LiteFold/GO huggingface dataset:
nuclear body organization (GO:0030575)
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 any of the extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
Synonyms: nuclear body organisation; nuclear body organization and biogenesis
Cajal body organization (GO:0030576)
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 Cajal bodies, nuclear bodies that appear ultrastructurally as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter and are enriched in ribonucleoproteins, and certain general RNA polymerase II transcription factors.
Synonyms: Cajal body organisation; Cajal body organization and biogenesis
Comment: See also the cellular component term 'Cajal body ; GO:0015030'.
Lands organization (GO:0030577)
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 Lands, a class of nuclear body that react against SP140 auto-antibodies.
Synonyms: Lands organisation; Lands organization and biogenesis; LYSP100-associated nuclear domain organization
Comment: See also the cellular component term 'Lands ; GO:0016606'.
PML body organization (GO:0030578)
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 PML bodies, a class of nuclear body; they react against SP100 auto-antibodies (PML = promyelocytic leukemia).
Synonyms: PML body organisation; PML body organization and biogenesis
Comment: See also the cellular component term 'PML body ; GO:0016605'.
obsolete ubiquitin-dependent SMAD protein catabolic process (GO:0030579)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome.
Synonyms: ubiquitin-dependent SMAD protein breakdown; ubiquitin-dependent SMAD protein catabolism; ubiquitin-dependent SMAD protein degradation
Comment: The reason for obsoletion is that the substrate should be captured as the input.
obsolete quinone cofactor methyltransferase activity (GO:0030580)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the transfer of a methyl group from S-adenosylmethionine during the synthesis of quinone cofactors such as ubiquinone (coenzyme Q), menaquinone (vitamin K2), plastoquinone and phylloquinone (vitamin K1).
Comment: This term was obsoleted because it was an unnecessary grouping class.
symbiont intracellular protein transport in host (GO:0030581)
Namespace: biological_process
Definition: The directed movement of a symbiont's proteins within a cell of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: host cell protein transport; intracellular protein transport in host; intracellular protein transport in other organism during symbiotic interaction; intracellular protein transport in other organism involved in symbiotic interaction
reproductive fruiting body development (GO:0030582)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of a reproductive fruiting body over time, from its formation to the mature structure. A reproductive fruiting body is a multicellular reproductive structure that contains spores.
Synonyms: fruiting body formation
Comment: This term describes the development of a fruiting body that is a spore-bearing organ. It is not intended to describe the development of myxococcal fruiting bodies.
myxococcal fruiting body development (GO:0030583)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the myxococcal fruiting body over time, from its formation to the mature structure. The process begins when myxococci respond to a lack of nutrients in the environment and ends when the myxococcal fruiting body is a mature structure.
Synonyms: fruiting body development in cellular response to starvation; fruiting body development in response to starvation
Comment: For example, as seen in myxobacterium. It is not intended to describe fruiting body development as is Dictyostelium.
sporocarp development (GO:0030584)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of a sporocarp over time, from its formation to the mature structure. The sporocarp is a spore bearing fruiting body organ. An example of this process is found in the Fungal species Coprinopsis cinerea.
Synonyms: fruiting body development
phosphoenolpyruvate carboxykinase (diphosphate) activity (GO:0030585)
Namespace: molecular_function
Definition: Catalysis of the reaction: diphosphate + oxaloacetate = CO2 + phosphate + phosphoenolpyruvate.
Synonyms: diphosphate:oxaloacetate carboxy-lyase (transphosphorylating); diphosphate:oxaloacetate carboxy-lyase (transphosphorylating; phosphoenolpyruvate-forming); PEP carboxyphosphotransferase activity; PEPCTrP; phosphoenolpyruvate carboxykinase (pyrophosphate) activity; phosphoenolpyruvate carboxylase (pyrophosphate); phosphoenolpyruvate carboxyphosphotransferase activity; phosphoenolpyruvate carboxytransphosphorylase activity; phosphoenolpyruvic carboxykinase; phosphoenolpyruvic carboxykinase (pyrophosphate); phosphoenolpyruvic carboxylase (pyrophosphate); phosphoenolpyruvic carboxytransphosphorylase activity; phosphopyruvate carboxykinase; phosphopyruvate carboxykinase (pyrophosphate); phosphopyruvate carboxylase (pyrophosphate)
[methionine synthase] reductase (NADPH) activity (GO:0030586)
Namespace: molecular_function
Definition: Catalysis of the reaction: [methionine synthase]-cob(II)alamin + NADPH + H+ + S-adenosyl methionine = [methionine synthase]-methylcob(I)alamin + S-adenosylhomocysteine + NADP+.
Synonyms: 5-methyltetrahydrofolate-homocysteine methyltransferase reductase; [methionine synthase]-cobalamin methyltransferase (cob(II)alamin reducing) activity; methionine synthase cob(II)alamin reductase (methylating) activity; methionine synthase reductase activity; methionine synthase-cobalamin methyltransferase (cob(II)alamin reducing); methionine synthase-methylcob(I)alamin,S-adenosylhomocysteine:NADP+ oxidoreductase activity
sorocarp development (GO:0030587)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the sorocarp over time, from its formation to the mature structure. The process begins with the aggregation of individual cells and ends with the mature sorocarp. The sorocarp is a structure containing a spore-bearing sorus that sits on top of a stalk. An example of this process is found in Dictyostelium discoideum.
Synonyms: fruiting body development; fruiting body formation; sorocarp biosynthesis; sorocarp formation
pseudocleavage (GO:0030588)
Namespace: biological_process
Definition: Partial constriction of the cytoplasm of a cell to form a furrow that resembles a cleavage furrow but does not complete cytokinesis.
pseudocleavage involved in syncytial blastoderm formation (GO:0030589)
Namespace: biological_process
Definition: Formation of furrows in the cytoplasm between nuclei during cell cycles in embryos that contribute to the formation of the syncytial blastoderm. An example of this process is found in Drosophila melanogaster.
Synonyms: pseudocleavage during syncytial blastoderm formation
2'-deoxyguanosine DNA ADP-ribosyltransferase activity (GO:0030591)
Namespace: molecular_function
Definition: Catalysis of the transfer of the ADP-ribose group of NAD+ to the amino group at N2 of 2'-deoxyguanosine to yield N2-(alpha-ADP-ribos-1-yl)-2'-deoxyguanosine and its beta form.
Synonyms: NAD DNA ADP-ribosyltransferase activity
DNA ADP-ribosylation (GO:0030592)
Namespace: biological_process
Definition: The covalent attachment of an ADP-ribosyl group to a residue in double-stranded DNA.
neutrophil chemotaxis (GO:0030593)
Namespace: biological_process
Definition: The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
neurotransmitter receptor activity (GO:0030594)
Namespace: molecular_function
Definition: Combining with a neurotransmitter and transmitting the signal to initiate a change in cell activity.
Comment: A strict definition of neurotransmitter receptor activity would limit its use to receptor activity at the postsynaptic membrane as part of synaptic transmission, but we recognize that usage is often much broader than this. For the strict use case, please see 'postsynaptic neurotransmitter receptor activity'
leukocyte chemotaxis (GO:0030595)
Namespace: biological_process
Definition: The movement of a leukocyte in response to an external stimulus.
Synonyms: immune cell chemotaxis; leucocyte chemotaxis
alpha-L-rhamnosidase activity (GO:0030596)
Namespace: molecular_function
Definition: Catalysis of the hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides.
Synonyms: alpha-L-rhamnosidase N; alpha-L-rhamnosidase T; alpha-L-rhamnoside rhamnohydrolase activity
RNA glycosylase activity (GO:0030597)
Namespace: molecular_function
Definition: Catalysis of the hydrolysis of N-glycosidic bonds in an RNA molecule.
rRNA N-glycosylase activity (GO:0030598)
Namespace: molecular_function
Definition: Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
Synonyms: gelonin; mirabilis antiviral protein; momorcochin-S; nigrin b; ribosomal ribonucleate N-glycosidase activity; ricin; RNA N-glycosidase activity; rRNA N-glycohydrolase activity; rRNA N-glycosidase activity; saporins
pectinesterase activity (GO:0030599)
Namespace: molecular_function
Definition: Catalysis of the reaction: pectin + n H2O = n methanol + pectate.
Synonyms: pectase activity; pectin demethoxylase activity; pectin methoxylase activity; pectin methyl esterase activity; pectin methylesterase activity; pectin pectylhydrolase activity; pectinoesterase activity
obsolete aminopeptidase B activity (GO:0030601)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the release of N-terminal Arg and Lys from oligopeptides when P1' is not Pro. Also acts on arylamides of Arg and Lys.
Synonyms: aminopeptidase B activity; arginyl aminopeptidase activity; arylamidase II; Cl--activated arginine aminopeptidase activity; cytosol aminopeptidase IV; L-arginine aminopeptidase activity
Comment: This term was made obsolete because it represents a gene product.
obsolete chymosin activity (GO:0030602)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the lysis of peptide bonds with broad specificity similar to that of pepsin A. Clots milk by cleavage of a single Ser-Phe-l-Met-Ala bond in kappa-casein.
Synonyms: chymosin activity; rennin; rennin (but this should be avoided since it leads to confusion with renin)
Comment: This term was made obsolete because it represents a gene product.
1-deoxy-D-xylulose-5-phosphate reductoisomerase activity (GO:0030604)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + H+ + NADPH.
Synonyms: 1-deoxy-D-xylulose-5-phosphate isomeroreductase activity; 1-deoxyxylulose-5-phosphate reductoisomerase activity; 2-C-methyl-D-erythritol-4-phosphate:NADP+ oxidoreductase (isomerizing); 2C-methyl-D-erythritol-4-phosphate (MEP) synthase activity; DOXP reductoisomerase activity; DXP-reductoisomerase activity
arsenate reductase activity (GO:0030611)
Namespace: molecular_function
Definition: Catalysis of the reaction: arsenite + A + H2O = arsenate + AH2 + H+.
Synonyms: arsenate reductase (donor) activity; arsenate:(acceptor) oxidoreductase activity; arsenate:acceptor oxidoreductase activity
arsenate reductase (thioredoxin) activity (GO:0030612)
Namespace: molecular_function
Definition: Catalysis of the reaction: arsenate + [thioredoxin]-dithiol + H+ = arsenite + [thioredoxin]-disulfide + H2O.
obsolete transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)
Namespace: molecular_function
Definition: OBSOLETE. A TGF-beta cytoplasmic mediator that forms a complex with a phosphorylated pathway-specific mediator. The heterocomplex translocates to the nucleus to regulate transcription.
Synonyms: co-SMAD protein; common mediator SMAD protein; common partner SMAD protein; common-mediator SMAD protein; common-partner SMAD protein; TGF-beta receptor, common-partner cytoplasmic mediator activity; TGFbeta receptor, common-partner cytoplasmic mediator activity
Comment: This term was obsoleted because it is redundant with other terms.
obsolete transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)
Namespace: molecular_function
Definition: OBSOLETE. A TGF-beta cytoplasmic mediator that inhibits the signaling function of common-partner and pathway-specific mediators.
Synonyms: inhibitory SMAD protein; TGF-beta receptor, inhibitory cytoplasmic mediator activity; TGFbeta receptor, inhibitory cytoplasmic mediator activity
Comment: This term was obsoleted because it represents the same activity as GO:0140416 ; DNA-binding transcription factor inhibitor activity', occurs in cytosol.
obsolete transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)
Namespace: molecular_function
Definition: OBSOLETE. A TGF-beta cytoplasmic mediator that is phosphorylated by a TGFbeta receptor and complexes with a common-partner mediator. The- heterocomplex translocates to the nucleus to regulate transcription.
Synonyms: pathway restricted SMAD protein; pathway-restricted SMAD protein; pathway-specific SMAD protein; receptor regulated SMAD protein; receptor-regulated SMAD protein; TGF-beta receptor, pathway-specific cytoplasmic mediator activity; TGFbeta receptor, pathway-specific cytoplasmic mediator activity
Comment: This term was obsoleted because it is redundant with other terms.
U1 snRNA binding (GO:0030619)
Namespace: molecular_function
Definition: Binding to a U1 small nuclear RNA (U1 snRNA).
Comment: Note that this term may be useful for annotating other small nuclear RNAs (snRNAs).
U2 snRNA binding (GO:0030620)
Namespace: molecular_function
Definition: Binding to a U2 small nuclear RNA (U2 snRNA).
U4 snRNA binding (GO:0030621)
Namespace: molecular_function
Definition: Binding to a U4 small nuclear RNA (U4 snRNA).
U4atac snRNA binding (GO:0030622)
Namespace: molecular_function
Definition: Binding to a U4atac small nuclear RNA (U4atac snRNA).
U5 snRNA binding (GO:0030623)
Namespace: molecular_function
Definition: Binding to a U5 small nuclear RNA (U5 snRNA).
U6atac snRNA binding (GO:0030624)
Namespace: molecular_function
Definition: Binding to a U6atac small nuclear RNA (U6atac snRNA).
U11 snRNA binding (GO:0030625)
Namespace: molecular_function
Definition: Binding to a U11 small nuclear RNA (U11 snRNA).
U12 snRNA binding (GO:0030626)
Namespace: molecular_function
Definition: Binding to a U12 small nuclear RNA (U12 snRNA).
pre-mRNA 5'-splice site binding (GO:0030627)
Namespace: molecular_function
Definition: Binding to a pre-mRNA 5' splice site sequence.
Synonyms: pre-mRNA 5' splice site binding
pre-mRNA 3'-splice site binding (GO:0030628)
Namespace: molecular_function
Definition: Binding to a pre-mRNA 3' splice site sequence.
Synonyms: pre-mRNA 3' splice site binding
U6 snRNA 3'-end binding (GO:0030629)
Namespace: molecular_function
Definition: Binding to a U6 small nuclear RNA (U6 snRNA) at the 3' end.
Synonyms: U6 snRNA 3' end binding
Comment: Note that this term may be useful for annotating small nuclear RNAs (snRNAs).
pyrrolysine incorporation (GO:0030631)
Namespace: biological_process
Definition: The incorporation of pyrrolysine, also known as lysine methylamine methyltransferase cofactor adduct, into a peptide; uses a special tRNA that recognizes the UAG codon as a modified lysine, rather than as a termination codon. Pyrrolysine may be synthesized as a free amino acid or synthesized from a lysine charged tRNA before its incorporation; it is not a posttranslational modification of peptidyl-lysine; this modification is found in several Methanosarcina methylamine methyltransferases.
Synonyms: lysine methylamine methyltransferase cofactor adduct incorporation; monomethylamine methyltransferase cofactor lysine adduct incorporation
D-alanine biosynthetic process (GO:0030632)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
Synonyms: D-alanine anabolism; D-alanine biosynthesis; D-alanine formation; D-alanine synthesis
obsolete D-alanine family amino acid catabolic process (GO:0030633)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-alanine and related amino acids.
Synonyms: D-alanine family amino acid breakdown; D-alanine family amino acid catabolism; D-alanine family amino acid degradation
Comment: This term was obsoleted because it represents an unnecessary grouping class.
carbon fixation by acetyl-CoA pathway (GO:0030634)
Namespace: biological_process
Definition: A pathway of carbon dioxide fixation in which one molecule of acetyl-CoA is completely synthesized from two molecules of carbon dioxide (CO2).
Synonyms: acetyl CoA pathway; Ljungdahl-Wood pathway; reductive acetyl CoA pathway
obsolete acetate derivative metabolic process (GO:0030635)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving derivatives of acetic acid.
Synonyms: acetate derivative metabolic process; acetate derivative metabolism
Comment: This term was made obsolete because it is an unnecessary grouping term, and has been replaced by terms to describe metabolism of specific compounds.
obsolete acetate derivative biosynthetic process (GO:0030636)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of derivatives of acetic acid.
Synonyms: acetate derivative anabolism; acetate derivative biosynthesis; acetate derivative biosynthetic process; acetate derivative formation; acetate derivative synthesis
Comment: This term was made obsolete because it is an unnecessary grouping term and has been replaced by terms to describe metabolism of specific compounds.
obsolete acetate derivative catabolic process (GO:0030637)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of derivatives of acetic acid.
Synonyms: acetate derivative breakdown; acetate derivative catabolic process; acetate derivative catabolism; acetate derivative degradation
Comment: This term was made obsolete because it is an unnecessary grouping term and has been replaced by terms to describe metabolism of specific compounds.
polyketide metabolic process (GO:0030638)
Namespace: biological_process
Definition: The chemical reactions and pathways involving polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones, which are themselves formed by repetitive head-to-tail addition of acetyl (or substituted acetyl) units indirectly derived from acetate (or a substituted acetate) by a mechanism similar to that for fatty acid biosynthesis but without the intermediate reductive steps.
Synonyms: polyketide metabolism
polyketide biosynthetic process (GO:0030639)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones, which are themselves formed by repetitive head-to-tail addition of acetyl (or substituted acetyl) units indirectly derived from acetate (or a substituted acetate) by a mechanism similar to that for fatty acid biosynthesis but without the intermediate reductive steps.
Synonyms: polyketide anabolism; polyketide biosynthesis; polyketide formation; polyketide synthesis
polyketide catabolic process (GO:0030640)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones, which are themselves formed by repetitive head-to-tail addition of acetyl (or substituted acetyl) units indirectly derived from acetate (or a substituted acetate) by a mechanism similar to that for fatty acid biosynthesis but without the intermediate reductive steps.
Synonyms: polyketide breakdown; polyketide catabolism; polyketide degradation
obsolete regulation of cellular pH (GO:0030641)
Namespace: biological_process
Definition: OBSOLETE. Any process involved in the maintenance of an internal equilibrium of hydrogen ions (protons) within a cell or between a cell and its external environment.
Comment: The reason for obsoletion is that this term is equivalent to 'regulation of intracellular pH' (GO:0051453). The terms 'cellular pH' and 'intracellular pH' refer to the same concept, and GO:0051453 is the more appropriate term with a proper logical definition.
intracellular phosphate ion homeostasis (GO:0030643)
Namespace: biological_process
Definition: A homeostatic process involved in the maintenance of a steady state level of phosphate ions within a cell.
Synonyms: cellular phosphate ion homeostasis; intracellular phosphate homeostasis; intracellular Pi homeostasis
intracellular chloride ion homeostasis (GO:0030644)
Namespace: biological_process
Definition: A homeostatic process involved in the maintenance of a steady state level of chloride ions within a cell.
Synonyms: cellular chloride ion homeostasis
acetyl-CoA fermentation to butanoate (GO:0030645)
Namespace: biological_process
Definition: The anaerobic chemical reactions and pathways resulting in the production of acetic acid, butyric acid, and dihydrogen from acetyl-CoA; effected by some saccharolytic species of Clostridium, e.g. C. butyricum.
Synonyms: butyrate fermentation; glucose catabolic process to butyrate; glucose fermentation to butyrate
obsolete aminoglycoside antibiotic metabolic process (GO:0030647)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving an aminoglycoside antibiotic, any member of a group of broad spectrum antibiotics, of similar toxicity and pharmacology, that contain an aminodeoxysugar, an amino- or guanidino-substituted inositol ring, and one or more residues of other sugars. The group includes streptomycin, neomycin, framycetin, kanamycin, paromomycin, and gentamicin.
Synonyms: aminoglycoside antibiotic metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
aminoglycoside antibiotic biosynthetic process (GO:0030648)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of an aminoglycoside antibiotic, any member of a group of broad spectrum antibiotics, of similar toxicity and pharmacology, that contain an aminodeoxysugar, an amino- or guanidino-substituted inositol ring, and one or more residues of other sugars. The group includes streptomycin, neomycin, framycetin, kanamycin, paromomycin, and gentamicin.
Synonyms: aminoglycoside antibiotic anabolism; aminoglycoside antibiotic biosynthesis; aminoglycoside antibiotic formation; aminoglycoside antibiotic synthesis
obsolete peptide antibiotic metabolic process (GO:0030650)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving peptides with antibiotic activity.
Synonyms: peptide antibiotic metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.