LiteFold/GO huggingface dataset:
Ire1 complex (GO:1990332)
Namespace: cellular_component
Definition: A type-I transmembrane protein complex located in the endoplasmic reticulum (ER) consisting of an IRE1-IRE1 dimer, which forms in response to the accumulation of unfolded protein in the ER. The dimeric complex has endoribonuclease (RNase) activity and evokes the unfolded protein response (UPR) by cleaving an intron of a mRNA coding for the transcription factor HAC1 in yeast or XBP1 in mammals; the complex cleaves a single phosphodiester bond in each of two RNA hairpins (with non-specific base paired stems and loops of consensus sequence CNCNNGN, where N is any base) to remove an intervening intron from the target transcript.
Synonyms: ER-bound kinase/endoribonuclease (RNase), inositol-requiring enzyme-1; ERN1 complex; Ire1 complex dimer; Ire1 complex homodimer; Ire1 complex homooligomer; IRE1 dimer
Comment: An example of this is Ire1 in S. cerevisiae (P32361) in PMID:18191223 (inferred from direct assay).
mitotic checkpoint complex, CDC20-MAD2 subcomplex (GO:1990333)
Namespace: cellular_component
Definition: A protein complex involved in the spindle checkpoint, preventing the activation of the anaphase-promoting complex until all chromosomes are correctly attached in a bipolar fashion to the mitotic spindle. In budding yeast this complex consists of Mad2p and Cdc20p, and in mammalian cells it consists of MAD2 and CDC20.
Synonyms: CDC20-MAD2 complex
Comment: An example of this is cdc20 in Saccharomyces cerevisiae (P26309) in PMID:15879521 (inferred from direct assay).
Bfa1-Bub2 complex (GO:1990334)
Namespace: cellular_component
Definition: A protein complex that acts as a two-component GTPase-activating protein for Tem1 GTPase, thus regulating a signal transduction cascade, called the mitotic exit network (MEN), which is required for mitotic exit and cytokinesis. Bub2/Bfa1 keeps Tem1 inactive until the spindle is properly oriented, thus inhibiting MEN activation.
laminin-522 trimer (GO:1990339)
Namespace: cellular_component
Definition: A laminin complex composed of alpha5, beta2 and gamma2 polypeptide chains.
Synonyms: laminin-522; laminin-522 complex
laminin-523 trimer (GO:1990340)
Namespace: cellular_component
Definition: A laminin complex composed of alpha5, beta2 and gamma3 polypeptide chains.
Synonyms: laminin-15 complex; laminin-523
thrombospondin complex (GO:1990341)
Namespace: cellular_component
Definition: A homotrimeric or homopentameric glycoprotein that functions at the interface of the cell membrane and the extracellular matrix through its interactions with proteins and proteoglycans, such as collagens, integrins and fibronectin, to regulate matrix structure and cellular behaviour.
heterochromatin island (GO:1990342)
Namespace: cellular_component
Definition: A region of facultative heterochromatin formed dynamically at specific loci in response to environmental signals, independently of RNAi.
Comment: An example of this type of heterochromatin is found in Schizosaccharomyces pombe, where heterochromatin islands are formed at meiotic genes during vegetative (mitotic) growth.
secondary cell septum biogenesis (GO:1990344)
Namespace: biological_process
Definition: A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a secondary cell septum following nuclear division.
BID-BCL-xl complex (GO:1990346)
Namespace: cellular_component
Definition: A heterodimeric protein complex consisting of BID and BCL-xl, members of the Bcl-2 family of anti- and proapoptotic regulators.
obsolete G*/A mismatch-specific adenine-DNA glycosylase activity (GO:1990347)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the removal of adenine misinserted into nascent strand opposite 8-oxoG in the template by adenine DNA glycosylase activity. The reaction leaves an apyrimidinic (AP) site.
Synonyms: G*/A mismatch-specific adenine-DNA glycosylase activity
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete G/A mismatch specific adenine DNA glycosylase activity (GO:1990348)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the removal of adenine misinserted into nascent strand opposite guanine in the template by adenine DNA glycosylase activity. The reaction leaves an apurinic AP site. I also requested same term but for Go/A mismatch. If you think it is better to make one term for mismatched adenine that is fine by me.
Synonyms: G/A mismatch specific adenine DNA glycosylase activity
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
gap junction-mediated intercellular transport (GO:1990349)
Namespace: biological_process
Definition: The movement of substances between cells via gap junctions. A gap junction is a fine cytoplasmic channel, found in animal cells, that connects the cytoplasm of one cell to that of an adjacent cell, allowing ions and other molecules to pass freely between the two cells.
glucose transporter complex (GO:1990350)
Namespace: cellular_component
Definition: A protein complex facilitating glucose transport into, out of or within a cell, or between cells.
Comment: An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).
transporter complex (GO:1990351)
Namespace: cellular_component
Definition: A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.
Comment: An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).
BRE1 E3 ubiquitin ligase complex (GO:1990352)
Namespace: cellular_component
Definition: A homodimeric protein complex composed of the E3 ubiquitin-protein ligase BRE1. Plays a role in regulating association of RNA polymerase II with active genes.
Synonyms: BRE1 E3 ubiquitin-protein ligase complex; BRE1 oligomer
Comment: An example of this is BRE1 in Saccharomyces cerevisiae (UniProt symbol Q07457) in PMID:19531475 (inferred from direct assay).
Fused-Smurf ubiquitin ligase complex (GO:1990353)
Namespace: cellular_component
Definition: A ubiquitin ligase complex. In D. melanogaster, it regulates ubiquitination and proteolysis of the BMP receptor Thickveins in cystoblasts, potentially by controlling Tkv ubiquitination and degradation.
Comment: An example of this is FUSED in Drosophila melanogaster (UniProt symbol P23647) in PMID:21145463 (inferred from direct assay).
activated SUMO-E1 ligase complex (GO:1990354)
Namespace: cellular_component
Definition: A protein complex consisting of a SUMO protein bound to a SUMO activating enzyme complex. Activation by the E1 complex and linkage to the E2 enzyme UBE2I is required for the formation of covalent bonds between SUMO and its ultimate target proteins.
Synonyms: SUMO-SAE1/2 complex
Comment: An example of this is SAE1 in human (UniProt symbol Q9UBE0) in PMID:15660128 (inferred from direct assay).
obsolete L-methionine salvage from methionine sulphoxide (GO:1990355)
Namespace: biological_process
Definition: OBSOLETE. The generation of L-methionine from methionine sulphoxide.
Synonyms: methionine salvage from methionine sulphoxide
Comment: The reason for obsoletion is that the term represents a single step process and is not generally considered a salvage process.
obsolete sumoylated E2 ligase complex (GO:1990356)
Namespace: cellular_component
Definition: OBSOLETE. A protein complex consisting of a SUMO (small ubiquitin-related modifier) protein bound to a SUMO-conjugating E2 ligase. Sumoylation of the E2 ligase is an intermediate step required for the formation of covalent bonds between a SUMO protein and its ultimate protein target. SUMO is transferred to the E2 ligase by a SUMO-activating E1 enzyme. Sumoylation of the target protein is either facilitated directly by the sumoylated E2 ligase or aided by an optional E3 ligase.
Comment: This term was obsoleted because it is represents a complex with a modified (sumoylated) subunit; this is out of the scope of GO.
terminal web (GO:1990357)
Namespace: cellular_component
Definition: An actin-rich cytoskeletal network located beneath the microvilli of the apical plasma membrane of polarized epithelial cells. In addition to actin filaments, the terminal web may contain actin-binding proteins, myosin motor proteins, and intermediate filaments. The terminal web can function as a contractile structure that influences the spatial distribution of microvilli as well as the development and morphogenesis of tissues containing polarized epithelial cells.
xylanosome (GO:1990358)
Namespace: cellular_component
Definition: A multifunctional supermolecular complex, containing several proteins with hemicellulase activity. Functions to hydrolyze hemicellulose.
Synonyms: xylanolytic complex
stress response to zinc ion (GO:1990359)
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 disturbance in organismal or cellular homeostasis caused by a zinc ion stimulus.
Synonyms: response to zinc ion stress; response to zinc toxicity; stress response to zinc
PKM2 protein kinase complex (GO:1990360)
Namespace: cellular_component
Definition: A protein complex capable of phosphorylating a large number of protein targets. Contributes to cell proliferation under glycose starvation conditions. In human, the complex is present as a dimer.
Synonyms: PKM2-SAICAR complex; PKM2-SAICAR protein kinase complex
PKM2 pyruvate kinase complex (GO:1990361)
Namespace: cellular_component
Definition: A protein complex capable of pyruvate kinase activity. PKM2 only exists as homotetramer when bound to beta-d-fructofuranose 1,6-bisphosphate (CHEBI:28013).
Synonyms: PKM2 homotetramer
Comment: An example of this is PKM2 in human (P14618) in PMID:24606918 (inferred from direct assay).
butanol dehydrogenase (NAD+) activity (GO:1990362)
Namespace: molecular_function
Definition: Catalysis of the reaction: butan-1-ol + NAD+ = butanal + H+ + NADH.
Synonyms: butanol dehydrogenase activity
obsolete response to hydrolysate (GO:1990363)
Namespace: biological_process
Definition: OBSOLETE. 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 hydrolysate (any product of hydrolysis).
Synonyms: response to hydrolysate
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete response to aldehyde (GO:1990364)
Namespace: biological_process
Definition: OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldehyde.
Synonyms: response to aldehyde
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete response to phenol (GO:1990365)
Namespace: biological_process
Definition: OBSOLETE. 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 phenols.
Synonyms: response to phenol
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete response to organic acid (GO:1990366)
Namespace: biological_process
Definition: OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic acid.
Synonyms: response to organic acid
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete process resulting in tolerance to hydrolysate (GO:1990368)
Namespace: biological_process
Definition: OBSOLETE. A response that results in a state of tolerance to hydrolysate (product of hydrolysis).
Synonyms: process resulting in tolerance to hydrolysate
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete process resulting in tolerance to aldehyde (GO:1990370)
Namespace: biological_process
Definition: OBSOLETE. A response that results in a state of tolerance to aldehyde.
Comment: This term was obsoleted because it does not represent a clear process.
obsolete process resulting in tolerance to phenol (GO:1990371)
Namespace: biological_process
Definition: OBSOLETE. A response that results in a state of tolerance to phenol.
Comment: This term was obsoleted because it does not represent a clear process.
obsolete process resulting in tolerance to organic acid (GO:1990372)
Namespace: biological_process
Definition: OBSOLETE. A response that results in a state of tolerance to organic acid.
Comment: This term was obsoleted because it does not represent a clear process.
baculum development (GO:1990375)
Namespace: biological_process
Definition: The reproductive developmental process whose specific outcome is the progression of the baculum over time, from its formation to the mature structure.
Synonyms: os penis development; penile bone development; penis bone development
obsolete negative regulation of G1/S transition of mitotic cell cycle by positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation (GO:1990376)
Namespace: biological_process
Definition: OBSOLETE. A positive regulation of transcription from RNA polymerase II promoter in response to nitrogen starvation that results in negative regulation of mitotic G1/S transition.
Comment: This term was made obsolete because it would not be used for annotation.
organomineral extracellular matrix (GO:1990377)
Namespace: cellular_component
Definition: An extracellular matrix consisting of a densely packed organomineral assembly in which the mineral phase represents the majority of the material by weight.
Comment: An example is found in shell calcitic prisms of the Mediterranean fan mussel Pinna nobilis (PMID:15994301), but the term may also be useful to annotate bone and eggshell proteins.
lipid transport across blood-brain barrier (GO:1990379)
Namespace: biological_process
Definition: The directed movement of lipid molecules passing through the blood-brain barrier.
Synonyms: lipid transport across blood brain barrier
K48-linked deubiquitinase activity (GO:1990380)
Namespace: molecular_function
Definition: Hydrolysis of a ubiquitin unit from a ubiquitinated protein linked via the Lys48 residue of ubiquitin.
Synonyms: K48-specific deubiquitinase activity; K48-specific deubiquitinating activity; Lys48-specific deubiquitinase activity
ubiquitin-specific protease binding (GO:1990381)
Namespace: molecular_function
Definition: Binding to a ubiquitin-specific protease.
Synonyms: deubiquitinase binding; deubiquitinating enzyme binding
obsolete melanosome assembly (GO:1990382)
Namespace: biological_process
Definition: OBSOLETE. The aggregation, arrangement and bonding together of a set of components to form a melanosome, a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored.
Synonyms: melanosome biogenesis
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
cellular response to biotin starvation (GO:1990383)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of biotin.
hyaloid vascular plexus regression (GO:1990384)
Namespace: biological_process
Definition: The developmental process in which the hyaloid vascular plexus is destroyed as a part of its normal progression.
mitotic cleavage furrow ingression (GO:1990386)
Namespace: biological_process
Definition: Advancement of the mitotic cleavage furrow from the outside of the cell inward towards the center of the cell. The cleavage furrow acts as a 'purse string' which draws tight to separate daughter cells during mitotic cytokinesis and partition the cytoplasm between the two daughter cells. The furrow ingresses until a cytoplasmic bridge is formed.
isogloboside biosynthetic process (GO:1990387)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of isogobliosides that begins with the synthesis of a tetrasaccharide core GalNAc-beta-1,3Gal-alpha-1,3Gal-beta-1,4Glc-ceramide. This core can be further elongated with the sequential addition of various carbohydrate units.
Synonyms: isoglobo-series glycosphingolipid biosynthesis
CUE1-UBC7 ubiquitin-conjugating enzyme complex (GO:1990389)
Namespace: cellular_component
Definition: A protein complex capable of ubiquitin-conjugating enzyme activity during ER-associated protein degradation (ERAD). In S. cerevisiae, UBC7 is the ubiquitin-conjugating enzyme (E2) and requires binding to the ER surface by CUE1.
Synonyms: CUE1-UBC7 ubiquitin-conjugating enzyme (E2)
Comment: An example of this is UBC7 in Saccharomyces cerevisiae (Q02159) in PMID:16179953 (inferred from direct assay).
protein K33-linked ubiquitination (GO:1990390)
Namespace: biological_process
Definition: A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 33 of the ubiquitin monomers, is added to a protein.
DNA repair complex (GO:1990391)
Namespace: cellular_component
Definition: A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Synonyms: DNA damage repair complex; WHY1 complex
EFF-1 complex (GO:1990392)
Namespace: cellular_component
Definition: A trimeric cell-cell fusion complex that serves as a scaffold for zippering up the extracellular domains, bringing the transmembrane segments into close proximity such that they can continue zippering within the two membranes into one. Two prefusion monomers cluster at the surface of adjacent cells. Parallel EFF-1 interactions occur across cells and a third monomer, which can come from either cell, adds on to make an intermediate, extended trimer.
Comment: An example of this is eff-1 in C. elegans (G5ECA1) in PMID:24725407 (inferred from direct assay).
3M complex (GO:1990393)
Namespace: cellular_component
Definition: A protein complex, at least composed of CUL7, CCDC8 and OBSL1, that is required for maintaining microtubule and genome integrity.
cellular response to cell wall damage (GO:1990394)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of cell wall damage. The process begins with detection of the damage and ends with a change in state or activity of the cell.
meiotic spindle pole body organization (GO:1990395)
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 meiotic spindle pole body.
single-strand break repair via homologous recombination (GO:1990396)
Namespace: biological_process
Definition: The error-free repair of a single-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
obsolete queuosine salvage (GO:1990397)
Namespace: biological_process
Definition: OBSOLETE. Any process which produces queuosine from derivatives of it, without de novo synthesis.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
Cus cation efflux complex (GO:1990398)
Namespace: cellular_component
Definition: Transmembrane complex that mediates resistance to copper and silver by cation efflux directly from the cell using the proton-motive force. Spans the inner membrane, periplasm, and outer membrane. Primarily activated under anaerobic conditions by CusR and CusS but also expressed under extreme copper stress, in aerobic growth.
Synonyms: copper efflux complex; copper efflux system; Cus cation efflux system; silver efflux complex; silver efflux system
Comment: An example of this is CusA in E. coli (UniProt symbol P38054) in PMID:23122209.
epithelium regeneration (GO:1990399)
Namespace: biological_process
Definition: The regrowth of lost or destroyed epithelium.
Synonyms: regeneration of epithelium
mitochondrial ribosomal large subunit rRNA binding (GO:1990400)
Namespace: molecular_function
Definition: Binding to a mitochondrial large ribosomal subunit RNA (LSU rRNA).
Synonyms: 21S rRNA binding; mitochondrial LSU rRNA binding
Comment: In S. cerevisiae, this is the mitochondrial 21S rRNA
embryonic liver development (GO:1990402)
Namespace: biological_process
Definition: The process occurring during the embryonic phase whose specific outcome is the progression of the liver over time, from its formation to the mature structure.
embryonic brain development (GO:1990403)
Namespace: biological_process
Definition: The process occurring during the embryonic phase whose specific outcome is the progression of the brain over time, from its formation to the mature structure.
NAD+-protein mono-ADP-ribosyltransferase activity (GO:1990404)
Namespace: molecular_function
Definition: Catalysis of the reaction: amino acyl-[protein] + NAD+ = H+ + (ADP-D-ribosyl)-amino acyl-[protein] + nicotinamide.
Synonyms: NAD+ ADP-ribosyltransferase activity; NAD+-protein ADP-ribosyltransferase activity; protein ADP-ribosylase activity; protein ADP-ribosyltransferase activity; protein mono-ADP-ribosyltransferase activity; ribosylase activity
CGRP receptor complex (GO:1990406)
Namespace: cellular_component
Definition: A transmembrane, G protein-coupled signaling receptor complex recognized by calcitonin gene-related peptides (CGRP).
Synonyms: calcitonin gene-related polypeptide receptor complex; Calcitonin-gene-related peptide receptor complex; CGRP-R complex
Comment: An example of this is CALCRL in human (Q16602) in PMID:20826335 (inferred from direct assay).
calcitonin gene-related peptide binding (GO:1990407)
Namespace: molecular_function
Definition: Binding to calcitonin gene-related peptide (CGRP).
Synonyms: calcitonin-gene-related peptide binding; calcitonin-gene-related polypeptide binding; CGRP polypeptide binding
Comment: An example of this is CALCRL in human (Q16602) in PMID:10882736 (inferred from direct assay/mutant phenotype/etc.).
calcitonin gene-related peptide receptor signaling pathway (GO:1990408)
Namespace: biological_process
Definition: The series of molecular signals initiated by an extracellular calcitonin gene-related peptide (CGRP) combining with a calcitonin gene-related peptide receptor on the surface of the target cell. Calcitonin gene-related peptide receptors may form dimers, trimers or tetramers.
Synonyms: calcitonin-gene-related peptide receptor signaling pathway; calcitonin-gene-related polypeptide receptor signaling pathway; CGRP receptor signaling pathway
Comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
adrenomedullin binding (GO:1990409)
Namespace: molecular_function
Definition: Binding to adrenomedullin (AM).
Synonyms: AM binding
Comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
adrenomedullin receptor signaling pathway (GO:1990410)
Namespace: biological_process
Definition: The series of molecular signals initiated by an extracellular adrenomedullin combining with a dimeric adrenomedullin receptor on the surface of the target cell.
Synonyms: AM receptor signaling pathway
Comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) (GO:1990411)
Namespace: molecular_function
Definition: Catalysis of the reaction: hercynylcysteine sulfoxide + 2H+ = ergothioneine + pyruvate + ammonium.