LiteFold/GO huggingface dataset:
obsolete L-cysteine catabolic process via cystine, using cystine reductase (GO:0019455)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cystine reductase.
Synonyms: L-cysteine breakdown via cystine, using cystine reductase; L-cysteine degradation via cystine, using cystine reductase
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-cysteine catabolic process via cystine, using cysteine transaminase (GO:0019456)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cysteine transaminase.
Synonyms: L-cysteine breakdown via cystine, using cysteine transaminase; L-cysteine degradation via cystine, using cysteine transaminase
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-methionine catabolic process to succinyl-CoA (GO:0019457)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine into other compounds, including succinyl-CoA.
Synonyms: methionine breakdown to succinyl-CoA; methionine degradation to succinyl-CoA
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete glutamine catabolic process to fumarate (GO:0019460)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamine into other compounds, including fumarate.
Synonyms: glutamate catabolic process to fumarate; glutamine breakdown to fumarate; glutamine degradation to fumarate
Comment: The reason for obsoletion is that this term is the same as the parent term.
obsolete glutamine catabolic process to fumarate, using glutamate synthase (NADPH) (GO:0019461)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamine into fumarate, beginning with the conversion of glutamine to glutamate catalyzed by the enzyme glutamate synthase (NADPH) (EC:1.4.1.13).
Synonyms: glutamate catabolic process to fumarate, using glutamate synthase (NADPH); glutamine breakdown to fumarate, using glutamate synthase (NADPH); glutamine degradation to fumarate, using glutamate synthase (NADPH)
Comment: The reason for obsoletion is that this term is defined by a single-step process.
obsolete glutamine catabolic process to fumarate, using glutaminase (GO:0019462)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamine into fumarate, beginning with conversion of glutamine into glutamate catalyzed by the enzyme glutaminase (EC:3.5.1.2).
Synonyms: glutamate catabolic process to fumarate, using glutaminase; glutamine breakdown to fumarate, using glutaminase; glutamine degradation to fumarate, using glutaminase
Comment: The reason for obsoletion is that this term is defined by a single-step process.
obsolete glycine catabolic process to creatine (GO:0019463)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glycine into other compounds, including creatine.
Synonyms: glycine breakdown to creatine; glycine degradation to creatine
Comment: The reason for obsoletion is that there is no evidence that this process exists.
glycine decarboxylation via glycine cleavage system (GO:0019464)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
Synonyms: glycine cleavage system
obsolete aspartate transamidation (GO:0019465)
Namespace: biological_process
Definition: OBSOLETE. The exchange of the amino group of aspartate, the anion derived from aspartic acid, for another amino group.
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete L-ornithine catabolic process via proline (GO:0019466)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-ornithine, via the intermediate proline.
Synonyms: ornithine breakdown via proline; ornithine degradation via proline
Comment: This term was obsoleted because it represents a variant pathway of L-ornithine degradation and is out of scope for GO.
obsolete L-ornithine catabolic process, by decarboxylation (GO:0019467)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-ornithine by decarboxylation.
Synonyms: ornithine breakdown, by decarboxylation; ornithine degradation, by decarboxylation
Comment: This term was obsoleted because it represents a variant pathway of L-ornithine degradation and is out of scope for GO.
obsolete nopaline catabolic process (GO:0019468)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of nopaline (N-(I-carboxy-4-guanidinobutyl)glutamic acid), a rare amino-acid derivative.
Synonyms: nopaline breakdown; nopaline catabolism; nopaline degradation
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete octopine catabolic process (GO:0019469)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of octopine (N-(1-carboxy-4-guanidinobutyl)-L-alanine), an amino acid derived opine.
Synonyms: octopine breakdown; octopine catabolism; octopine degradation
Comment: The reason for obsoletion is that this term represents a molecular function.
trans-4-hydroxy-L-proline catabolic process (GO:0019470)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of trans-4-hydroxy-L-proline.
Synonyms: 4-hydroxyproline breakdown; 4-hydroxyproline catabolism; 4-hydroxyproline degradation
obsolete 4-hydroxyproline metabolic process (GO:0019471)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline. The presence of hydroxyproline is essential to produce stable triple helical tropocollagen, hence the problems caused by ascorbate deficiency in scurvy. This unusual amino acid is also present in considerable amounts in the major glycoprotein of primary plant cell walls.
Synonyms: 4-hydroxyproline metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete 4-hydroxyproline biosynthetic process (GO:0019472)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline.
Synonyms: 4-hydroxyproline anabolism; 4-hydroxyproline biosynthesis; 4-hydroxyproline formation; 4-hydroxyproline synthesis
Comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
obsolete L-lysine catabolic process to glutarate, by acetylation (GO:0019473)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including glutarate, by acetylation.
Synonyms: L-lysine breakdown to glutarate, by acetylation; L-lysine degradation to glutarate, by acetylation
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-lysine catabolic process to acetyl-CoA (GO:0019474)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA.
Synonyms: L-lysine breakdown to acetyl-CoA; L-lysine degradation to acetyl-CoA
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
L-lysine fermentation (GO:0019475)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-lysine into acetyl-CoA and butanoate. Acetyl-CoA can be further converted into acetate, releasing one ATP molecule.
Synonyms: 3-keto-5-aminohexanoate pathway; L-lysine breakdown to acetate; L-lysine catabolic process to butyrate and acetate; L-lysine degradation to acetate; L-lysine fermentation to acetic acid and butanoic acid
obsolete D-lysine catabolic process (GO:0019476)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-lysine, the D-enantiomer of lysine; i.e. (2R)-2,6-diaminohexanoic acid.
Synonyms: D-lysine breakdown; D-lysine catabolism; D-lysine degradation
Comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-lysine.
L-lysine catabolic process (GO:0019477)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-lysine.
Synonyms: L-lysine breakdown; L-lysine catabolism; L-lysine degradation
D-amino acid catabolic process (GO:0019478)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
Synonyms: D-amino acid breakdown; D-amino acid catabolism; D-amino acid degradation
obsolete L-alanine oxidation to D-lactate and ammonia (GO:0019479)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-alanine to D-lactate and ammonia.
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-alanine oxidation to pyruvate via D-alanine (GO:0019480)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-alanine to pyruvate, with D-alanine as an intermediate.
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete L-alanine catabolic process, by transamination (GO:0019481)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-alanine by transamination.
Synonyms: L-alanine breakdown, by transamination; L-alanine degradation, by transamination
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
beta-alanine metabolic process (GO:0019482)
Namespace: biological_process
Definition: The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins.
Synonyms: beta-alanine metabolism
beta-alanine biosynthetic process (GO:0019483)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins.
Synonyms: beta-alanine anabolism; beta-alanine biosynthesis; beta-alanine formation; beta-alanine synthesis
beta-alanine catabolic process (GO:0019484)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of beta-alanine.
Synonyms: beta-alanine breakdown; beta-alanine catabolism; beta-alanine degradation
obsolete beta-alanine catabolic process to L-alanine (GO:0019485)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including L-alanine.
Synonyms: beta-alanine breakdown to L-alanine; beta-alanine degradation to L-alanine
Comment: This term was obsoleted because it represents a variant pathway of beta-alanine degradation and is out of scope for GO.
anaerobic acetylene catabolic process (GO:0019487)
Namespace: biological_process
Definition: The chemical reactions and pathways involving acetylene, a colorless, volatile, explosive gas, that occur in the absence of oxygen.
Synonyms: anaerobic acetylene breakdown; anaerobic acetylene catabolism; anaerobic acetylene degradation; anaerobic ethyne catabolic process; anaerobic ethyne catabolism
ribitol catabolic process to D-xylulose 5-phosphate (GO:0019488)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of ribitol to form D-xylulose 5-phosphate. Ribitol is initially converted to D-ribulose, which is phosphorylated to form D-ribulose 5-phosphate, which is then converted into D-xylulose 5-phosphate.
Synonyms: ribitol breakdown to xylulose 5-phosphate; ribitol degradation to xylulose 5-phosphate; ribitol utilization
obsolete methylgallate metabolic process (GO:0019489)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving methylgallate, trihydroxymethylbenzoate, the anion of methylgallic acid.
Synonyms: methylgallate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
2-aminobenzenesulfonate desulfonation (GO:0019490)
Namespace: biological_process
Definition: The removal of the sulfonate group from 2-aminobenzenesulfonate, an aromatic sulfonate used in organic synthesis and in the manufacture of various dyes and medicines.
Synonyms: 2-aminobenzenesulphonate desulphonation
ectoine biosynthetic process (GO:0019491)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), a tetrahydropyrimidine commonly synthesized by halophilic bacteria.
Synonyms: ectoine anabolism; ectoine biosynthesis; ectoine formation; ectoine synthesis
obsolete L-arginine catabolic process to L-proline (GO:0019493)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-proline.
Synonyms: arginine breakdown to proline; arginine degradation to proline
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete proline catabolic process to 2-oxoglutarate (GO:0019495)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including 2-oxoglutarate.
Synonyms: proline breakdown to 2-oxoglutarate; proline catabolic process to 2-ketoglutarate; proline catabolic process to alpha-ketoglutarate; proline catabolic process to alpha-oxoglutarate; proline catabolism to 2-ketoglutarate; proline catabolism to alpha-ketoglutarate; proline catabolism to alpha-oxoglutarate; proline degradation to 2-oxoglutarate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
serine-isocitrate lyase pathway (GO:0019496)
Namespace: biological_process
Definition: A one-carbon metabolic process in which acetyl-CoA is produced from formaldehyde and carbon dioxide.
hexachlorocyclohexane metabolic process (GO:0019497)
Namespace: biological_process
Definition: The chemical reactions and pathways involving hexachlorocyclohexane, a cyclohexane derivative with 6 chlorine atoms attached to the hexane ring. Hexachlorocyclohexane consists of a mixture of 8 different isomers and was used a commercial insecticide. It is persistent in the environment, causing serious soil pollution.
Synonyms: hexachlorocyclohexane metabolism
n-octane oxidation (GO:0019498)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the conversion of n-octane to octanoyl-CoA.
cyanide metabolic process (GO:0019499)
Namespace: biological_process
Definition: The chemical reactions and pathways involving cyanide, NC-, the anion of hydrocyanic acid. Cyanide is a potent inhibitor of respiration, reacting with the ferric form of cytochrome aa3 and thus blocking the electron transport chain.
Synonyms: cyanide metabolism
cyanide catabolic process (GO:0019500)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of cyanide, NC-, the anion of hydrocyanic acid. Cyanide is a potent inhibitor of respiration.
Synonyms: cyanide breakdown; cyanide catabolism; cyanide degradation
arsonoacetate catabolic process (GO:0019501)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of arsonoacetate, a synthetic, organic compound containing a single arsenic atom.
Synonyms: arsonoacetate breakdown; arsonoacetate catabolism; arsonoacetate degradation
obsolete L-proline betaine metabolic process (GO:0019502)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline found in alfalfa, chrysanthemum, and citrus plants.
Synonyms: stachydrine metabolic process; stachydrine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete L-proline betaine biosynthetic process (GO:0019503)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline.
Synonyms: stachydrine anabolism; stachydrine biosynthesis; stachydrine biosynthetic process; stachydrine formation; stachydrine synthesis
Comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
L-proline betaine catabolic process (GO:0019504)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-proline betaine (stachydrine).
Synonyms: stachydrine breakdown; stachydrine catabolic process; stachydrine catabolism; stachydrine degradation
resorcinol metabolic process (GO:0019505)
Namespace: biological_process
Definition: The chemical reactions and pathways involving resorcinol (C6H4(OH)2), a benzene derivative with many applications, including dyes, explosives, resins and as an antiseptic.
Synonyms: 1,3-benzenediol metabolic process; 1,3-benzenediol metabolism; 1,3-dihydroxybenzene metabolic process; 1,3-dihydroxybenzene metabolism; resorcinol metabolism
phenylmercury acetate catabolic process (GO:0019506)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of phenylmercury acetate, an organomercurial compound composed of a mercury atom attached to a benzene ring and an acetate group.
Synonyms: phenylmercury acetate breakdown; phenylmercury acetate catabolism; phenylmercury acetate degradation
obsolete pyridine metabolic process (GO:0019507)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving pyridine, a nitrogenous base (C5H5N) obtained from the distillation of bone oil or coal tar, and by the decomposition of certain alkaloids, as a colorless liquid with a peculiar pungent odor.
Synonyms: pyridine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete 2,5-dihydroxypyridine catabolic process to fumarate (GO:0019508)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 2,5-dihydroxypyridine to form fumarate. 2,5-dihydroxypyridine is dioxygenated to give maleamate and formate; the maleamate from this reaction is then converted to maleate, which is then isomerized to fumurate.
Synonyms: 2,5-dihydroxypyridine breakdown to fumarate; 2,5-dihydroxypyridine degradation to fumarate; 2,5-dihydroxypyridine utilization; maleamate pathway; pyridine-2,5-diol catabolic process to fumarate
Comment: This term was obsoleted because it represents an intermediate in nicotinate catabolic process ; GO:1901848.
obsolete L-methionine salvage from methylthioadenosine (GO:0019509)
Namespace: biological_process
Definition: OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
Synonyms: methionine recycling; methionine regeneration; methionine salvage from methylthioadenosine; methionine salvage pathway
Comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
obsolete S-adenosylhomocysteine catabolic process (GO:0019510)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of S-adenosylhomocysteine, forming homocysteine and then methionine.
Synonyms: S-adenosylhomocysteine breakdown; S-adenosylhomocysteine catabolism; S-adenosylhomocysteine degradation
Comment: The reason for obsoletion is that the terms represent molecular functions and not biological processes.
peptidyl-proline hydroxylation (GO:0019511)
Namespace: biological_process
Definition: The hydroxylation of peptidyl-proline to form peptidyl-hydroxyproline.
lactose catabolic process via tagatose-6-phosphate (GO:0019512)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
Synonyms: lactose breakdown via tagatose-6-phosphate; lactose degradation via tagatose-6-phosphate
lactose catabolic process, using glucoside 3-dehydrogenase (GO:0019513)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lactose, catalyzed by the enzyme glucoside 3-dehydrogenase.
Synonyms: lactose breakdown, using glucoside 3-dehydrogenase; lactose degradation, using glucoside 3-dehydrogenase
obsolete lactose hydrolysis (GO:0019514)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: lactose hydrolysis
Comment: This term was made obsolete because hydrolysis is a reaction.
lactose catabolic process via UDP-galactose (GO:0019515)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate UDP-galactose.
Synonyms: lactose breakdown via UDP-galactose; lactose degradation via UDP-galactose
obsolete lactate oxidation (GO:0019516)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons.
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete L-threonine catabolic process to D-lactate (GO:0019517)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L- threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form the compound methylglyoxal, which is subsequently converted to D-lactate.
Synonyms: L-threonine breakdown to D-lactate; L-threonine catabolic process to (R)-lactate; L-threonine catabolic process to methylglyoxal; L-threonine catabolic process to pyruvate; L-threonine catabolism to D-lactate; L-threonine degradation to D-lactate; threonine catabolic process to D-lactate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.