LiteFold/GO huggingface dataset:
obsolete reduced coenzyme F420:NADP+ oxidoreductase activity (GO:0052808)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: NADP+ + 1,5-dihydrocoenzyme F420 = NADPH + H+ + coenzyme F420. 1,5-dihydrocoenzyme F420 is also known as reduced coenzyme F420.
Synonyms: coenzyme F420-dependent NADP oxidoreductase activity; coenzyme F420-dependent NADP reductase activity; F420H2:NADP oxidoreductase activity; F420H2:NADP+ oxidoreductase activity; NADP+:F420 oxidoreductase activity
Comment: This term was obsoleted because it represents the same activity as 8-hydroxy-5-deazaflavin:NADPH oxidoreductase activity ; GO:0102261.
1-phosphatidylinositol-5-kinase activity (GO:0052810)
Namespace: molecular_function
Definition: Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + ADP + H+.
Synonyms: 1-phosphatidylinositol 5-kinase activity
very long-chain fatty acyl-CoA hydrolase activity (GO:0052817)
Namespace: molecular_function
Definition: Catalysis of the reaction: a very long-chain fatty acyl-CoA + H2O = a very long-chain fatty acid + CoA + H+. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons.
Synonyms: very long-chain acyl coenzyme A hydrolase activity; very long-chain acyl-thioester hydrolase activity; very long-chain hydrolase activity; very long-chain-acyl-CoA hydrolase activity
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
2-hydroxy-6-oxonona-2,4,7-trienedioate hydrolase activity (GO:0052823)
Namespace: molecular_function
Definition: Catalysis of the reaction: (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate + H+.
Synonyms: (2E,4Z,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate fumarylhydrolase activity; 2-hydroxy-6-ketonona-2,4,7-trienedoic acid hydrolase activity
thiazole metabolic process (GO:0052838)
Namespace: biological_process
Definition: The chemical reactions and pathways involving thiazole, a five-membered heterocyclic ring structure containing a sulfur in the 1-position and a nitrogen in the 3-position.
Synonyms: thiazole metabolism
inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)
Namespace: molecular_function
Definition: Catalysis of the reaction: 1,5-bisdiphospho-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + phosphate + H+.
endo-1,3(4)-beta-glucanase activity (GO:0052861)
Namespace: molecular_function
Definition: Catalysis of the endohydrolysis of (1->3)- or (1->4)-linkages in beta-D-glucans when the glucose residue whose reducing group is involved in the linkage to be hydrolyzed is itself substituted at C-3. Substrates include laminarin, lichenin and cereal D-glucans.
Synonyms: 1,3-(1,3)-beta-D-glucan 3-glucanohydrolase activity; glucan endo-1,3-beta-glucanase activity, C-3 substituted reducing group; glucan endo-1,4-beta-glucanase activity, C-3 substituted reducing group; laminaranase activity; laminarinase activity
obsolete 1-deoxy-D-xylulose 5-phosphate catabolic process (GO:0052864)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 1-deoxy-D-xylulose 5-phosphate, the 5-phospho derivative of 1-deoxy-D-xylulose. 1-deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway and a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis.
Synonyms: (2R,3S)-2,3-dihydroxy-4-oxopentyl dihydrogen phosphate breakdown; (2R,3S)-2,3-dihydroxy-4-oxopentyl dihydrogen phosphate catabolic process; (2R,3S)-2,3-dihydroxy-4-oxopentyl dihydrogen phosphate catabolism; (2R,3S)-2,3-dihydroxy-4-oxopentyl dihydrogen phosphate degradation; 1-deoxy-D-xylulose 5-phosphate breakdown; 1-deoxy-D-xylulose 5-phosphate catabolism; 1-deoxy-D-xylulose 5-phosphate degradation
Comment: This term was obsoleted because it is an unnecessary grouping class.
aliphatic (S)-hydroxynitrile lyase activity (GO:0052891)
Namespace: molecular_function
Definition: Catalysis of the reaction: an aliphatic (S)-hydroxynitrile = an aliphatic aldehyde or ketone + cyanide.
Synonyms: (S)-cyanohydrin carbonyl-lyase (cyanide forming) activity; (S)-cyanohydrin producing hydroxynitrile lyase activity; (S)-hydroxynitrile lyase activity; (S)-oxynitrilase activity; (S)-selective hydroxynitrile lyase activity
obsolete N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: H2O + N(1),N(12)-diacetylspermine + O2 = 3-acetamidopropanal + H2O2 + N(1)-acetylspermidine.
Comment: This term was obsoleted because it represents a specific substrate of N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity ; GO:0052903.
obsolete spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: H2O + O2 + spermidine = 3-aminopropanal + H2O2 + putrescine.
Comment: This term was obsoleted because it represents a specific activity of spermine oxidase activity ; GO:0052901.
dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)
Namespace: molecular_function
Definition: Catalysis of the reaction: an alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphospho-di-trans,poly-cis-dolichol + a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate = an alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphospho-di-trans,poly-cis-dolichol + a di-trans,poly-cis-dolichyl phosphate + H+.
dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)
Namespace: molecular_function
Definition: Catalysis of the reaction: an alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphospho-di-trans,poly-cis-dolichol + a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate = an alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc-diphospho-di-trans,poly-cis-dolichol + a di-trans,poly-cis-dolichyl phosphate + H+.
Synonyms: dolichylphosphomannose-dependent ALG9 mannosyltransferase activity
alcohol dehydrogenase (cytochrome c) activity (GO:0052934)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2 [Fe(III)cytochrome c] + a primary alcohol = 2 [Fe(II)cytochrome c] + an aldehyde + 2 H+.
Synonyms: 2-chloroethanol:cytochrome c oxidoreductase activity; alcohol dehydrogenase (acceptor) activity; alcohol:(acceptor) oxidoreductase activity; alcohol:acceptor oxidoreductase activity; alcohol:cytochrome c oxidoreductase activity; ethanol:cytochrome c oxidoreductase activity; PQQ-dependent alcohol dehydrogenase activity; quinoprotein alcohol dehydrogenase activity
cardiac muscle cell differentiation (GO:0055007)
Namespace: biological_process
Definition: The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
Synonyms: cardiomyocyte differentiation; heart muscle cell differentiation
ventricular cardiac muscle tissue morphogenesis (GO:0055010)
Namespace: biological_process
Definition: The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
Synonyms: cardiac ventricle muscle morphogenesis; ventricular heart muscle morphogenesis
hypochord development (GO:0055016)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the hypochord over time, from its formation to the mature structure. The hypochord is a transient rod-like structure in the embryos of fish, lampreys and amphibians that is located immediately ventral to the notochord. The hypochord may play a role in positioning the dorsal aorta.
Synonyms: subnotochordal rod development
positive regulation of cardiac muscle fiber development (GO:0055020)
Namespace: biological_process
Definition: Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development.
Synonyms: activation of cardiac muscle fiber development; positive regulation of cardiac muscle fibre development; positive regulation of heart muscle fiber development; stimulation of cardiac muscle fiber development; up regulation of cardiac muscle fiber development; up-regulation of cardiac muscle fiber development; upregulation of cardiac muscle fiber development
regulation of cardiac muscle tissue growth (GO:0055021)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of cardiac muscle growth.
generative cell mitosis (GO:0055047)
Namespace: biological_process
Definition: The process in which the generative cell divides by mitosis to form two haploid cells. These will subsequently differentiate into sperm cells.
ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing (GO:0055052)
Namespace: cellular_component
Definition: A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP.
mannose:proton symporter activity (GO:0055053)
Namespace: molecular_function
Definition: Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: mannose + H+ = mannose + H+.
Synonyms: mannose:hydrogen symporter activity
sulfate ion homeostasis (GO:0055063)
Namespace: biological_process
Definition: Any process involved in the maintenance of an internal steady state of sulfate ions within an organism or cell.
Synonyms: sulfate homeostasis; sulphate ion homeostasis
obsolete monovalent inorganic cation homeostasis (GO:0055067)
Namespace: biological_process
Definition: OBSOLETE. Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell.
Comment: This term was obsoleted because it is an unnecessary grouping class.
obsolete zinc ion homeostasis (GO:0055069)
Namespace: biological_process
Definition: OBSOLETE. Any process involved in the maintenance of an internal steady state of zinc ions within an organism or cell.
Synonyms: zinc homeostasis
Comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. For homeostasis terms, we would like to specify whether the homeostasis takes place intracellularly or at the level of the organism.
calcium ion homeostasis (GO:0055074)
Namespace: biological_process
Definition: Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
Synonyms: regulation of calcium ion concentration
monoatomic anion homeostasis (GO:0055081)
Namespace: biological_process
Definition: Any process involved in the maintenance of an internal steady state of monoatomic anions within an organism or cell. Monatomic anions (also called simple anions) are anions consisting of exactly one atom.
Synonyms: anion homeostasis
high density lipoprotein particle mediated signaling (GO:0055097)
Namespace: biological_process
Definition: The series of molecular signals mediated by the detection of high density lipoprotein particle.
Synonyms: high density lipoprotein mediated signalling; high density lipoprotein particle mediated signal transduction; high density lipoprotein particle-mediated signaling
ligase inhibitor activity (GO:0055104)
Namespace: molecular_function
Definition: Binds to and stops, prevents or reduces the activity of a ligase.
ubiquitin-protein transferase regulator activity (GO:0055106)
Namespace: molecular_function
Definition: Binds to and modulates the activity of a ubiquitin-protein transferase, an enzyme that catalyzes the covalent attachment of ubiquitin to lysine in a substrate protein.
obsolete oxidation-reduction process (GO:0055114)
Namespace: biological_process
Definition: OBSOLETE. A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
Synonyms: oxidation reduction; oxidoreductase process
Comment: This term was obsoleted because it represents a molecular function.
negative regulation of cardiac muscle contraction (GO:0055118)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
plus-end directed microfilament motor activity (GO:0060002)
Namespace: molecular_function
Definition: A motor activity that generates movement along a microfilament towards the plus end, driven by ATP hydrolysis. The minus end of an actin filament is the end that does not preferentially add actin monomers.
Synonyms: barbed-end directed actin-filament motor activity; plus-end directed actin filament motor activity; plus-end directed actin-filament motor activity
radial glial cell differentiation (GO:0060019)
Namespace: biological_process
Definition: The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the brain. Differentiation includes the processes involved in commitment of a cell to a specific fate.
dorsal convergence (GO:0060030)
Namespace: biological_process
Definition: The directed migration of individual cells and small groups of cells toward the dorsal midline during gastrulation. This process does not require cell rearrangement.
notochord regression (GO:0060032)
Namespace: biological_process
Definition: The developmental process in which the structure of the notochord is destroyed in an embryo.
notochord cell differentiation (GO:0060034)
Namespace: biological_process
Definition: The process in which relatively unspecialized cells acquire specialized structural and/or functional features cells that make up the notochord. Differentiation includes the processes involved in commitment of a cell to a notochord cell fate.
retina morphogenesis in camera-type eye (GO:0060042)
Namespace: biological_process
Definition: The process in which the anatomical structure of the retina is generated and organized.
Synonyms: retina morphogenesis in camera-style eye; retinogenesis
oviduct development (GO:0060066)
Namespace: biological_process
Definition: The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism.
Synonyms: fallopian tube development; Mullerian tract development
obsolete collagen and cuticulin-based cuticle extracellular matrix part (GO:0060103)
Namespace: cellular_component
Definition: OBSOLETE. Any constituent part of the collagen and cuticulin-based cuticle extracellular matrix, a collagen and cuticulin-based noncellular, multilayered structure that is synthesized by an underlying ectodermal (hypodermal) cell layer.
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.
cortical layer of collagen and cuticulin-based cuticle extracellular matrix (GO:0060106)
Namespace: cellular_component
Definition: The cuticle layer that lies directly beneath the lipid-containing epicuticle. The cortical layer contains collagens and insoluble, non-collagenous cuticulins and is characterized by a distinct annular pattern consisting of regularly spaced annular ridges delineated by annular furrows. An example of this component is found in Caenorhabditis elegans.
corticotropin hormone secreting cell differentiation (GO:0060128)
Namespace: biological_process
Definition: The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a corticotropic hormone secreting cell. An corticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces corticotropin.
Synonyms: adrenocorticotrophic hormone secreting cell differentiation; adrenocorticotropic hormone secreting cell differentiation; corticotrope differentiation; corticotroph differentiation; corticotrophin hormone secreting cell differentiation
positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)
Namespace: biological_process
Definition: Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
peroxisome localization (GO:0060151)
Namespace: biological_process
Definition: Any process in which a peroxisome is transported to, and/or maintained in, a specific location. A peroxisome is a small membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
Synonyms: peroxisome localisation
obsolete cellular process regulating host cell cycle in response to virus (GO:0060154)
Namespace: biological_process
Definition: OBSOLETE. Any cellular process that modulates the rate or extent of progression through the cell cycle in response to a virus.
Comment: The reason for obsoletion is that based on the definition, it is not clear that this process exists.
platelet dense granule organization (GO:0060155)
Namespace: biological_process
Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a platelet dense granule. A platelet dense granule is an electron-dense granule occurring in blood platelets that stores and secretes adenosine nucleotides and serotonin. They contain a highly condensed core consisting of serotonin, histamine, calcium, magnesium, ATP, ADP, pyrophosphate and membrane lysosomal proteins.
Synonyms: bull's eye body organization and biogenesis; platelet dense body organization and biogenesis; platelet dense granule organisation; platelet dense granule organization and biogenesis
urinary bladder development (GO:0060157)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the urinary bladder over time, from its formation to the mature structure. The urinary bladder is an elastic, muscular sac situated in the anterior part of the pelvic cavity in which urine collects before excretion.
positive regulation of adenosine receptor signaling pathway (GO:0060168)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of the adenosine receptor signaling pathway. The adenosine receptor pathway is the series of molecular signals generated as a consequence of an adenosine receptor binding to one of its physiological ligands.
Synonyms: positive regulation of adenosine receptor signalling pathway
obsolete regulation of lipase activity (GO:0060191)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of lipase activity, the hydrolysis of a lipid or phospholipid.
Comment: This term was obsoleted because it represents a molecular function.
clathrin-sculpted glutamate transport vesicle lumen (GO:0060204)
Namespace: cellular_component
Definition: The volume enclosed by the membrane of the clathrin-sculpted glutamate transport vesicle.
Synonyms: clathrin sculpted glutamate constitutive secretory pathway transport vesicle lumen; clathrin sculpted glutamate transport vesicle lumen
regulation of retinal cone cell fate commitment (GO:0060222)
Namespace: biological_process
Definition: Any process that modulates the process in which a cell becomes committed to a retinal cone cell fate. Retinal cone cell fate commitment is the process in which the developmental fate of a cell becomes restricted such that it will develop into a retinal cone cell.
positive regulation of retinal rod cell fate commitment (GO:0060225)
Namespace: biological_process
Definition: Any process that increases the process in which the developmental fate of a cell becomes restricted such that it will develop into a retinal rod cell. A retinal rod cell is one of the two photoreceptor subtypes in a camera-type eye.
obsolete regulation of signal transduction involved in conjugation with cellular fusion (GO:0060238)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the rate, frequency or extent of pheromone-dependent signal transduction during conjugation with cellular fusion.
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
contact inhibition (GO:0060242)
Namespace: biological_process
Definition: The series of events in which information about the density of cells in a population is received by direct cell-cell contact and is converted into a molecular signal, resulting in the cessation of cell growth or proliferation.
Synonyms: detection of cell density by contact stimulus; detection of cell density by contact stimulus involved in contact inhibition
negative regulation of cell proliferation involved in contact inhibition (GO:0060244)
Namespace: biological_process
Definition: Any process that stops, prevents or reduces the rate or extent of cell proliferation in response to cell density.
regulation of macromolecule metabolic process (GO:0060255)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
cilium assembly (GO:0060271)
Namespace: biological_process
Definition: The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Synonyms: ciliogenesis; cilium biogenesis; cilium formation; cilium morphogenesis; cilium organization; microtubule-based flagellum assembly
Comment: Note that we deem cilium and microtubule-based flagellum to be equivalent.
obsolete flagellar cell motility (GO:0060286)
Namespace: biological_process
Definition: OBSOLETE. Cell motility due to the motion of one or more flagella.
Synonyms: flagellar cell motility
Comment: This term was made obsolete because microtubule-based flagellum (GO:0009434) and motile cilium (GO:0031514), as referenced by this term, were determined to be equivalent and merged. When a merge for this term was considered, it was noticed that both eukaryotic and prokaryotic proteins are annotated to it because its meaning had been ambiguous so obsoletion was considered safest.
cilium movement involved in cell motility (GO:0060294)
Namespace: biological_process
Definition: Movement of cilia mediated by motor proteins that contributes to the movement of a cell.