BiPOm 1. Copyright of ontology The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Université Paris-Sud/CNRS, France and by the Département MMIP AgroParisTech of the INRA, France. INRA, Agroparistech and Université Paris-Sud own the copyright of the ontology BiPOm. 2. License terms The ontology BiPOm is licensed under the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. 3. Notice This product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, licensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/). This product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. This product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. This product contains references to classes of the Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, licensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php). This product contains references to properties of the Relation Ontology (RO) (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/). This product contains references to properties of the Basic Formal Ontology (BFO) (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium, licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/). 4. Contact For questions and remarks concerning BiPOm: Anne Goelzer Anne.Goelzer
Relation between occurrents, shares an end boundary with.
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
has output
a core relation that holds between a whole and its part
has part
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
input of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
output of
a core relation that holds between a part and its whole
part of
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
preceded by
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
Relation between occurrents, shares a start boundary with.
starts
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
assembly of proteins in a complex that requires an energy dependent chaperoning activity
ATP-dependent chaperone mediated protein complex assembly
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
complex V (mitochondrial electron transport)
Trafficking of GluR2-containing AMPA receptors to synapse, Canis familiaris
Trafficking of GluR2-containing AMPA receptors to synapse, Bos taurus
Trafficking of GluR2-containing AMPA receptors to synapse, Danio rerio
Trafficking of GluR2-containing AMPA receptors to synapse, Xenopus tropicalis
Trafficking of GluR2-containing AMPA receptors to synapse, Homo sapiens
Trafficking of GluR2-containing AMPA receptors to synapse, Gallus gallus
Trafficking of GluR2-containing AMPA receptors to synapse, Mus musculus
Trafficking of GluR2-containing AMPA receptors to synapse, Drosophila melanogaster
Trafficking of GluR2-containing AMPA receptors to synapse, Rattus norvegicus
Trafficking of GluR2-containing AMPA receptors to synapse, Taeniopygia guttata
Any action that can, in the context of a study or a post-marketing investigation, be defined, planned, scheduled or performed. EXAMPLE(S): surgical procedure, laboratory test, administration of a drug.
An active process; excludes processes and mechanisms which fulfill biological functions.
a protein that combines with a coenzyme to form an active enzyme [http://wordnet.princeton.edu/perl/webwn?s=apoenzyme]
apoenzyme
A linked series of non-equivalent biochemical interactions and enzymatic reactions, and/or a linked series of biochemical processes.
In living cells, chemical reactions that help sustain life and allow cells to grow.
A chemical process, typically mediated by an enzyme, in which one or more substances (a substrate) are transformed by covalent modification into another substance(s) (a product) or in which the state of a substance is transformed.
ATP Hydrolysis is the cleavage of a high-energy phosphate bond of adenosine triphosphate by the addition of water. The energy derived from hydrolysis of ATP is used to drive metabolic reactions including nucleic acid and protein synthesis, to move molecules against concentration gradients (active transport), and to produce mechanical motion (contraction of microfibrils and microtubules).
A series of actions among molecules in a cell that leads to a certain end point or cell function.
A series of biochemical reactions which occurs in a known sequence and can result in all or part of the initiation, progression or completion of a biological process or function.
Cytoplasmic proteins of both prokaryotes and eukaryotes that bind to nascent or unfolded polypeptides and ensure correct folding or transport. Chaperone proteins do not covalently bind to their targets and do not form part of the finished product. Heat-shock proteins are an important sub set of chaperones. Three major families are recognised, the chaperonins (groEL and hsp60), the hsp70 family and the hsp90 family. Outside these major families are other proteins with similar functions including nucleoplasmin, secB and T-cell receptor associated protein.
chemical
A protein that speeds up chemical reactions in the body.
Molecules that catalyze a chemical reaction. They are usually proteins, although catalytic RNA and DNA molecules have been identified.
A protein, RNA or a complex that contains proteins and/or RNA.
In NCI Thesaurus: includes Proteins, Functional RNAs, Protein Complexes, and Riboprotein Complexes
A protein that has sugar molecules attached to it.
A conjugated protein having a carbohydrate component.
A complete and catalytically active enzyme consisting of all subunits. (i.e. Holoenzyme = Apoenzyme + Cofactor).
holoenzyme
Enzymes (EC class 3) cleaving substrates with addition of H2O at the point of cleavage; e.g., esterases, phosphatases, nucleases, peptidases. SYN hydrolyzing enzymes.
An enzyme that transfers functional groups to catalyze the geometric or structural rearrangement of atoms within a given molecule to form an isomer of the original molecule.
Major class of enzymes that catalyze the linking together of two molecules (EC class 6) for example DNA ligases that link two fragments of DNA by forming a phosphodiester bond.
An important class of serum proteins in which a spherical hydrophobic core of triglycerides or cholesterol esters surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Classified according to density: chylomicrons, large low density particles, very low density, low density and high density species. Important in lipid transport, especially cholesterol transport in the blood stream. Abnormalities in lipoprotein metabolism have been implicated in certain heart diseases.
Trivial name applied, together with dehydratase, to certain hydro-lyases (EC class 4.2.1) catalyzing hydration-dehydration.
The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics. source: PW:PW_0000002
conversion of simple chemical (without loss of matter)
The class of all enzymes catalyzing oxidoreduction reactions (EC class 1). The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor: acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
Proteins that contain phosphate groups esterified to serine, threonine or tyrosine. The phosphate group usually regulates protein function.
Used for classifying a protein or peptide that does not have a perceptible function before it is assembled into a functional complex.
Transferases are enzymes transferring a group, for example, the methyl group or a glycosyl group, from one compound (generally regarded as donor) to another compound (generally regarded as acceptor). The classification is based on the scheme "donor: acceptor group transferase". (EC 2 class)
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
enzyme enabling a biological process to occur
molecule encoded by a gene and enabling a biological process to occur
Covalent reaction that results in the addition of a chemical group on a molecule.
Added on September 13 2006 by Nicolas Le Novere based on Patika ontology.
An apoprotein is a protein devoid of its characteristic prosthetic group or metal.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
biological process that needs some cellular machinery to occur
biological reaction that needs some cellular machinery to occur
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
biological process occurring independent of catalyst (non-mediated process)
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
process resulting in protein modification
The aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex.
cellular chaperone-mediated protein complex assembly
protein complex assembly, multichaperone pathway
chaperone-mediated protein complex assembly
assembly of proteins in a complex that requires a chaperoning activity but no cofactor
chaperone-mediated protein complex assembly independent of cofactor
modification of a protein that requires a chaperone activity
chaperone-mediated protein modification reaction
A ligand with two or more separate binding sites that can bind to a single metallic central atom, forming a chelate.
recruitment of an organic molecule as a cofactor
A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Chaperone involved in recruitment of protein complex units and the assembly of the complex
Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion.
Part of a complex that mediates a process
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
A small molecule which increases (activator) or decreases (inhibitor) the activity of an (allosteric) enzyme by binding to the enzyme at the regulatory site (which is different from the substrate-binding catalytic site).
dissociation of a cofactor that was associated to an enzyme
Metabolic reaction mediated by one catalyst
Post-translational modification of a protein that requires a enzymatic activity
enzymatic post-translational protein modification
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
A macromolecular complex composed of precisely two identical monomeric units, which are usually non-covalently bound.
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
Hydrolysis of phosphatidylcholine, Bos taurus
Partial proteolysis of antigen in phagolysosomes, Homo sapiens
Hydrolysis of phosphatidylcholine, Homo sapiens
Hydrolysis of phosphatidylcholine, Danio rerio
Hydrolysis of phosphatidylcholine, Xenopus tropicalis
Hydrolysis of phosphatidylcholine, Gallus gallus
Hydrolysis of phosphatidylcholine, Canis familiaris
Hydrolysis of phosphatidylcholine, Mus musculus
Hydrolysis of phosphatidylcholine, Taeniopygia guttata
Hydrolysis of phosphatidylcholine, Rattus norvegicus
A molecular entity having a net electric charge.
Interacting selectively and non-covalently with ions, charged atoms or groups of atoms.
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
Note that enzymes of class EC:5.99.-.- should also be annotated to this term.
Any molecule or ion capable of binding to a central metal atom to form coordination complexes.
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
Ligation of DNA at sites of patch replacement, Gallus gallus
Ligation of newly synthesized repair patch to incised DNA in GG-NER, Gallus gallus
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
Note that enzymes of class EC:4.99.-.- should also be annotated to this term.
addition of a chemical group that do require other factors
loss of a chemical bond in a metabolite that is mediated by water
modification of the arrangements of the atoms of a metabolite
addition o a covalent bound between two metabolites
modification of chemical bonds of a metablite throught an elimination reaction
metabolic reaction consisting in an electron transfer
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
rupture of a metabolite that is linked to a new molecule
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
Metabolite interacting non-covalently with metabolites.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Elemental activities that needs a mediator to occur, such as catalysis or chaperoning. A given process may require one or more molecular functions.
Non-covalent association between several simple chemicals
Entity composed of several independant components that are not linked by covalent bonds.
Created on November 10 2006 by Nicolas Le Novere.
Chemical independent to genetic attribute, that is unrecognizable from a species to another.
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
oxidoreductase activity, acting on other substrates
Note that enzymes of class EC:1.97.-.- should also be annotated to this term.
Diiodinated tyrosine can be deiodinated, Mus musculus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Canis familiaris
Monoiodinated tyrosine can be deiodinated, Canis familiaris
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Danio rerio
Monoiodinated tyrosine can be deiodinated, Danio rerio
Monoiodinated tyrosine can be deiodinated, Caenorhabditis elegans
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Rattus norvegicus
Monoiodinated tyrosine can be deiodinated, Rattus norvegicus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Sus scrofa
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Rattus norvegicus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Taeniopygia guttata
Monoiodinated tyrosine can be deiodinated, Bos taurus
Diiodinated tyrosine can be deiodinated, Rattus norvegicus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Drosophila melanogaster
Monoiodinated tyrosine can be deiodinated, Homo sapiens
Diiodinated tyrosine can be deiodinated, Homo sapiens
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Homo sapiens
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Homo sapiens
Diiodinated tyrosine can be deiodinated, Canis familiaris
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Mus musculus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Gallus gallus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Bos taurus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Mus musculus
Monoiodinated tyrosine can be deiodinated, Mus musculus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Taeniopygia guttata
Diiodinated tyrosine can be deiodinated, Gallus gallus
Monoiodinated tyrosine can be deiodinated, Xenopus tropicalis
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Bos taurus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Gallus gallus
Diiodinated tyrosine can be deiodinated, Xenopus tropicalis
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Arabidopsis thaliana
Monoiodinated tyrosine can be deiodinated, Gallus gallus
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Xenopus tropicalis
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Canis familiaris
Diiodinated tyrosine can be deiodinated, Drosophila melanogaster
Diiodinated tyrosine can be deiodinated, Taeniopygia guttata
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR2], Danio rerio
Monoiodinated tyrosine can be deiodinated, Sus scrofa
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Caenorhabditis elegans
Diiodinated tyrosine can be deiodinated, Caenorhabditis elegans
Diiodinated tyrosine can be deiodinated, Sus scrofa
Diiodinated tyrosine can be deiodinated, Bos taurus
Monoiodinated tyrosine can be deiodinated, Drosophila melanogaster
palmitoyl-CoA + 2 NADPH + 2 H+ => hexadecanol + 2 NADP+ [FAR1], Oryza sativa
Diiodinated tyrosine can be deiodinated, Danio rerio
Monoiodinated tyrosine can be deiodinated, Taeniopygia guttata
Something who takes part in a process (input,output or mediator)
The process of covalently altering one or more amino acids in a protein after the protein has been completely translated and released from the ribosome.
post-translational amino acid modification
posttranslational amino acid modification
This term should only be used to annotate a protein modification process that occurs after the protein has been released from the ribosome, and is therefore strictly post-translational. Modification of a free protein (one not attached to a ribosome) and modification of a C-terminal residue are post-translational processes. Some protein modifications occur while the protein is still in the ribosome but before translation has been completed; these modification processes are considered co-translational and should not be annotated using this term.
Post-translational protein modification, Canis familiaris
Post-translational protein modification, Arabidopsis thaliana
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Saccharomyces cerevisiae
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Schizosaccharomyces pombe
Post-translational protein modification, Saccharomyces cerevisiae
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Danio rerio
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Homo sapiens
Post-translational protein modification, Gallus gallus
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Caenorhabditis elegans
Post-translational protein modification, Homo sapiens
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Gallus gallus
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Drosophila melanogaster
Post-translational protein modification, Dictyostelium discoideum
Post-translational protein modification, Danio rerio
Post-translational protein modification, Taeniopygia guttata
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Oryza sativa
Post-translational protein modification, Xenopus tropicalis
Post-translational protein modification, Sus scrofa
Post-translational protein modification, Caenorhabditis elegans
Post-translational protein modification, Schizosaccharomyces pombe
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Mus musculus
Post-translational protein modification, Bos taurus
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Xenopus tropicalis
Post-translational protein modification, Plasmodium falciparum
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Taeniopygia guttata
Post-translational protein modification, Drosophila melanogaster
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Sus scrofa
Post-translational protein modification, Mus musculus
Post-translational protein modification, Rattus norvegicus
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Canis familiaris
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Rattus norvegicus
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Bos taurus
Post-translational protein modification, Oryza sativa
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Arabidopsis thaliana
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation, Dictyostelium discoideum
Substance that is produced in a reaction. In a chemical\nequation the Products are the elements or compounds on the right hand side\nof the reaction equation. A product can be produced and consumed by the\nsame reaction, its global quantity remaining unchanged.
A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
a complex involving a protein and a cofactor
A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events.
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
alpha-2 macroglobulin receptor-associated protein activity
Formation of the IGF:IGFBP-4 Complex, Canis familiaris
Formation of the IGF:IGFBP-3:ALS Complex, Rattus norvegicus
Formation of the IGF:IGFBP-5:ALS Complex, Mus musculus
An anchoring protein, SARA, recruits SMAD2/3, Canis familiaris
Type II receptor recruits type I receptor, Xenopus tropicalis
Formation of the IGF:IGFBP-6 Complex, Bos taurus
Type II receptor recruits type I receptor, Sus scrofa
Formation of the IGF:IGFBP-3:ALS Complex, Danio rerio
Formation of the IGF:IGFBP-4 Complex, Bos taurus
Formation of the IGF:IGFBP-2 Complex, Bos taurus
Formation of the IGF:IGFBP-5:ALS Complex, Gallus gallus
Formation of the IGF:IGFBP-4 Complex, Mus musculus
Formation of the IGF:IGFBP-4 Complex, Xenopus tropicalis
Formation of the IGF:IGFBP-3:ALS Complex, Gallus gallus
Type II receptor recruits type I receptor, Bos taurus
Formation of the IGF:IGFBP-3:ALS Complex, Sus scrofa
Formation of the IGF:IGFBP-1 Complex, Homo sapiens
Formation of the IGF:IGFBP-4 Complex, Homo sapiens
Formation of the IGF:IGFBP-5:ALS Complex, Homo sapiens
Formation of the IGF:IGFBP-3:ALS Complex, Homo sapiens
Formation of the IGF:IGFBP-2 Complex, Homo sapiens
Formation of the IGF:IGFBP-6 Complex, Homo sapiens
Traversal of the cortical actin network and docking at plasma membrane, Homo sapiens
Traversal of the cortical actin network., Mus musculus
Formation of the IGF:IGFBP-4 Complex, Sus scrofa
Formation of the IGF:IGFBP-6 Complex, Danio rerio
Formation of the IGF:IGFBP-2 Complex, Taeniopygia guttata
Formation of the IGF:IGFBP-3:ALS Complex, Taeniopygia guttata
Formation of the IGF:IGFBP-6 Complex, Rattus norvegicus
Type II receptor recruits type I receptor, Danio rerio
An anchoring protein, SARA, recruits SMAD2/3, Mus musculus
Formation of the IGF:IGFBP-1 Complex, Canis familiaris
An anchoring protein, SARA, recruits SMAD2/3, Rattus norvegicus
Formation of the IGF:IGFBP-1 Complex, Danio rerio
An anchoring protein, SARA, recruits SMAD2/3, Homo sapiens
Type II receptor recruits type I receptor, Homo sapiens
Formation of the IGF:IGFBP-1 Complex, Mus musculus
Formation of the IGF:IGFBP-6 Complex, Canis familiaris
Formation of the IGF:IGFBP-5:ALS Complex, Canis familiaris
Formation of the IGF:IGFBP-1 Complex, Rattus norvegicus
Type II receptor recruits type I receptor, Mus musculus
Type II receptor recruits type I receptor, Rattus norvegicus
Formation of the IGF:IGFBP-5:ALS Complex, Sus scrofa
Formation of the IGF:IGFBP-2 Complex, Xenopus tropicalis
Formation of the IGF:IGFBP-2 Complex, Canis familiaris
Formation of the IGF:IGFBP-2 Complex, Gallus gallus
An anchoring protein, SARA, recruits SMAD2/3, Danio rerio
An anchoring protein, SARA, recruits SMAD2/3, Xenopus tropicalis
Formation of the IGF:IGFBP-6 Complex, Sus scrofa
Formation of the IGF:IGFBP-5:ALS Complex, Bos taurus
Formation of the IGF:IGFBP-3:ALS Complex, Canis familiaris
Formation of the IGF:IGFBP-5:ALS Complex, Danio rerio
Formation of the IGF:IGFBP-1 Complex, Sus scrofa
Formation of the IGF:IGFBP-4 Complex, Taeniopygia guttata
Formation of the IGF:IGFBP-2 Complex, Rattus norvegicus
Formation of the IGF:IGFBP-1 Complex, Xenopus tropicalis
An anchoring protein, SARA, recruits SMAD2/3, Sus scrofa
Type II receptor recruits type I receptor, Canis familiaris
Formation of the IGF:IGFBP-4 Complex, Rattus norvegicus
Formation of the IGF:IGFBP-1 Complex, Gallus gallus
Formation of the IGF:IGFBP-5:ALS Complex, Rattus norvegicus
Formation of the IGF:IGFBP-5:ALS Complex, Taeniopygia guttata
Formation of the IGF:IGFBP-6 Complex, Mus musculus
Formation of the IGF:IGFBP-3:ALS Complex, Mus musculus
Formation of the IGF:IGFBP-5:ALS Complex, Xenopus tropicalis
Formation of the IGF:IGFBP-3:ALS Complex, Bos taurus
Formation of the IGF:IGFBP-2 Complex, Mus musculus
Formation of the IGF:IGFBP-2 Complex, Danio rerio
Formation of the IGF:IGFBP-1 Complex, Taeniopygia guttata
An anchoring protein, SARA, recruits SMAD2/3, Bos taurus
The addition of a carbamoyl group to a protein amino acid. A carbamoyl group is the acyl group -CO-NH2.
activity of a process that assists the maturation of a protein
A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
The aggregation, arrangement and bonding together of a set of components to form a protein complex.
activity of a process that assists complex formation of proteins by other proteins
Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
The disaggregation of a protein complex into its constituent components. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
glycoprotein-specific chaperone activity
non-chaperonin molecular chaperone ATPase activity
Chaperonin-mediated protein folding, Arabidopsis thaliana
Chaperonin-mediated protein folding, Caenorhabditis elegans
Chaperonin-mediated protein folding, Rattus norvegicus
Chaperonin-mediated protein folding, Canis familiaris
Chaperonin-mediated protein folding, Mus musculus
Formation of tubulin folding intermediates by CCT/TriC, Canis familiaris
Chaperonin-mediated protein folding, Drosophila melanogaster
Formation of tubulin folding intermediates by CCT/TriC, Drosophila melanogaster
Chaperonin-mediated protein folding, Gallus gallus
Formation of tubulin folding intermediates by CCT/TriC, Bos taurus
Formation of tubulin folding intermediates by CCT/TriC, Rattus norvegicus
Formation of tubulin folding intermediates by CCT/TriC, Homo sapiens
Formation of tubulin folding intermediates by CCT/TriC, Mus musculus
Chaperonin-mediated protein folding, Homo sapiens
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding, Bos taurus
N-glycan trimming in the ER and Calnexin/Calreticulin cycle, Homo sapiens
Chaperonin-mediated protein folding, Oryza sativa
Chaperonin-mediated protein folding, Saccharomyces cerevisiae
Chaperonin-mediated protein folding, Schizosaccharomyces pombe
Chaperonin-mediated protein folding, Plasmodium falciparum
Formation of tubulin folding intermediates by CCT/TriC, Saccharomyces cerevisiae
Formation of tubulin folding intermediates by CCT/TriC, Gallus gallus
Formation of tubulin folding intermediates by CCT/TriC, Caenorhabditis elegans
Chaperonin-mediated protein folding, Dictyostelium discoideum
Formation of tubulin folding intermediates by CCT/TriC, Sus scrofa
Formation of tubulin folding intermediates by CCT/TriC, Plasmodium falciparum
Formation of tubulin folding intermediates by CCT/TriC, Arabidopsis thaliana
Formation of tubulin folding intermediates by CCT/TriC, Schizosaccharomyces pombe
Formation of tubulin folding intermediates by CCT/TriC, Dictyostelium discoideum
Chaperonin-mediated protein folding, Xenopus tropicalis
Chaperonin-mediated protein folding, Taeniopygia guttata
Formation of tubulin folding intermediates by CCT/TriC, Taeniopygia guttata
Formation of tubulin folding intermediates by CCT/TriC, Danio rerio
Chaperonin-mediated protein folding, Sus scrofa
Chaperonin-mediated protein folding, Danio rerio
Chaperonin-mediated protein folding, Bos taurus
Formation of tubulin folding intermediates by CCT/TriC, Xenopus tropicalis
Formation of tubulin folding intermediates by CCT/TriC, Oryza sativa
The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage.
Any process leading to the attainment of the full functional capacity of a protein.
The transfer of an assembled iron-sulfur cluster from a scaffold protein to an acceptor protein that contributes to the attainment of the full functional capacity of a protein.
protein maturation by iron-sulfur cluster transfer
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
The modification of a protein amino acid by oxidation.
The process of introducing a phosphate group on to a protein.
Covalent reaction that results in the removal of a chemical group from a molecule.
Dissociation of simple chemical non-covalent complex (simple chemical dissociation)
Non-covalent binding between at least two metabolites.
activity that do not require other factors
addition of a chemical group that do not require other factors
spontaneous addition of a chemical group
recruitment of a cofactor that do no requires other factor
formation of a covalent bond that do not require external factors
rupture of a covalent bond that does not require external factors
metabolic reaction that do not require external factors
formation of a molecular interaction that does not require external factors
assembly of proteins in a complex (not involving cofactors) that do no require other factors
spontaneous protein-protein complex assembly
dissociation of polypeptidic chain from protein complex that do no require other factors
spontaneous protein-protein complex disassembly
assembly of proteins in a complex that do no require other factors
dissociation of a protein with any bounded entity that do no require other factors
Molecule which is acted upon by an enzyme. The substrate binds with the enzyme's active site, and the enzyme catalyzes a chemical reaction involving the substrate.
Covalent reaction that results in the transfer of a chemical group from one molecule to another.
loss of a disulfide bond that is compensated by a new one
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
Molybdenum ion transfer onto molybdopterin, Homo sapiens
A pathway is a collection/cascade of events, its initiation is triggered by some event and it results in some event/outcome. A pathway may have other pathways as its parts. More than 1 pathway may be triggered by the initial event or any intermediate event.
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20633 A series of biochemical reactions which occurs in a known sequence and can result in all or part of the initiation, progression or completion of a biological process or function.
Interaction between several biochemical entities that results in the formation of a non-covalent complex
"non-covalent" added on February 26 2008 by Nicolas Le Novere.nadded synonym [SF req #3503970]
Transformation of a non-covalent complex that results in the formation of several independent biochemical entities
"Relationship between molecular entities, based on contacts, direct or indirect. [src_code:NR]
Created on February 26 2008 by Nicolas Le Novere on the suggestion of Samuel Kerrien.
"EC:4 catalyzed process\n\n[STKE:0456] Enzyme that catalyzes the cleavage of C-C, C-O, C-S, C-N or other bonds by other means than by hydrolysis or oxidation, with two substrates in one reaction direction, and one in the other. In the latter direction, a molecule (of carbon dioxide, water, etc) is eliminated, thus creating a new double bond or a new ring.\n\n[GO:0016829] Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [GO:0016829, STKE:0456]
"Terms aiming to represent biochemical reactions referring to their resulting product modifications." [MI:0414]
ADP
ATP
phosphate(3-)
proton
water