LiteFold/GO huggingface dataset:
obsolete anaerobic L-glutamate catabolic process (GO:0019670)
Namespace: biological_process
Definition: OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of L-glutamate, yielding energy in the form of ATP.
Synonyms: glutamate fermentation
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
obsolete glutamate catabolic process via mesaconate and citramalate (GO:0019671)
Namespace: biological_process
Definition: OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of glutamate via the intermediates mesaconate and S-citramalate, yielding energy in the form of ATP.
Synonyms: glutamate fermentation via mesaconate and citramalate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
acetyl-CoA fermentation to butyrate (GO:0019672)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of acetyl-CoA to butyrate, yielding energy in the form of ATP. Butanoate is secreted by the cell.
NAD+ metabolic process (GO:0019674)
Namespace: biological_process
Definition: The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.
Synonyms: NAD (oxidized) metabolic process; NAD (oxidized) metabolism; NAD metabolic process; NAD metabolism; NAD phosphorylation and dephosphorylation; nicotinamide adenine dinucleotide metabolic process; nicotinamide adenine dinucleotide metabolism; oxidized NAD metabolic process; oxidized NAD metabolism; oxidized nicotinamide adenine dinucleotide metabolic process; oxidized nicotinamide adenine dinucleotide metabolism
obsolete NAD phosphorylation and dephosphorylation (GO:0019675)
Namespace: biological_process
Definition: OBSOLETE. The addition or removal of a phosphate group from nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
Synonyms: NAD phosphorylation and dephosphorylation; nicotinamide adenine dinucleotide phosphorylation and dephosphorylation
Comment: This term was made obsolete because it represents a process, NAD dephosphorylation, that does not exist.
ammonia assimilation cycle (GO:0019676)
Namespace: biological_process
Definition: The pathway by which ammonia is processed and incorporated into a cell. In an energy-rich (glucose-containing), nitrogen-poor environment, glutamine synthetase and glutamate synthase form an ammonia assimilatory cycle, in which ammonia is incorporated into L-glutamate to form L-glutamine, which then combines with alpha-ketoglutarate to regenerate L-glutamate. This ATP-dependent cycle is essential for nitrogen-limited growth and for steady-state growth with some sources of nitrogen.
Synonyms: glutamate metabolic process via glutamine and ammonia; glutamate metabolism via glutamine and ammonia
NAD+ catabolic process (GO:0019677)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions.
Synonyms: NAD (oxidized) catabolic process; NAD (oxidized) catabolism; NAD (reduced) catabolic process; NAD (reduced) catabolism; NAD breakdown; NAD catabolic process; NAD catabolism; NAD degradation; NADH catabolic process; NADH catabolism; nicotinamide adenine dinucleotide catabolic process; nicotinamide adenine dinucleotide catabolism; oxidized NAD catabolic process; oxidized NAD catabolism; oxidized nicotinamide adenine dinucleotide catabolic process; oxidized nicotinamide adenine dinucleotide catabolism; reduced NAD catabolic process; reduced NAD catabolism; reduced nicotinamide adenine dinucleotide catabolic process; reduced nicotinamide adenine dinucleotide catabolism
obsolete propionate metabolic process, methylmalonyl pathway (GO:0019678)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving propionate that occur in the methylmalonyl pathway.
Synonyms: methylmalonyl pathway; propanoyl CoA degradation; propionate metabolism, methylmalonyl pathway
Comment: The reason for obsoletion is that the meaning of the term is too narrow.
obsolete propionate metabolic process, methylcitrate cycle (GO:0019679)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving propionate that occur in the methylcitrate cycle.
Synonyms: propionate metabolism, methylcitrate cycle
Comment: The reason for obsoletion is that the meaning of the term is too narrow.
L-methylmalonyl-CoA biosynthetic process (GO:0019680)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-methylmalonyl-CoA, the L-enantiomer of 2-carboxypropanoyl-CoA.
Synonyms: L-methylmalonyl-CoA anabolism; L-methylmalonyl-CoA biosynthesis; L-methylmalonyl-CoA formation; L-methylmalonyl-CoA synthesis
acetyl-CoA assimilation pathway (GO:0019681)
Namespace: biological_process
Definition: The pathways by which acetyl-CoA is processed and converted into alpha-ketoglutarate (2-oxoglutarate); methanogenic archaea use these pathways to assimilate acetyl-CoA into the cell.
Synonyms: acetyl-CoA catabolic process to 2-ketoglutarate; acetyl-CoA catabolic process to 2-oxoglutarate; acetyl-CoA catabolic process to alpha-ketoglutarate; acetyl-CoA catabolic process to alpha-oxoglutarate; acetyl-CoA catabolism to 2-ketoglutarate; acetyl-CoA catabolism to 2-oxoglutarate; acetyl-CoA catabolism to alpha-ketoglutarate; acetyl-CoA catabolism to alpha-oxoglutarate
glyceraldehyde-3-phosphate metabolic process (GO:0019682)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
Synonyms: glyceraldehyde 3-phosphate metabolic process; glyceraldehyde 3-phosphate metabolism; glyceraldehyde-3-phosphate metabolism
glyceraldehyde-3-phosphate catabolic process (GO:0019683)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
Synonyms: glyceraldehyde 3-phosphate catabolic process; glyceraldehyde 3-phosphate catabolism; glyceraldehyde-3-phosphate breakdown; glyceraldehyde-3-phosphate catabolism; glyceraldehyde-3-phosphate degradation
photosynthesis, dark reaction (GO:0019685)
Namespace: biological_process
Definition: A complex cycle of enzyme-mediated reactions which catalyzes the reduction of carbon dioxide to sugar. As well as carbon dioxide the cycle requires reducing power in the form of reduced nicotinamide adenine dinucleotide phosphate (NADP) and chemical energy in the form of adenosine triphosphate (ATP). The reduced NADP (NADPH) and ATP are produced by the 'light' reactions.
purine nucleoside interconversion (GO:0019686)
Namespace: biological_process
Definition: The chemical reactions and pathways by which a purine nucleoside is synthesized from another purine nucleoside.
pyruvate biosynthetic process from acetate (GO:0019687)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of pyruvate from other compounds, including acetate.
Synonyms: pyruvate anabolism from acetate; pyruvate formation from acetate; pyruvate synthesis from acetate
purine deoxyribonucleoside interconversion (GO:0019688)
Namespace: biological_process
Definition: The chemical reactions and pathways by which a purine deoxyribonucleoside is synthesized from another purine deoxyribonucleoside.
pyrimidine nucleoside interconversion (GO:0019689)
Namespace: biological_process
Definition: The chemical reactions and pathways by which a pyrimidine nucleoside is synthesized from another pyrimidine nucleoside.
pyrimidine deoxyribonucleoside interconversion (GO:0019690)
Namespace: biological_process
Definition: The chemical reactions and pathways by which a pyrimidine deoxyribonucleoside is synthesized from another deoxyribopyrimidine nucleoside.
obsolete deoxyribose phosphate metabolic process (GO:0019692)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose.
Synonyms: deoxyribose phosphate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
ribose phosphate metabolic process (GO:0019693)
Namespace: biological_process
Definition: The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.
Synonyms: ribose phosphate metabolism
alkanesulfonate metabolic process (GO:0019694)
Namespace: biological_process
Definition: The chemical reactions and pathways involving alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group.
Synonyms: alkanesulfonate metabolism; alkanesulphonate metabolic process; alkanesulphonate metabolism
choline metabolic process (GO:0019695)
Namespace: biological_process
Definition: The chemical reactions and pathways involving choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
Synonyms: choline metabolism
xylitol catabolic process to D-xylulose 5-phosphate (GO:0019697)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of xylitol to form xylulose 5-phosphate.
Synonyms: L-arabitol and xylitol degradation; xylitol breakdown to xylulose 5-phosphate; xylitol degradation to xylulose 5-phosphate; xylitol utilization
Comment: Note that xylitol is a meso compound, thus there are no L or D-versions.
D-galacturonate catabolic process (GO:0019698)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of D-galacturonate, the D-enantiomer of galacturonate, the anion of galacturonic acid.
Synonyms: D-galacturonate breakdown; D-galacturonate catabolism; D-galacturonate degradation
organic phosphonate catabolic process (GO:0019700)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Catabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.
Synonyms: organophosphonate catabolic process; phosphonate breakdown; phosphonate catabolism; phosphonate degradation
obsolete peptidyl-arginine N5-methylation (GO:0019701)
Namespace: biological_process
Definition: OBSOLETE. The methylation of peptidyl-arginine on the internal nitrogen-5 (N5) atom (also called delta-nitrogen) to form peptidyl-N5-methyl-L-arginine.
Synonyms: peptidyl-arginine delta-N-methylation
Comment: This term was obsoleted because it represents a molecular function.
protein arginine N5-methyltransferase activity (GO:0019702)
Namespace: molecular_function
Definition: Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the delta-nitrogen atom of peptidyl-arginine residues. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N5-methyl-L-arginine.
Synonyms: protein arginine N5-methylase activity; protein-arginine delta-N-methyltransferase activity; protein-arginine N5-methyltransferase activity; S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-N5-methyl-L-arginine-forming); type IV PRMT activity; type IV protein arginine methyltransferase activity
Comment: This enzyme, characterized from the yeast Saccharomyces cerevisiae, methylates the delta-nitrogen atom of arginine residues within proteins. Among its substrates are R67 of the ribosomal protein L12.
obsolete coenzyme A-peptidyl-cysteine covalent linking (GO:0019703)
Namespace: biological_process
Definition: OBSOLETE. The covalent linkage of coenzyme A and peptidyl-cysteine to form L-cysteine coenzyme A disulfide.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-L-cysteine S-myristoylation (GO:0019704)
Namespace: biological_process
Definition: OBSOLETE. The modification of peptidyl-cysteine to form peptidyl-S-myristoyl-L-cysteine.
Synonyms: peptidyl-S-myristoyl-L-cysteine anabolism from peptidyl-cysteine; peptidyl-S-myristoyl-L-cysteine biosynthetic process from peptidyl-cysteine; peptidyl-S-myristoyl-L-cysteine formation from peptidyl-cysteine; peptidyl-S-myristoyl-L-cysteine synthesis from peptidyl-cysteine
Comment: This term was obsoleted because it represents a molecular function.
protein-cysteine S-palmitoyltransferase activity (GO:0019706)
Namespace: molecular_function
Definition: Catalysis of the transfer of a palmitoyl (systematic name, hexadecanoyl) group to a sulfur atom on the cysteine of a protein molecule, in the reaction hexadecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-hexadecanoyl-L-cysteinyl-[protein].
Synonyms: protein-cysteine S-palmitoleyltransferase activity
protein-cysteine S-acyltransferase activity (GO:0019707)
Namespace: molecular_function
Definition: Catalysis of the transfer of an acyl group to a sulfur atom on the cysteine of a protein molecule.
obsolete peptidyl-glycine cholesteryl ester biosynthesis from peptidyl-glycine (GO:0019708)
Namespace: biological_process
Definition: OBSOLETE. The synthesis of peptidyl-glycine cholest-5-en-3-beta-ol ester at the carboxy-terminus of autolytically cleaved proteins.
Synonyms: peptidyl-glycine cholesteryl ester anabolism from peptidyl-glycine; peptidyl-glycine cholesteryl ester formation from peptidyl-glycine; peptidyl-glycine cholesteryl ester synthesis from peptidyl-glycine
Comment: This term was obsoleted because it represents a molecular function.
obsolete iron incorporation into iron-sulfur cluster via pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide (GO:0019709)
Namespace: biological_process
Definition: OBSOLETE. The incorporation of iron into a nickel-iron-sulfur cluster via pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide, found in carbon monoxide dehydrogenase.
Synonyms: iron incorporation into iron-sulphur cluster via pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulphide
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-asparagine methylation (GO:0019710)
Namespace: biological_process
Definition: OBSOLETE. The methylation of peptidyl-asparagine to form peptidyl-N4-methyl-L-asparagine or peptidyl-N4,N4-dimethyl-L-asparagine.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-beta-carboxyaspartic acid biosynthetic process from peptidyl-aspartic acid (GO:0019711)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of peptidyl-beta-carboxyaspartic acid from other compounds, including peptidyl-aspartic acid.
Synonyms: peptidyl-beta-carboxyaspartic acid anabolism from peptidyl-aspartic acid; peptidyl-beta-carboxyaspartic acid formation from peptidyl-aspartic acid; peptidyl-beta-carboxyaspartic acid synthesis from peptidyl-aspartic acid
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamic acid (GO:0019712)
Namespace: biological_process
Definition: OBSOLETE. The methyl esterification of peptidyl-glutamic acid.
Synonyms: peptidyl-L-glutamic acid 5-methyl ester anabolism from glutamic acid; peptidyl-L-glutamic acid 5-methyl ester formation from glutamic acid; peptidyl-L-glutamic acid 5-methyl ester synthesis from glutamic acid
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-L-glutamic acid 5-methyl ester biosynthetic process from glutamine (GO:0019713)
Namespace: biological_process
Definition: OBSOLETE. The coupled methyl esterification and deamidation of peptidyl-glutamine.
Synonyms: peptidyl-L-glutamic acid 5-methyl ester anabolism from glutamine; peptidyl-L-glutamic acid 5-methyl ester formation from glutamine; peptidyl-L-glutamic acid 5-methyl ester synthesis from glutamine
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-glutamine esterification (GO:0019714)
Namespace: biological_process
Definition: OBSOLETE. The addition of an ester group to a glutamine residue in a protein.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-aspartic acid hydroxylation to form L-erythro-beta-hydroxyaspartic acid (GO:0019715)
Namespace: biological_process
Definition: OBSOLETE. The hydroxylation of peptidyl-aspartic acid to form peptidyl-L-erythro-beta-hydroxyaspartic acid; catalyzed by peptide-aspartate beta-dioxygenase (EC:1.14.11.16).
Comment: This term was obsoleted because it represents a molecular function.
obsolete N-terminal peptidyl-alanine monomethylation (GO:0019716)
Namespace: biological_process
Definition: OBSOLETE. The monomethylation of the N-terminal alanine of proteins to form the derivative peptidyl-N-methyl-L-alanine.
Comment: This term was obsoleted because it represents a molecular function.
obsolete synaptosome (GO:0019717)
Namespace: cellular_component
Definition: OBSOLETE. Any of the discrete particles (nerve-ending particles) formed from the clublike presynaptic nerve endings that resist disruption and are snapped or torn off their attachments when brain tissue is homogenized in media isosmotic to plasma.
Synonyms: synaptosome
Comment: This term was made obsolete because it refers to a result of cell homogenization and not a bona fide cellular component.
obsolete rough microsome (GO:0019718)
Namespace: cellular_component
Definition: OBSOLETE. Vesicular particles formed from disrupted endoplasmic reticulum membranes and studded with ribosomes on the outside.
Synonyms: rough microsome
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
obsolete smooth microsome (GO:0019719)
Namespace: cellular_component
Definition: OBSOLETE. Vesicular particles formed from disrupted endoplasmic reticulum and plasma membranes without any adhering ribosomes.
Synonyms: smooth microsome
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
Mo-molybdopterin cofactor metabolic process (GO:0019720)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
Synonyms: Mo-molybdopterin cofactor metabolism; Moco metabolic process; Moco metabolism
calcium-mediated signaling (GO:0019722)
Namespace: biological_process
Definition: Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
Synonyms: calcium ion signaling; calcium signaling; calcium signalling; calcium-mediated signalling
B cell mediated immunity (GO:0019724)
Namespace: biological_process
Definition: Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.
Synonyms: B lymphocyte mediated immune effector process; B lymphocyte mediated immunity; B-cell mediated immune effector process; B-cell mediated immunity; B-lymphocyte mediated immune effector process; B-lymphocyte mediated immunity
cellular homeostasis (GO:0019725)
Namespace: biological_process
Definition: Any process involved in the maintenance of an internal steady state at the level of the cell.
obsolete mevaldate reductase (NADPH) activity (GO:0019726)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: (R)-mevalonate + NADP+ = H+ + mevaldate + NADPH.
Synonyms: (R)-mevalonate:NADP+ oxidoreductase; mevaldate (reduced nicotinamide adenine dinucleotide phosphate) reductase
Comment: This term was obsoleted because the associated EC number has been deleted (EC 1.1.1.33), based on PMID:4463942 where the enzyme has been shown to actually belong to EC 1.1.1.2.
obsolete peptidyl-allysine oxidation to 2-aminoadipic acid (GO:0019728)
Namespace: biological_process
Definition: OBSOLETE. The oxidation of allysine to 2-aminoadipic acid.
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptide cross-linking via 2-imino-glutaminyl-5-imidazolinone glycine (GO:0019729)
Namespace: biological_process
Definition: OBSOLETE. The formation of the fluorescent protein FP583 chromophore cross-link from the alpha-carboxyl carbon of residue n, a glutamine, to the alpha-amino nitrogen of residue n+2, a glycine, and a dehydration to form a double bond to the alpha-amino nitrogen of residue n+1. This cross-linking is coupled with a dehydrogenation of residue n+1 to form a double bond between the alpha and beta carbons.
Synonyms: biosynthesis of protein-protein cross-link via 2-imino-glutaminyl-5-imidazolinone glycine; biosynthetic process of protein-protein cross-link via 2-imino-glutaminyl-5-imidazolinone glycine
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined in RESID.
antibacterial humoral response (GO:0019731)
Namespace: biological_process
Definition: An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
antifungal humoral response (GO:0019732)
Namespace: biological_process
Definition: An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
obsolete peptidyl-sarcosine incorporation (GO:0019736)
Namespace: biological_process
Definition: OBSOLETE. The incorporation of sarcosine (N-methylglycine) into non-coded peptides.
Comment: This term was obsoleted because it represents a molecular function.
nitrogen utilization (GO:0019740)
Namespace: biological_process
Definition: A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.
pentacyclic triterpenoid catabolic process (GO:0019741)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings.
Synonyms: pentacyclic triterpenoid breakdown; pentacyclic triterpenoid catabolism; pentacyclic triterpenoid degradation
pentacyclic triterpenoid metabolic process (GO:0019742)
Namespace: biological_process
Definition: The chemical reactions and pathways involving pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings.
Synonyms: pentacyclic triterpenoid metabolism
hopanoid catabolic process (GO:0019743)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of hopanoids, pentacyclic sterol-like compounds based on the hopane nucleus.
Synonyms: hopanoid breakdown; hopanoid catabolism; hopanoid degradation
obsolete hopanoid metabolic process (GO:0019744)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving hopanoids, pentacyclic sterol-like compounds based on the hopane nucleus.
Synonyms: hopanoid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.