LiteFold/GO huggingface dataset:
dimeric ribonuclease P complex (GO:0030680)
Namespace: cellular_component
Definition: A ribonuclease P complex that contains a single RNA molecule that is necessary and usually sufficient for catalysis, and a single protein molecule. Examples of this complex are found in Bacterial species.
Synonyms: dimeric RNase P complex
preribosome (GO:0030684)
Namespace: cellular_component
Definition: Any complex of pre-rRNAs, ribosomal proteins, and associated proteins formed during ribosome biogenesis.
preribosome, large subunit precursor (GO:0030687)
Namespace: cellular_component
Definition: A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.
Synonyms: 66S preribosome
Comment: Note that this complex is 66S in Saccharomyces.
obsolete caspase activity (GO:0030693)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the hydrolysis of a peptide bond on the carboxyl side of an aspartate residue.
Synonyms: caspase activity; caspase-1 activity; caspase-10 activity; caspase-2 activity; caspase-3 activity; caspase-4 activity; caspase-5 activity; caspase-6 activity; caspase-7 activity; caspase-8 activity; caspase-9 activity; effector caspase activity; signaling (initiator) caspase activity
Comment: This term was made obsolete because it represents a gene product.
glycine reductase activity (GO:0030699)
Namespace: molecular_function
Definition: Catalysis of the reaction: acetyl phosphate + H2O + NH4 + thioredoxin disulfide = glycine + H+ + phosphate + thioredoxin.
Synonyms: acetyl-phosphate ammonia:thioredoxin disulfide oxidoreductase (glycine-forming)
anterior/posterior axis specification, follicular epithelium (GO:0030714)
Namespace: biological_process
Definition: Polarization of the follicle cells of an insect ovary along the anterior/posterior axis.
Synonyms: anterior/posterior axis determination, follicular epithelium
spectrosome organization (GO:0030721)
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 the spectrosome, a germline specific spherical organelle that is the precursor to the fusome.
Synonyms: spectrosome organisation; spectrosome organization and biogenesis
ovarian fusome organization (GO:0030723)
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 the fusome of ovarian cells, an organelle derived from the spectrosome. It anchors the mitotic spindle pole to provide orientation during cystoblast cell divisions.
Synonyms: ovarian fusome organisation; ovarian fusome organization and biogenesis
(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase activity (GO:0030776)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline = S-adenosyl-L-homocysteine + N-methyl-(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline.
Synonyms: (RS)-tetrahydrobenzylisoquinoline N-methyltransferase activity; norreticuline N-methyltransferase activity; S-adenosyl-L-methionine:(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase activity
(S)-tetrahydroprotoberberine N-methyltransferase activity (GO:0030782)
Namespace: molecular_function
Definition: Catalysis of the reaction: an (S)-7,8,13,14-tetrahydroprotoberberine + S-adenosyl-L-methionine = an (S)-cis-N-methyl-7,8,13,14-tetrahydroprotoberberine + S-adenosyl-L-homocysteine.
Synonyms: S-adenosyl-L-methionine:(S)-7,8,13,14-tetrahydroprotoberberine cis-N-methyltransferase activity; tetrahydroprotoberberine cis-N-methyltransferase activity
(RS)-norcoclaurine 6-O-methyltransferase activity (GO:0030786)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + (RS)-norcoclaurine = S-adenosyl-L-homocysteine + (RS)-coclaurine.
Synonyms: S-adenosyl-L-methionine:(RS)-norcoclaurine 6-O-methyltransferase activity
methyl jasmonate methylesterase activity (GO:0030795)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + a jasmonate = S-adenosyl-L-homocysteine + a methyljasmonate.
Synonyms: jasmonic acid carboxyl methyltransferase activity; S-adenosyl-L-methionine:jasmonate O-methyltransferase activity; S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase activity
obsolete positive regulation of cyclic nucleotide catabolic process (GO:0030807)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of chemical reactions and pathways resulting in the breakdown of cyclic nucleotides.
Synonyms: activation of cyclic nucleotide catabolic process; positive regulation of cyclic nucleotide breakdown; positive regulation of cyclic nucleotide catabolism; positive regulation of cyclic nucleotide degradation; stimulation of cyclic nucleotide catabolic process; up regulation of cyclic nucleotide catabolic process; up-regulation of cyclic nucleotide catabolic process; upregulation of cyclic nucleotide catabolic process
Comment: The reason for obsoletion is that this term represents the regulation of a signaling pathway, not regulation of metabolism.
obsolete positive regulation of cAMP metabolic process (GO:0030816)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
Synonyms: activation of cAMP metabolic process; positive regulation of 3',5' cAMP metabolic process; positive regulation of 3',5' cAMP metabolism; positive regulation of 3',5'-cAMP metabolic process; positive regulation of 3',5'-cAMP metabolism; positive regulation of adenosine 3',5'-cyclophosphate metabolic process; positive regulation of adenosine 3',5'-cyclophosphate metabolism; positive regulation of cAMP metabolism; positive regulation of cyclic AMP metabolic process; positive regulation of cyclic AMP metabolism; stimulation of cAMP metabolic process; up regulation of cAMP metabolic process; up-regulation of cAMP metabolic process; upregulation of cAMP metabolic process
Comment: The reason for obsoletion is that this term represents the regulation of a signaling pathway, not regulation of metabolism.
obsolete positive regulation of cAMP catabolic process (GO:0030822)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
Synonyms: activation of cAMP catabolic process; positive regulation of 3',5' cAMP catabolic process; positive regulation of 3',5' cAMP catabolism; positive regulation of 3',5'-cAMP catabolic process; positive regulation of 3',5'-cAMP catabolism; positive regulation of adenosine 3',5'-cyclophosphate catabolic process; positive regulation of adenosine 3',5'-cyclophosphate catabolism; positive regulation of cAMP breakdown; positive regulation of cAMP catabolism; positive regulation of cAMP degradation; positive regulation of cyclic AMP catabolic process; positive regulation of cyclic AMP catabolism; stimulation of cAMP catabolic process; up regulation of cAMP catabolic process; up-regulation of cAMP catabolic process; upregulation of cAMP catabolic process
Comment: The reason for obsoletion is that this term represents the regulation of a signaling pathway, not regulation of metabolism.
regulation of actin filament length (GO:0030832)
Namespace: biological_process
Definition: Any process that controls the length of actin filaments in a cell.
Comment: Note that the syntax of the definition of this term is different from the usual regulation syntax because it describes regulation of a trait rather than regulation of a process.
regulation of actin filament polymerization (GO:0030833)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
Synonyms: regulation of actin polymerization
negative regulation of intermediate filament depolymerization (GO:0030843)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of intermediate filament depolymerization.
Synonyms: down regulation of intermediate filament depolymerization; down-regulation of intermediate filament depolymerization; downregulation of intermediate filament depolymerization; inhibition of intermediate filament depolymerization; negative regulation of intermediate filament polymerization and/or depolymerization
Comment: Note that this term was split from 'negative regulation of intermediate filament polymerization and/or depolymerization ; GO:0045825' (sibling term 'negative regulation of intermediate filament polymerization ; GO:0030840').
negative regulation of epithelial cell differentiation (GO:0030857)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation.
Synonyms: down regulation of epithelial cell differentiation; down-regulation of epithelial cell differentiation; downregulation of epithelial cell differentiation; inhibition of epithelial cell differentiation
mammary gland development (GO:0030879)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages.
Synonyms: mammogenesis
retromer complex (GO:0030904)
Namespace: cellular_component
Definition: A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
response to deep water (GO:0030912)
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 deep water stimulus, being immersed in standing deep water throughout the life cycle.
Comment: Note that this term should not be confused with 'response to flooding ; GO:0009413'; which refers to immersion in water on a shorter time scale.
midbrain-hindbrain boundary development (GO:0030917)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages.
Synonyms: isthmic organizer development; isthmomesencephalic boundary development; isthmus development; MHB development; midbrain-hindbrain orgainizer development
obsolete metal incorporation into metallo-oxygen cluster (GO:0030923)
Namespace: biological_process
Definition: OBSOLETE. The formation of a cluster of several metal atoms, including manganese or calcium, with one or more bridging (mu-bond) oxygen atoms; amino acids residues in proteins that may ligate the metal oxygen cluster are histidine, aspartate, and glutamate.
Comment: This term represents a molecular function.
obsolete sheet-forming collagen trimer (GO:0030935)
Namespace: cellular_component
Definition: OBSOLETE. A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers assemble into a sheet.
Synonyms: hexagonal network-forming collagen
Comment: This term was obsoleted because it was an unnecessary grouping term.
obsolete protein tyrosine phosphatase activity, via thiol-phosphate intermediate (GO:0030945)
Namespace: molecular_function
Definition: OBSOLETE. The catalysis of phosphate removal from a phosphotyrosine using cysteine as a nucleophile and proceed by means of a thiol-phosphate intermediate.
Comment: This term was obsoleted because it represents a specific substrate of protein tyrosine phosphatase activity ; GO:0004725.
protein tyrosine phosphatase activity, metal-dependent (GO:0030946)
Namespace: molecular_function
Definition: Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate. This reaction requires metal ions.
alpha-glucan catabolic process (GO:0030980)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of alpha-glucans.
Synonyms: alpha-glucan breakdown; alpha-glucan catabolism; alpha-glucan degradation
high molecular weight kininogen binding (GO:0030985)
Namespace: molecular_function
Definition: Binding to a kininogen of high molecular mass.
Synonyms: HK binding; HMW kininogen binding
potassium ion-transporting ATPase complex (GO:0031004)
Namespace: cellular_component
Definition: Protein complex that carries out the reaction: ATP + H2O + K+(out) = ADP + phosphate + K+(in). It is a high affinity potassium uptake system. The E. coli complex consists of 4 proteins: KdpA is the potassium ion translocase, KdpB is the ATPase, and KdpC and KdpF seem to be involved in assembly and stabilization of the complex.
Synonyms: Kdp system complex
pre-miRNA processing (GO:0031054)
Namespace: biological_process
Definition: A process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
Synonyms: pre-microRNA processing
obsolete positive regulation of histone methylation (GO:0031062)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of the covalent addition of methyl groups to histones.
Synonyms: activation of histone methylation; stimulation of histone methylation; up regulation of histone methylation; up-regulation of histone methylation; upregulation of histone methylation
Comment: This term was obsoleted because it represents a molecular function.
obsolete positive regulation of histone deacetylation (GO:0031065)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of the removal of acetyl groups from histones.
Synonyms: activation of histone deacetylation; stimulation of histone deacetylation; up regulation of histone deacetylation; up-regulation of histone deacetylation; upregulation of histone deacetylation
Comment: This term was obsoleted because it represents a molecular function.
cysteine desulfurase activity (GO:0031071)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
Synonyms: cysteine desulfurylase activity; IscS; L-cysteine:enzyme cysteine sulfurtransferase activity; NIFS; SufS
BLOC-1 complex (GO:0031083)
Namespace: cellular_component
Definition: A protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules. Many of the protein subunits are conserved between mouse and human; the mouse complex contains the Pallidin, Muted, Cappuccino, Dysbindin, Snapin, BLOS1, BLOS2, AND BLOS3 proteins.
nuclear-transcribed mRNA catabolic process, deadenylation-independent decay (GO:0031086)
Namespace: biological_process
Definition: A pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of steps that is independent of deadenylation, but requires decapping followed by transcript decay, and that can regulate mRNA stability.
Synonyms: deadenylation-independent mRNA decay; deadenylylation-independent mRNA decay; mRNA breakdown, deadenylation-independent decay; mRNA catabolic process, deadenylation-independent; mRNA catabolic process, deadenylylation-independent; mRNA catabolism, deadenylation-independent; mRNA catabolism, deadenylation-independent decay; mRNA catabolism, deadenylylation-independent; mRNA degradation, deadenylation-independent decay; nuclear mRNA catabolic process, deadenylation-independent decay
stress-activated protein kinase signaling cascade (GO:0031098)
Namespace: biological_process
Definition: The series of molecular signals in which a stress-activated protein kinase (SAPK) cascade relays a signal.
Synonyms: JNK signaling pathway; JNK signalling pathway; SAPK signaling pathway; SAPK signalling pathway; stress-activated protein kinase signaling pathway; stress-activated protein kinase signalling pathway
fin regeneration (GO:0031101)
Namespace: biological_process
Definition: The regrowth of fin tissue following its loss or destruction.
rRNA 3'-end processing (GO:0031125)
Namespace: biological_process
Definition: Any process involved in forming the mature 3' end of an rRNA molecule.
Synonyms: rRNA 3' end processing
regulation of axon diameter (GO:0031133)
Namespace: biological_process
Definition: Any process that modulates the rate, direction or extent of axon growth such that the correct diameter is attained and maintained.
histone H3K79 methyltransferase activity (GO:0031151)
Namespace: molecular_function
Definition: Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). This reaction is the addition of a methyl group to the lysine residue at position 79 of the histone H3 protein.
Synonyms: histone H3K79 methylase activity; histone lysine N-methyltransferase activity (H3-K79 specific); histone methylase activity (H3-K79 specific); histone methyltransferase activity (H3-K79 specific); histone-H3K79 methyltransferase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
post-translational protein targeting to membrane, docking (GO:0031203)
Namespace: biological_process
Definition: The process in which the signal sequence of a translated protein binds to and forms a complex with the Sec complex.
Synonyms: posttranslational protein membrane targeting, docking; posttranslational protein targeting to membrane, docking; protein docking during posttranslational protein targeting to membrane; Sec-translated protein complex assembly
obsolete anchored component of membrane (GO:0031225)
Namespace: cellular_component
Definition: OBSOLETE. The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
Synonyms: anchored to membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
obsolete intrinsic component of external side of plasma membrane (GO:0031233)
Namespace: cellular_component
Definition: OBSOLETE. The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
Synonyms: intrinsic to external leaflet of plasma membrane; intrinsic to external side of plasma membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
pseudopodium membrane (GO:0031260)
Namespace: cellular_component
Definition: The portion of the plasma membrane surrounding a pseudopodium.
obsolete ATPase-coupled amine transporter activity (GO:0031263)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: ATP + H2O + amine(out) = ADP + phosphate + amine(in).
Synonyms: amine ABC transporter; amine-transporting ATPase activity; ATP-dependent amine transporter activity
Comment: This term was obsoleted because it corresponds to a wide range of substrates not necessarily transported by the same transporter. See https://en.wikipedia.org/wiki/Amine.
obsolete regulation of guanylate cyclase activity (GO:0031282)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of guanylate cyclase activity.
Comment: This term was obsoleted because it represents a molecular function. Consider molecular function regulator activity ; GO:0098772 or a child.
negative regulation of sorocarp stalk cell differentiation (GO:0031286)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of sorocarp stalk cell differentiation. An example of this process is found in Dictyostelium discoideum.
Synonyms: down regulation of stalk cell differentiation; down-regulation of stalk cell differentiation; downregulation of stalk cell differentiation; inhibition of stalk cell differentiation; negative regulation of stalk cell differentiation
obsolete integral component of mitochondrial outer membrane (GO:0031307)
Namespace: cellular_component
Definition: OBSOLETE. The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
Synonyms: integral to mitochondrial outer membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
obsolete integral component of nuclear outer membrane (GO:0031309)
Namespace: cellular_component
Definition: OBSOLETE. The component of the nuclear outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
Synonyms: integral to nuclear outer membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
detection of cAMP (GO:0031319)
Namespace: biological_process
Definition: The series of events in which a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus is received by a cell and converted into a molecular signal; cAMP is the nucleotide cyclic AMP.
Synonyms: 3',5'-cAMP detection; 3',5'-cAMP sensing; cAMP detection; cAMP sensing; cyclic AMP detection; detection of 3',5' cAMP; detection of 3',5'-cAMP; detection of adenosine 3',5'-cyclophosphate; detection of cyclic AMP
obsolete negative regulation of sulfur amino acid metabolic process (GO:0031336)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids.
Synonyms: down regulation of sulfur amino acid metabolic process; down-regulation of sulfur amino acid metabolic process; downregulation of sulfur amino acid metabolic process; inhibition of sulfur amino acid metabolic process; negative regulation of sulfur amino acid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
regulation of cell killing (GO:0031341)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism.