaffold-like cullin molecule; adaptor proteins; and a target recognizing subunit that binds substrates.

Pathway Name: Sulfur relay system
Pathway ID	ko04122
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	Ubiquitin and ubiquitin-like proteins (Ubls) are signalling messengers that control many cellular functions; such as cell proliferation; apoptosis; and DNA repair. It is suggested that Ub-protein modification evolved from prokaryotic sulfurtransfer systems. Molybdenum cofactor (Moco) and thiamin are sulfur-containing cofactors whose biosynthesis includes a key sulfur transfer step that uses unique sulfur carrier proteins; MoaD and ThiS. Ubiquitin; MoaD; and ThiS are all structurally related proteins whose C-termini are activated through adenylation by homologous E1-like enzymes. s2T biosynthesis may share similar chemistry with Moco and thiamin synthesis. In Saccharomyces cerevisiae; Urm1 and Uba4 function as part of a ubl protein conjugation system; though they have sequence homology to bacterial sulfur-transfer enzymes and the ability to function in sulfur transfer.

Pathway Name: SNARE interactions in vesicular transport
Pathway ID	ko04130
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	SNARE interactions in vesicular transport

Pathway Name: Protein processing in endoplasmic reticulum
Pathway ID	ko04141
Class & Sub-Class	Class: Genetic Information Processing Sub-Class: Folding sorting and degradation
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Description	The endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylated. Correctly folded proteins are packaged into transport vesicles that shuttle them to the Golgi complex. Misfolded proteins are retained within the ER lumen in complex with molecular chaperones. Proteins that are terminally misfolded bind to BiP and are directed toward degradation through the proteasome in a process called ER-associated degradation (ERAD). Accumulation of misfolded proteins in the ER causes ER stress and activates a signaling pathway called the unfolded protein response (UPR). In certain severe situations; however; the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis.

Pathway Name: ABC transporters
Pathway ID	ko02010
Class & Sub-Class	Class: Environmental Information Processing Sub-Class: Membrane transport
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Description	The ATP-binding cassette (ABC) transporters form one of the largest known protein families; and are widespread in bacteria; archaea; and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions; sugars; lipids; sterols; peptides; proteins; and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments; two peripheral proteins that bind and hydrolyze ATP; and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand; in a typical eukaryotic ABC transporter; the membrane spanning protein and the ATP-binding protein are fused; forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD).

Pathway Name: MAPK signaling pathway - plant
Pathway ID	ko04016
Class & Sub-Class	Class: Environmental Information Processing Sub-Class: Signal transduction
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Description	Mitogen-activated protein kinase (MAPK) cascades; the evolutionarily conserved signaling modules in all eukaryotes; serve in transducing extracellular signals to the nucleus or cytoplasm for appropriate cellular responses; including cell division; differentiation; programmed cell death; and adaption to various stresses. In plant; several cascades are triggered by different biotic and abiotic stress stimuli such as pathogen infection; wounding; low temperature; drought; osmotic shock; high salinity; and reactive oxygen species. MAPK pathways also play pivotal roles in processes such as hormonal and developmental signaling. Multiple functional pathways initiated from distinct receptors often share the same kinase components while maintaining their signaling specificity. In contrast to those of animals and fungi; all the plant MAPK genes that have been reported belong to extracellular signal-regulated kinase (ERK) subfamily.

Pathway Name: Plant hormone signal transduction
Pathway ID	ko04075
Class & Sub-Class	Class: Environmental Information Processing Sub-Class: Signal transduction
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Description	Plant hormone signal transduction

Pathway Name: Autophagy - other
Pathway ID	ko04136
Class & Sub-Class	Class: Cellular Processes Sub-Class: Transport and catabolism
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Description	Autophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells; and is characterized by the formation of a double-membrane structure called the autophagosome; either in a housekeeping capacity or during stress and senescence. The process of autophagy could be divided into several stages: induction; vesicle nucleation; elongation and closure; and fusion and digestion. Most essential autophagic machineries are conserved throughout eukaryotes (see map04140 for animals and map04138 for fungi). This map is for other eukaryotes including plants and protists; where autophagy related genes (ATGs) play similar roles in the life cycle. However; autophagy has been relatively less studied in lower eukaryotes.

Pathway Name: Plant-pathogen interaction
Pathway ID	ko04626
Class & Sub-Class	Class: Organismal Systems Sub-Class: Environmental adaptation
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Description	Plants lack animal-like adaptive immunity mechanisms; and therefore have evolved a specific system with multiple layers against invading pathogens. The primary response includes the perception of pathogens by cell-surface pattern-recognition receptors (PRRs) and is referred to as PAMP-triggered immunity (PTI). Activation of FLS2 and EFR triggers MAPK signaling pathway that activates defense genes for antimictobial compounds. The increase in the cytosolic Ca2+ concentration is also a regulator for production of reactive oxygen species and localized programmed cell death/hypersensitive response. The secondary response is called effector-triggered immunity (ETI). Pathogens can acquire the ability to suppress PTI by directly injecting effector proteins into the plant cell through secretion systems. In addition; pathogens can manipulate plant hormone signaling pathways to evade host immune responses using coronatine toxin. Some plants possess specific intracellular surveillance proteins (R proteins) to monitor the presence of pathogen virulence proteins. This ETI occurs with localized programmed cell death to arrest pathogen growth; resulting in cultivar-specific disease resistance.

Pathway Name: Circadian rhythm - plant
Pathway ID	ko04712
Class & Sub-Class	Class: Organismal Systems Sub-Class: Environmental adaptation
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Description	The circadian system is an endogenous rhythm with the period of about 24 hours to provide temporal organization of biological activity. In Arabidopsis the circadian oscillator at the core of this system is composed of the interlocked feedback loop formed by the major transcriptional factors CCA1 (circadian clock associated); LHY (late elongated hypocotyl) and TOC1 (timing of cab); a pseudo response regulator (PRR). The morning-expressed CCA1/LHY Myb transcription factors suppress TOC1 expression by binding to its promoter. Moreover; CCA1/LHY activates the expression of PRR7/9 in the morning and then PRR7/9 repress the transcription of CCA1/LHY during the rest of the day. By contrast; the evening-expressed TOC1 activates the expression of CCA1/LHY.