LiteFold/GO huggingface dataset:
histidyl-tRNA aminoacylation (GO:0006427)
Namespace: biological_process
Definition: The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA.
isoleucyl-tRNA aminoacylation (GO:0006428)
Namespace: biological_process
Definition: The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
leucyl-tRNA aminoacylation (GO:0006429)
Namespace: biological_process
Definition: The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
methionyl-tRNA aminoacylation (GO:0006431)
Namespace: biological_process
Definition: The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
phenylalanyl-tRNA aminoacylation (GO:0006432)
Namespace: biological_process
Definition: The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
prolyl-tRNA aminoacylation (GO:0006433)
Namespace: biological_process
Definition: The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA.
seryl-tRNA aminoacylation (GO:0006434)
Namespace: biological_process
Definition: The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA.
tryptophanyl-tRNA aminoacylation (GO:0006436)
Namespace: biological_process
Definition: The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
valyl-tRNA aminoacylation (GO:0006438)
Namespace: biological_process
Definition: The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
obsolete aminoacyl-tRNA hydrolase reaction (GO:0006439)
Namespace: biological_process
Definition: OBSOLETE. Hydrolysis of the peptidyl-tRNA by aminoacyl-tRNA hydrolase upon termination of translation. Analogous to usual peptidyl transfer during elongation, except that the acceptor is H2O instead of an aminoacyl-tRNA.
Synonyms: aminoacyl-tRNA hydrolase reaction
Comment: This term was made obsolete because it represents a molecular function.
obsolete binding to mRNA cap (GO:0006441)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: binding to mRNA cap
Comment: This term was made obsolete because it represents a function rather than a process.
regulation of translational initiation (GO:0006446)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of translational initiation.
regulation of translational initiation by iron (GO:0006447)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the translation of certain mRNAs involved in iron metabolism; regulated by the concentration of iron.
regulation of translational termination (GO:0006449)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of translational termination.
regulation of translational fidelity (GO:0006450)
Namespace: biological_process
Definition: Any process that modulates the ability of the translational apparatus to interpret the genetic code.
Synonyms: regulation of translational accuracy
translational readthrough (GO:0006451)
Namespace: biological_process
Definition: The continuation of translation beyond a stop codon by the use of a special tRNA that recognizes the UAG and UGA codons as modified amino acids, rather than as termination codons.
Synonyms: natural nonsense suppression
translational frameshifting (GO:0006452)
Namespace: biological_process
Definition: A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon.
protein folding (GO:0006457)
Namespace: biological_process
Definition: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
Synonyms: alpha-tubulin folding; beta-tubulin folding; chaperone activity; chaperonin ATPase activity; chaperonin-mediated tubulin folding; co-chaperone activity; co-chaperonin activity; glycoprotein-specific chaperone activity; non-chaperonin molecular chaperone ATPase activity; protein complex assembly, multichaperone pathway
'de novo' protein folding (GO:0006458)
Namespace: biological_process
Definition: The process of assisting in the folding of a nascent peptide chain into its correct tertiary structure.
Synonyms: nascent chain protein folding
obsolete binding unfolded ER proteins (GO:0006459)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: binding unfolded ER proteins
Comment: This term was made obsolete because it represents a function rather than a process.
obsolete protein complex assembly, multichaperone pathway (GO:0006462)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: protein complex assembly, multichaperone pathway
Comment: This term was made obsolete because the string was ambiguous and the original meaning of the term was hence unknown.
obsolete signal peptide processing (GO:0006465)
Namespace: biological_process
Definition: OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
Synonyms: leader peptide processing
Comment: This term was obsoleted because it reprenset a molecular function, signal peptidase activity ; GO:0009003.
obsolete protein disulfide-isomerase reaction (GO:0006466)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: protein disulfide-isomerase reaction; protein disulphide-isomerase reaction
Comment: This term was made obsolete because it presents a molecular function.
protein phosphorylation (GO:0006468)
Namespace: biological_process
Definition: The process of introducing a phosphate group on to a protein.
Synonyms: protein amino acid phosphorylation
negative regulation of protein kinase activity (GO:0006469)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
Synonyms: down regulation of protein kinase activity; down-regulation of protein kinase activity; downregulation of protein kinase activity; inhibition of protein kinase activity
obsolete protein ADP-ribosylation (GO:0006471)
Namespace: biological_process
Definition: OBSOLETE. The transfer, from NAD, of ADP-ribose to protein amino acids.
Synonyms: protein amino acid ADP-ribosylation
Comment: This term was obsoleted because it represents a molecular function.
protein acetylation (GO:0006473)
Namespace: biological_process
Definition: The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
Synonyms: protein amino acid acetylation
N-terminal protein amino acid acetylation (GO:0006474)
Namespace: biological_process
Definition: The acetylation of the N-terminal amino acid of proteins.
Synonyms: N(alpha)-terminal acetylation
internal protein amino acid acetylation (GO:0006475)
Namespace: biological_process
Definition: The addition of an acetyl group to a non-terminal amino acid in a protein.
protein deacetylation (GO:0006476)
Namespace: biological_process
Definition: The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
Synonyms: protein amino acid deacetylation
protein sulfation (GO:0006477)
Namespace: biological_process
Definition: The addition of a sulfate group as an ester to a protein amino acid.
Synonyms: protein amino acid sulfation; protein amino acid sulphation
protein methylation (GO:0006479)
Namespace: biological_process
Definition: The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
Synonyms: protein amino acid methylation
N-terminal protein amino acid methylation (GO:0006480)
Namespace: biological_process
Definition: The methylation of the N-terminal amino acid of a protein.
C-terminal protein methylation (GO:0006481)
Namespace: biological_process
Definition: The methylation of the C-terminal amino acid of a protein.
Synonyms: C-terminal protein amino acid methylation
protein demethylation (GO:0006482)
Namespace: biological_process
Definition: The removal of a methyl group, from a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
Synonyms: protein amino acid demethylation
obsolete peptidyl-aspartic acid/asparagine hydroxylation (GO:0006483)
Namespace: biological_process
Definition: OBSOLETE. The hydroxylation of peptidyl-aspartic acid or asparagine.
Synonyms: aspartic acid/asparagine hydroxylation; peptidyl-aspartic acid/asparagine hydroxylation
Comment: This term was made obsolete because it is a redundant grouping term.
obsolete protein cysteine-thiol oxidation (GO:0006484)
Namespace: biological_process
Definition: OBSOLETE. Oxidation of two cysteine sulfhydryl groups (thiols) in one protein by a disulfide bond in a second protein to form a disulfide bond in the first protein and two reduced sulfhydryls in the second. The oxidized cysteines linked by a disulfide bond is known as cystine.
Synonyms: protein cysteine-thiol oxidation
Comment: This term was made obsolete because it represents a single activity.
obsolete protein glycosylation (GO:0006486)
Namespace: biological_process
Definition: OBSOLETE. A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
Synonyms: protein amino acid glycosylation
Comment: The reason for obsoletion is that this term represents a molecular function.
protein N-linked glycosylation (GO:0006487)
Namespace: biological_process
Definition: A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of an asparagine residue.
Synonyms: N-glycan biosynthesis; N-glycan metabolism; protein amino acid N-linked glycosylation
dolichol-linked oligosaccharide biosynthetic process (GO:0006488)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dolichol-linked oligosaccharide, usually by a stepwise addition of glycosyl chains to endoplasmic reticulum membrane-bound dolichol-P.
Synonyms: dolichol-linked oligosaccharide anabolism; dolichol-linked oligosaccharide biosynthesis; dolichol-linked oligosaccharide formation; dolichol-linked oligosaccharide synthesis; N-linked glycan precursor biosynthesis; N-linked glycan precursor biosynthetic process; oligosaccharide-PP-dolichol assembly
dolichyl diphosphate biosynthetic process (GO:0006489)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of dolichyl diphosphate, a diphosphorylated dolichol derivative.
Synonyms: dolichyl diphosphate anabolism; dolichyl diphosphate biosynthesis; dolichyl diphosphate formation; dolichyl diphosphate synthesis
obsolete oligosaccharide-lipid intermediate biosynthetic process (GO:0006490)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of an oligosaccharide-lipid intermediate, such as a molecule of dolichol-P-man or dolicol-P-Glc used in N-linked glycosylation.
Synonyms: oligosaccharide-lipid intermediate assembly
Comment: This term was obsoleted because it is an unnecessary grouping term
N-glycan processing (GO:0006491)
Namespace: biological_process
Definition: The conversion of N-linked glycan (N = nitrogen) structures from the initially transferred oligosaccharide to a mature form, by the actions of glycosidases and glycosyltransferases. The early processing steps are conserved and play roles in glycoprotein folding and trafficking.
Synonyms: glycoprotein trimming involved in glycoprotein maturation; N-linked glycoprotein maturation
protein O-linked glycosylation (GO:0006493)
Namespace: biological_process
Definition: A glycoprotein biosynthetic process starting with the covalent linkage of carbohydrate or carbohydrate derivative unit via a glycosidic bond to the oxygen atom of a serine, threonine, hydroxylysine, hydroxyproline or tyrosine side chain in a protein, which can be further elongated with the sequential addition of sugar units resulting in the formation of a protein O-linked glycan.
Synonyms: protein amino acid O-linked glycosylation
obsolete protein amino acid terminal glycosylation (GO:0006494)
Namespace: biological_process
Definition: OBSOLETE. A protein amino acid glycosylation process in which a sugar unit is added to a free alpha-amino or alpha-carboxyl terminal of a peptide.
Synonyms: protein amino acid terminal glycosylation
Comment: This term was made obsolete because the term name is ambiguous.
obsolete terminal O-glycosylation (GO:0006495)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: terminal O-glycosylation
Comment: This term was made obsolete because there is no evidence for the existence of this process.
obsolete protein amino acid terminal N-glycosylation (GO:0006496)
Namespace: biological_process
Definition: OBSOLETE. The glycosylation of a nitrogen atom of a free alpha amino terminal of a peptide.
Synonyms: protein amino acid terminal N-glycosylation
Comment: This term was made obsolete because the term name is ambiguous.
protein lipidation (GO:0006497)
Namespace: biological_process
Definition: The covalent attachment of lipid groups to an amino acid in a protein.
Synonyms: lipid:protein modification; protein amino acid lipidation
Comment: For non-covalent interactions with a lipid, consider instead the term 'lipid binding ; GO:0008289' and its children.
N-terminal protein lipidation (GO:0006498)
Namespace: biological_process
Definition: The covalent attachment of a lipid group to the amino terminus of a protein.
N-terminal protein myristoylation (GO:0006499)
Namespace: biological_process
Definition: The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.
N-terminal protein palmitoylation (GO:0006500)
Namespace: biological_process
Definition: The covalent attachment of a palmitoyl group to the N-terminal amino acid residue of a protein.
C-terminal protein lipidation (GO:0006501)
Namespace: biological_process
Definition: The covalent attachment of a lipid group to the carboxy-terminus of a protein.
obsolete C-terminal protein prenylation (GO:0006502)
Namespace: biological_process
Definition: OBSOLETE. The covalent or non-covalent attachment of a prenyl group to the carboxy-terminus of a protein; geranyl, farnesyl, or geranylgeranyl groups may be added.
Synonyms: C-terminal protein prenylation
Comment: This term was made obsolete because the process is not exclusive to the carboxy-terminus of a protein.
obsolete C-terminal protein farnesylation (GO:0006503)
Namespace: biological_process
Definition: OBSOLETE. The covalent or non-covalent attachment of a farnesyl group to the carboxy terminus of a protein.
Synonyms: C-terminal protein farnesylation
Comment: This term was made obsolete because the process is not exclusive to the carboxy-terminus of a protein.
obsolete C-terminal protein geranylgeranylation (GO:0006504)
Namespace: biological_process
Definition: OBSOLETE. The covalent or non-covalent attachment of a geranylgeranyl group to the carboxy-terminus of a protein.
Synonyms: C-terminal protein geranylgeranylation
Comment: This term was made obsolete because the process is not exclusive to the carboxy-terminus of a protein.
GPI anchor metabolic process (GO:0006505)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glycosylphosphatidylinositol anchors, molecular mechanisms for attaching membrane proteins to the lipid bilayer of cell membranes. Structurally they consist of a molecule of phosphatidylinositol to which is linked, via the C-6 hydroxyl of the inositol, a carbohydrate chain. This chain is in turn linked to the protein through an ethanolamine phosphate group, the amino group of which is in amide linkage with the C-terminal carboxyl of the protein chain, the phosphate group being esterified to the C-6 hydroxyl of the terminal mannose of the core carbohydrate chain.
Synonyms: glycosylphosphatidylinositol metabolic process; glycosylphosphatidylinositol metabolism; GPI anchor metabolism; GPI/GSI anchor metabolic process; GPI/GSI anchor metabolism
GPI anchor biosynthetic process (GO:0006506)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a glycosylphosphatidylinositol (GPI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The phosphatidylinositol group is linked via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via an ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GPI anchors have variants on this canonical linkage.
Synonyms: glycosylphosphatidylinositol biosynthesis; glycosylphosphatidylinositol biosynthetic process; GPI anchor anabolism; GPI anchor biosynthesis; GPI anchor formation; GPI anchor synthesis; GPI/GSI anchor biosynthesis; GPI/GSI anchor biosynthetic process
proteolysis (GO:0006508)
Namespace: biological_process
Definition: The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
Synonyms: ATP-dependent proteolysis; peptidolysis
Comment: This term was intentionally placed under 'protein metabolic process ; GO:0019538' rather than 'protein catabolic process ; GO:0030163' to cover all processes centered on breaking peptide bonds, including those involved in protein processing.
membrane protein ectodomain proteolysis (GO:0006509)
Namespace: biological_process
Definition: The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
Synonyms: ectoderm shedding; ectodomain cleavage; membrane protein solubilization; receptor shedding
obsolete ATP-dependent proteolysis (GO:0006510)
Namespace: biological_process
Definition: OBSOLETE. The hydrolysis of a peptide bond or bonds within a protein using energy from the hydrolysis of ATP.
Synonyms: ATP-dependent peptidolysis; ATP-dependent proteolysis
Comment: This term was made obsolete because it represents a molecular function.
ubiquitin-dependent protein catabolic process (GO:0006511)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
Synonyms: myofibrillar protein ubiquitination during ubiquitin-dependent protein breakdown; myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolic process; myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolism; myofibrillar protein ubiquitination during ubiquitin-dependent protein degradation; protein degradation tagging activity; protein ubiquitination during ubiquitin-dependent protein breakdown; protein ubiquitination during ubiquitin-dependent protein catabolic process; protein ubiquitination during ubiquitin-dependent protein catabolism; protein ubiquitination during ubiquitin-dependent protein degradation; protein ubiquitination involved in ubiquitin-dependent protein catabolic process; protein ubiquitinylation during ubiquitin-dependent protein catabolic process; protein ubiquitinylation during ubiquitin-dependent protein catabolism; protein ubiquitylation during ubiquitin-dependent protein catabolic process; protein ubiquitylation during ubiquitin-dependent protein catabolism; ubiquitin-dependent protein breakdown; ubiquitin-dependent protein catabolism; ubiquitin-dependent protein degradation; ubiquitin-dependent proteolysis
obsolete ubiquitin cycle (GO:0006512)
Namespace: biological_process
Definition: OBSOLETE. The cyclical process by which one or more ubiquitin groups are added to (ubiquitination) and removed from (deubiquitination) a protein.
Synonyms: ubiquitin cycle
Comment: This term was made obsolete because it implies that every protein that is ubiquitinated is also subsequently deubiquinitated, which is not true. Also, the process ontology does not include analogous terms for other small modifiers.
protein monoubiquitination (GO:0006513)
Namespace: biological_process
Definition: Addition of a single ubiquitin group to a protein.
Synonyms: protein monoubiquitinylation; protein monoubiquitylation
glycoprotein catabolic process (GO:0006516)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
Synonyms: glycoprotein breakdown; glycoprotein catabolism; glycoprotein degradation
protein deglycosylation (GO:0006517)
Namespace: biological_process
Definition: The removal of sugar residues from a glycosylated protein.
Synonyms: glycoprotein deglycosylation
peptide metabolic process (GO:0006518)
Namespace: biological_process
Definition: The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
Synonyms: peptide metabolism
amino acid metabolic process (GO:0006520)
Namespace: biological_process
Definition: The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
Synonyms: amino acid and derivative metabolism; cellular amino acid and derivative metabolic process; cellular amino acid metabolic process; cellular amino acid metabolism
alanine biosynthetic process (GO:0006523)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid.
Synonyms: alanine anabolism; alanine biosynthesis; alanine formation; alanine synthesis