LiteFold/GO huggingface dataset:
protein import into peroxisome matrix, docking (GO:0016560)
Namespace: biological_process
Definition: The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
Synonyms: peroxisome matrix protein import, docking; peroxisome receptor docking; protein docking during peroxisome matrix protein import; protein docking during protein import into peroxisome matrix; protein docking during protein transport into peroxisome matrix; protein transport into peroxisome matrix, docking
protein import into peroxisome matrix, translocation (GO:0016561)
Namespace: biological_process
Definition: The process in which proteins are moved across the peroxisomal membrane into the matrix. It is likely that the peroxisome targeting sequence receptor remains associated with cargo proteins during translocation.
Synonyms: peroxisome matrix protein import, translocation; peroxisome receptor translocation; protein translocation during peroxisome matrix protein import; protein translocation during protein import into peroxisome matrix; protein translocation during protein transport into peroxisome matrix; protein transport into peroxisome matrix, translocation
protein import into peroxisome matrix, receptor recycling (GO:0016562)
Namespace: biological_process
Definition: The process in which peroxisome targeting sequence receptors dissociates from cargo proteins and are returned to the cytosol.
Synonyms: peroxisome matrix protein import, receptor recycling; peroxisome receptor recycling; protein transport into peroxisome matrix, receptor recycling; PTS receptor recycling; receptor recycling during peroxisome matrix protein import; receptor recycling during protein import into peroxisome matrix; receptor recycling during protein transport into peroxisome matrix
obsolete transcription activator activity (GO:0016563)
Namespace: molecular_function
Definition: OBSOLETE. Any transcription regulator activity required for initiation or upregulation of transcription.
Synonyms: transcription activating factor; transcription activator activity; transcriptional activator activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete transcription repressor activity (GO:0016564)
Namespace: molecular_function
Definition: OBSOLETE. Any transcription regulator activity that prevents or downregulates transcription.
Synonyms: negative transcriptional regulator activity; transcription repressor activity; transcriptional repressor activity
Comment: This term was obsoleted because it is essentially identical to a Process term (specifically the Biological Process term which has been selected as a term to consider for reannotation), i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of this gene product is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete general transcriptional repressor activity (GO:0016565)
Namespace: molecular_function
Definition: OBSOLETE. Any activity that stops or downregulates transcription of genes globally, and is not specific to a particular gene or gene set.
Synonyms: general transcriptional repressor activity
Comment: This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of your repressor is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
obsolete specific transcriptional repressor activity (GO:0016566)
Namespace: molecular_function
Definition: OBSOLETE. Any activity that stops or downregulates transcription of specific genes or sets of genes.
Synonyms: specific transcriptional repressor activity
Comment: This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism. To transfer all annotations without review, the BP term indicated is considered to be equivalent and thus the only appropriate destination for all annotations. To reannotate to a MF term, you will probably need to revisit the original literature or other primary data because this "MF" term was not defined in terms of mechanism of action and there are multiple possibilities in the revised MF structure. In reannotation, please also consider descendent terms of the suggested MF terms as a more specific term may be more appropriate than the MF terms indicated. Please be aware that you may wish to request a new term if the mechanism of action of your repressor is not yet represented or if you are annotating for an RNAP different than one for which there is a specific suggested term. Also note that if there is no information about how the gene product acts, it may be appropriate to annotate to the root term for molecular_function.
protein ubiquitination (GO:0016567)
Namespace: biological_process
Definition: The process in which one or more ubiquitin groups are added to a protein.
Synonyms: protein ubiquitinylation; protein ubiquitylation
obsolete covalent chromatin modification (GO:0016569)
Namespace: biological_process
Definition: OBSOLETE. The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups.
Synonyms: chromatin modification
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone modification (GO:0016570)
Namespace: biological_process
Definition: OBSOLETE. The covalent alteration of one or more amino acid residues within a histone protein.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone methylation (GO:0016571)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by addition of methyl groups.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone phosphorylation (GO:0016572)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by addition of phosphate groups.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone acetylation (GO:0016573)
Namespace: biological_process
Definition: OBSOLETE. The modification of a histone by the addition of an acetyl group.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone deacetylation (GO:0016575)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by removal of acetyl groups.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone dephosphorylation (GO:0016576)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by removal of phosphate groups.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone demethylation (GO:0016577)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by removal of methyl groups.
Comment: This term was obsoleted because it represents a molecular function.
obsolete histone deubiquitination (GO:0016578)
Namespace: biological_process
Definition: OBSOLETE. The modification of histones by removal of ubiquitin groups.
Synonyms: histone deubiquitinylation; histone deubiquitylation
Comment: This term was obsoleted because it represents a molecular function.
protein deubiquitination (GO:0016579)
Namespace: biological_process
Definition: The removal of one or more ubiquitin groups from a protein.
Synonyms: deubiquitination; protein deubiquitinylation; protein deubiquitylation
obsolete Sin3 complex (GO:0016580)
Namespace: cellular_component
Definition: OBSOLETE. A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
Comment: This term was added in error and is ambiguous.
NuRD complex (GO:0016581)
Namespace: cellular_component
Definition: An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
Synonyms: Mi-2 complex; NRD complex; nucleosome remodeling and histone deacetylation complex
obsolete non-covalent chromatin modification (GO:0016582)
Namespace: biological_process
Definition: OBSOLETE. The alteration of DNA or protein in chromatin by the non-covalent addition or removal of chemical groups.
Comment: This term was made obsolete because it was added in error; its usefulness is unclear.
obsolete nucleosome modeling (GO:0016583)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: nucleosome modeling
Comment: This term was made obsolete because it has been replaced by more specific terms.
obsolete nucleosome positioning (GO:0016584)
Namespace: biological_process
Definition: OBSOLETE. Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another.
Synonyms: nucleosome spacing
Comment: This term was obsoleted because it represents a molecular function.
obsolete chromatin remodeling complex (GO:0016585)
Namespace: cellular_component
Definition: OBSOLETE. Any complex that mediates dynamic changes in eukaryotic chromatin.
Synonyms: chromatin remodeling complex; chromatin remodelling complex; nucleosome remodeling complex
Comment: This term was made obsolete because its definition no longer reflects and cannot be modified to be consistent with the current state of knowledge.
RSC-type complex (GO:0016586)
Namespace: cellular_component
Definition: A SWI/SNF-type complex that contains a bromodomain containing-protein, such as yeast Rsc1 or Rsc4 or mammalian PB1/BAF180. The RSC complex is generally recruited to RNA polymerase III promoters and is specifically recruited to RNA polymerase II promoters by transcriptional activators and repressors; it is also involved in non-homologous end joining.
Synonyms: PBAF complex; Polybromo- and BAF containing complex; SWI/SNF complex B
NURF complex (GO:0016589)
Namespace: cellular_component
Definition: An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
Synonyms: nucleosome remodeling factor complex
ACF complex (GO:0016590)
Namespace: cellular_component
Definition: An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and generally no other subunits, though Xenopus is an exception with a third non-conserved subunit. ACF plays roles in regulation of RNA polymerase II transcription and in DNA replication and repair.
Synonyms: ATP-utilizing chromatin assembly and remodeling factor complex
RNA polymerase II, holoenzyme (GO:0016591)
Namespace: cellular_component
Definition: A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
Synonyms: DNA-directed RNA polymerase II, holoenzyme
mediator complex (GO:0016592)
Namespace: cellular_component
Definition: A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
Synonyms: CDK8-containing TRAP/mediator complex; L mediator complex; Srb-mediator complex; TRAP complex
Cdc73/Paf1 complex (GO:0016593)
Namespace: cellular_component
Definition: A multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.
Synonyms: Paf1 complex; Paf1p complex
glycine binding (GO:0016594)
Namespace: molecular_function
Definition: Binding to glycine, aminoethanoic acid.
Synonyms: aminoacetic acid binding; aminoethanoic acid binding; Gly binding
thienylcyclohexylpiperidine binding (GO:0016596)
Namespace: molecular_function
Definition: Binding to thienylcyclohexylpiperidine.
Synonyms: TCP binding
amino acid binding (GO:0016597)
Namespace: molecular_function
Definition: Binding to an amino acid, organic acids containing one or more amino substituents.
protein arginylation (GO:0016598)
Namespace: biological_process
Definition: The conjugation of arginine to the N-terminal aspartate or glutamate of a protein; required for the degradation of the protein via the ubiquitin pathway.
Synonyms: protein amino acid arginylation
flotillin complex (GO:0016600)
Namespace: cellular_component
Definition: A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.
Comment: See also the cellular component term 'caveola ; GO:0005901'.
Rac protein signal transduction (GO:0016601)
Namespace: biological_process
Definition: An intracellular signaling cassette in which a small monomeric GTPase of the Rac subfamily relays a signal.
Synonyms: Rac mediated signal transduction
CCAAT-binding factor complex (GO:0016602)
Namespace: cellular_component
Definition: A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
Synonyms: CBF complex; NF-Y transcription factor complex; nuclear transcription factor Y complex
glutaminyl-peptide cyclotransferase activity (GO:0016603)
Namespace: molecular_function
Definition: Catalysis of the reaction: N-terminal L-glutaminyl-[peptide] = N-terminal 5-oxo-L-prolyl-[peptide] + NH4+.
Synonyms: glutaminyl cyclase activity; glutaminyl-transfer ribonucleate cyclotransferase activity; glutaminyl-tRNA cyclotransferase activity; L-glutaminyl-peptide gamma-glutamyltransferase (cyclizing)
nuclear body (GO:0016604)
Namespace: cellular_component
Definition: Membraneless organelle present in the nucleoplasm and usually visible by confocal microscopy.
PML body (GO:0016605)
Namespace: cellular_component
Definition: A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
Synonyms: ND10; nuclear dot; PML NB; PML nuclear body
nuclear speck (GO:0016607)
Namespace: cellular_component
Definition: A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
Synonyms: nuclear speckle; nuclear speckles; speckle domain; speckle focus; splicing speckle
growth hormone-releasing hormone activity (GO:0016608)
Namespace: molecular_function
Definition: The action characteristic of growth hormone-releasing hormone, any of a family of peptide hormones that act on the anterior pituitary to stimulate the secretion of growth hormone and exert a trophic effect on the gland.
Synonyms: GHRF activity; GHRH activity
nitrogenase complex (GO:0016610)
Namespace: cellular_component
Definition: An enzyme complex composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase is tetrameric with an alpha2-beta2 structure and nitrogenase reductase is a homodimer, and both are associated with metal ions, which differ between species. Both proteins are required for the enzyme activity of the complex, the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen.
iron-iron nitrogenase complex (GO:0016611)
Namespace: cellular_component
Definition: An enzyme complex containing an iron-iron cluster found in species such as the photosynthetic bacterium Rhodobacter capsulatus. It is composed of two main subunits, dinitrogenase and nitrogenase reductase. Dinitrogenase, the iron-iron containing subunit, has an alpha1-beta2 or alpha2-beta2 structure, and the nitrogenase reductase subunit is a homodimer. Functions in the catalysis of the formation of oxidized ferredoxin and ammonia from reduced ferredoxin and nitrogen.
Comment: Note that it is not established whether the nitrogenase exists in vivo in a specific particle or whether the nitrogenase proteins are bound nonspecifically to the membranes of some cells.
molybdenum-iron nitrogenase complex (GO:0016612)
Namespace: cellular_component
Definition: An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.
Synonyms: molybdenum-iron nitrogenase activity
vanadium-iron nitrogenase complex (GO:0016613)
Namespace: cellular_component
Definition: An enzyme complex containing a vanadium-iron cluster found in some species, such as Azotobacter vinelandii. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the vanadium-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.
Synonyms: vanadium-iron nitrogenase activity
oxidoreductase activity, acting on CH-OH group of donors (GO:0016614)
Namespace: molecular_function
Definition: Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
Synonyms: oxidoreductase activity, acting on the CH-OH group of donors, other acceptors
malate dehydrogenase activity (GO:0016615)
Namespace: molecular_function
Definition: Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)
Namespace: molecular_function
Definition: Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
4-oxoproline reductase activity (GO:0016617)
Namespace: molecular_function
Definition: Catalysis of the reaction: 4-hydroxy-L-proline + NAD+ = 4-oxoproline + NADH + H+.
Synonyms: 4-hydroxy-L-proline:NAD+ oxidoreductase activity; hydroxy-L-proline oxidase activity; hydroxyproline oxidase activity