LiteFold/GO huggingface dataset:
acetyl-CoA carboxylase complex (GO:0009317)
Namespace: cellular_component
Definition: A protein complex that catalyzes the first step in long-chain fatty acid biosynthesis. For example, in E. coli the complex is heterohexameric and composed of biotin carbonyl carrier protein, biotin carboxylase and the acetate CoA-transferase complex.
Synonyms: ACCase complex
cytochrome o ubiquinol oxidase complex (GO:0009319)
Namespace: cellular_component
Definition: A protein complex that possesses cytochrome o ubiquinol oxidase activity; consists of four polypeptide subunits and associated prosthetic groups.
Comment: See also the molecular function term 'cytochrome o ubiquinol oxidase activity ; GO:0008827'.
phosphoribosylaminoimidazole carboxylase complex (GO:0009320)
Namespace: cellular_component
Definition: A protein complex that possesses phosphoribosylaminoimidazole carboxylase activity.
Comment: See also the molecular function term 'phosphoribosylaminoimidazole carboxylase activity ; GO:0004638'.
alkyl hydroperoxide reductase complex (GO:0009321)
Namespace: cellular_component
Definition: An enzyme complex, usually a homodimer, which directly reduces cellular levels of organic hydroperoxides.
Comment: See also the molecular function term 'alkyl hydroperoxide reductase activity ; GO:0008785'.
obsolete trimethylamine-N-oxide reductase complex (GO:0009322)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the reduction of trimethylamine N-oxide to trimethylamine.
Comment: This term was obsoleted because there is no evidence that this complex exists.
obsolete ribosomal-protein-alanine N-acetyltransferase complex (GO:0009323)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the transfer of an acetyl group to ribosomal-protein alanine, forming ribosomal-protein acetylalanine.
Comment: This term was obsoleted because there is no evidence that this complex exists. Enzymes with that activity, such as E. coli rimJ (UniProt:P0A948), act as monomers.
D-amino-acid dehydrogenase complex (GO:0009324)
Namespace: cellular_component
Definition: A protein complex that possesses D-amino-acid dehydrogenase activity.
Comment: See also the molecular function term 'D-amino-acid oxidase activity ; GO:0003884'.
nitrate reductase complex (GO:0009325)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the formation of nitrate from nitrite with the concomitant reduction of an acceptor.
formate dehydrogenase complex (GO:0009326)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2).
obsolete NAD(P)+ transhydrogenase complex (AB-specific) (GO:0009327)
Namespace: cellular_component
Definition: OBSOLETE. A protein complex that possesses NAD(P)+ transhydrogenase (AB-specific) activity. Homodimeric, trimeric, and heterotetrameric complexes have been identified.
Comment: This term was obsoleted because there is no evidence that this activity exists as part of a complex.
phenylalanine-tRNA ligase complex (GO:0009328)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe).
acetate CoA-transferase complex (GO:0009329)
Namespace: cellular_component
Definition: A heterotetrameric enzyme complex made up of two alpha subunits and two beta subunits. Part of the acetyl-CoA carboxylase complex. Catalyzes the transfer of a carboxyl group to form malonyl-CoA.
DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex (GO:0009330)
Namespace: cellular_component
Definition: Complex that possesses DNA topoisomerase II (double strand cut, ATP-hydrolyzing) activity.
glycerol-3-phosphate dehydrogenase (FAD) complex (GO:0009331)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the oxidation of sn-glycerol 3-phosphate to dihydroxyacetone phosphate, with concurrent reduction of flavin adenine dinucleotide (FAD) to FADH2. In E. coli, the complex is either a GlpA-GlpB-GlpC heterotrimer that functions in anaerobic conditions, or a GlpD homodimer that functions in aerobic conditions.
Synonyms: aerobic glycerol 3-phosphate dehydrogenase; anaerobic glycerol-3-phosphate dehydrogenase; glycerol-3-phosphate dehydrogenase complex
glutamate-tRNA ligase complex (GO:0009332)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the ligation of glutamate and tRNA(Glu) to form glutamyl-tRNA(Glu).
cysteine synthase complex (GO:0009333)
Namespace: cellular_component
Definition: Cysteine synthase is a multienzyme complex made up, in E. coli, of the heteromeric hexamer serine acetyltransferase and the homodimer O-acetylserine (thiol)-lyase A.
3-phenylpropionate dioxygenase complex (GO:0009334)
Namespace: cellular_component
Definition: Enzyme complex consisting of four proteins: the two subunits of the hydroxylase component (hcaE and hcaF), a ferredoxin (hcaC) and a ferredoxin reductase (hcaD). Converts 3-phenylpropionic acid (PP) into cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol (PP-dihydrodiol).
Comment: See also the molecular function term '3-phenylpropionate dioxygenase activity ; GO:0008695'.
obsolete holo-[acyl-carrier protein] synthase complex (GO:0009335)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the formation of holo-[acyl-carrier protein] from CoA and apo-[acyl-carrier protein].
Synonyms: holo-[acyl-carrier protein] synthase complex; holo-ACP synthase complex
Comment: This term was made obsolete because the catalytic activity resides in a single polypeptide rather than a complex, and the complex is represented by a different GO term.
sulfate adenylyltransferase complex (ATP) (GO:0009336)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the formation adenylylsulfate from sulfate and ATP.
Synonyms: sulphate adenylyltransferase complex (ATP)
sulfite reductase complex (NADPH) (GO:0009337)
Namespace: cellular_component
Definition: A multisubunit iron flavoprotein, which in yeast is composed of 2 alpha and 2 beta subunits. Catalyzes the reduction of sulfite to sulfide.
Synonyms: sulphite reductase complex (NADPH)
Comment: See also the molecular function term 'sulfite reductase (NADPH) activity ; GO:0004783'.
exodeoxyribonuclease V complex (GO:0009338)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA.
glycolate oxidase complex (GO:0009339)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and H2O2. The enzyme is a flavoprotein (FMN).
DNA topoisomerase IV complex (GO:0009340)
Namespace: cellular_component
Definition: A heterodimeric enzyme, which in most bacterial species is composed of two subunits, ParC and ParE. Functions in chromosome segregation and can relax supercoiled DNA.
beta-galactosidase complex (GO:0009341)
Namespace: cellular_component
Definition: A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species.
glutamate synthase complex (NADPH) (GO:0009342)
Namespace: cellular_component
Definition: A complex that possesses glutamate synthase (NADPH) activity.
obsolete biotin carboxylase complex (GO:0009343)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the formation of carboxybiotin-carboxyl-carrier protein from biotin-carboxyl-carrier protein and carbon dioxide (CO2).
Comment: This term was obsoleted because it represents a homomer.
nitrite reductase complex [NAD(P)H] (GO:0009344)
Namespace: cellular_component
Definition: Complex that possesses nitrite reductase [NAD(P)H] activity.
Comment: See also the molecular function term 'nitrite reductase [NAD(P)H] activity ; GO:0008942'.
glycine-tRNA ligase complex (GO:0009345)
Namespace: cellular_component
Definition: A multimeric enzyme complex which, in bacteria, is usually a tetramer of two alpha and two beta chains and in eukaryotes, is usually a homodimer. Functions in the ligation of glycine and tRNA(Gly) to form glycyl-tRNA(Gly).
Synonyms: glycine-tRNA synthetase complex
ATP-independent citrate lyase complex (GO:0009346)
Namespace: cellular_component
Definition: Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria.
Synonyms: citrate lyase complex; citrate synthase complex
Comment: Note that this complex has only been found in bacteria. For eukaryotic cytrate lyases, consider GO:0140615 ; ATP-dependent citrate lyase complex.
aspartate carbamoyltransferase complex (GO:0009347)
Namespace: cellular_component
Definition: A multienzyme complex that catalyzes the formation N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate. It exhibits a variety of architectural organizations, but in all microorganisms the core catalytic component is a homotrimer of approximately 34 kDa polypeptides.
Comment: Note that in eukaryotes, aspartate carbamoyltransferase is usually a single polypeptide, not a complex, and should therefore not be annotated to this component term.
obsolete ornithine carbamoyltransferase complex (GO:0009348)
Namespace: cellular_component
Definition: OBSOLETE. A homotrimeric protein complex that catalyzes the transfer of a carbamoyl group to ornithine, forming citrulline.
Comment: This term was obsoleted because it represents a homomer.
riboflavin synthase complex (GO:0009349)
Namespace: cellular_component
Definition: An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
ethanolamine ammonia-lyase complex (GO:0009350)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the breakdown of ethanolamine to form acetaldehyde and ammonia.
obsolete dihydrolipoamide S-acyltransferase complex (GO:0009351)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the transfer of an acyl group from coenzyme A to dihydrolipoamide.
Synonyms: dihydrolipoamide S-acyltransferase complex
Comment: This term was made obsolete because dihydrolipoamide S-acyltransferase activity resides in a single polypeptide.
obsolete dihydrolipoyl dehydrogenase complex (GO:0009352)
Namespace: cellular_component
Definition: OBSOLETE. Complex that possesses dihydrolipoyl dehydrogenase activity.
Synonyms: dihydrolipoamide dehydrogenase complex; dihydrolipoyl dehydrogenase complex
Comment: This term was made obsolete because the activity dihydrolipoamide dehydrogenase is held by a single protein (Lpd1 in yeast), which is one of the components of three different complexes: 2-oxoglutarate dehydrogenase, pyruvate dehydrogenase, and branch chain amino acid dehydrogenase, so dihydrolipoamide dehydrogenase is not a complex itself.
obsolete mitochondrial oxoglutarate dehydrogenase complex (GO:0009353)
Namespace: cellular_component
Definition: OBSOLETE. A mitochondrial complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix.
Comment: This term is unnecessarily taxon-specific.
obsolete dihydrolipoamide S-succinyltransferase complex (GO:0009354)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the transfer of succinyl-CoA to dihydrolipoamide to form S-succinyldihydrolipoamide. The enzyme is a component of the multienzyme 2-oxoglutarate dehydrogenase complex.
Synonyms: dihydrolipoamide S-succinyltransferase complex
Comment: This term was made obsolete because dihydrolipoamide S-succinyltransferase itself is not a complex, it is a component of the 2-oxoglutarate dehydrogenase complex, the activity dihydrolipoamide S-succinyltransferase is contained in a single polypeptide.
DNA polymerase V complex (GO:0009355)
Namespace: cellular_component
Definition: A DNA polymerase complex that contains two UmuD' and one UmuC subunits, and acts in translesion DNA synthesis.
aminodeoxychorismate synthase complex (GO:0009356)
Namespace: cellular_component
Definition: A heterodimeric protein complex that possesses 4-amino-4-deoxychorismate synthase activity.
Synonyms: 4-amino-4-deoxychorismate synthase complex; ADC synthase complex; p-aminobenzoate synthetase complex
protein-N(PI)-phosphohistidine-sugar phosphotransferase complex (GO:0009357)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the transfer of a phosphate from protein N(PI)-phosphohistidine to a sugar molecule. It is enzyme II of the phosphotransferase system.
type II site-specific deoxyribonuclease complex (GO:0009359)
Namespace: cellular_component
Definition: A protein complex that functions as an endonuclease to cleave DNA at or near a specific recognition site, when that site is unmethylated. These complexes may be dimers or tetramers; it is also possible for the endonuclease to be in a complex with the corresponding methyltransferase that methylates the recognition site. DNA restriction systems such as this are used by bacteria to defend against phage and other foreign DNA that may enter a cell.
Synonyms: type II restriction enzyme complex
DNA polymerase III complex (GO:0009360)
Namespace: cellular_component
Definition: The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
Synonyms: DNA polymerase III holoenzyme complex
succinate-CoA ligase complex (ADP-forming) (GO:0009361)
Namespace: cellular_component
Definition: A heterodimeric enzyme complex, composed of an alpha and beta chain, most usually found in (but not limited to) bacteria. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP.
Synonyms: succinyl-CoA synthetase, ADP-forming
protein histidine kinase complex (GO:0009365)
Namespace: cellular_component
Definition: A complex that possesses protein histidine kinase activity.
enterobactin synthetase complex (GO:0009366)
Namespace: cellular_component
Definition: A multienzyme complex usually composed of four proteins, EntB, EntD, EntE and EntF. Plays a role in the enterobactin biosynthesis pathway.
Synonyms: enterochelin synthetase complex
obsolete prepilin peptidase complex (GO:0009367)
Namespace: cellular_component
Definition: OBSOLETE. An enzyme complex that catalyzes the cleavage of a Gly-Phe bond to release an N-terminal, basic peptide of 5-8 residues from type IV prepilin, and then N-methylates the new N-terminal amino group.
Synonyms: prepilin peptidase complex
Comment: This term was made obsolete because prepilin peptidase is a single gene product, and there is no evidence that it acts as a multimer.
endopeptidase Clp complex (GO:0009368)
Namespace: cellular_component
Definition: A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form.
quorum sensing (GO:0009372)
Namespace: biological_process
Definition: The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
Synonyms: cell-cell signaling involved in quorum sensing; detection of cell density by secreted molecule; quorum sensing system
obsolete regulation of transcription by pheromones (GO:0009373)
Namespace: biological_process
Definition: OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent of transcription.
Comment: This term has been obsoleted because it represents a GO-CAM model.
biotin binding (GO:0009374)
Namespace: molecular_function
Definition: Binding to biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
Synonyms: vitamin B7 binding; vitamin H binding
ferredoxin hydrogenase complex (GO:0009375)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances.
four-way junction helicase activity (GO:0009378)
Namespace: molecular_function
Definition: Unwinding a DNA helix of DNA containing four-way junctions, including Holliday junctions, driven by ATP hydrolysis.
Synonyms: ATP-dependent four-way junction DNA helicase activity; ATP-dependent four-way junction helicase activity; ATP-dependent Holliday junction helicase activity; Holliday junction helicase activity
Holliday junction helicase complex (GO:0009379)
Namespace: cellular_component
Definition: A DNA helicase complex found at Holliday junctions where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.
excinuclease repair complex (GO:0009380)
Namespace: cellular_component
Definition: Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.
Synonyms: excinuclease ABC complex; UvrABC excinuclease complex
excinuclease ABC activity (GO:0009381)
Namespace: molecular_function
Definition: Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
imidazoleglycerol-phosphate synthase complex (GO:0009382)
Namespace: cellular_component
Definition: Complex that possesses imidazoleglycerol-phosphate synthase activity.
Synonyms: imidazoleglycerol phosphate synthase complex
Comment: See also the molecular function term 'imidazoleglycerol-phosphate synthase activity ; GO:0000107'.
rRNA (cytosine-C5-)-methyltransferase activity (GO:0009383)
Namespace: molecular_function
Definition: Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to cytosine to form 5-methylcytosine in small subunit ribosomal RNA.
Synonyms: rRNA (cytosine-C5-967)-methyltransferase activity; rRNA m5C967 methyltransferase activity
N-acylmannosamine kinase activity (GO:0009384)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + N-acyl-D-mannosamine = ADP + N-acyl-D-mannosamine 6-phosphate.
Synonyms: acetylamidodeoxymannokinase activity; acetylmannosamine kinase activity; acylaminodeoxymannokinase activity; acylmannosamine kinase (phosphorylating); acylmannosamine kinase activity; ATP:N-acetylmannosamine 6-phosphotransferase activity; ATP:N-acyl-D-mannosamine 6-phosphotransferase activity; N-acetylmannosamine kinase activity; N-acyl-D-mannosamine kinase activity
obsolete N-acylmannosamine-6-phosphate 2-epimerase activity (GO:0009385)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: N-acetyl-D-mannosamine-6-phosphate = N-acetyl-D-glucosamine-6-phosphate.
Synonyms: N-acylmannosamine-6-P epimerase activity
Comment: This term was obsoleted because it represents the same activity as N-acylglucosamine-6-phosphate 2-epimerase activity ; GO:0047465.
translational attenuation (GO:0009386)
Namespace: biological_process
Definition: Translational attenuation is a regulatory mechanism analogous to ribosome-mediated transcriptional attenuation. The system requires the presence of a short ORF, called a leader peptide, encoded in the mRNA upstream of the ribosome-binding site and start codon of the gene whose translation is to be regulated. Certain conditions, such as presence of the antibiotic tetracycline in bacteria or amino acid starvation, may cause slowing or stalling of the ribosome translating the leader peptide. The stalled ribosome masks a region of the mRNA and affects which of two alternative mRNA folded structures will form, therefore controlling whether or not a ribosome will bind and initiate translation of the downstream gene. Translational attenuation is analogous to ribosome-mediated transcriptional attenuation, in which mRNA remodeling caused by ribosome stalling regulates transcriptional termination rather than translational initiation.
obsolete antisense RNA (GO:0009388)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: antisense RNA
Comment: This term was made obsolete because it represents a gene product.
dimethyl sulfoxide reductase activity (GO:0009389)
Namespace: molecular_function
Definition: Catalysis of the reaction: dimethyl sulfide + a menaquinone + H2O = dimethyl sulfoxide + a menaquinol.
Synonyms: dimethyl sulphoxide reductase activity; respiratory dimethylsulfoxide reductase
dimethyl sulfoxide reductase complex (GO:0009390)
Namespace: cellular_component
Definition: An enzyme complex that catalyzes the formation of dimethyl sulfide from dimethyl sulfoxide.
Synonyms: dimethyl sulphoxide reductase complex
N-acetyl-anhydromuramoyl-L-alanine amidase activity (GO:0009392)
Namespace: molecular_function
Definition: Catalysis of the reaction: GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-Ala + H2O glcNAc-1,6-anhMurNAc + L-Ala-gamma-D-Glu-DAP-D-Ala.
2'-deoxyribonucleotide metabolic process (GO:0009394)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a 2'-deoxyribonucleotide, a compound consisting of 2'-deoxyribonucleoside (a base linked to a 2'-deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
Synonyms: 2'-deoxyribonucleotide metabolism