LiteFold/GO huggingface dataset:
obsolete L-threonine catabolic process to glycine (GO:0019518)
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 2-amino-3-oxobutanoate, which is subsequently converted to glycine.
Synonyms: glycine biosynthetic process from L-threonine; L-threonine breakdown to glycine; L-threonine catabolic process to pyruvate; L-threonine catabolism to glycine; L-threonine degradation to glycine; threonine catabolic process to glycine
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete aldonic acid metabolic process (GO:0019520)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving aldonic acid, a monocarboxylic acid with a chain of three or more carbon atoms, derived from an aldose by oxidation of the aldehydic group.
Synonyms: aldonic acid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
D-gluconate metabolic process (GO:0019521)
Namespace: biological_process
Definition: The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
Synonyms: D-gluconate metabolism
obsolete ketogluconate metabolic process (GO:0019522)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving ketogluconate, the anion of ketogluconic acid, an aldonic acid derived from glucose containing a ketonic carbonyl group.
Synonyms: ketogluconate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete L-idonate metabolic process (GO:0019523)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving L-idonate, the anion of idonic acid, an aldonic acid derived from L-idose, an aldohexose which is epimeric with D-glucose.
Synonyms: L-idonate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
keto-D-gluconate catabolic process (GO:0019524)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of keto-D-gluconate, the anion of keto-D-gluconic acid, an aldonic acid derived from glucose.
Synonyms: keto-D-gluconate breakdown; keto-D-gluconate catabolism; keto-D-gluconate degradation
obsolete keto-D-gluconate metabolic process (GO:0019525)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving keto-D-gluconate, the anion of keto-D-gluconic acid, an aldonic acid derived from glucose.
Synonyms: keto-D-gluconate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
pentitol biosynthetic process (GO:0019526)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of pentitols, any alditol with a chain of five carbon atoms in the molecule.
Synonyms: pentitol anabolism; pentitol biosynthesis; pentitol formation; pentitol synthesis
pentitol catabolic process (GO:0019527)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of pentitols, any alditol with a chain of five carbon atoms in the molecule.
Synonyms: pentitol breakdown; pentitol catabolism; pentitol degradation
D-arabitol catabolic process to D-xylulose 5-phosphate (GO:0019528)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of D-arabitol to form D-xylulose 5-phosphate. D-arabitol is converted into D-xylulose, which is then phosphorylated to form D-xylulose-5-phosphate.
Synonyms: D-arabitol breakdown to xylulose 5-phosphate; D-arabitol degradation; D-arabitol degradation to xylulose 5-phosphate; D-arabitol utilization
taurine catabolic process (GO:0019529)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of taurine (2-aminoethanesulfonic acid), a sulphur-containing amino acid derivative important in the metabolism of fats.
Synonyms: taurine breakdown; taurine catabolism; taurine degradation
taurine metabolic process (GO:0019530)
Namespace: biological_process
Definition: The chemical reactions and pathways involving taurine (2-aminoethanesulfonic acid), a sulphur-containing amino acid derivative important in the metabolism of fats.
Synonyms: taurine metabolism
oxalate transmembrane transporter activity (GO:0019531)
Namespace: molecular_function
Definition: Enables the transfer of oxalate from one side of a membrane to the other. Oxalate, or ethanedioic acid, occurs in many plants and is highly toxic to animals.
Synonyms: oxalic acid transporter activity
oxalate transport (GO:0019532)
Namespace: biological_process
Definition: The directed movement of oxalate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oxalate, or ethanedioic acid, occurs in many plants and is highly toxic to animals.
Synonyms: ethanedioate transport; ethanedioic acid transport; oxalic acid transport
cellobiose transport (GO:0019533)
Namespace: biological_process
Definition: The directed movement of cellobiose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Cellobiose, or 4-O-beta-D-glucopyranosyl-D-glucose, is a disaccharide that represents the basic repeating unit of cellulose.
toxin transmembrane transporter activity (GO:0019534)
Namespace: molecular_function
Definition: Enables the transfer of a toxin from one side of a membrane to the other. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
ferric-vibriobactin transmembrane transporter activity (GO:0019535)
Namespace: molecular_function
Definition: Enables the transfer of ferric-vibriobactin ions from one side of a membrane to the other.
vibriobactin metabolic process (GO:0019536)
Namespace: biological_process
Definition: The chemical reactions and pathways involving vibriobactin, the major siderophore produced by Vibrio cholerae.
Synonyms: vibriobactin metabolism
vibriobactin biosynthetic process (GO:0019537)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of vibriobactin, the major siderophore produced by Vibrio cholerae.
Synonyms: vibriobactin anabolism; vibriobactin biosynthesis; vibriobactin biosynthetic process, peptide formation; vibriobactin biosynthetic process, peptide modification; vibriobactin formation; vibriobactin synthesis
protein metabolic process (GO:0019538)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a protein. Includes protein modification.
Synonyms: cellular protein metabolic process; cellular protein metabolism; multicellular organismal protein metabolic process; protein metabolic process and modification; protein metabolism; protein metabolism and modification
Comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
hydroxymate-containing siderophore biosynthetic process (GO:0019539)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a siderophore from other compounds, including hydroxamic acid. Hydroxamate is one of the three major chemical groups incorporated into siderophore structures with catechol and a-hydroxycarboxylate, each having a high selectivity for iron(3+).
propionate metabolic process (GO:0019541)
Namespace: biological_process
Definition: The chemical reactions and pathways involving propionate, the anion derived from propionic (propanoic) acid, a carboxylic acid important in the energy metabolism of ruminants.
Synonyms: propanoate metabolic process; propanoate metabolism; propionate metabolism
propionate biosynthetic process (GO:0019542)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of propionate, the anion derived from propionic acid.
Synonyms: propionate anabolism; propionate biosynthesis; propionate formation; propionate synthesis
propionate catabolic process (GO:0019543)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of propionate, the anion derived from propionic acid.
Synonyms: propionate breakdown; propionate catabolism; propionate degradation
obsolete L-arginine catabolic process to succinate (GO:0019545)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including succinate.
Synonyms: arginine breakdown to succinate; arginine degradation to succinate
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-arginine deiminase pathway (GO:0019546)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including ornithine and CO2, using the enzyme arginine deiminase.
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete arginine catabolic process to ornithine (GO:0019547)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
Synonyms: arginine breakdown to ornithine; arginine degradation to ornithine
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete glutamate catabolic process to succinate via succinate semialdehyde (GO:0019549)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into succinate, that includes the conversion of 4-aminobutyrate to succinate semialdehyde by the pyruvate-dependent gamma aminobutyrate (GABA) transaminase.
Comment: The reason for obsoletion is that this term was added in error (unnecessary specificity, these are steps in a single pathway)
obsolete glutamate catabolic process to 2-oxoglutarate (GO:0019551)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including 2-oxoglutarate.
Synonyms: glutamate breakdown to 2-oxoglutarate; glutamate catabolic process to 2-ketoglutarate; glutamate catabolic process to alpha-ketoglutarate; glutamate catabolic process to alpha-oxoglutarate; glutamate catabolism to 2-ketoglutarate; glutamate catabolism to alpha-ketoglutarate; glutamate catabolism to alpha-oxoglutarate; glutamate degradation to 2-oxoglutarate
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete L-glutamate fermentation via 2-hydroxyglutarate (GO:0019552)
Namespace: biological_process
Definition: OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate 2-hydroxyglutarate, yielding acetyl-CoA and butanoate. Acetyl-CoA can be further converted into acetate, releasing one ATP molecule.
Synonyms: L-glutamate catabolic process via 2-hydroxyglutarate
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-glutamate fermentation via L-citramalate (GO:0019553)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate L-citramalate.
Synonyms: glutamate breakdown via L-citramalate; glutamate degradation via L-citramalate; L-glutamate catabolic process via L-citramalate
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-glutamate catabolic process to ornithine (GO:0019555)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including ornithine.
Synonyms: glutamate breakdown to ornithine; glutamate degradation to ornithine
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-histidine catabolic process to glutamate and formamide (GO:0019556)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formamide.
Synonyms: histidine breakdown to glutamate and formamide; histidine catabolic process to glutamate and formamide; histidine degradation to glutamate and formamide
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-histidine catabolic process to glutamate and formate (GO:0019557)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formate.
Synonyms: histidine breakdown to glutamate and formate; histidine catabolic process to glutamate and formate; histidine degradation to glutamate and formate
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-histidine catabolic process to 2-oxoglutarate (GO:0019558)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including 2-oxoglutarate.
Synonyms: histidine breakdown to 2-oxoglutarate; histidine catabolic process to 2-ketoglutarate; histidine catabolic process to 2-oxoglutarate; histidine catabolic process to alpha-ketoglutarate; histidine catabolic process to alpha-oxoglutarate; histidine catabolism to 2-ketoglutarate; histidine catabolism to alpha-ketoglutarate; histidine catabolism to alpha-oxoglutarate; histidine 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.
obsolete L-histidine catabolic process to imidazol-5-yl-lactate (GO:0019559)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including imidazol-5-yl-lactate.
Synonyms: histidine breakdown to imidazol-5-yl-lactate; histidine degradation to imidazol-5-yl-lactate
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-histidine catabolic process to hydantoin-5-propionate (GO:0019560)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including hydantoin-5-propionate.
Synonyms: histidine breakdown to hydantoin-5-propionate; histidine degradation to hydantoin-5-propionate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete anaerobic L-phenylalanine oxidation (GO:0019561)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-phenylalanine under anaerobic conditions; occurs via the intermediates phenylpyruvate and phenylacetaldehyde.
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-phenylalanine catabolic process to phosphoenolpyruvate (GO:0019562)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-phenylalanine into other compounds, including phosphoenolpyruvate.
Synonyms: phenylalanine breakdown to phosphoenolpyruvate; phenylalanine degradation to phosphoenolpyruvate
Comment: The reason for obsoletion is that there is no evidence that this is a real process.
obsolete aerobic glycerol catabolic process (GO:0019564)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, in the presence of oxygen.
Synonyms: aerobic glycerol breakdown; aerobic glycerol catabolism; aerobic glycerol degradation; aerobic glycerol fermentation
Comment: This term was obsoleted because it represents the same process as glycerol catabolic process to glycerone phosphate ; GO:0061610.
arabinose metabolic process (GO:0019566)
Namespace: biological_process
Definition: The chemical reactions and pathways involving arabinose, arabino-pentose. L-Arabinose occurs both free, for example in the heartwood of many conifers, and in the combined state, as a constituent of plant hemicelluloses, bacterial polysaccharides etc. D-arabinose is a constituent of arabinonucleosides.
Synonyms: arabinose metabolism
L-arabinose catabolic process to D-xylulose 5-phosphate (GO:0019569)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate.
Synonyms: L-arabinose breakdown to xylulose 5-phosphate; L-arabinose degradation to xylulose 5-phosphate
L-arabinose catabolic process to 2-oxoglutarate (GO:0019570)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-arabinose into other compounds, including 2-oxoglutarate.
Synonyms: L-arabinose breakdown to 2-oxoglutarate; L-arabinose catabolic process to 2-ketoglutarate; L-arabinose catabolic process to alpha-ketoglutarate; L-arabinose catabolic process to alpha-oxoglutarate; L-arabinose catabolism to 2-ketoglutarate; L-arabinose catabolism to alpha-ketoglutarate; L-arabinose catabolism to alpha-oxoglutarate; L-arabinose degradation to 2-oxoglutarate
L-arabinose catabolic process (GO:0019572)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-arabinose, the L-enantiomer of arabino-pentose.
Synonyms: L-arabinose breakdown; L-arabinose catabolism; L-arabinose degradation
D-arabinose catabolic process to D-xylulose 5-phosphate (GO:0019573)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of D-arabinose to form D-xylulose 5-phosphate. D-arabinose is converted into D-ribulose, which is phosphorylated to D-ribulose-5-phosphate, which is isomerized to give D-xylulose-5-phosphate.
Synonyms: D-arabinose breakdown to xylulose 5-phosphate; D-arabinose degradation to xylulose 5-phosphate
obsolete sucrose catabolic process via 3'-ketosucrose (GO:0019574)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds via the conversion of sucrose to 3'-ketosucrose. 3'-ketosucrose is hydrolyzed to 3-ketoglucose and fructose, and the 3-ketoglucose is then be converted to glucose.
Synonyms: sucrose breakdown, using glucoside 3-dehydrogenase; sucrose catabolic process to D-glucose; sucrose catabolic process, using glucoside 3-dehydrogenase; sucrose catabolism, using glucoside 3-dehydrogenase; sucrose degradation, using glucoside 3-dehydrogenase
Comment: This term was obsoleted because it represents a specific pathway out of scope for GO.
obsolete sucrose catabolic process, using beta-fructofuranosidase (GO:0019575)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose, catalyzed by the enzyme beta-fructofuranosidase (EC:3.2.1.26).
Synonyms: sucrose breakdown, using beta-fructofuranosidase; sucrose catabolic process, using beta-fructofuranosidase; sucrose catabolism, using beta-fructofuranosidase; sucrose degradation, using beta-fructofuranosidase
Comment: This term was made obsolete because beta-fructofuranosidase (also known as invertase) catalyzes the first step in multiple routes of sucrose catabolism.
obsolete aerobic fructose catabolic process (GO:0019576)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fructose that occurs in the presence of oxygen.
Synonyms: aerobic fructose breakdown; aerobic fructose catabolism; aerobic fructose degradation
Comment: The reason for obsoletion is that this term is not clearly defined the meaning is ambiguous.
obsolete aldaric acid metabolic process (GO:0019577)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving aldaric acid, any dicarboxylic acid formed by oxidation of by the terminal groups of an aldose to carboxyl group.
Synonyms: aldaric acid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
aldaric acid biosynthetic process (GO:0019578)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of aldaric acid, any dicarboxylic acid formed by oxidation of by the terminal groups of an aldose to carboxyl group.
Synonyms: aldaric acid anabolism; aldaric acid biosynthesis; aldaric acid formation; aldaric acid synthesis
aldaric acid catabolic process (GO:0019579)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of aldaric acid, any dicarboxylic acid formed by oxidation of by the terminal groups of an aldose to carboxyl group.
Synonyms: aldaric acid breakdown; aldaric acid catabolism; aldaric acid degradation
galactarate metabolic process (GO:0019580)
Namespace: biological_process
Definition: The chemical reactions and pathways involving galactarate, an anion of galactaric acid, the meso-aldaric acid derived from both D- and L-galactose.
Synonyms: D-galactarate metabolic process; D-galactarate metabolism; galactarate metabolism; mucic acid metabolic process; mucic acid metabolism
obsolete galactonate metabolic process (GO:0019583)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving galactonate, the anion of galactonic acid, an organic acid derived from the sugar galactose.
Synonyms: galactonate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
galactonate catabolic process (GO:0019584)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of galactonate, the anion of galactonic acid.
Synonyms: galactonate breakdown; galactonate catabolism; galactonate degradation
glucuronate metabolic process (GO:0019585)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glucuronate, any salt or ester of glucuronic acid, the uronic acid formally derived from glucose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group.
Synonyms: glucuronate metabolism
obsolete galacturonate metabolic process (GO:0019586)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving galacturonate, the anion of galacturonic acid, the uronic acid formally derived from galactose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group.
Synonyms: galacturonate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
anaerobic glycerol catabolic process (GO:0019588)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol, yielding energy in the form of ATP.
Synonyms: glycerol fermentation
anaerobic glycerol catabolic process to 1,3-propanediol and glycerone phosphate (GO:0019589)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol into 1,3-propanediol and glycerone phosphate.
Synonyms: glycerol fermentation to 1,3-propanediol; glycerol fermentation to propane-1,3-diol