LiteFold/GO huggingface dataset:
SeqA-DNA complex (GO:1990097)
Namespace: cellular_component
Definition: A protein-DNA complex that contains an oligomer of SeqA bound to GATC sites in methylated or newly-synthesized, hemi-methylated double-stranded DNA, with preference for the latter. Binding of SeqA to hemimethylated DNA sequesters oriC, prevents re-methylation of DNA by Dam and in turn stops premature re-initiation of replication during one replication cycle.
Synonyms: SeqA-dsDNA complex; SeqA-hemimethylated DNA complex; SeqA-hemimethylation dsDNA complex
core primosome complex (GO:1990098)
Namespace: cellular_component
Definition: A protein-DNA complex containing at least one DNA helicase and one primase. Can also contain associated proteins. The helicase component continues to unwind the double-stranded DNA (dsDNA) and the primase component synthesizes a RNA primer during initiation or restart of replication.
Synonyms: core primosome
Comment: The core primosome refers to a helicase-primase complex, and should not be confused with the more general GO term 'primosome complex ; GO:1990077'.
pre-primosome complex (GO:1990099)
Namespace: cellular_component
Definition: Any of the protein-DNA complexes that contain a DNA helicase and associated protein(s) at the origin of replication, and build up to assembling the core primosome. The associated protein(s) chaperone the helicase to the DNA, and assembly of the pre-primosome is essential for the initiation or restart of replication. Pre-primosome complexes lack a primase component.
Synonyms: pre-priming complex; pre-primosome; pre-replication complex; preprimosome; preprimosome complex; prereplication complex
DnaB-DnaC complex (GO:1990100)
Namespace: cellular_component
Definition: A protein complex containing homohexameric DNA helicase DnaB, and the DNA helicase loader DnaC. The helicase loader DnaC delivers DnaB to the chromosomal origin (oriC).
Synonyms: DnaB6-DnaC3 complex; DnaB6-DnaC6 complex; helicase-loading complex
Comment: DnaB and DnaC may be present in different ratios in different forms of the DnaB-DnaC complex, including a DnaB6-DnaC3 complex active at the oriC, and a DnaB6-DnaC6 complex.
DnaA-oriC complex (GO:1990101)
Namespace: cellular_component
Definition: A protein-DNA complex containing the initiator protein DnaA bound to high-affinity recognition sites in the unique origin of replication, oriC. DnaA-oriC binding is the first step in assembly of a bacterial pre-replicative complex (pre-RC) and is responsible for the timely initiation of replication once per cell cycle.
Synonyms: DnaA-DNA complex
DnaA-DiaA complex (GO:1990102)
Namespace: cellular_component
Definition: A protein-DNA complex containing a tetramer of DiaA attached to multiple DnaA molecule bound to oriC DNA. Regulates timely initiation of chromosomal replication during the cell cycle by stimulating assembly of DnaA-oriC complexes, conformational changes in ATP-DnaA initiation complexes, and unwinding of oriC duplex DNA.
Synonyms: DnaA-DiaA-DNA complex
DnaA-HU complex (GO:1990103)
Namespace: cellular_component
Definition: A protein-DNA complex containing DNA-bound DnaA attached to HU. HU is a dimer encoded by two closely related genes. Essential for the initiation of replication in bacteria; stimulates the DnaA-dependent unwinding of oriC.
Synonyms: DnaA-HU-DNA complex
DNA bending complex (GO:1990104)
Namespace: cellular_component
Definition: A protein-DNA complex that contains DNA in combination with a protein which binds to and bends DNA. Often plays a role in DNA compaction.
Synonyms: histone-like DNA binding complex
obsolete regulation of voltage-gated potassium channel activity (GO:1990105)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of voltage-gated potassium channel activity.
Synonyms: regulation of voltage-gated potassium channel activity
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
thiazole synthase activity (GO:1990107)
Namespace: molecular_function
Definition: Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + [sulfur-carrier protein ThiS]-C-terminal Gly-NH-CH2-C(O)SH = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS]-C-terminal Gly-Gly + 2 H+ + 2 H2O.
Synonyms: 1-deoxy-D-xylulose 5-phosphate:thiol sulfurtransferase activity
Comment: Part of the pathway for thiamine biosynthesis.
protein linear deubiquitination (GO:1990108)
Namespace: biological_process
Definition: A protein deubiquitination process in which a linear polymer of ubiquitin, formed by the amino-terminal methionine (M1) of one ubiquitin molecule and by the carboxy-terminal glycine (G76) of the next, is removed from a protein.
callus formation (GO:1990110)
Namespace: biological_process
Definition: The process by which a callus is formed at a wound site. A plant callus is a portion of plant tissue that consists of mass of undifferentiated plant cells. It consists primarily of parenchyma cells but possibly contains other cell types as the callus begins to differentiate.
spermatoproteasome complex (GO:1990111)
Namespace: cellular_component
Definition: A proteasome specifically found in mammalian testis. Contains the proteasome activator PA200 in the regulatory particle, and beta1i, beta2i, beta5i and/or alpha4s in the core (20S) subunit. Beta1i, beta2i and beta5i are inducible catalytic subunits, closely related to beta1, beta2 and beta5. Alpha4s is a sperm-specific 20S subunit, but unlike other alternative 20S subunits alpha4s lies in the outer alpha-ring and lacks catalytic activity.
RQC complex (GO:1990112)
Namespace: cellular_component
Definition: A multiprotein complex that forms a stable complex with large ribosomal subunits (60S in eukaryotes and 50S in prokaryotes) containing stalled polypeptides and triggers their degradation (ribosomal quality control). In budding yeast, this complex includes Cdc48p, Rkr1p, Tae2p, Rqc1p, Npl4p and Ufd1p proteins.
Synonyms: ribosome quality control complex; ribosome-bound quality control complex
RNA polymerase I assembly (GO:1990113)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase I complex.
Synonyms: DNA-directed RNA polymerase I complex assembly; RNA Polymerase I complex assembly
RNA polymerase II core complex assembly (GO:1990114)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase II core complex.
Synonyms: DNA-directed RNA polymerase II, core complex assembly; RNA Polymerase II assembly
RNA polymerase III assembly (GO:1990115)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase III complex.
Synonyms: DNA-directed RNA polymerase III complex assembly; RNA Polymerase III complex assembly
ribosome-associated ubiquitin-dependent protein catabolic process (GO:1990116)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a protein or peptide encoded by an aberrant message and associated with a stalled ribosome. Degradation is initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the ribosome-associated protein.
Synonyms: RAD; ribosome-associated degradation; ribosome-associated ubiquitin-dependent protein breakdown; ribosome-associated ubiquitin-dependent protein catabolism; ribosome-associated ubiquitin-dependent protein degradation
B cell receptor apoptotic signaling pathway (GO:1990117)
Namespace: biological_process
Definition: An extrinsic apoptotic signaling pathway initiated by the cross-linking of an antigen receptor on a B cell.
Synonyms: B cell receptor extrinsic apoptotic signaling pathway; extrinsic apoptotic signaling pathway via B cell antigen receptor; extrinsic apoptotic signaling pathway via BCR
RNA helicase inhibitor activity (GO:1990119)
Namespace: molecular_function
Definition: Binds to and stops, prevents or reduces the activity of an RNA helicase.
Synonyms: ATP-dependent RNA helicase inhibitor activity
obsolete messenger ribonucleoprotein complex assembly (GO:1990120)
Namespace: biological_process
Definition: OBSOLETE. The aggregation, arrangement and bonding together of proteins and messenger RNA (mRNA) molecules to form a messenger ribonucleoprotein (mRNP) complex.
Comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
H-NS complex (GO:1990121)
Namespace: cellular_component
Definition: A multimer of H-NS proteins that is involved in bacterial nucleoid condensation and negative regulation of global gene expression by directly binding to promoter regions. Recognizes both structural and sequence-specific motifs in double-stranded DNA and has binding preference for bent DNA.
Synonyms: DNA-binding protein H-NS complex; histone-like protein H-NS complex
obsolete messenger ribonucleoprotein complex (GO:1990124)
Namespace: cellular_component
Definition: OBSOLETE. A ribonucleoprotein complex containing both protein and messenger RNA (mRNA) molecules.
Synonyms: messenger ribonucleoprotein particle; mRNA-protein complex; mRNP; mRNP complex
Comment: This term was obsoleted becasue it does not represent a specific complex
DiaA complex (GO:1990125)
Namespace: cellular_component
Definition: A homotetrameric protein complex consisting of a symmetrical pair of DiaA homodimers. Facilitates DnaA binding to the origin of replication during replication initiation.
Synonyms: DiaA homotetramer
intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1990127)
Namespace: biological_process
Definition: The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of osmotic stress, and ends when the execution phase of apoptosis is triggered.
obsolete pre-primosome complex involved in replication initiation (GO:1990128)
Namespace: cellular_component
Definition: OBSOLETE. A protein-DNA complex involved in replication initiation at the origin of replication.
Synonyms: pre-primosome complex involved in replication initiation
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete pre-primosome complex involved in replication restart (GO:1990129)
Namespace: cellular_component
Definition: OBSOLETE. A protein-DNA complex involved in replication restart after a stalled replication fork has been repaired.
Synonyms: pre-primosome complex involved in replication restart
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
GATOR1 complex (GO:1990130)
Namespace: cellular_component
Definition: A GTPase-activating protein (GAP) complex that regulates TORC1 signaling by interacting with the Rag GTPase. In human, the GATOR1 complex consists of DEPDC5, NPRL2, and NPRL3. In S. cerevisiae, this complex is referred to as SEACIT and contains the Iml1p, Npr2p, and Npr3p proteins.
Synonyms: IML1 complex; SEACIT complex
Comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
obsolete release of misfolded protein from chaperone (GO:1990132)
Namespace: biological_process
Definition: OBSOLETE. The release of misfolded proteins that are being held by the chaperone heat shock protein (Hsp) and targeting them for destruction by the Ub-proteasome machinery.
Synonyms: release of misfolded protein from chaperone
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
molybdopterin adenylyltransferase complex (GO:1990133)
Namespace: cellular_component
Definition: A heterotetrameric protein complex which adenylates two molecules of the sulfur carrier subunit of the molybdopterin cofactor synthase using ATP as part of molybdopterin cofactor (Moco) biosynthesis. In E. coli the subunits are MoeB and MoaD; in human the subunits are MOCS3 and MOCS2A. Moco biosynthesis and its constituent molecules are evolutionarily conserved.
Synonyms: molybdopterin cofactor (Moco) biosynthesis adenylyltransferase complex; MPT adenylyltransferase complex
epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)
Namespace: biological_process
Definition: An apoptotic process in a palatal shelf epithelial cell that contributes to the shaping of the palatal shelf.
linoleate 9S-lipoxygenase activity (GO:1990136)
Namespace: molecular_function
Definition: Catalysis of the reaction: linoleate + O2 = (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate.
Synonyms: 9-lipoxygenase activity; 9S-lipoxygenase activity; linoleate 9-lipoxygenase activity; linoleate:oxygen 9S-oxidoreductase activity
plant seed peroxygenase activity (GO:1990137)
Namespace: molecular_function
Definition: Catalysis of the reaction: RH + ROOH = ROH + ROH.
Synonyms: peroxygenase activity; plant seed peroxidase activity
neuron projection extension (GO:1990138)
Namespace: biological_process
Definition: Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
Synonyms: neurite extension; neuron process extension; neuron protrusion extension; neuronal cell projection extension
protein localization to nuclear periphery (GO:1990139)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, a location within the nuclear periphery.
molybdopterin synthase complex (GO:1990140)
Namespace: cellular_component
Definition: A heterotetrameric protein complex that catalyses sulfur transfer from the sulfur carrier subunit of molybdopterin synthase to precursor Z to synthesize molybdopterin as part of molybdopterin cofactor (Moco) biosynthesis. In E. coli the subunits are MoaE and MoaD; in human, MOCS2B and MOCS2A. Moco biosynthesis and its constituent molecules are evolutionarily conserved.
Synonyms: molybdopterin cofactor (Moco) biosynthesis sulfurtransferase complex; molybdopterin converting factor complex; MPT synthase complex
CoA-synthesizing protein complex (GO:1990143)
Namespace: cellular_component
Definition: A multisubunit complex likely involved in the synthesis of coenzyme A (CoA). In S. cerevisiae, the complex consists of at least Cab2, Cab3, Cab4 and Cab5 but may also include Sis2 and Vhs3. The latter subunits are shared by the GO:0071513 phosphopantothenoylcysteine decarboxylase complex that catalyses the third step of the coenzyme A (CoA) biosynthetic pathway.
Synonyms: CoA-SPC; coenzyme A-synthesizing protein complex
intrinsic apoptotic signaling pathway in response to hypoxia (GO:1990144)
Namespace: biological_process
Definition: The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to hypoxia (lowered oxygen tension). Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level. The pathway ends when the execution phase of apoptosis is triggered.
maintenance of translational fidelity (GO:1990145)
Namespace: biological_process
Definition: Suppression of the occurrence of translational errors, such as codon-anticodon mis-paring, during the process of translation of a protein using an mRNA template.
protein localization to rhabdomere (GO:1990146)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, a location within a rhabdomere.
talin binding (GO:1990147)
Namespace: molecular_function
Definition: Binding to a talin, a family of related cytoskeletal proteins that play a role in assembly of actin filaments and migration of various cell types.
glutamate dehydrogenase complex (GO:1990148)
Namespace: cellular_component
Definition: A homomeric protein complex that possesses glutamate dehydrogenase activity. This complex is evolutionarily conserved except that the number of homoprotomers per complex varies.
Synonyms: dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate)) complex; glutamate dehydrogenase (NADP+) complex; glutamic acid dehydrogenase complex; glutamic dehydrogenase complex; L-glutamate dehydrogenase complex; L-glutamate:NADP+ oxidoreductase (deaminating) complex; L-glutamic acid dehydrogenase complex; NAD(P)-glutamate dehydrogenase complex; NAD(P)H-dependent glutamate dehydrogenase complex
obsolete COPI vesicle coating (GO:1990149)
Namespace: biological_process
Definition: OBSOLETE. The addition of COPI proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
Synonyms: COPI vesicle coating
Comment: This term was obsoleted at the TermGenie Gatekeeper stage because COPI vesicles are formed on Golgi membranes, and the existing term 'COPI coating of Golgi vesicle ; GO:0048205' describes this process.
VEGF-A complex (GO:1990150)
Namespace: cellular_component
Definition: A homodimeric, extracellular protein complex containing two VEGF-A monomers. Binds to and activates a receptor tyrosine kinase.
Synonyms: vascular endothelial growth factor A complex
maintenance of protein localization to heterochromatin (GO:1990153)
Namespace: biological_process
Definition: A process in which a protein is maintained in a location in telomeric heterochromatin.
Synonyms: maintenance of protein localisation to heterochromatin; maintenance of protein location in heterochromatin
enzyme IIA-maltose transporter complex (GO:1990154)
Namespace: cellular_component
Definition: A protein complex consisting of the pentameric maltose transporter complex bound to two enzyme IIA (EIIA) molecules. EIIA is a component of the glucose-specific phosphotransferase system that inhibits maltose transport from the periplasm to the cytoplasm. When EIIA-bound, the maltose transporter remains in the open, inward-facing conformation, which prevents binding of maltose-loaded maltose binding protein (MBP) to the transporter.
Synonyms: EIIA(Glc)-MalFGK2 complex; EIIA(Glc)-maltose transporter complex; maltose transporter inhibitor complex
Dsc E3 ubiquitin ligase complex assembly (GO:1990155)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a Dsc E3 ubiquitin ligase complex, an E3 ubiquitin ligase complex localized to the ER and Golgi membrane.
Synonyms: Dsc complex assembly
DnaA-DnaB-DnaC complex (GO:1990157)
Namespace: cellular_component
Definition: A protein-DNA complex consisting of the helicase loading complex DnaB-DnaC bound to the DNA-bound DNA replication initiation protein DnaA. Essential for DNA replication initiation.
DnaB-DnaC-DnaT-PriA-PriB complex (GO:1990158)
Namespace: cellular_component
Definition: A protein-DNA complex consisting of the helicase loading complex DnaB-DnaC, replication restart proteins DnaT, PriA and PriB, and associated DNA. Involved in the restart of DNA replication after a stalled replication fork has been repaired.
Synonyms: DnaB-DnaC-DnaT-PriA-PriB preprimosome; phi-X174-type preprimosome
DnaB-DnaC-DnaT-PriA-PriC complex (GO:1990159)
Namespace: cellular_component
Definition: A protein-DNA complex consisting of the helicase loading complex DnaB-DnaC, replication restart proteins DnaT, PriA and PriC, and associated DNA. Involved in the restart of DNA replication after a stalled replication fork has been repaired.
Synonyms: DnaB-DnaC-DnaT-PriA-PriC preprimosome; phi-X174-type preprimosome
DnaB-DnaC-Rep-PriC complex (GO:1990160)
Namespace: cellular_component
Definition: A protein-DNA complex consisting of the helicase loading complex DnaB-DnaC, replication restart proteins Rep and PriC, and associated DNA. Involved in the restart of DNA replication after a stalled replication fork has been repaired.
Synonyms: DnaB-DnaC-Rep-PriC preprimosome; phi-X174-type preprimosome
DnaB helicase complex (GO:1990161)
Namespace: cellular_component
Definition: A homohexameric protein complex that possesses DNA helicase activity; functions during DNA replication and repair.
Synonyms: DnaB hexamer
histone H3K4 deacetylase activity, hydrolytic mechanism (GO:1990162)
Namespace: molecular_function
Definition: Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 4) + H2O = histone H3 L-lysine (position 4) + acetate. This reaction represents the removal of an acetyl group from lysine at position 4 of the histone H3 protein.
Synonyms: histone deacetylase activity (H3-K4 specific); histone H3-K4 deacetylase activity; histone H3K14 deacetylase 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.
obsolete histone H2A phosphorylation (GO:1990164)
Namespace: biological_process
Definition: OBSOLETE. The modification of histone H2A by the addition of a phosphate group.
Comment: This term was obsoleted because it represents a molecular function.
single-strand break-containing DNA binding (GO:1990165)
Namespace: molecular_function
Definition: Binding to damaged DNA containing single-strand breaks (SSBs).
Synonyms: single-strand break-containing damaged DNA binding; SSB-containing DNA binding
protein localization to site of double-strand break (GO:1990166)
Namespace: biological_process
Definition: Any process in which a protein is transported to, or maintained at, a region of a chromosome at which a DNA double-strand break has occurred.
Synonyms: protein localisation to site of double-strand break; protein localization to double-strand break site; protein localization to site of DSB
protein K27-linked deubiquitination (GO:1990167)
Namespace: biological_process
Definition: A protein deubiquitination process in which a K27-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 27 of the ubiquitin monomers, is removed from a protein.
protein K33-linked deubiquitination (GO:1990168)
Namespace: biological_process
Definition: A protein deubiquitination process in which a K33-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 33 of the ubiquitin monomers, is removed from a protein.
stress response to copper ion (GO:1990169)
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 copper ion stimulus.
Synonyms: response to copper ion stress; response to copper toxicity; stress response to copper
stress response to cadmium ion (GO:1990170)
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 cadmium ion stimulus.
Synonyms: response to cadmium ion stress; response to cadmium toxicity; stress response to cadmium
G protein-coupled receptor catabolic process (GO:1990172)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a G protein-coupled receptor.
Synonyms: G-protein coupled receptor catabolic process
protein localization to nucleoplasm (GO:1990173)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, a location within the nucleoplasm.
Synonyms: nucleolus to nucleoplasm transport; protein localisation to nucleoplasm
phosphodiesterase decapping endonuclease activity (GO:1990174)
Namespace: molecular_function
Definition: Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA.
Synonyms: G(5')pppN pyrophosphatase activity