LiteFold/GO huggingface dataset:
bisphenol A catabolic process (GO:0043636)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of bisphenol A, 4,4'-(propane-2,2-diyl)diphenol, a synthetic, aromatic organic compound used as a monomer in the manufacture of polycarbonate plastic and in the manufacture of epoxy resins.
Synonyms: bisphenol-A catabolic process; bisphenol-A catabolism
obsolete puromycin metabolic process (GO:0043637)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving puromycin, 3'-deoxy-N,N-dimethyl-3'-(O-methyl-L-tyrosinamido)adenosine, an aminonucleoside antibiotic that is a potent inhibitor of translation; produced by the bacterium Streptomyces alboniger.
Synonyms: puromycin metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
puromycin biosynthetic process (GO:0043638)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of puromycin, an aminonucleoside antibiotic that is a potent inhibitor of translation; produced by the bacterium Streptomyces alboniger.
benzoate catabolic process (GO:0043639)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.
Synonyms: benzoate breakdown; benzoate catabolism; benzoate degradation
benzoate catabolic process via hydroxylation (GO:0043640)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of benzoate, by its hydroxylation to cis-1,2-dihydroxybenzoate followed by dehydrogenation to catechol.
Synonyms: benzoate breakdown via hydroxylation; benzoate degradation via hydroxylation
obsolete novobiocin metabolic process (GO:0043641)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving novobiocin, a coumarin antibiotic produced by the bacterium Gyrasestreptomyces spheroides, that acts by inhibiting DNA gyrase.
Synonyms: novobiocin metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
novobiocin biosynthetic process (GO:0043642)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of novobiocin, a coumarin antibiotic produced by the bacterium Gyrasestreptomyces spheroides, that acts by inhibiting DNA gyrase.
obsolete tetracycline metabolic process (GO:0043643)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles).
Synonyms: tetracyclin metabolic process; tetracyclin metabolism; tetracycline metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
tetracycline biosynthetic process (GO:0043644)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of tetracycline, (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide, a broad-spectrum antibiotic produced by streptomyces bacteria that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles).
Synonyms: tetracyclin biosynthesis; tetracyclin biosynthetic process
obsolete cephalosporin metabolic process (GO:0043645)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria.
Synonyms: cephalosporin metabolism
Comment: This term was obsoleted because it is an unnecessary grouping term.
cephalosporin biosynthetic process (GO:0043646)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a cephalosporin, any of large class of tetracyclic triterpene broad-spectrum antibiotics similar both chemically and in their mode of action to penicillin, first isolated from the culture filtrates of mediterranean fungus acremonium (cephalosporium acremonium), and effective against gram-positive bacteria.
inositol phosphate metabolic process (GO:0043647)
Namespace: biological_process
Definition: The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
Synonyms: inositol phosphate metabolism; myo-inositol phosphate metabolic process; myo-inositol phosphate metabolism
dicarboxylic acid metabolic process (GO:0043648)
Namespace: biological_process
Definition: The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-).
Synonyms: dicarboxylate metabolic process; dicarboxylate metabolism; dicarboxylic acid metabolism
dicarboxylic acid biosynthetic process (GO:0043650)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups.
Synonyms: dicarboxylate biosynthesis; dicarboxylate biosynthetic process; dicarboxylic acid anabolism; dicarboxylic acid biosynthesis; dicarboxylic acid formation; dicarboxylic acid synthesis
linoleic acid metabolic process (GO:0043651)
Namespace: biological_process
Definition: The chemical reactions and pathways involving linoleic acid, an unsaturated omega-6 fatty acid that has the molecular formula C18H32O2.
Synonyms: linoleic acid metabolism
engulfment of apoptotic cell (GO:0043652)
Namespace: biological_process
Definition: The removal of the apoptotic cell by phagocytosis, by a neighboring cell or by a phagocyte.
Synonyms: engulfment of apoptotic cell corpse; engulfment of cell corpse
Comment: This term should be used to annotate gene products from the engulfing cell that facilitate phagocytosis of apoptotic cells. It should not be mistaken with GO:0070782 'phosphatidylserine exposure on apoptotic cell surface', a process occurring in apoptotic cells that acts as a signal for engulfing cells. If gene products involved in such instances of phosphatidylserine exposure are shown to have a positive effect on engulfment, they may be annotated to GO:1901076 'positive regulation of engulfment of apoptotic cell'.
mitochondrial fragmentation involved in apoptotic process (GO:0043653)
Namespace: biological_process
Definition: The change in the morphology of the mitochondria in an apoptotic cell from a highly branched network to a fragmented vesicular form.
Synonyms: mitochondrial fission during apoptosis; mitochondrial fragmentation involved in apoptosis
Comment: Although most of the processes described under 'apoptotic mitochondrial changes' take place during the signaling phase of apoptosis, 'mitochondrial fragmentation involved in apoptotic process' cannot be confidently placed there. It is still controversial whether this process is involved in the signaling phase of apoptosis or not, so it was placed under the more generic 'apoptotic mitochondrial changes' parent rather than linked to the signaling or the execution phase until further research clarifies the matter.
host extracellular region (GO:0043655)
Namespace: cellular_component
Definition: The space within a host but external to the plasma membrane of host cells, e.g. host bloodstream.
Synonyms: extracellular space of host; host extracellular space
host intracellular region (GO:0043656)
Namespace: cellular_component
Definition: That space within the plasma membrane of a host cell.
Synonyms: host intracellular; intracellular region of host
host cell (GO:0043657)
Namespace: cellular_component
Definition: A cell within a host organism. Includes the host plasma membrane and any external encapsulating structures such as the host cell wall and cell envelope.
host symbiosome (GO:0043658)
Namespace: cellular_component
Definition: A double-enveloped cell compartment, composed of the endosymbiont with its plasmalemma (as inner envelope) and an outer envelope (the perisymbiontic membrane) derived from the host cell.
symbiosome (GO:0043659)
Namespace: cellular_component
Definition: A double-enveloped cell compartment, composed of an endosymbiont with its plasmalemma (as inner envelope) and a non-endosymbiotic outer envelope (the perisymbiontic membrane).
bacteroid-containing symbiosome (GO:0043660)
Namespace: cellular_component
Definition: A symbiosome containing any of various structurally modified bacteria, such as those occurring on the root nodules of leguminous plants.
peribacteroid membrane (GO:0043661)
Namespace: cellular_component
Definition: A membrane that surrounds one or more bacteroids (such as nitrogen-fixing bacteroids within legume root nodule cells).
peribacteroid fluid (GO:0043662)
Namespace: cellular_component
Definition: The soluble material inside the peribacteroid membrane, but outside of the bacteroid, within a bacteroid-containing symbiosome.
host bacteroid-containing symbiosome (GO:0043663)
Namespace: cellular_component
Definition: A symbiosome containing any of various structurally modified bacteria, such as those occurring on the root nodules of leguminous plants, of a host cell.
host peribacteroid membrane (GO:0043664)
Namespace: cellular_component
Definition: A host-derived membrane that surrounds one or more bacteroids (such as nitrogen-fixing bacteroids within legume root nodule cells).
host peribacteroid fluid (GO:0043665)
Namespace: cellular_component
Definition: The soluble material inside the peribacteroid membrane, but outside of the bacteroid, within a bacteroid-containing symbiosome of a host cell.
exine (GO:0043668)
Namespace: cellular_component
Definition: The outer layer of the pollen grain wall which is composed primarily of sporopollenin.
Comment: Note that the exine is highly resistant to strong acids and bases.
ectexine (GO:0043669)
Namespace: cellular_component
Definition: The outer part of the exine, which stains positively with basic fuchsin in optical microscopy and has higher electron density in conventionally prepared TEM sections.
Comment: Note that ectexine is distinguished on staining properties; compare with 'sexine ; GO:0043673'. See also 'endexine ; GO:0043671'.
foot layer (GO:0043670)
Namespace: cellular_component
Definition: The inner layer of the ectexine.
Synonyms: nexine 1
endexine (GO:0043671)
Namespace: cellular_component
Definition: The inner part of the exine, which stains.
Comment: Note that endexine is distinguished on staining properties; compare with 'sexine ; GO:0043673'. See also 'ectexine ; GO:0043669'.
nexine (GO:0043672)
Namespace: cellular_component
Definition: The inner, non-sculptured part of the exine which lies below the sexine.
Comment: Note that nexine is distinguished on purely morphological criteria; compare with 'endexine ; GO:0043671'. See also 'sexine ; GO:0043673'.
sexine (GO:0043673)
Namespace: cellular_component
Definition: The outer, sculptured layer of the exine, which lies above the nexine.
Comment: Note that the sexine sometimes consists of 5 layers, but of those, 3 layers are the most common (sexine 1 = columellae; sexine 2 = tectum; sexine 3 = sculpture elements). Sexine is distinguished on purely morphological criteria; compare with 'ectexine ; GO:0043669'. See also 'nexine ; GO:0043672'.
columella (GO:0043674)
Namespace: cellular_component
Definition: A rod-like element of the sexine and ectexine, supporting either the tectum (the layer of sexine which forms a roof over the columella), or supporting a caput (an architectural element on top of a columella).
Synonyms: sexine 1
sculpture element (GO:0043675)
Namespace: cellular_component
Definition: The third layer of the sexine.
tectum (GO:0043676)
Namespace: cellular_component
Definition: The layer of sexine which forms a roof over the columella, granules or other infratectal elements.
Synonyms: sexine 2
obsolete germination pore (GO:0043677)
Namespace: cellular_component
Definition: OBSOLETE. A small pore in the outer wall of a mycelial spore through which the germ tube exits upon germination. It can be apical or eccentric in its location.
Synonyms: germ pore
Comment: This term was made obsolete because it was poorly named and poorly defined.
intine (GO:0043678)
Namespace: cellular_component
Definition: The innermost of the major layers of the pollen grain wall which underlies the exine and borders the cytoplasm.
Comment: Note that the intine is not acetolysis resistant and is therefore absent in conventionally prepared palynological material.
axon terminus (GO:0043679)
Namespace: cellular_component
Definition: Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
Synonyms: axon terminal; axon terminal specialization; nerve ending
filiform apparatus (GO:0043680)
Namespace: cellular_component
Definition: A complex of cell wall invaginations in a synergid cell, similar to those in transfer cells.
P-type divalent copper transporter activity (GO:0043682)
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: ATP + H2O + Cu2+(in) = ADP + phosphate + Cu2+(out).
Synonyms: copper exporting ATPase activity; copper transmembrane transporter activity, phosphorylative mechanism; copper-exporting ATPase activity; copper-translocating P-type ATPase activity; copper-transporting ATPase activity; Cu(2+)-exporting ATPase activity; Cu2+-exporting ATPase activity
type IV pilus assembly (GO:0043683)
Namespace: biological_process
Definition: The assembly from its constituent parts of a type IV pilus.
Synonyms: type IV fimbria assembly; type IV fimbria biogenesis; type IV fimbriae assembly; type IV fimbriae biogenesis; type IV fimbrial assembly; type IV fimbrial biogenesis; type IV fimbrium assembly; type IV fimbrium biogenesis; type IV pilus biogenesis
type IV secretion system complex (GO:0043684)
Namespace: cellular_component
Definition: A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of DNA or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s).
Synonyms: T4SS complex; type IV protein secretion system complex
conversion of glutamyl-tRNA to glutaminyl-tRNA (GO:0043685)
Namespace: biological_process
Definition: The modification process that results in the conversion of glutamate charged on a tRNA(Gln) to glutaminyl-tRNA.
Comment: Note that this process has been observed in some archaeal and bacterial species.
obsolete co-translational protein modification (GO:0043686)
Namespace: biological_process
Definition: OBSOLETE. The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
Synonyms: co-translational amino acid modification; co-translational modification; cotranslational amino acid modification; cotranslational modification; cotranslational protein modification
Comment: This term was obsoleted because it represents a molecular function, and not a specific biological process.
post-translational protein modification (GO:0043687)
Namespace: biological_process
Definition: The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome.
Synonyms: post-translational amino acid modification; post-translational modification; posttranslational amino acid modification; posttranslational modification; posttranslational protein modification; PTM
Comment: This term should only be used to annotate a protein modification process that occurs after the protein has been released from the ribosome, and is therefore strictly post-translational. Modification of a free protein (one not attached to a ribosome) and modification of a C-terminal residue are post-translational processes. Some protein modifications occur while the protein is still in the ribosome but before translation has been completed; these modification processes are considered co-translational and should not be annotated using this term.
conversion of aspartyl-tRNA to asparaginyl-tRNA (GO:0043688)
Namespace: biological_process
Definition: The modification process that results in the conversion of aspartate charged on a tRNA(Asn) to asparaginyl-tRNA.
Comment: Note that this process has been observed in some archaeal and bacterial species.
reverse cholesterol transport (GO:0043691)
Namespace: biological_process
Definition: The directed movement of peripheral cell cholesterol, cholest-5-en-3-beta-ol, towards the liver for catabolism.
monoterpene metabolic process (GO:0043692)
Namespace: biological_process
Definition: The chemical reactions and pathways involving monoterpenes, terpenes with a C10 structure.
Synonyms: monoterpene metabolism
monoterpene biosynthetic process (GO:0043693)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of monoterpenes, terpenes with a C10 structure.
Synonyms: monoterpene biosynthesis
monoterpene catabolic process (GO:0043694)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of monoterpenes, terpenes with a C10 structure.
Synonyms: monoterpene catabolism
detection of pheromone (GO:0043695)
Namespace: biological_process
Definition: The series of events in which a pheromone stimulus is received by a cell and converted into a molecular signal.
dedifferentiation (GO:0043696)
Namespace: biological_process
Definition: The process in which a specialized structure (cell, tissue or organ) loses structural or functional features that characterize it in the mature organism, or some other relatively stable phase of the organism's life history. Under certain conditions, these structures can revert back to the features of their ancestors.
cell dedifferentiation (GO:0043697)
Namespace: biological_process
Definition: The process in which a specialized cell loses the structural or functional features that characterize it in the mature organism, or some other relatively stable phase of the organism's life history. Under certain conditions, these cells can revert back to the features of the stem cells that were their ancestors.
Comment: Note that this term should be used to annotate gene products involved in dedifferentiation that occurs as part of a normal process, such as regeneration. It should not be used for dedifferentiation that occurs in an abnormal or disease state such as cancer.
iridosome (GO:0043698)
Namespace: cellular_component
Definition: A tissue-specific, membrane-bounded cytoplasmic organelle within which purines crystalize in reflective stacks. Iridosomes are synthesized in iridophore cells and are silver, gold or iridescent in appearance.
Synonyms: reflecting platelet
leucosome (GO:0043699)
Namespace: cellular_component
Definition: A tissue-specific, membrane-bounded cytoplasmic organelle within which uric acid and/or purines crystalize in reflective stacks. Leucosomes are synthesized in leucophore cells and have a whitish cast.
Synonyms: refractosome
pterinosome (GO:0043700)
Namespace: cellular_component
Definition: A tissue-specific, membrane-bounded cytoplasmic organelle within which pteridine pigments are synthesized and stored. Pterinosomes are synthesized in xanthophores and erythrophore cells and are yellow, orange or red in appearance.
cyanosome (GO:0043701)
Namespace: cellular_component
Definition: A tissue-specific, membrane-bounded cytoplasmic organelle within which an unknown blue pigment is localized. Cyanosomes are synthesized in cyanophores and are blue in appearance.
photoreceptor cell fate determination (GO:0043703)
Namespace: biological_process
Definition: The process in which a cell becomes capable of differentiating autonomously into a photoreceptor cell regardless of its environment; upon determination, the cell fate cannot be reversed.
photoreceptor cell fate specification (GO:0043704)
Namespace: biological_process
Definition: The process in which a cell becomes capable of differentiating autonomously into a photoreceptor cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.
obsolete cyanophycin metabolic process (GO:0043705)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving cyanophycin, a non-protein, non-ribosomally produced amino acid polymer composed of an aspartic acid backbone and arginine side groups.
Synonyms: cyanophycin metabolism; multi-L-arginyl-poly(L-aspartic acid) metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
cell adhesion involved in biofilm formation (GO:0043708)
Namespace: biological_process
Definition: The attachment of a cell to a solid substrate, via cell adhesion molecules, contributing to the formation of a biofilm.
Synonyms: cell adhesion during biofilm formation
cell adhesion involved in single-species biofilm formation (GO:0043709)
Namespace: biological_process
Definition: The attachment of a cell to a solid substrate, via cell adhesion molecules, during the formation of a biofilm composed of microorganisms of the same species.
Synonyms: cell adhesion during single-species biofilm formation
pilus organization (GO:0043711)
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 pilus, a short filamentous structure on a bacterial cell, flagella-like in structure and generally present in many copies.
Synonyms: pilus organisation; pilus organization and biogenesis
Comment: Note that this term should not be used for direct annotation. Please use one of the children, GO:0009297 ; pilus assembly or GO:0043108 ; pilus retraction.
(R)-2-hydroxyisocaproate dehydrogenase activity (GO:0043713)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2-oxoisocaproate + NADH + H+ = (R)-2-hydroxyisocaproate + NAD+.
(R)-citramalate synthase activity (GO:0043714)
Namespace: molecular_function
Definition: Catalysis of the reaction: pyruvate + acetyl-CoA + H2O = (R)-citramalate + CoA.
Synonyms: citramalate synthase
2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity (GO:0043715)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2,3-diketo-5-methylthiopentyl-1-phosphate = H+ + 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate. 2,3-diketo-5-methylthiopentyl-1-phosphate is also known as DK-MTP-1-P, and 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate as HK-MTPenyl-1-P.
Synonyms: DK-MTP-1-P enolase activity; E-1; MasA; mtnW
Comment: This function is part of the process of methionine salvage.
2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity (GO:0043716)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2-hydroxy-5-methylsulfanyl-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate.
Synonyms: 2-hydroxy-3-keto-5-methylthio-phosphopentene phosphatase activity; HK-MTPenyl-1-P phosphatase activity
2-hydroxyglutaryl-CoA dehydratase activity (GO:0043717)
Namespace: molecular_function
Definition: Catalysis of the reaction: (R)-2-hydroxyglutaryl-CoA = H2O + glutaconyl-CoA.
Synonyms: (R)-2-hydroxyglutaryl-CoA dehydratase activity