LiteFold/GO huggingface dataset:
obsolete hydrogen-translocating V-type ATPase activity (GO:0000260)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out). Found in vacuoles of eukaryotes and in bacteria.
Synonyms: hydrogen-translocating V-type ATPase activity
Comment: This term was made obsolete because it represents a gene product.
obsolete sodium-translocating V-type ATPase activity (GO:0000261)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: ATP + H2O + Na+(in) = ADP + phosphate + Na+(out). Found in vacuoles of eukaryotes and in bacteria.
Synonyms: sodium-translocating V-type ATPase activity
Comment: This term was made obsolete because it represents a gene product.
mitochondrial chromosome (GO:0000262)
Namespace: cellular_component
Definition: A chromosome found in the mitochondrion of a eukaryotic cell.
Synonyms: mitochondrial DNA; mitochondrial genome; mtDNA
obsolete heterotrimeric G-protein GTPase, alpha-subunit (GO:0000263)
Namespace: molecular_function
Definition: OBSOLETE. Subunit of a heterotrimeric G-protein GTPase that contains the guanine nucleotide binding site and possesses GTPase activity.
Synonyms: heterotrimeric G-protein GTPase, alpha-subunit
Comment: This term was made obsolete because it does not represent a molecular function.
obsolete heterotrimeric G-protein GTPase, beta-subunit (GO:0000264)
Namespace: molecular_function
Definition: OBSOLETE. Subunit of a heterotrimeric G-protein GTPase; associates tightly with the gamma subunit.
Synonyms: heterotrimeric G-protein GTPase, beta-subunit
Comment: This term was made obsolete because it does not represent a molecular function.
obsolete heterotrimeric G-protein GTPase, gamma-subunit (GO:0000265)
Namespace: molecular_function
Definition: OBSOLETE. Smallest subunit of a heterotrimeric G-protein GTPase; associates tightly with the beta subunit.
Synonyms: heterotrimeric G-protein GTPase, gamma-subunit
Comment: This term was made obsolete because it does not represent a molecular function.
mitochondrial fission (GO:0000266)
Namespace: biological_process
Definition: The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
Synonyms: mitochondrial division; mitochondrial proliferation
obsolete cell fraction (GO:0000267)
Namespace: cellular_component
Definition: OBSOLETE. A generic term for parts of cells prepared by disruptive biochemical techniques.
Synonyms: cell fraction
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
peroxisome targeting sequence binding (GO:0000268)
Namespace: molecular_function
Definition: Binding to a peroxisomal targeting sequence, a sequence of amino acids within a protein that acts as a signal for the localization of a protein into the peroxisome.
Synonyms: peroxisome targeting signal receptor; PTS binding; PTS receptor
toxin export channel activity (GO:0000269)
Namespace: molecular_function
Definition: Enables the energy independent passage of toxins, sized less than 1000 Da, across a membrane towards the outside of the cell. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
peptidoglycan metabolic process (GO:0000270)
Namespace: biological_process
Definition: The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
Synonyms: murein metabolic process; murein metabolism; peptidoglycan metabolism
polysaccharide biosynthetic process (GO:0000271)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
Synonyms: glycan biosynthesis; glycan biosynthetic process; polysaccharide anabolism; polysaccharide biosynthesis; polysaccharide formation; polysaccharide synthesis
polysaccharide catabolic process (GO:0000272)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
Synonyms: multicellular organismal polysaccharide catabolic process; polysaccharide breakdown; polysaccharide catabolism; polysaccharide degradation
obsolete mitochondrial proton-transporting ATP synthase, stator stalk (GO:0000274)
Namespace: cellular_component
Definition: OBSOLETE. One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the mitochondrial membrane-associated F0 proteins; is thought to prevent futile rotation of the catalytic core.
Synonyms: mitochondrial proton-transporting ATP synthase, peripheral stalk
Comment: The reason for obsoletion is that this term unnecssarily specified a cellular compartment.
obsolete mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) (GO:0000275)
Namespace: cellular_component
Definition: OBSOLETE. The catalytic sector of the mitochondrial hydrogen-transporting ATP synthase; it comprises the catalytic core and central stalk, and is peripherally associated with the mitochondrial inner membrane when the entire ATP synthase is assembled.
Synonyms: hydrogen-transporting ATP synthase, F1 sector; proton-transporting ATP synthase complex, catalytic core F(1)
Comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.\nThe reason for obsoletion is that this term unnecssarily specified a cellular compartment
obsolete mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)
Namespace: cellular_component
Definition: OBSOLETE. All non-F1 subunits of the mitochondrial hydrogen-transporting ATP synthase, including integral and peripheral mitochondrial inner membrane proteins.
Comment: The reason for obsoletion is that this term unnecssarily specified a cellular compartment.
[cytochrome c]-lysine N-methyltransferase activity (GO:0000277)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + cytochrome c L-lysine = S-adenosyl-L-homocysteine + cytochrome c N6-methyl-L-lysine. This is the addition of a methyl group to the N6 atom of a lysine residue in cytochrome c.
Synonyms: cytochrome c (lysine) methyltransferase activity; cytochrome c methyltransferase activity; cytochrome c-lysine N-methyltransferase activity; cytochrome c-specific protein methylase III activity; cytochrome c-specific protein-lysine methyltransferase activity; S-adenosyl-L-methionine:cytochrome c-L-lysine 6-N-methyltransferase activity; S-adenosyl-L-methionine:cytochrome c-L-lysine N6-methyltransferase activity
M phase (GO:0000279)
Namespace: biological_process
Definition: A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
Synonyms: M-phase
Comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
nuclear division (GO:0000280)
Namespace: biological_process
Definition: The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
Synonyms: karyokinesis
mitotic cytokinesis (GO:0000281)
Namespace: biological_process
Definition: A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
Synonyms: cytokinesis after mitosis
cellular bud site selection (GO:0000282)
Namespace: biological_process
Definition: The specification of the site where a daughter cell will form, in organisms that reproduce by budding. An example of this process is found in Saccharomyces cerevisiae.
Synonyms: bud site selection/establishment of cell polarity
Comment: Note that this term was split from 'bud site selection/establishment of cell polarity (sensu Saccharomyces) ; GO:0007115' (a sibling term, 'establishment of cell polarity (sensu Saccharomyces) ; GO:0000283', was created but has since been merged with 'establishment of cell polarity' ; GO:0030010).
obsolete shmoo orientation (GO:0000284)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: shmoo orientation
Comment: This term was made obsolete because it is an organism specific term. The entire branch of the ontology was reorganized to be more generally applicable.
1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)
Namespace: molecular_function
Definition: Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + H+.
Synonyms: ATP:1-phosphatidyl-1D-myo-inositol-3-phosphate 5-phosphotransferase activity; phosphatidylinositol 3-phosphate 5-kinase activity; phosphatidylinositol-3-phosphate 5-kinase activity; type III PIP kinase activity
L-alanine dehydrogenase (NAD+) activity (GO:0000286)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-alanine + NAD+ + H2O = pyruvate + NH4+ + NADH + H+.
Synonyms: AlaDH; alanine dehydrogenase activity; alanine oxidoreductase activity; alpha-alanine dehydrogenase activity; L-alanine dehydrogenase activity; L-alanine:NAD+ oxidoreductase (deaminating); NAD-dependent alanine dehydrogenase activity; NAD-linked alanine dehydrogenase activity; NADH-dependent alanine dehydrogenase activity
magnesium ion binding (GO:0000287)
Namespace: molecular_function
Definition: Binding to a magnesium (Mg) ion.
Synonyms: magnesium binding; Mg binding
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)
Namespace: biological_process
Definition: A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
Synonyms: deadenylation-dependent mRNA decay; mRNA breakdown, deadenylation-dependent decay; mRNA catabolic process, deadenylation-dependent; mRNA catabolic process, deadenylylation-dependent; mRNA catabolism, deadenylation-dependent; mRNA catabolism, deadenylylation-dependent; mRNA degradation, deadenylation-dependent decay; nuclear mRNA catabolic process, deadenylation-dependent decay
nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)
Namespace: biological_process
Definition: Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
Synonyms: 3' to 5' mRNA deadenylation; mRNA deadenylation; nuclear mRNA poly(A) tail shortening
deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)
Namespace: biological_process
Definition: Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
Synonyms: deadenylation-dependent decapping of nuclear mRNA; deadenylylation-dependent decapping
obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic (GO:0000291)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail.
Synonyms: exonucleolytic degradation of mRNA; mRNA breakdown, exonucleolytic; mRNA degradation, exonucleolytic; nuclear mRNA catabolic process, exonucleolytic
Comment: The reason for obsoletion is that this represents an unnecessary grouping term
RNA fragment catabolic process (GO:0000292)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a fragment of RNA, such as excised introns or sequences removed from ribosomal RNA during processing.
Synonyms: group I intron catabolic process; RNA fragment breakdown; RNA fragment catabolism; RNA fragment degradation
ferric-chelate reductase activity (GO:0000293)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2 Fe3+-siderophore + electron donor = 2 Fe2+-siderophore + electron acceptor.
Synonyms: ferric chelate reductase activity; iron chelate reductase activity
nuclear-transcribed mRNA catabolic process, RNase MRP-dependent (GO:0000294)
Namespace: biological_process
Definition: A minor MRP-dependent nuclear-transcribed mRNA degradation pathway that begins with an endonucleolytic cleavage to generate unprotected ends.
Synonyms: nuclear mRNA catabolic process, endonucleolytic cleavage-dependent decay; nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay
adenine nucleotide transmembrane transporter activity (GO:0000295)
Namespace: molecular_function
Definition: Enables the transfer of adenine nucleotides (AMP, ADP, and ATP) from one side of a membrane to the other.
spermine transport (GO:0000296)
Namespace: biological_process
Definition: The directed movement of spermine, N,N-bis(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to spermidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
spermine transmembrane transporter activity (GO:0000297)
Namespace: molecular_function
Definition: Enables the transfer of spermine from one side of a membrane to the other. Spermine is a polybasic amine found in human sperm, in ribosomes and in some viruses, which is involved in nucleic acid packaging. Synthesis is regulated by ornithine decarboxylase which plays a key role in control of DNA replication.
endopolyphosphatase activity (GO:0000298)
Namespace: molecular_function
Definition: Catalysis of the reaction: polyphosphate + n H2O = (n+1) oligophosphate. The product contains 4 or 5 phosphate residues.
Synonyms: metaphosphatase activity; polymetaphosphatase activity; polyphosphatase activity; polyphosphate depolymerase activity; polyphosphate polyphosphohydrolase activity
obsolete integral to membrane of membrane fraction (GO:0000299)
Namespace: cellular_component
Definition: OBSOLETE. Integral to that fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes; require detergents, such as Triton X-100, to be released from membranes.
Synonyms: integral to membrane of membrane fraction
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
obsolete peripheral to membrane of membrane fraction (GO:0000300)
Namespace: cellular_component
Definition: OBSOLETE. Peripheral to that fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes; can be extracted from membrane fraction with high concentrations of salt or high pH.
Synonyms: peripheral to membrane of membrane fraction
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
retrograde transport, vesicle recycling within Golgi (GO:0000301)
Namespace: biological_process
Definition: The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi.
Synonyms: retrograde (vesicle recycling within Golgi) transport
response to reactive oxygen species (GO:0000302)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
Synonyms: response to active oxygen species; response to AOS; response to reactive oxidative species; response to reactive oxygen intermediate; response to ROI; response to ROS
response to superoxide (GO:0000303)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.
response to singlet oxygen (GO:0000304)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a singlet oxygen stimulus. Singlet oxygen is a dioxygen (O2) molecule in which two 2p electrons have similar spin. Singlet oxygen is more highly reactive than the form in which these electrons are of opposite spin, and it is produced in mutant chloroplasts lacking carotenoids and by leukocytes during metabolic burst.
response to oxygen radical (GO:0000305)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen radical stimulus. An oxygen radical is any oxygen species that carries a free electron; examples include hydroxyl radicals and the superoxide anion.
obsolete extrinsic component of vacuolar membrane (GO:0000306)
Namespace: cellular_component
Definition: OBSOLETE. The component of a vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
Synonyms: extrinsic to vacuolar membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
cyclin-dependent protein kinase holoenzyme complex (GO:0000307)
Namespace: cellular_component
Definition: Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
Synonyms: CDK holoenzyme
cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)
Namespace: cellular_component
Definition: Cyclin-dependent protein kinase (CDK) complex found in the cytoplasm.
Synonyms: CDK holoenzyme
xanthine phosphoribosyltransferase activity (GO:0000310)
Namespace: molecular_function
Definition: Catalysis of the reaction: diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine.
Synonyms: 5-phospho-alpha-D-ribose-1-diphosphate:xanthine phospho-D-ribosyltransferase activity; Xan phosphoribosyltransferase activity; xanthine-guanine phosphoribosyltransferase activity; xanthosine 5'-phosphate pyrophosphorylase activity; xanthylate pyrophosphorylase activity; xanthylic pyrophosphorylase activity; XMP pyrophosphorylase activity; XMP:diphosphate 5-phospho-alpha-D-ribosyltransferase activity
plastid large ribosomal subunit (GO:0000311)
Namespace: cellular_component
Definition: The larger of the two subunits of a plastid ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site).
plastid small ribosomal subunit (GO:0000312)
Namespace: cellular_component
Definition: The smaller of the two subunits of a plastid ribosome.
organellar small ribosomal subunit (GO:0000314)
Namespace: cellular_component
Definition: The smaller of the two subunits of an organellar ribosome.
organellar large ribosomal subunit (GO:0000315)
Namespace: cellular_component
Definition: The larger of the two subunits of an organellar ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site).
sulfite transmembrane transport (GO:0000316)
Namespace: biological_process
Definition: The directed movement of sulfite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Synonyms: sulphite transport
sulfite transmembrane transporter activity (GO:0000319)
Namespace: molecular_function
Definition: Enables the transfer of sulfite ions from one side of a membrane to the other.
Synonyms: sulphite transporter activity
re-entry into mitotic cell cycle (GO:0000320)
Namespace: biological_process
Definition: The resumption of the mitotic cell division cycle by cells that were in a quiescent or other non-dividing state.
re-entry into mitotic cell cycle after pheromone arrest (GO:0000321)
Namespace: biological_process
Definition: The resumption of the mitotic cell division cycle by pheromone-arrested cells that have not mated. An example of this process is found in Saccharomyces cerevisiae.
fungal-type vacuole (GO:0000324)
Namespace: cellular_component
Definition: A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
Synonyms: vacuole, cell cycle-correlated morphology
plant-type vacuole (GO:0000325)
Namespace: cellular_component
Definition: A closed structure that is completely surrounded by a unit membrane, contains liquid, and retains the same shape regardless of cell cycle phase. An example of this structure is found in Arabidopsis thaliana.
Synonyms: vacuole, cell cycle-independent morphology
protein storage vacuole (GO:0000326)
Namespace: cellular_component
Definition: A storage vacuole that contains a lytic vacuole; identified in plants.
lytic vacuole within protein storage vacuole (GO:0000327)
Namespace: cellular_component
Definition: A membrane-bounded compartment containing crystals of phytic acid and proteins characteristic of a lytic vacuole, found within a storage vacuole.
fungal-type vacuole lumen (GO:0000328)
Namespace: cellular_component
Definition: The volume enclosed within the vacuolar membrane of a vacuole, the shape of which correlates with cell cycle phase. An example of this structure is found in Saccharomyces cerevisiae.
Synonyms: lumen of vacuole with cell cycle-correlated morphology
fungal-type vacuole membrane (GO:0000329)
Namespace: cellular_component
Definition: The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
Synonyms: fungal-type vacuolar membrane; membrane of vacuole with cell cycle-correlated morphology
plant-type vacuole lumen (GO:0000330)
Namespace: cellular_component
Definition: The volume enclosed within the vacuolar membrane of a vacuole that retains the same shape regardless of cell cycle phase. An example of this is found in Arabidopsis thaliana.
Synonyms: lumen of vacuole with cell cycle-independent morphology