LiteFold/GO huggingface dataset:
obsolete sulfide oxidation, using siroheme sulfite reductase (GO:0019424)
Namespace: biological_process
Definition: OBSOLETE. A sulfide oxidation process that proceeds via the reaction catalyzed by siroheme sulfite reductase.
Synonyms: sulfide oxidation, using sirohaem sulfite reductase; sulfur oxidation, using sirohaem sulfite reductase; sulfur oxidation, using siroheme sulfite reductase; sulphide oxidation, using siroheme sulphite reductase; sulphur oxidation, using siroheme sulphite reductase
Comment: This term was obsoleted because the corresponding MetaCyc pathway was deprecated.
obsolete L-methionine catabolic process via 2-oxobutanoate (GO:0019458)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine, via the intermediate 2-oxobutanoate.
Synonyms: methionine breakdown via 2-oxobutanoate; methionine degradation via 2-oxobutanoate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete beta-alanine catabolic process to mevalonate semialdehyde, by transamination (GO:0019486)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including mevalonate semialdehyde, by transamination.
Synonyms: beta-alanine breakdown to mevalonate semialdehyde, by transamination; beta-alanine degradation to mevalonate semialdehyde, by transamination
Comment: This term was obsoleted because it represents a variant pathway of beta-alanine degradation and is out of scope for GO.
obsolete L-proline salvage (GO:0019492)
Namespace: biological_process
Definition: OBSOLETE. Any process which produces L-proline from derivatives of it, without de novo synthesis.
Synonyms: proline cycling
Comment: The reason for obsoletion is that this term represents a GO-CAM model.
pentitol metabolic process (GO:0019519)
Namespace: biological_process
Definition: The chemical reactions and pathways involving pentitols, any alditol with a chain of five carbon atoms in the molecule.
Synonyms: pentitol metabolism
catechol-containing siderophore biosynthetic process (GO:0019540)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a siderophore from other compounds, including catechol. Catechol is one of the three major chemical groups incorporated into siderophore structures with hydroxamate and a-hydroxycarboxylate, each having a high selectivity for iron(3+).
obsolete L-arginine catabolic process to L-glutamate (GO:0019544)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-glutamate.
Synonyms: arginine breakdown to glutamate; arginine degradation to glutamate
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 spermine (GO:0019548)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including spermine.
Synonyms: arginine breakdown to spermine; arginine degradation to spermine
Comment: The reason for obsoletion is that this term was added in error.
obsolete L-glutamate catabolic process to aspartate (GO:0019550)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including aspartate.
Synonyms: glutamate breakdown to aspartate; glutamate degradation to aspartate
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
obsolete glutamate catabolic process to oxaloacetate (GO:0019554)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including oxaloacetate.
Synonyms: glutamate breakdown to oxaloacetate; glutamate degradation to oxaloacetate
Comment: The reason for obsoletion is that there is no evidence that this function/process/component exists.
glycerol catabolic process (GO:0019563)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
Synonyms: glycerol breakdown; glycerol catabolism; glycerol degradation
arabinose biosynthetic process (GO:0019567)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of arabinose, arabino-pentose.
Synonyms: arabinose anabolism; arabinose biosynthesis; arabinose formation; arabinose synthesis
arabinose catabolic process (GO:0019568)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of arabinose, arabino-pentose.
Synonyms: arabinose breakdown; arabinose catabolism; arabinose degradation
D-arabinose catabolic process (GO:0019571)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of D-arabinose, the D-enantiomer of arabino-pentose.
Synonyms: D-arabinose breakdown; D-arabinose catabolism; D-arabinose degradation
L-arabitol catabolic process to D-xylulose 5-phosphate (GO:0019590)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-arabitol to form D-xylulose 5-phosphate. L-arabitol is converted into L-xylulose, which is then phosphorylated to L-xylulose-5-phosphate. This is converted to D-xylulose-5-phosphate via the intermediate L-ribulose-5-phosphate.
Synonyms: L-arabitol and xylitol degradation; L-arabitol breakdown to xylulose 5-phosphate; L-arabitol degradation to xylulose 5-phosphate; L-arabitol utilization
(R)-mandelate catabolic process to benzoate (GO:0019597)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of (R)-mandelate into other compounds, including benzoate.
Synonyms: (R)-mandelate breakdown to benzoate; (R)-mandelate degradation to benzoate
(R)-4-hydroxymandelate catabolic process (GO:0019599)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of (R)-4-hydroxymandelate, the anion of (R)-4-hydroxymandelic acid.
Synonyms: (R)-4-hydroxymandelate breakdown; (R)-4-hydroxymandelate catabolism; (R)-4-hydroxymandelate degradation
toluene oxidation to catechol (GO:0019604)
Namespace: biological_process
Definition: The formation from toluene of catechol, dihydroxybenzene, by successive oxidations followed by loss of carbon dioxide (CO2).
obsolete 4-toluenecarboxylate metabolic process (GO:0019611)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving 4-toluenecarboxylate, 4-methylbenzenecarboxylate, the anion of carboxylic acid attached to a methylbenzene molecule.
Synonyms: 4-toluenecarboxylate metabolism; p-toluate metabolic process; p-toluate metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
organophosphate metabolic process (GO:0019637)
Namespace: biological_process
Definition: The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound.
Synonyms: organophosphate metabolism
pyruvate fermentation to acetate (GO:0019654)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of acetate, yielding energy in the form of ATP.
Synonyms: acetate fermentation
pyruvate fermentation to propionate (GO:0019657)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of pyruvate into to propionate, an alternative to the acrylate pathway to produce propionate.
Synonyms: glycolytic fermentation to propionate; succinate-propionate fermentation
bifid shunt (GO:0019658)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of glucose to lactate and acetate, yielding energy in the form of ATP.
Synonyms: bifidum pathway; glucose catabolic process to lactate and acetate; glucose fermentation to lactate and acetate
amino acid fermentation (GO:0019665)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids to ammonia, CO2, H2, acetate and short chain fatty acids, under anoxic conditions.
Synonyms: anaerobic amino acid catabolic process
anaerobic catabolism of pairs of amino acids (GO:0019668)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids; in these reactions, one amino acid is oxidised (acts as an electron donor) and a different amino acid is reduced (acts as an electron acceptor); oxidation of the electron-donating amino acid yields energy in the form of ATP.
Synonyms: cofermentation of pairs of amino acids; Stickland reaction
GDP-mannose metabolic process (GO:0019673)
Namespace: biological_process
Definition: The chemical reactions and pathways involving GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
Synonyms: GDP-mannose metabolism
photosynthesis, light reaction (GO:0019684)
Namespace: biological_process
Definition: The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I.
Synonyms: photolysis
toluene oxidation via toluene-cis-1,2-dihydrodiol (GO:0019696)
Namespace: biological_process
Definition: The degradation of toluene to form pyruvate and acetaldehyde; the first step in the pathway is the oxidation of toluene to form toluene-cis-1,2-dihydrodiol.
protein-cysteine S-myristoyltransferase activity (GO:0019705)
Namespace: molecular_function
Definition: Catalysis of the transfer of a myristoyl (systematic name, tetradecanoyl) group to a sulfur atom on a cysteine residue of a protein molecule in the reaction: tetradecanoyl-CoA + L-cysteinyl-[protein] = CoA + S-tetradecanoyl-L-cysteinyl-[protein].
obsolete mevaldate reductase (NADH) activity (GO:0019727)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: (R)-mevalonate + NAD+ = H+ + mevaldate + NADH.
Comment: This term was obsoleted because it is believed to be a spontaneous reaction.
antimicrobial humoral response (GO:0019730)
Namespace: biological_process
Definition: An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus.
high-affinity IgE receptor activity (GO:0019768)
Namespace: molecular_function
Definition: Combining with high affinity with an immunoglobulin of the IgE isotype via the Fc region, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
Synonyms: high affinity Fc receptor activity; high affinity IgE receptor activity
Atg12 transferase activity (GO:0019777)
Namespace: molecular_function
Definition: Catalysis of the transfer of ATG12 from one protein to another via the reaction X-ATG12 + Y = Y-ATG12 + X, where both X-ATG12 and Y-ATG12 are covalent linkages.
Synonyms: APG12 conjugating enzyme activity; APG12 ligase activity; Atg12 conjugating enzyme activity; Atg12 ligase activity
NEDD8 activating enzyme activity (GO:0019781)
Namespace: molecular_function
Definition: Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade.
Synonyms: RUB1 activating enzyme activity
SUMO transferase activity (GO:0019789)
Namespace: molecular_function
Definition: Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y = Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
Synonyms: SMT3 conjugating enzyme; SUMO conjugating enzyme activity
obsolete APG12 hydrolase activity (GO:0019792)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: APG12 hydrolase activity
Comment: This term was made obsolete because it cannot be determined what its intended meaning was, because the term name is not found in the literature.
obsolete nonprotein amino acid metabolic process (GO:0019794)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving any amino acid not found, or rarely found, in peptide linkage in proteins.
Synonyms: nonprotein amino acid metabolic process; nonprotein amino acid metabolism
Comment: This term was made obsolete because it was a grouping term that was poorly defined and did not provide a particularly meaningful grouping, since even for those amino acids commonly found in proteins, not all molecules necessarily end up incorporated into proteins. The term also violated the principle of positivity.
polyamine binding (GO:0019808)
Namespace: molecular_function
Definition: Binding to a polyamine, an organic compound containing two or more amino groups.
P3 peroxisome (GO:0019821)
Namespace: cellular_component
Definition: A subform of peroxisome that corresponds to an intermediate in a peroxisome assembly pathway, which operates by conversion of peroxisomal subforms in the direction P1, P2 -> P3 -> P4 -> P5 -> P6. P3 peroxisomes are formed by fusion of P1 and P2 peroxisomes, and are distinguished from the other subforms on the bases of buoyant density and protein content.
Synonyms: peroxisome vesicle
Comment: Note that this peroxisome assembly pathway is described in the yeast Yarrowia lipolytica. See also the cellular component terms 'P1 peroxisome ; GO:0019819', 'P2 peroxisome ; GO:0019820', 'P4 peroxisome ; GO:0019822', 'P5 peroxisome ; GO:0019823', and 'P6 peroxisome ; GO:0019824'.
obsolete chromate sensitivity/resistance (GO:0019831)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: chromate sensitivity/resistance
Comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
ice nucleation activity (GO:0019833)
Namespace: molecular_function
Definition: Catalysis of the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation. This process is commonly found in certain bacteria, such as Pseudomonas syringae, and plays roles in environmental adaptation and plant pathogenesis.
Comment: Note that this term was reinstated from obsolete.
symbiont-mediated hemolysis of host erythrocyte (GO:0019836)
Namespace: biological_process
Definition: The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: haemolysis in host; hemolysin activity; hemolysis by symbiont of host erythrocytes; hemolysis by symbiont of host RBCs; hemolysis by symbiont of host red blood cells; pathogenesis; regulation of cytolysis of host cells by symbiont
obsolete conotoxin activity (GO:0019848)
Namespace: molecular_function
Definition: OBSOLETE. Acts to inhibit neural function in another organism by inhibiting voltage-gated calcium ion channels and neurotransmitter release. This function is thought to be specific to the venom of two marine snail species.
Synonyms: conotoxin activity
Comment: This term was made obsolete because it represents a gene product.
obsolete cytotoxin activity (GO:0019849)
Namespace: molecular_function
Definition: OBSOLETE. Acts as to cause injury to other living cells.
Synonyms: cytotoxin activity
Comment: This term was made obsolete because it represents a class of gene products.
L-ascorbic acid biosynthetic process (GO:0019853)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions.
Synonyms: ascorbate biosynthesis; ascorbate biosynthetic process; L-ascorbic acid anabolism; L-ascorbic acid biosynthesis; L-ascorbic acid formation; L-ascorbic acid synthesis; vitamin C biosynthesis; vitamin C biosynthetic process
obsolete flagellum (GO:0019861)
Namespace: cellular_component
Definition: OBSOLETE. Long whiplike or feathery structures borne either singly or in groups by the motile cells of many bacteria and unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms, which propel the cell through a liquid medium.
Synonyms: flagellum
Comment: This term was made obsolete because it was an unnecessary grouping term. Eukaryotic flagella were deemed to be equivalent to cilia and merged, so the only remaining child to this term was 'bacterial-type flagellum ; GO:0009288'.
chloride channel inhibitor activity (GO:0019869)
Namespace: molecular_function
Definition: Binds to and stops, prevents, or reduces the activity of a chloride channel.
potassium channel inhibitor activity (GO:0019870)
Namespace: molecular_function
Definition: Binds to and stops, prevents, or reduces the activity of a potassium channel.
6-aminohexanoate-cyclic-dimer hydrolase activity (GO:0019874)
Namespace: molecular_function
Definition: Catalysis of the reaction: 1,8-diazacyclotetradecane-2,9-dione + H2O = N-(6-aminohexanoyl)-6-aminohexanoate.
Synonyms: 1,8-diazacyclotetradecane-2,9-dione lactamhydrolase activity
obsolete diaminopimelate biosynthetic process (GO:0019877)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
Synonyms: diaminopimelate anabolism; diaminopimelate biosynthesis; diaminopimelate formation; diaminopimelate synthesis
Comment: This term was obsoleted because it represents an intermediate in L-leucine biosynthesis.
obsolete bacteriocin susceptibility/resistance (GO:0019880)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: bacteriocin susceptibility/resistance
Comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
protein kinase binding (GO:0019901)
Namespace: molecular_function
Definition: Binding to a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
protein phosphatase binding (GO:0019903)
Namespace: molecular_function
Definition: Binding to a protein phosphatase.
obsolete peptidyl-D-alanine racemization via peptidyl-L-serine (GO:0019917)
Namespace: biological_process
Definition: OBSOLETE. The dehydration of peptidyl-serine, followed by hydrogenation to produce peptidyl-D-alanine.
Comment: This term was obsoleted because it represents a molecular function.
peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)
Namespace: biological_process
Definition: The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N'(omega)-dimethyl-L-arginine.
obsolete peptidyl-1-thioglycine biosynthetic process, internal (GO:0019920)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of internal peptidyl-1-thioglycine, which has an internal C=S bond, instead of an internal C=O bond, in the peptide.
Synonyms: peptidyl-1-thioglycine anabolism, internal; peptidyl-1-thioglycine formation, internal; peptidyl-1-thioglycine synthesis, internal
Comment: This term was obsoleted because it represents a molecular function.
obsolete peptidyl-tryptophan oxidation to tryptophyl quinone (GO:0019926)
Namespace: biological_process
Definition: OBSOLETE. The oxidation of peptidyl-tryptophan to form tryptophan-6,7-dione, otherwise known as tryptophyl quinone, which is further modified by cross-linking to either tryptophan or cysteine.
Comment: This term was obsoleted because it represents a cofactor, see PMID:2028257.
obsolete peptide cross-linking via 4'-(S-L-cysteinyl)-L-tryptophyl quinone (GO:0019927)
Namespace: biological_process
Definition: OBSOLETE. The cross-linking of a cysteine residue to tryptophyl quinone to form 4'-(S-L-cysteinyl)-L-tryptophyl quinone, a cofactor found at the active site of amine dehydrogenase.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete peptide cross-linking via 3-(S-L-cysteinyl)-L-aspartic acid (GO:0019928)
Namespace: biological_process
Definition: OBSOLETE. The cross-linking of a cysteine residue to an aspartic acid residue to form 3-(S-L-cysteinyl)-L-aspartic acid.
Comment: This term was obsoleted because it represents a molecular function; however the enzyme responsible for this reaction has not been defined.
obsolete cyclic-nucleotide-mediated signaling (GO:0019935)
Namespace: biological_process
Definition: OBSOLETE. An intracellular signaling cassette that starts with production or release of the cyclic nucleotide, and ends with the activation of downstream effectors that further transmit the signal within the cell.
Synonyms: cyclic-nucleotide-mediated signalling
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete SUMO-dependent protein catabolic process (GO:0019940)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: SUMO-dependent protein breakdown; SUMO-dependent protein catabolic process; SUMO-dependent protein catabolism; SUMO-dependent protein degradation
Comment: This term was made obsolete because it does not reflect an accurate biological process, as sumoylation of a protein does not lead to catabolism of that protein.
obsolete NEDD8 class-dependent protein catabolic process (GO:0019942)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to the target protein.
Synonyms: NEDD8 class-dependent protein breakdown; NEDD8 class-dependent protein catabolic process; NEDD8 class-dependent protein catabolism; NEDD8 class-dependent protein degradation; RUB1-dependent protein catabolic process; RUB1-dependent protein catabolism; RUB1-dependent protein degradation
Comment: This term was made obsolete because NEDD8-class tags do not target proteins for proteolytic destruction.
C-X-C chemokine binding (GO:0019958)
Namespace: molecular_function
Definition: Binding to a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif.
interleukin-4 binding (GO:0019979)
Namespace: molecular_function
Definition: Binding to interleukin-4.
Synonyms: IL-4 binding
diacylglycerol binding (GO:0019992)
Namespace: molecular_function
Definition: Binding to a diacylglycerol, a diester of glycerol and two fatty acids.
conoid (GO:0020010)
Namespace: cellular_component
Definition: A spiral cytoskeletal structure located at the apical end of the apical complex in some apicomplexan parasites. Fibers form a left-handed spiral, and are comprised of tubulin protofilaments organized in a ribbon-like structure that differs from the conventional tubular structure characteristic of microtubules.