LiteFold/GO huggingface dataset:
glycolytic process (GO:0006096)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
Synonyms: anaerobic glycolysis; Embden-Meyerhof pathway; Embden-Meyerhof-Parnas pathway; glycolysis; modified Embden-Meyerhof pathway
glyoxylate cycle (GO:0006097)
Namespace: biological_process
Definition: A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
Synonyms: glyoxylate bypass
pentose-phosphate shunt (GO:0006098)
Namespace: biological_process
Definition: The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).
Synonyms: hexose monophosphate pathway; pentose phosphate pathway; pentose phosphate shunt; pentose-phosphate pathway
tricarboxylic acid cycle (GO:0006099)
Namespace: biological_process
Definition: A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
Synonyms: citric acid cycle; Krebs cycle; oxidative TCA cycle; TCA cycle
obsolete tricarboxylic acid cycle intermediate metabolic process (GO:0006100)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving intermediates of the tricarboxylic acid cycle.
Synonyms: citric acid cycle intermediate metabolic process; citric acid cycle intermediate metabolism; Krebs cycle intermediate metabolic process; Krebs cycle intermediate metabolism; TCA intermediate metabolic process; TCA intermediate metabolism; tricarboxylic acid cycle intermediate metabolic process; tricarboxylic acid cycle intermediate metabolism
Comment: This term was made obsolete because it is a grouping term that is not useful, but has caused true path violations.
citrate metabolic process (GO:0006101)
Namespace: biological_process
Definition: The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboxylate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
Synonyms: citrate metabolism
isocitrate metabolic process (GO:0006102)
Namespace: biological_process
Definition: The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
Synonyms: isocitrate metabolism
2-oxoglutarate metabolic process (GO:0006103)
Namespace: biological_process
Definition: The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
Synonyms: 2-ketoglutarate metabolic process; 2-ketoglutarate metabolism; 2-oxoglutarate metabolism; alpha-ketoglutarate metabolic process; alpha-ketoglutarate metabolism; alpha-oxoglutarate metabolic process; alpha-oxoglutarate metabolism
succinyl-CoA metabolic process (GO:0006104)
Namespace: biological_process
Definition: The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.
Synonyms: succinyl-CoA metabolism
succinate metabolic process (GO:0006105)
Namespace: biological_process
Definition: The chemical reactions and pathways involving succinate, also known as butanedioate or ethane dicarboxylate, the dianion of succinic acid. Succinate is an important intermediate in metabolism and a component of the TCA cycle.
Synonyms: succinate metabolism
fumarate metabolic process (GO:0006106)
Namespace: biological_process
Definition: The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
Synonyms: fumarate metabolism
oxaloacetate metabolic process (GO:0006107)
Namespace: biological_process
Definition: The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.
Synonyms: oxaloacetate metabolism
malate metabolic process (GO:0006108)
Namespace: biological_process
Definition: The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
Synonyms: malate metabolism
regulation of glycolytic process (GO:0006110)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of glycolysis.
Synonyms: regulation of glycolysis involved in cellular glucose homeostasis
regulation of gluconeogenesis (GO:0006111)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
Synonyms: regulation of gluconeogenesis involved in cellular glucose homeostasis; regulation of glucose biosynthesis; regulation of glucose biosynthetic process
fermentation (GO:0006113)
Namespace: biological_process
Definition: The metabolic process that uses oxidation-reduction reactions of organic compounds and substrate-level phosphorylation for the generation of adenosine triphosphate (ATP), without consuming oxygen and is independent of electron transport chains.
Comment: PMID:38821505 mentions exceptions regarding organic compounds and electron transport chain. Fermentation sub-processes exclude glycolysis to prevent redundancy with the glycolytic pathway.
glycerol biosynthetic process (GO:0006114)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
Synonyms: glycerol anabolism; glycerol biosynthesis; glycerol formation; glycerol synthesis
ethanol biosynthetic process (GO:0006115)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ethanol, CH3-CH2-OH, a colorless, water-miscible, flammable liquid produced by alcoholic fermentation.
Synonyms: ethanol anabolism; ethanol biosynthesis; ethanol formation; ethanol synthesis
obsolete NADH oxidation (GO:0006116)
Namespace: biological_process
Definition: OBSOLETE. A metabolic process that results in the oxidation of reduced nicotinamide adenine dinucleotide, NADH, to the oxidized form, NAD+.
Synonyms: NAD (reduced) dehydrogenation; NAD (reduced) oxidation; NADH dehydrogenation; reduced NAD dehydrogenation; reduced NAD oxidation; reduced nicotinamide adenine dinucleotide dehydrogenation; reduced nicotinamide adenine dinucleotide oxidation
Comment: This term was obsoleted because it represents a reactant in oxidoreductase reactions.
acetaldehyde metabolic process (GO:0006117)
Namespace: biological_process
Definition: The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol.
Synonyms: acetaldehyde metabolism; ethanal metabolic process; ethanal metabolism
obsolete electron transport (GO:0006118)
Namespace: biological_process
Definition: OBSOLETE. The transport of electrons from an electron donor to an electron acceptor.
Synonyms: 6-phosphofructokinase reduction; dihydrobiopterin reduction; dihydrolipoamide reduction; dihydrolipoylprotein reduction; dihydropteridine reduction; electron transfer; electron transport; other pathways of electron transport; oxidized glutathione reduction; protein-disulfide reduction
Comment: This term was made obsolete because it describes a molecular function.
oxidative phosphorylation (GO:0006119)
Namespace: biological_process
Definition: The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
Synonyms: respiratory-chain phosphorylation
mitochondrial electron transport, NADH to ubiquinone (GO:0006120)
Namespace: biological_process
Definition: The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation.
Synonyms: complex I (NADH to ubiquinone); oxidative phosphorylation, NADH to ubiquinone
mitochondrial electron transport, succinate to ubiquinone (GO:0006121)
Namespace: biological_process
Definition: The transfer of electrons from succinate to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex II.
Synonyms: complex II (succinate to ubiquinone); mitochondrial electron transport, succinate to coenzyme Q; oxidative phosphorylation, succinate to ubiquinone
mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)
Namespace: biological_process
Definition: The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
Synonyms: complex III (ubiquinone to cytochrome c)
mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)
Namespace: biological_process
Definition: The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
Synonyms: complex IV (reduction of O2)
ferredoxin metabolic process (GO:0006124)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ferredoxin, any simple, nonenzymatic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur. Iron and sulfur atoms are present in one or two clusters of two or four atoms of each.
Synonyms: ferredoxin metabolism
obsolete thioredoxin pathway (GO:0006125)
Namespace: biological_process
Definition: OBSOLETE. This term was not defined before being made obsolete.
Synonyms: thioredoxin pathway; thioredoxin reduction
Comment: This term was made obsolete because it is not clear what it is intended to represent.
obsolete other pathways of electron transport (GO:0006126)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: other pathways of electron transport
Comment: This term was made obsolete because it was an unnecessary grouping term.
glycerol-3-phosphate shuttle (GO:0006127)
Namespace: biological_process
Definition: The process of transferring reducing equivalents from NADH in the cytosol into the mitochondria via glycerol-3-phosphate. Cytosolic glycerol-3-phosphate dehydrogenase uses NADH to convert dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate (G3P) in the cytosol; G3P then diffuses into the mitochondria where mitochondrial glycerol-3-phosphate dehydrogenase uses FAD to convert G3P back to DHAP; the electrons on the reduced FADH2 are then available for use in the electron transport chain, and DHAP returns to the cytosol to complete the cycle.
Synonyms: glycerol phosphate shuttle; glycerophosphate shuttle
obsolete protein-disulfide reduction (GO:0006129)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: protein-disulfide reduction; protein-disulphide reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete 6-phosphofructokinase reduction (GO:0006130)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: 6-phosphofructokinase reduction
Comment: This term was made obsolete because the term string was ambiguous and the term may represent a molecular function.
obsolete dihydrolipoamide reduction (GO:0006131)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: dihydrolipoamide reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete dihydrolipoylprotein reduction (GO:0006132)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: dihydrolipoylprotein reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete dihydrobiopterin reduction (GO:0006134)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: dihydrobiopterin reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
obsolete dihydropteridine reduction (GO:0006135)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: dihydropteridine reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
nucleobase-containing compound metabolic process (GO:0006139)
Namespace: biological_process
Definition: Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
Synonyms: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism; nucleobase, nucleoside and nucleotide metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolism
regulation of nucleotide metabolic process (GO:0006140)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides.
Synonyms: regulation of nucleotide metabolism
obsolete regulation of pyrimidine nucleobase metabolic process (GO:0006142)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases.
Synonyms: regulation of pyrimidine base metabolic process; regulation of pyrimidine base metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete purine metabolic process (GO:0006143)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: purine metabolic process
Comment: This term was made obsolete because more appropriate terms were created.
purine nucleobase metabolic process (GO:0006144)
Namespace: biological_process
Definition: The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
Synonyms: purine base metabolic process; purine base metabolism; purine metabolic process; purine metabolism
purine nucleobase catabolic process (GO:0006145)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
Synonyms: purine base breakdown; purine base catabolic process; purine base catabolism; purine base degradation
adenine catabolic process (GO:0006146)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of adenine, 6-aminopurine, one of the 5 main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
Synonyms: adenine breakdown; adenine catabolism; adenine degradation
guanine catabolic process (GO:0006147)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
Synonyms: guanine breakdown; guanine catabolism; guanine degradation
inosine catabolic process (GO:0006148)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs.
Synonyms: inosine breakdown; inosine catabolism; inosine degradation
deoxyinosine catabolic process (GO:0006149)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of deoxyinosine, hypoxanthine deoxyriboside.
Synonyms: deoxyinosine breakdown; deoxyinosine catabolism; deoxyinosine degradation
purine nucleoside catabolic process (GO:0006152)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
Synonyms: purine nucleoside breakdown; purine nucleoside catabolism; purine nucleoside degradation
adenosine catabolic process (GO:0006154)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
Synonyms: adenosine breakdown; adenosine catabolism; adenosine degradation; adenosine phosphorolysis
obsolete adenosine deaminase reaction (GO:0006155)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: adenosine deaminase reaction
Comment: This term was made obsolete because it represents a molecular function.
deoxyadenosine catabolic process (GO:0006157)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA.
Synonyms: deoxyadenosine breakdown; deoxyadenosine catabolism; deoxyadenosine degradation; deoxyadenosine phosphorolysis
obsolete deoxyadenosine deaminase reaction (GO:0006158)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: deoxyadenosine deaminase reaction
Comment: This term was made obsolete because it represents a molecular function.
deoxyguanosine catabolic process (GO:0006161)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of deoxyguanosine, a nucleoside consisting of the base guanine and the sugar deoxyribose.
Synonyms: deoxyguanosine breakdown; deoxyguanosine catabolism; deoxyguanosine degradation
obsolete purine/pyrimidine nucleoside diphosphate reduction (GO:0006162)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: purine/pyrimidine nucleoside diphosphate reduction
Comment: This term was made obsolete because it represents a molecular function rather than a biological process.
purine nucleotide metabolic process (GO:0006163)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
Synonyms: purine metabolic process; purine metabolism; purine nucleotide metabolism
purine nucleotide biosynthetic process (GO:0006164)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
Synonyms: purine nucleotide anabolism; purine nucleotide biosynthesis; purine nucleotide formation; purine nucleotide synthesis
obsolete nucleoside diphosphate phosphorylation (GO:0006165)
Namespace: biological_process
Definition: OBSOLETE. The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
Comment: The reason for obsoletion is that this term represents a single step MF.
purine ribonucleoside salvage (GO:0006166)
Namespace: biological_process
Definition: Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
adenine salvage (GO:0006168)
Namespace: biological_process
Definition: Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
Synonyms: adenine salvage pathway; adenine, hypoxanthine and their nucleoside salvage
adenosine salvage (GO:0006169)
Namespace: biological_process
Definition: Any process that generates adenosine, adenine riboside, from derivatives of it without de novo synthesis.
Synonyms: adenine, hypoxanthine and their nucleoside salvage
dAMP biosynthetic process (GO:0006170)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dAMP, deoxyadenosine monophosphate (2'-deoxyadenosine 5'-phosphate).
Synonyms: dAMP anabolism; dAMP biosynthesis; dAMP formation; dAMP synthesis
ADP biosynthetic process (GO:0006172)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
Synonyms: ADP anabolism; ADP biosynthesis; ADP formation; ADP synthesis
dADP biosynthetic process (GO:0006173)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate).
Synonyms: dADP anabolism; dADP biosynthesis; dADP formation; dADP synthesis
obsolete dADP phosphorylation (GO:0006174)
Namespace: biological_process
Definition: OBSOLETE. The process of introducing a phosphate group into dADP, deoxyadenosine diphosphate, to produce dATP.
Comment: The reason for obsoletion is that this term represents a single step MF.
dATP biosynthetic process (GO:0006175)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
Synonyms: dATP anabolism; dATP biosynthesis; dATP formation; dATP synthesis
dATP biosynthetic process from ADP (GO:0006176)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate) from other compounds, including ADP, adenosine diphosphate.
Synonyms: dATP anabolism from ADP; dATP formation from ADP; dATP synthesis from ADP
GMP biosynthetic process (GO:0006177)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
Synonyms: GMP anabolism; GMP biosynthesis; GMP formation; GMP synthesis