LiteFold/GO huggingface dataset:
obsolete alanine catabolic process (GO:0006524)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of alanine, 2-aminopropanoic acid.
Synonyms: alanine breakdown; alanine catabolism; alanine degradation
Comment: The reason for obsoletion is that a more specific term has been created.
arginine metabolic process (GO:0006525)
Namespace: biological_process
Definition: The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
Synonyms: arginine metabolism
L-arginine biosynthetic process (GO:0006526)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
Synonyms: arginine anabolism; arginine biosynthesis; arginine formation; arginine synthesis
L-arginine catabolic process (GO:0006527)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-arginine.
Synonyms: arginine breakdown; arginine catabolism; arginine degradation
asparagine metabolic process (GO:0006528)
Namespace: biological_process
Definition: The chemical reactions and pathways involving asparagine, 2-amino-3-carbamoylpropanoic acid.
Synonyms: asparagine metabolism
obsolete asparagine biosynthetic process (GO:0006529)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine, 2-amino-3-carbamoylpropanoic acid.
Synonyms: asparagine anabolism; asparagine biosynthesis; asparagine formation; asparagine synthesis
Comment: The reason for obsoletion is that more specific terms were created.
aspartate metabolic process (GO:0006531)
Namespace: biological_process
Definition: The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
Synonyms: aspartate metabolism
L-aspartate biosynthetic process (GO:0006532)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
Synonyms: aspartate anabolism; aspartate biosynthesis; aspartate formation; aspartate synthesis
obsolete cysteine metabolic process (GO:0006534)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
Synonyms: cysteine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
obsolete L-cysteine biosynthetic process from L-serine (GO:0006535)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine.
Synonyms: cysteine anabolism from serine; cysteine formation from serine; cysteine synthesis from serine
Comment: This term was obsoleted because it is too specific and is outside the scope of GO.
glutamate metabolic process (GO:0006536)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
Synonyms: glutamate metabolism; glutamic acid metabolic process; glutamic acid metabolism
obsolete glutamate biosynthetic process (GO:0006537)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
Synonyms: glutamate anabolism; glutamate biosynthesis; glutamate biosynthesis, using glutamate dehydrogenase (NAD(P)+); glutamate biosynthesis, using glutamate synthase (NADPH); glutamate biosynthetic process, using glutamate dehydrogenase (NAD(P)+); glutamate biosynthetic process, using glutamate synthase (NADPH); glutamate formation; glutamate synthesis; glutamic acid biosynthesis; glutamic acid biosynthetic process
Comment: This is a duplicate term.
L-glutamate catabolic process (GO:0006538)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-glutamate.
Synonyms: glutamate breakdown; glutamate catabolism; glutamate deamidation; glutamate degradation; glutamic acid catabolic process; glutamic acid catabolism
obsolete glutamate catabolic process via 2-oxoglutarate (GO:0006539)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate 2-oxoglutarate.
Synonyms: glutamate breakdown via 2-oxoglutarate; glutamate catabolic process via 2-ketoglutarate; glutamate catabolic process via alpha-ketoglutarate; glutamate catabolic process via alpha-oxoglutarate; glutamate catabolism via 2-ketoglutarate; glutamate catabolism via alpha-ketoglutarate; glutamate catabolism via alpha-oxoglutarate; glutamate degradation via 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.
GABA shunt (GO:0006540)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of succinate from L-glutamate via gamma-aminobutyrate (GABA), bypassing two steps of the TCA cycle. It operates through the sequential conversion of glutamate to GABA by glutamate decarboxylase, transamination of GABA to succinic semialdehyde by GABA transaminase, and oxidation of succinic semialdehyde to succinate by succinate semialdehyde dehydrogenase.
Synonyms: 4-aminobutyrate shunt; gamma aminobutyrate shunt; gamma-aminobutyrate shunt; glutamate decarboxylation to succinate
L-glutamine metabolic process (GO:0006541)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
Synonyms: glutamine metabolism
obsolete glutamine biosynthetic process (GO:0006542)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamine, 2-amino-4-carbamoylbutanoic acid.
Synonyms: glutamine anabolism; glutamine biosynthesis; glutamine formation; glutamine synthesis
Comment: This is a duplicate term.
L-glutamine catabolic process (GO:0006543)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-glutamine.
Synonyms: glutamine breakdown; glutamine catabolism; glutamine degradation
glycine metabolic process (GO:0006544)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glycine, aminoethanoic acid.
Synonyms: glycine metabolism
glycine biosynthetic process (GO:0006545)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
Synonyms: glycine anabolism; glycine biosynthesis; glycine formation; glycine synthesis
glycine catabolic process (GO:0006546)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glycine.
Synonyms: glycine breakdown; glycine catabolism; glycine degradation
obsolete L-histidine metabolic process (GO:0006547)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
Synonyms: histidine metabolic process; histidine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
L-histidine catabolic process (GO:0006548)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-histidine.
Synonyms: histidine breakdown; histidine catabolic process; histidine catabolism; histidine degradation
isoleucine metabolic process (GO:0006549)
Namespace: biological_process
Definition: The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
Synonyms: isoleucine metabolism
L-isoleucine catabolic process (GO:0006550)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-isoleucine.
Synonyms: isoleucine breakdown; isoleucine catabolism; isoleucine degradation
L-leucine metabolic process (GO:0006551)
Namespace: biological_process
Definition: The chemical reactions and pathways involving L-leucine, 2-amino-4-methylpentanoic acid.
Synonyms: L-leucine metabolism; leucine metabolic process
L-leucine catabolic process (GO:0006552)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-leucine.
Synonyms: L-leucine breakdown; L-leucine catabolism; L-leucine degradation; leucine catabolic process
obsolete lysine metabolic process (GO:0006553)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid.
Synonyms: lysine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
obsolete lysine catabolic process (GO:0006554)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid.
Synonyms: lysine breakdown; lysine catabolism; lysine degradation
Comment: The reason for obsoletion is that more specific terms were created.
L-methionine metabolic process (GO:0006555)
Namespace: biological_process
Definition: The chemical reactions and pathways involving L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
Synonyms: methionine and threonine metabolic process; methionine and threonine metabolism; methionine metabolism
S-adenosylmethionine biosynthetic process (GO:0006556)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
Synonyms: S-adenosyl methionine biosynthesis; S-adenosyl methionine biosynthetic process; S-adenosylmethionine anabolism; S-adenosylmethionine biosynthesis; S-adenosylmethionine formation; S-adenosylmethionine synthesis; SAM biosynthetic process
obsolete S-adenosylmethioninamine biosynthetic process (GO:0006557)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of S-adenosylmethioninamine, (5-deoxy-5-adenosyl)(3-aminopropyl) methylsulfonium salt.
Synonyms: S-adenosylmethioninamine anabolism; S-adenosylmethioninamine biosynthesis; S-adenosylmethioninamine formation; S-adenosylmethioninamine synthesis
Comment: This term was obsoleted because it represents a molecular function.
L-phenylalanine metabolic process (GO:0006558)
Namespace: biological_process
Definition: The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
Synonyms: L-phenylalanine metabolism; phenylalanine metabolic process; phenylalanine metabolism
L-phenylalanine catabolic process (GO:0006559)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-phenylalanine.
Synonyms: L-phenylalanine breakdown; L-phenylalanine catabolism; L-phenylalanine degradation; phenylalanine catabolic process; phenylalanine catabolism
L-proline metabolic process (GO:0006560)
Namespace: biological_process
Definition: The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
Synonyms: proline metabolism
L-proline catabolic process (GO:0006562)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-proline.
Synonyms: proline breakdown; proline catabolism; proline degradation
L-serine metabolic process (GO:0006563)
Namespace: biological_process
Definition: The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
Synonyms: L-serine metabolism
L-serine catabolic process (GO:0006565)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-serine.
Synonyms: L-serine breakdown; L-serine catabolism; L-serine degradation
L-threonine metabolic process (GO:0006566)
Namespace: biological_process
Definition: The chemical reactions and pathways involving threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
Synonyms: methionine and threonine metabolic process; methionine and threonine metabolism; threonine metabolism
L-threonine catabolic process (GO:0006567)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-threonine.
Synonyms: threonine breakdown; threonine catabolism; threonine degradation
L-tryptophan metabolic process (GO:0006568)
Namespace: biological_process
Definition: The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
Synonyms: tryptophan metabolic process; tryptophan metabolism
L-tryptophan catabolic process (GO:0006569)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-tryptophan.
Synonyms: tryptophan breakdown; tryptophan catabolic process; tryptophan catabolic process, using tryptophanase; tryptophan catabolism; tryptophan catabolism, using tryptophanase; tryptophan degradation
tyrosine metabolic process (GO:0006570)
Namespace: biological_process
Definition: The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
Synonyms: tyrosine metabolism
L-tyrosine biosynthetic process (GO:0006571)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
Synonyms: tyrosine anabolism; tyrosine biosynthesis; tyrosine formation; tyrosine synthesis
L-tyrosine catabolic process (GO:0006572)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-tyrosine.
Synonyms: tyrosine breakdown; tyrosine catabolism; tyrosine degradation
valine metabolic process (GO:0006573)
Namespace: biological_process
Definition: The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid.
Synonyms: valine metabolism
L-valine catabolic process (GO:0006574)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-valine.
Synonyms: valine breakdown; valine catabolism; valine degradation
modified amino acid metabolic process (GO:0006575)
Namespace: biological_process
Definition: The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents.
Synonyms: amino acid derivative metabolic process; cellular amino acid derivative metabolic process; cellular amino acid derivative metabolism; cellular modified amino acid metabolic process; cellular modified amino acid metabolism; modified amino acid metabolism
biogenic amine metabolic process (GO:0006576)
Namespace: biological_process
Definition: The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters.
Synonyms: biogenic amine metabolism; cellular biogenic amine metabolic process
amino-acid betaine metabolic process (GO:0006577)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid.
Synonyms: betaine metabolic process; betaine metabolism
amino-acid betaine catabolic process (GO:0006579)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of any betaine, the N-trimethyl derivative of an amino acid.
Synonyms: betaine breakdown; betaine catabolic process; betaine catabolism; betaine degradation
ethanolamine metabolic process (GO:0006580)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ethanolamine (2-aminoethanol), an important water-soluble base of phospholipid (phosphatidylethanolamine).
Synonyms: ethanolamine metabolism
acetylcholine catabolic process (GO:0006581)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of acetylcholine, the acetic acid ester of the organic base choline.
Synonyms: acetylcholine breakdown; acetylcholine catabolism; acetylcholine degradation
melanin metabolic process (GO:0006582)
Namespace: biological_process
Definition: The chemical reactions and pathways involving melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.
Synonyms: melanin metabolism
melanin biosynthetic process from tyrosine (GO:0006583)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of melanin from other compounds, including tyrosine.
Synonyms: melanin anabolism from tyrosine; melanin formation from tyrosine; melanin synthesis from tyrosine
catecholamine metabolic process (GO:0006584)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
Synonyms: catecholamine metabolism
dopamine biosynthetic process from tyrosine (GO:0006585)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dopamine (3,4-dihydroxyphenylethylamine) from L-tyrosine, via the metabolic precursor 3,4-dihydroxy-L-phenylalanine (L-dopa). Dopamine is a catecholamine neurotransmitter and a metabolic precursor of norepinephrine and epinephrine.
Synonyms: dopamine anabolism from tyrosine; dopamine formation from tyrosine; dopamine synthesis from tyrosine
obsolete indolalkylamine metabolic process (GO:0006586)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving indolalkylamines, indole or indole derivatives containing a primary, secondary, or tertiary amine group.
Synonyms: indolalkylamine metabolism; indolamine metabolic process; indolamine metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
serotonin biosynthetic process from L-tryptophan (GO:0006587)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation from L-tryptophan of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
Synonyms: serotonin anabolism from tryptophan; serotonin formation from tryptophan; serotonin synthesis from tryptophan
obsolete activation of tryptophan 5-monooxygenase activity (GO:0006588)
Namespace: biological_process
Definition: OBSOLETE. The process in which the tryptophan 5-monooxygenase enzyme is changed so that it can carry out its enzymatic activity.
Synonyms: tryptophan hydroxylase activation
Comment: This term was obsoleted because it represents a molecular function.
octopamine biosynthetic process (GO:0006589)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of octopamine, 1-(p-hydroxyphenyl)-2-aminoethanol. The D enantiomer is about one-tenth as active as norepinephrine and is found in the salivary glands of Octopus and Eledone species.
Synonyms: octopamine anabolism; octopamine biosynthesis; octopamine formation; octopamine synthesis
thyroid hormone generation (GO:0006590)
Namespace: biological_process
Definition: The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones.
Comment: Note that this term does not fall under the general GO definition for biosynthetic processes, which is 'The chemical reactions and pathways resulting in the formation of... ', because thyroid hormones can only be formed by the proteolysis of a larger molecule (see term definition). The word 'generation' is therefore used in place of biosynthesis.
ornithine metabolic process (GO:0006591)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
Synonyms: ornithine metabolism
ornithine biosynthetic process (GO:0006592)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
Synonyms: ornithine anabolism; ornithine biosynthesis; ornithine formation; ornithine synthesis
L-ornithine catabolic process (GO:0006593)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-ornithine.
Synonyms: ornithine breakdown; ornithine catabolism; ornithine degradation
polyamine metabolic process (GO:0006595)
Namespace: biological_process
Definition: The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.
Synonyms: polyamine metabolism
polyamine biosynthetic process (GO:0006596)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
Synonyms: polyamine anabolism; polyamine biosynthesis; polyamine formation; polyamine synthesis
spermine biosynthetic process (GO:0006597)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses and involved in nucleic acid packaging.
Synonyms: spermine anabolism; spermine biosynthesis; spermine formation; spermine synthesis
obsolete phosphagen metabolic process (GO:0006599)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving phosphagen, any of a group of guanidine phosphates that occur in muscle and can be used to regenerate ATP from ADP during muscular contraction.
Synonyms: phosphagen metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
creatine metabolic process (GO:0006600)
Namespace: biological_process
Definition: The chemical reactions and pathways involving creatine (N-(aminoiminomethyl)-N-methylglycine), a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle.
Synonyms: creatine metabolism
creatine biosynthetic process (GO:0006601)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle.
Synonyms: creatine anabolism; creatine biosynthesis; creatine formation; creatine synthesis