None Mobilome Ontology 2023-04-13 definition definition If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive database_cross_reference has_exact_synonym is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 RO:part_of external part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external has_part has_part has part has part preceded by 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. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes 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 inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity 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. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true w 'has component' p if 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. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 RO:regulates external regulates regulates regulates regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by inverse of has input input of inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation 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. Considering relabeling as 'pairwise interacts with' 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. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic sequence has_quality The relationship between a feature and an attribute. has_quality entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) function material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA. https://github.com/geneontology/go-ontology/issues/20964 Reactome:R-HSA-912458 recombinase activity strand transferase molecular_function RecA-family recombinase activity strand exchange activity GO:0000150 Note that this term represents activities that do not break or form phosphodiester bonds, and is therefore not a parent of 'site-specific recombinase activity ; GO:0009009'. DNA strand exchange activity Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA. GOC:elh Reactome:R-HSA-912458 Formation of meiotic heteroduplex A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. GOC:pdt A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt 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. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity 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. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element. GO:0004804 P-element encoded transposase activity molecular_function GO:0004803 transposase activity Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element. GOC:bm ISBN:0198506732 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0055132 DNA metabolism cellular DNA metabolism biological_process GO:0006259 DNA metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. ISBN:0198506732 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. biological_process GO:0006310 DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. ISBN:0198506732 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 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. 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 'no data' (ND), is used to indicate this. biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt 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. jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process 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. GOC:go_curators ISBN:0198547684 Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GO:0034960 GO:0043283 GO:0044259 biopolymer metabolic process macromolecule metabolism organismal macromolecule metabolism multicellular organismal macromolecule metabolic process biological_process GO:0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. GOC:mah biopolymer metabolic process GOC:mtg_chebi_dec09 The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198506732 The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah Any cellular metabolic process involving nucleic acids. tb 2010-04-07T10:18:47Z biological_process GO:0090304 nucleic acid metabolic process Any cellular metabolic process involving nucleic acids. GOC:dph GOC:tb Catalytic activity that acts to modify DNA. https://github.com/geneontology/go-ontology/issues/14225 pg 2017-09-14T12:03:51Z molecular_function GO:0140097 catalytic activity, acting on DNA Catalytic activity that acts to modify DNA. GOC:molecular_function_refactoring GOC:pdt Catalytic activity that acts to modify a nucleic acid. https://github.com/geneontology/go-ontology/issues/21402 pg 2021-05-11T06:31:07Z molecular_function GO:0140640 catalytic activity, acting on a nucleic acid Catalytic activity that acts to modify a nucleic acid. GOC:pg The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie Mobile genetic elements (MGEs) are a type of genetic material, a segment of DNA or RNA, that is capable of movement around a genome or that can be transferred from one species or replicon to another. These include transposons, plasmids, bacteriophages, and genomic islands. The mechanism of movement may be self-encoded or may rely on other enzymes and structures, such as a pilus. In bacteria, MGEs are often associated with the movement of antibiotic resistance genes and virulence factors from one species to another, for example by plasmid-mediated transfer. mobile genetic element A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. Plasmids have a wide range of lengths, from roughly one thousand DNA base pairs to hundreds of thousands of base pairs. plasmid A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the same genetic material. Transposons were originally discovered as "jumping genes" by Barbara McClintock. transposon transposable element Bacteriophage are viral infectious agents with bacterial host organisms. Bacteriophage infect and replicate inside bacterial host cells, causing cell lysis as viral particles replicate. Bacteriophage are involved in DNA transfer between host organisms at low frequency through transduction: when segments of host DNA is accidentally packaged with the viral DNA, then integrated into a new host genome and later inherited. bacteriophage These plasmids contain genes that code for bacteriocins, proteins that can kill other bacteria. Col Plasmids Fertility F-plasmids contain tra genes and are capable of conjugation resulting in the expression of sex pilli. Fertility F-Plasmids These plasmids contain genes that provide resistance against antibiotics or poisons. Historically known as R-factors, before the nature of plasmids was understood. Resistance Plasmids These plasmids enable the digestion of unusual substances, e.g. toluene and salicylic acid. Degradative Plasmids which turn the bacterium into a pathogen Virulence Plasmids The set of specific processes that needed for plasmid partition, stability, replication, and mobility. These are all processes that allow for the plasmid to move between organisms. mechanism of plasmid maintenance Any process or set of processes through which plasmid replication is initiated. mechanism of replication Replication by the Theta Mechanism - opening of the strands followed by RNA priming theta type strand displacement replication. Opening of the strands followed by RNA priming strand displacement A mechanism of plasmid replication in which the two strands are asynchronously copied, with one strand initially forming a single-stranded circle. rolling circle replication Molecular mechanisms involved in the intracellular and intercellular transfer, integration, stabilization and recombination of mobile genetic elements. process or mechanism of genetic mobility Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient. Conjugation conjugative transfer Stabilization mechanisms facilitate and promote the survival of plasmids in their host cells. This includes mechanisms that allow for the survival of the host cell itself in harsh conditions. mechanism of stabilization Transformation refers to process of free DNA uptake by competent cells and subsequent integration and functional expression of genes. Extracellular DNA continually enters the environment upon release from decomposing cells, disrupted cells, viral particles or excretion from living cells. transformation A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable anti-toxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK). Toxin-antitoxin system Type I toxin-antitoxin systems rely on the base-pairing of complementary antitoxin RNA with the toxin's mRNA. Translation of the mRNA is then inhibited either by degradation via RNase III or by occluding the Shine-Dalgarno sequence or ribosome binding site. Type I TA System In this system a labile protein antitoxin tightly binds and inhibits the activity of a stable toxin. Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. Type II TA System Type III toxin-antitoxin systems rely on direct interaction between a toxic protein and an RNA antitoxin. The toxic effects of the protein are neutralised by the RNA gene. Type III TA System The process of conjugation requires several different types of subunits and complexes. conjugal transfer subunit or complex Protein involved in the conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. pilX7 Protein involved in the conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. PMID:18375554 PMID:19717626 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. pilX8 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. PMID:18375554 PMID:19717626 Colicin immunity proteins are plasmid encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress colicin immunity protein Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. pilX9 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. PMID:18375554 PMID:19717626 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to type IV secretory pathway VirB10 protein pilX10 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to type IV secretory pathway VirB10 protein PMID:18375554 PMID:19717626 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to P-type DNA transfer ATPase VirB11. pilX11 Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to P-type DNA transfer ATPase VirB11. PMID:18375554 PMID:19717626 conjugal transfer protein - conjugal transfer protein TraG taxB conjugal transfer protein - conjugal transfer protein TraG PMID:18375554 Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity. RelE Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity. PMID:12526800 PMID:15576765 PMID:18375554 PMID:21324908 PMID:22210768 PMID:9767574 Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA. They bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands. DNA topoisomerase The traE gene, first identified in plasmid RP4, is a homologue of E. coli DNA topoisomerase III. traE The traE gene, first identified in plasmid RP4, is a homologue of E. coli DNA topoisomerase III. PMID:18375554 Molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures. Chaperones are present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly. The chaperones are concerned primarily with protein folding. One major function of chaperones is to prevent both newly synthesized polypeptide chains and assembled subunits from aggregating into nonfunctional structures. Many chaperones are heat shock proteins because the tendency to aggregate increases as proteins are denatured by stress. Molecular chaperones have been shown to be involved in both the assembly and disassembly of DNA replication complexes. Molecular Chaperone Chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins. Hsp40 DnaJ Chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins. PMID:18375554 Class 2 transposons encode transposase, which is an enzyme that binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism. transposase This protein is a specific topoisomerase involved in initiating replication. This protein is specifically required and may be rate-limiting for replication of the plasmid in vivo. repC replication initiation protein RepC These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters Chromate transport protein Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group shuttle required for the de novo synthesis of purines, thymidylic acid, and certain amino acids. DfrA Dihydrofolate reductase Class 1 Integrase is a site-specific recombination enzyme that is part of the class 1 integron system. It recognizes the recombination site, attI1, which is where it will catalyze the insertion of gene casettes. Intl1 Class 1 Integrase Class 1 Integrase is a site-specific recombination enzyme that is part of the class 1 integron system. It recognizes the recombination site, attI1, which is where it will catalyze the insertion of gene casettes. PMID:18193080 PMID:8574395 Integrons are genetic mechanisms that allow bacteria to adapt and evolve rapidly through the acquisition, stockpiling and differential expression of new genes. Additionally, an integron will usually contain one or more gene cassettes that have been incorporated into it. integron DNA-binding transcriptional regulator. Protein that is involved in negative regulation of phenolic acid metabolism. PadR family transcriptional regulator transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. transcriptional regulator of operons found in MGEs protein required for initiation of replication replication initiation protein This protein is essential for plasmid replication; it is involved in copy control functions RepA replication initiation protein RepA papB may act as both positive and negative regulator of the pyelonephritis-associated pili (pap) pilin gene transcription. It is found in the pap operon. Major pili subunit operon regulatory protein papB Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. antitoxin Type II post-segregation antitoxin transcriptional regulator C protein Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. Type II toxin Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB. CcdA Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB. PMID:27357537 Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA. CcdB Replication initiator in the monomeric form, and autogenous repressor in the dimeric form. RepE replication initiation protein RepE A plasmid partition system is the mechanism that assures the stable transmission of plasmids during bacterial cell division. Each plasmid has its independent replication system which control the number of copy of a plasmid in a cell. plasmid partition system This system is also used by most bacteria for chromosome segregation. Type I partition system are composed of an ATPase which contains Walker motifs and a CBP which is structurally distinct in type Ia and Ib. ATPases and CBP from type Ia are longer than the one from type Ib, but both CBPs contain an arginine finger in their N-terminal part. ParA proteins from different plasmids and bacterial species show 25 to 30% of sequence identity to the protein ParA of the plasmid P1. The partition of type I system uses a "diffusion-ratchet" mechanism. Type 1 Partition System Type I Partition System def Type Ia Partition System partition system Type Ib partition system This system is composed of an actin-like ATPase, ParM, and a CBP called ParR. The centromere-like site, parC contains two sets of five 11 base pair direct repeats separated by the parMR promoter. The amino-acid sequence identity can go down to 15% between ParM and other actin-like ATPase. Type II Partition System This mechanism is composed of tubulin-like GTPase termed TubZ, and the CBP is termed TubR. Amino-acid sequence identity can go down to 21% for TubZ proteins Type III Partition System The partition system of the plasmid R388 has been found within the stb operon. This operon is composed of three genes, stbA, stbB and stbC R388 Partition System pSK1 is plasmid from Staphylococcus aureus. This plasmid has a partition system determined by a single gene, par, previously known as orf245. This gene has effect neither on the plasmid copy number nor on the growth rate (excluding its implication in a post-segregational killing system). A centromere-like binding sequence is present upstream the par gene, and is composed of seven direct repeats and one inverted repeat. pSK1 partition system Partitioning protein - ATPase ParA PifA is encoded on plasmid F and is responsible for the exclusion of phage T7. E. coli cells that carry plasmid F inhibit the growth of bacteriophage T7. pifA PifA is encoded on plasmid F and is responsible for the exclusion of phage T7. E. coli cells that carry plasmid F inhibit the growth of bacteriophage T7. PMID:7883717 Is essential for plasmid replication. Nicks the positive strand at the plus origin of replication. Pi protein RepB pir replication initiation protein RepB Is essential for plasmid replication. Nicks the positive strand at the plus origin of replication. PMID:18375554 regulates replication replication regulatory protein This protein is involved in the determination of copy number in gene replication. It binds to the repA promoter thus inhibiting the synthesis of the mRNA for the initiator protein RepA. repA2 This protein is essential for plasmid partition. It ensures the proper distribution of newly replicated plasmids to daughter cells during cell division. SopA is trans-acting and binds to a sequence in the sopAB operon, thus regulating the expression of the operon. SopA This protein is essential for plasmid partition. It ensures the proper distribution of newly replicated plasmids to daughter cells during cell division. SopA is trans-acting and binds to a sequence in the sopAB operon, thus regulating the expression of the operon. PMID:25753630 PMID:2670941 SopB is involved in the control of plasmid partitioning. It is trans-acting and binds specifically with the DNA segment containing the sopC region. The presence of SopB in the SopAB complex enhances SopA binding to the target DNA sequence. SopB SopB is involved in the control of plasmid partitioning. It is trans-acting and binds specifically with the DNA segment containing the sopC region. The presence of SopB in the SopAB complex enhances SopA binding to the target DNA sequence. PMID:25753630 PMID:2670941 Bacterial cells often contain type I DNA and restriction modification (RM) systems that degrade foreign DNA during bacterial conjugation. KlcA could be involved in inhibiting the RM systems and enhancing the success of conjugation. antirestriction protein KlcA Bacterial cells often contain type I DNA and restriction modification (RM) systems that degrade foreign DNA during bacterial conjugation. KlcA could be involved in inhibiting the RM systems and enhancing the success of conjugation. PMID:20007596 Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain followed by an RNA-binding maturase domain. These proteins play a role in site-specific DNA insertion. group II intron reverse transcriptase/maturase An enzyme that catalyzes the hydrolysis of a particular substrate. Many hydrolases participate in the inactivation of antibiotics. hydrolase An enzyme that catalyzes the hydrolysis of a particular substrate. Many hydrolases participate in the inactivation of antibiotics. PMID:25753630 Single-strand DNA-binding protein (SSB) binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. single stranded DNA binding protein Single-strand DNA-binding protein (SSB) binds to single-stranded regions of deoxyribonucleic acid (DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. PMID:25753630 The PsiB protein inhibits the functional activity of RecA by binding to it. By doing so, this prevents RecA by catalyzing the autocleavage of LexA, which triggers the SOS response. PsiB The PsiB protein inhibits the functional activity of RecA by binding to it. By doing so, this prevents RecA by catalyzing the autocleavage of LexA, which triggers the SOS response. PMID:19818715 PMID:25753630 PsiA is a protein encoded in the Psi region, which also encodes the PsiB protein. PsiA and PsiB are most likely transcribed in a polycistronic manner. The role of PsiA has not been identified, however it does not seem to influence SOS inhibition mediated by PsiB. PsiA PsiA is a protein encoded in the Psi region, which also encodes the PsiB protein. PsiA and PsiB are most likely transcribed in a polycistronic manner. The role of PsiA has not been identified, however it does not seem to influence SOS inhibition mediated by PsiB. PMID:2201950 PMID:25753630 The process of bacterial conjugation involves the transfer of a conjugative plasmid as a single strand. The potentially deleterious SOS response, which is normally triggered by the appearance of single-stranded DNA, is suppressed in the recipient cell by a complex involving the PsiB protein. This complex inhibits the activity of RecA, preventing RecA from catalyzing the auto-cleavage of LexA, which activates the SOS response. SOS inhibition allows for the successful transfer of plasmid genetic information between bacterial cells through conjugation. Plasmid SOS inhibition toxin Type I Toxin Type I antitoxins are RNA molecules that are complementary to the toxin mRNA, thus binding to the toxin and inhibiting its translation. Type I Antitoxin The CcdA/CCdB Type II Toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division (post-segregational killing). CcdA/CcdB Type II Toxin-antitoxin system The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli to maintain a low copy number. Hok/sok system host killing - a long lived (half-life 20 minutes) toxin Hok host killing - a long lived (half-life 20 minutes) toxin PMID:25753630 The mok reading frame in the hok/sok locus overlaps with the hok reading frame and is needed for the transcription of the hok gene. Mok The mok reading frame in the hok/sok locus overlaps with the hok reading frame and is needed for the transcription of the hok gene. PMID:25753630 Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair. TraM Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Cooperatively binds 3 regions in the F plasmid oriT locus; 2 are required for autoregulation while the other is required for plasmid transfer. Bends oriT DNA less than 50 degrees. Plasmid specificity is conferred by the TraD-TraM pair. PMID:25753630 TraJ is a conjugal transfer transcriptional regulator.It recruits the relaxasome complex to the oriT site TraJ TraJ is a conjugal transfer transcriptional regulator.It recruits the relaxasome complex to the oriT site PMID:25753630 TraY is a subunit of the relaxosome. It facilitates the binding of the relaxase to the oriT, and enhances cleaving activity. TraY TraY is a subunit of the relaxosome. It facilitates the binding of the relaxase to the oriT, and enhances cleaving activity. PMID:25753630 The traA gene codes for relaxase, which is an enzyme that initiates plasmid DNA transfer during bacterial conjugation. Relaxase forms a relaxosome complex with auxiliary proteins to initiate conjugation. Relaxosome binds to the origin of transfer (oriT) sequence and cleaves the DNA strand that will be transferred (the T strand). TraA The traA gene codes for relaxase, which is an enzyme that initiates plasmid DNA transfer during bacterial conjugation. Relaxase forms a relaxosome complex with auxiliary proteins to initiate conjugation. Relaxosome binds to the origin of transfer (oriT) sequence and cleaves the DNA strand that will be transferred (the T strand). PMID:25753630 Membrane protein involved in F pilin formation TraL Membrane protein involved in F pilin formation PMID:25753630 conjugal transfer protein traK conjugal transfer protein PMID:25753630 conjugal transfer protein TraB conjugal transfer protein PMID:25753630 A family of nucleases involved in resolution during DNA recombination. Resolvase enzymes resolve DNA intermediates known as junctions. Some resolvases have also been identified as repressors of transposase enzymes. recombinase resolvase resolvase ResD resolvase PMID:25753630 A helicase is an enzyme that participates in separating the strands of a nucleic acid duplex, which is required for processes such as DNA replication, transcription, recombination, and repair. helicase UvrD is a helicase that participates in nucleotide excision repair and other DNA repair and replication processes. UvrD UvrD is a helicase that participates in nucleotide excision repair and other DNA repair and replication processes. PMID:17190599 tranposase - Family IS1 IS1 InsA tranposase - Family IS1 PMID:25753630 tranposase - family IS1 IS1 InsB DNA resolvase DNA resolvase DNA resolvase PMID:25753630 Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to its cognate PemK endoribonuclease toxin and neutralizes its activity. Responsible for the stable maintenance of the plasmid during cell division. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis. PemI Antitoxin component of a type II toxin-antitoxin (TA) module. Labile antitoxin that binds to its cognate PemK endoribonuclease toxin and neutralizes its activity. Responsible for the stable maintenance of the plasmid during cell division. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis. PMID:17416361 PMID:25753630 Toxic component of a type II toxin-antitoxin (TA) module. Probably functions as an endoribonuclease. Responsible for the stable maintenance of the plasmid during cell division by postsegregational killing of plasmid-less daughter cells. Neutralized by coexpression with cognate antitoxin PemI. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis. PemK Toxic component of a type II toxin-antitoxin (TA) module. Probably functions as an endoribonuclease. Responsible for the stable maintenance of the plasmid during cell division by postsegregational killing of plasmid-less daughter cells. Neutralized by coexpression with cognate antitoxin PemI. Both PemI and PemK proteins bind to the promoter region of the pem operon to autoregulate their synthesis. PMID:17416361 PMID:25753630 Associated with replication initiation. RepA4 Arginine repressor ArgR ArgR family transcriptional regulator Arginine repressor PMID:25753630 TraI codes for a relaxase of F plasmids, which cleaves the DNA in the initiationof plasmid conjugation. It has also been identified as DNA helicase I. DNA helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA TraI TraI codes for a relaxase of F plasmids, which cleaves the DNA in the initiationof plasmid conjugation. It has also been identified as DNA helicase I. DNA helicase I is a potent, highly processive DNA-dependent ATPase, able to unwind about 1.1 kb dsDNA per second in a 5' to 3' manner. TraI forms a covalent 5'-phosphotyrosine intermediate linkage to the ssDNA. The transesterified T-strand moves from the donor cell to the recipient cell in a 5'to 3' direction, with the DNA helicase activity of TraI unwinding the DNA PMID:26899414 conjugal transfer protein - pilus acetylase TraX conjugal transfer protein - pilus acetylase PMID:25753630 Members of the Multiple Antibiotic Resistance Regulator (MarR) family. MarR regulates an operon that encodes a drug efflux pump, and mutations in proteins that partcipate in this system lead to a multiple antibiotic resistance phenotype. MarR proteins are members of the winged helix-turn-helix family of transcription factors. Some MarR homologs activate transcription, while most repress gene activity. MarR famiy transcriptional regulator Recombinases are genetic recombination enzymes. DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene expression. recombinase Serine recombinases can rearrange DNA sequences with topological selectivity. Sin Serine recombinases can rearrange DNA sequences with topological selectivity. PMID:11994145 resolvase/integrase a nuclease which is involved in DNA recombination. bin A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. AbiK functions as a transcriptional repressor of an arsenic resistance operon ArsR family transcriptional regulator Enzyme that repress transposases transposon DNA invertase The transposase produces nicks at the donor and the recipient sites. The 3' end of the transposon is ligated to the 5' end of the target sequence. The transposon is duplicated after DNA replication. IS6 family transposase Resolvase catalyzes the resolution (a site-specific recombination) of the cointegrated replicon to yield the final transposition products transposon Tn552 resolvase Topoisomerase III can introduce single-strand breaks that are required for DNA to be exchanged by adjacent chromosomes. Topoisomerase III Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element. transposase IS66 family protein Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element. Tn3 family transposase Catalysis of the transposition of transposable elements or transposons. Transposases are involved in recombination required for transposition and are site-specific for the transposon/transposable element. PMID:26899414 Initiates plasmid replication. IncFII family plasmid replication intiator RepA Initiates plasmid replication. PMID:26899414 One of the components on the FinOP fertility inhibition complex, which inhibits the expression of traJ gene, which in turn regulates the expression of some 20 transfer genes. The transfer genes are responsible for the process, called conjugal transfer, in which DNA is transmitted from one bacterial host to another. RNA-binding that interacts with the traJ mRNA and its antisense RNA, finP, stabilizing finP against endonucleolytic degradation and facilitating sense-antisense RNA recognition. FinO Fertility inhibition protein One of the components on the FinOP fertility inhibition complex, which inhibits the expression of traJ gene, which in turn regulates the expression of some 20 transfer genes. The transfer genes are responsible for the process, called conjugal transfer, in which DNA is transmitted from one bacterial host to another. RNA-binding that interacts with the traJ mRNA and its antisense RNA, finP, stabilizing finP against endonucleolytic degradation and facilitating sense-antisense RNA recognition. PMID:25753630 PMID:26899414 PMID:9819055 Enzymes that catalyze the cleavage of phosphodiester bonds in DNA in a site- and strand- specific manner, creating nicks that initiate either the processes of plasmid conjugation or rolling circle replication. relaxase The nicks produced by Rep relaxases initiate plasmid or virus RCR replicative relaxase Mob relaxases nick at origin of transfer (oriT) to initiate the process of DNA mobilization and transfer known as bacterial conjugation. Mob relaxases are part of the relaxosome. mobility relaxase Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Couples the transferosome to a type IV secretion system. Probably forms a pore through which single-stranded plasmid DNA is transferred to the secretion system. The last 37 residues are important for determining plasmid specificity and transfer efficiency, with additional specificity conferred by the TraD-TraM pair. Coupling protein TraD Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Couples the transferosome to a type IV secretion system. Probably forms a pore through which single-stranded plasmid DNA is transferred to the secretion system. The last 37 residues are important for determining plasmid specificity and transfer efficiency, with additional specificity conferred by the TraD-TraM pair. PMID:26899414 Antitoxin component of a type II toxin-antitoxin (TA) module. Counteracts the effect of cognate toxin RelE via direct protein-protein interaction, preventing RelE from entering the ribosome A site and thus inhibiting its endoribonuclease activity. An autorepressor of relBE operon transcription. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity. Increased transcription rate of relBE and activation of relE is consistent with a lower level of RelB in starved cells due to degradation of RelB by protease Lon. DinJ RelB RelB is the antitoxin component of a type II toxin-antitoxin (TA) module. Counteracts the effect of cognate toxin RelE via direct protein-protein interaction, preventing RelE from entering the ribosome A site and thus inhibiting its endoribonuclease activity. An autorepressor of relBE operon transcription. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity. Increased transcription rate of relBE and activation of relE is consistent with a lower level of RelB in starved cells due to degradation of RelB by protease Lon.RelE is the toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity. RelB/RelE Type II toxin-antitoxin system Toxin Antitoxin system Type II PemI/PemK type II Toxin-antitoxin system HicA is a toxin part of the HicA/HicB toxin-antitoxin system overexpression of the HicA toxin, which exhibits mRNA interferase activity, causes cleavage of mRNAs and an arrest of cell growth HicA HicA is a toxin part of the HicA/HicB toxin-antitoxin system overexpression of the HicA toxin, which exhibits mRNA interferase activity, causes cleavage of mRNAs and an arrest of cell growth PMID:25917909 The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer mobC The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer PMID:24905728 Relaxosome is the complex of proteins that initiates bacterial conjugation. The subunits that make up the relaxosome are encoded by the tra gene in the origin of transfer, oriT, region on the plasmid, and in the host cell genome. relaxosome DNA strand transferase,conjugal transfer relaxase TraA,Ti-type conjugative transfer relaxase TraA,MobA/MobL family mobA MobB promotes the specific transfer of the plasmid in the presence of conjugative plasmids. MobB The parDE type II toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). ParDE type II toxin-antitoxin system Toxin component of a toxin-antitoxin (TA) module involved in plasmid partition. Acts by inhibiting DNA gyrase, converting supercoiled plasmid DNA into a singly cleaved linear form in an ATP-dependent fashion. To do so it probably interacts with one of the gyrase subunits. Gyrase inhibition is prevented by antitoxin ParD, and is reversed in vitro by incubation with ParD. In cells that have lost the plasmid filamentation and growth inhibition occur; this is suppressed when ParD is supplied in trans. The parDE operon alone is capable of stabilizing an RK2-derived minireplicon under defined growth conditions in several different Gram-negative bacteria. It does so by the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. ParE Toxin component of a toxin-antitoxin (TA) module involved in plasmid partition. Acts by inhibiting DNA gyrase, converting supercoiled plasmid DNA into a singly cleaved linear form in an ATP-dependent fashion. To do so it probably interacts with one of the gyrase subunits. Gyrase inhibition is prevented by antitoxin ParD, and is reversed in vitro by incubation with ParD. In cells that have lost the plasmid filamentation and growth inhibition occur; this is suppressed when ParD is supplied in trans. The parDE operon alone is capable of stabilizing an RK2-derived minireplicon under defined growth conditions in several different Gram-negative bacteria. It does so by the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. PMID:25232178 PMID:26823590 Antitoxin of the VagCD toxin-antitoxin system VagC Antitoxin of the VagCD toxin-antitoxin system PMID:23733457 Toxin of the VagCD toxin antitoxin system VagD Toxin of the VagCD toxin antitoxin system PMID:23733457 A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. VagCD Type II Toxin-antitoxin system an antibody that counteracts a toxin Acinetobacter baumannii ACICU plasmid pACICU1 addiction module antitoxin an antibody that counteracts a toxin PMID:18411315 The product of the prevent host death (phd) gene is a type II antitoxin that is part of the doc/phd TA system. phd The product of the prevent host death (phd) gene is a type II antitoxin that is part of the doc/phd TA system. PMID:10358024 The product of the death on curing (doc) gene is a type II toxin. doc Involved in plasmid partition. Localize to both poles of the predivisional cell following completion of DNA replication. Binds to the DNA origin of replication. ParB a nuclease which is involved in DNA recombination. ResA a nuclease which is involved in DNA recombination. PMID:23733457 Mediator of plasmid stability StbB Mediator of plasmid stability PMID:25232178 plasmid stability protein StbA plasmid stability protein PMID:25232178 Type II toxin Zeta Type II toxin PMID:25845845 Part of the PhdYeFM antitoxin toxin system StbD Suppression of killing - a short lived (half-life 30 seconds) RNA antitoxin Sok Toxin of the Flm toxin/antitoxin system - F-plasmid homologues of hok/mok TA system FlmA Toxin of the Flm toxin/antitoxin system - F-plasmid homologues of hok/mok TA system PMID:7612932 ParD is a plasmid anti-toxin that forms a ribbon-helix-helix DNA binding structure. It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). ParD ParD is a plasmid anti-toxin that forms a ribbon-helix-helix DNA binding structure. It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). PMID:17320955 Epsilon antitoxin, produced by various prokaryotes, forms part of a post-segregational killing system, which is involved in the initiation of programmed cell death of plasmid-free cells. Epsilon Epsilon antitoxin, produced by various prokaryotes, forms part of a post-segregational killing system, which is involved in the initiation of programmed cell death of plasmid-free cells. PMID:20660665 PndA encodes toxin proteins containing single transmembrane domains. It is part of the PndA-PndB (promotion of nucleic acid acid degradation) TA. PndA PndA encodes toxin proteins containing single transmembrane domains. It is part of the PndA-PndB (promotion of nucleic acid acid degradation) TA. PMID:19052321 toxin type II YafO type II toxin HipA type II toxin PMID:22720069 antitoxin type II HicB antitoxin type II PMID:25917909 Type II antitoxin MazE Type II antitoxin PMID:41136 Type II toxin MazF Type II toxin PMID:24275114 Type II TA mediator Omega Type II TA mediator PMID:18511120 Mediator of TA systems Type II TA mediator antitoxin of YafO-YafN TA system YafN antitoxin of YafO-YafN TA system PMID:16397293 PMID:16738553 PMID:19617347 PMID:9278503 conjugal transfer mating pair stabilization protein TraG conjugal transfer mating pair stabilization protein PMID:11150665 TraS is an entry exclusion protein, involved in blocking the transfer of redundant DNA between donor cells. TraS TraS is an entry exclusion protein, involved in blocking the transfer of redundant DNA between donor cells. PMID:11150665 PMID:337311 conjugal transfer pilus assembly protein TraH conjugal transfer pilus assembly protein PMID:11150665 conjugal transfer pilin assembly thiol-disulfide isomerase TrbB conjugal transfer pilin assembly thiol-disulfide isomerase PMID:11150665 conjugal transfer pilin chaperone TraQ conjugal transfer pilin chaperone PMID:11150665 conjugal transfer pilus assembly protein TraF conjugal transfer pilus assembly protein PMID:11150665 conjugal transfer mating-pair stabilization protein TraN conjugal transfer mating-pair stabilization protein PMID:11150665 conjugal transfer pilus assembly protein TrbC conjugal transfer pilus assembly protein PMID:11150665 conjugal transfer pilus assembly protein TraU conjugal transfer pilus assembly protein PMID:11150665 conjugal transfer protein TrbI conjugal transfer protein PMID:11150665 TraC is an ATPase TraC TraC is an ATPase PMID:11150665 conjugal transfer pilus assembly protein TraW conjugal transfer protein TraP conjugal transfer protein PMID:11150665 conjugal transfer protein TraV conjugal transfer protein PMID:11150665 MazG is transcribed in the same polycistronic mRNA as MazE and MazF. It is a nucleotide pyrophosphohydrolase and breaks down guanosine 3',5'-bispyrophosphate (ppGpp). The activity of MazG is inhibited by the MazEF complex. However, it is hypothesized that MazG reduces the deleterious effect of the MazF toxin. MazG MazG is transcribed in the same polycistronic mRNA as MazE and MazF. It is a nucleotide pyrophosphohydrolase and breaks down guanosine 3',5'-bispyrophosphate (ppGpp). The activity of MazG is inhibited by the MazEF complex. However, it is hypothesized that MazG reduces the deleterious effect of the MazF toxin. PMID:16390452 PMID:24459253 Type II toxin-antitoxin system MazEF Type II toxin-antitoxin system Type II toxin-antitoxin system PMID:27259116 RecA is a protein that binds single-stranded DNA, forming a nucleoprotein filament. When bound, RecA may either target a homologous double-stranded DNA sequence and catalyze recombination, or it catalyzes the autocleavage of LexA. This allows for the expression of SOS genes. RecA RecA is a protein that binds single-stranded DNA, forming a nucleoprotein filament. When bound, RecA may either target a homologous double-stranded DNA sequence and catalyze recombination, or it catalyzes the autocleavage of LexA. This allows for the expression of SOS genes. PMID:16000023 PMID:24459253 PMID:6244554 DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. DNA polymerase conjugal transfer protein the forms the bulk of type IV secretion complex that spans outer membrane and periplasm TraO conjugal transfer protein the forms the bulk of type IV secretion complex that spans outer membrane and periplasm PMID:23357767 ISNCY family-transposase tnpA A transcription termination factor transcription termination factor NusG Hin belongs to the serine recombinase family of DNA invertases in which it relies on the active site serine to initiate DNA cleavage and recombination. DNA-invertase hin Hin belongs to the serine recombinase family of DNA invertases in which it relies on the active site serine to initiate DNA cleavage and recombination. PMID:24905728 LexA is a transcriptional repressor that represses SOS response genes coding primarily for error-prone DNA polymerases, DNA repair enzymes and cell division inhibitors. LexA forms de facto a two-component regulatory system with RecA, which senses DNA damage at stalled replication forks, forming monofilaments and acquiring an active conformation capable of binding to LexA and causing LexA to cleave itself, in a process called autoproteolysis LexA adiY is a DNA-binding transcriptional activator of the adi system. Implicated in arginine-dependent acid resistance in Escherichia coli. adiY adiY is a DNA-binding transcriptional activator of the adi system. Implicated in arginine-dependent acid resistance in Escherichia coli. PMID:12867448 PMID:8704970 During the process of conjugation, the coupling protein link the relaxosome and the mating pair formation complex to facilitate the movement of the DNA transfer intermediate through the channel between the cells. conjugation coupling protein During the process of conjugation, the coupling protein link the relaxosome and the mating pair formation complex to facilitate the movement of the DNA transfer intermediate through the channel between the cells. PMID:26104193 Subunits of relaxosomes, which are needed for conjugation of plasmids. subunit of relaxosome Subunits of mating pair formation complexes, which are needed for conjugation of plasmids. subunit of mating pair formation complex Genes, proteins, other biological or chemical compounds, their shared components, and their associated mechanisms as they relate to mobile genetic element molecular biology and evolution. process or component of mobile genetic element biology or chemistry Proteins that participate in the partition, movement, stabilization, and replication of plasmids. complex or subunit involved in plasmid maitenance Proteins that are involved in the partitioning of plasmids. partitioning protein Proteins that are needed for the replication of plasmids. subunit or complex involved in plasmid DNA replication Proteins that are encoded on plasmids and that are promote the stability of the plasmid in the host cell, or confer advantages to the host cell in certain conditions. subunit or complex involved in stabilization Proteins that are involved in the movement of genetic information between different regions on a chromosome, different chromosomes, or different organisms through processes such as genetic recombination. subunit or complex involved in genetic mobility Proteins, and genes, and RNAs that are part of toxin-antitoxin systems encoded on plasmids. component of a TA system This system is comprised of the toxin - Doc, and the antitoxin - Phd. Doc/Phd Type II TA System Genes that allow bacteria to resist infection by bacteriophages have been discovered to be encoded on plasmids. protein conferring phage resistance Proteins that are involved in the SOS response, which is a global response to DNA damage. SOS response protein Proteins that repress the SOS response in bacterial cells to allow for successful bacterial conjugation. SOS response inhibitor The mechanisms that mediate the intercellular movement of plasmids. mechanism of plasmid mobility Activity and mechanisms related to recombination in mobile genetic elements, including bacteriophage, plasmids and transposons recombinase activity DDE-based recombinase activity refers to DNA transposases with RNase H-like catalytic domains. The active site of such transposases contains an amino acid motif, DDE or sometimes DDD, which coordinates nucleophilic cleavage of a phosphodiester bond and joining by transesterification. DDE-based recombinase activity DNA cleavage by serine recombinases involves an active site serine nucleophile that attacks a phosphate group, without requiring a cofactor. serine-based recombinase activity A mechanism of transposition and recombination whereby DNA is cleaved by an active site tyrosine residue. tyrosine-based recombinase activity Group II introns are mobile genetic elements and mobile ribozymes that self-splice from precursor RNA to produce intron lariat RNA. A reverse transcriptase encoded by the intron stabilize the RNA structure for forward and reverse splicing, then the integrated intron RNA is converted back to DNA. group II intron Group I introns on mobile genetic elements and self-splicing ribozymes. In group I introns, self-splicing is assisted and catalyzed by guanosine-initiated processes, unlike group II introns. group I intron A genomic island is a type of mobile genetic element with evidence of horizontal gene transfer. Genomic islands are often large segments of DNA which carry accessory genes. These accessory genes may be integrase enzymes related to plasmid conjugation or bacteriophages, insertion elements or transposons for mobilization, and/or selective advantages. Genomic islands are well-known to carry genes associated with pathogenicity, symbiosis, metabolic fitness and/or antibiotic resistance. genomic island A class I transposable element, or Retrotransposon, uses an RNA intermediate to facilitate movement and copying. The transposable element is first transcribed from DNA to RNA, and the RNA copy is inserted into the genome via reverse transcription catalyzed by reverse transcriptase. The reverse transcriptase enzyme is generally encoded by the transposon retrotransposon class I transposable element Class II transposable elements, also known as DNA transposons, are catalyzed by transposase enzymes and do not use an RNA intermediate. The class II mechanism involves a staggered cut at a target site producing so-called "sticky ends" with a transposase. The DNA transposon can then be excised and ligated to the target site, where the gaps produced by "sticky ends" are filled by DNA polymerase. This produces a characteristic site duplication at the insertion site which may be identified by short direct repeats followed by inverted repeats. DNA transposon class II transposable element Transduction is a type of gene transfer mediate by a bacteriophage. When bacteriophage proteins assemble following replication, segments of host DNA may be accidentally included; this DNA is then injected into the next host, where it can recombine and be inherited. transduction Methods of classifying and separating plasmids based on given criteria. plasmid typing scheme Replicon typing schemes use genetic elements of the replicon region to type plasmids. This can be done through Southern blot hybridization, or through PCR-based replicon typing. replicon typing method A plasmid typing method using plasmid incompatibility groups. Plasmids with similar replication mechanisms are often unable to co-exist in a cell. Inc grouping MOB typing relies on the conserved N-terminal sequence of the relaxase proteins encoded by transmissible plasmids. MOB typing can make use of both in silico and PCR-based methods. MOB typing method A method wherein plasmids are classified according to Southern blot hybridizations using replicons as probes. This method lacks specificity when similar replicons are present; it is usually applied following PCR-based replicon typing (PBRT). replicon probe hybridization A plasmid typing method wherein allelic profiles are assessed at six loci. Plasmids are assigned a pMLST subtype nesting within the broader replicon type. This can be performed with PCR-based or in silico methods. replicon subtyping PCR-based degenerate primer MOB typing is used to type Proteobacterial and Enterococcal plasmids. PCR-based MOB typing in silico MOB typing using six N-terminal relaxase sequences are used as PSI-BLAST probes to detect relaxases from transmissible plasmids. Plasmids are then partitioned into six possible MOB types. in silico MOB typing A family of complex class II replicative transposons, often carrying genes for ampicillin or other beta-lactam resistance. Tn3-like family transposon Tn4401 is a Tn3-like transposon of which there are 5 subtypes (Tn4401a-e). Tn4401 has been shown to carry KPC family carbapenemases and are involved in KPC gene mobilization. Tn4401 Tn4401 is a Tn3-like transposon of which there are 5 subtypes (Tn4401a-e). Tn4401 has been shown to carry KPC family carbapenemases and are involved in KPC gene mobilization. PMID:21844325 A Tn3-like mosaic transposon carrying CTX-M and OXA beta-lactamase based resistance genes. Tn1999 A Tn3-like mosaic transposon carrying CTX-M and OXA beta-lactamase based resistance genes. PMID:23027715 A plasmid incompatibility group, IncA/C plasmids are large, low copy number, theta-replicating plasmids. IncA/C IncF plasmids are commonly carried by antibiotic-resistant Escherichia coli or other Enterobacteriaceae. These plasmids frequently harbour beta-lactam resistance genes from the CTX-M, TEM and OXA families. IncF IncI1 is a plasmid typing incompatibility group or replicon, associated with antibiotic resistance. IncI1 plasmids carry resistance genes from the CTX-M, CMY, TEM, SHV, and VIM beta-lactamase families, as well as other resistance genes. IncI1 IncL/M plasmid incompatibility group. IncL/M plasmids have been associated with aminoglycoside resistance, beta-lactam resistance (CTX-M, TEM, SHV, IMP) and fluoroquinolone resistance genes. IncL/M Resistance plasmids carrying KPC Carbapenemases found in Klebsiella pneumoniae pKPC-484 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. sequence sequence SO:0000001 region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. SO:ke A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. http://en.wikipedia.org/wiki/Transposable_element transposable element transposon sequence SO:0000101 transposable_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. http://www.sci.sdsu.edu/~smaloy/Glossary/T.html http://en.wikipedia.org/wiki/Transposable_element wiki Any extent of continuous biological sequence. INSDC_feature:misc_feature INSDC_note:other INSDC_note:sequence_feature located_sequence_feature sequence feature sequence located sequence feature SO:0000110 sequence_feature Any extent of continuous biological sequence. LAMHDI:mb SO:ke A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. plasmid sequence sequence SO:0000155 This term is mapped to MGED. Do not obsolete without consulting MGED ontology. plasmid A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. SO:ma The sequences extending on either side of a specific region. flanking region sequence SO:0000239 flanking_region The sequences extending on either side of a specific region. SO:ke The region of sequence surrounding a transposable element. transposable element flanking region sequence SO:0000364 transposable_element_flanking_region The region of sequence surrounding a transposable element. SO:ke A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. http://en.wikipedia.org/wiki/Integron sequence SO:0000365 integron A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. SO:as http://en.wikipedia.org/wiki/Integron wiki An attribute describes a quality of sequence. sequence attribute sequence SO:0000400 sequence_attribute An attribute describes a quality of sequence. SO:ke An attribute describing a located_sequence_feature. feature attribute sequence SO:0000733 feature_attribute An attribute describing a located_sequence_feature. SO:ke A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. http://en.wikipedia.org/wiki/Genomic_island genomic island sequence SO:0000772 Genomic islands are transmissible elements characterized by large size (>10kb). genomic_island A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. Phigo:at SO:ke http://en.wikipedia.org/wiki/Genomic_island wiki A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. http://en.wikipedia.org/wiki/Mobile_genetic_element INSDC_feature:mobile_element MGE mobile genetic element sequence SO:0001037 mobile_genetic_element A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. PMID:14681355 http://en.wikipedia.org/wiki/Mobile_genetic_element wiki An MGE that is not integrated into the host chromosome. extrachromosomal mobile genetic element sequence SO:0001038 extrachromosomal_mobile_genetic_element An MGE that is not integrated into the host chromosome. SO:ke An MGE that is integrated into the host chromosome. integrated mobile genetic element sequence SO:0001039 integrated_mobile_genetic_element An MGE that is integrated into the host chromosome. SO:ke The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. viral sequence virus sequence sequence SO:0001041 The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. viral_sequence The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. SO:ke The nucleotide sequence of a virus that infects bacteria. http://en.wikipedia.org/wiki/Bacteriophage bacteriophage phage phage sequence sequence SO:0001042 phage_sequence The nucleotide sequence of a virus that infects bacteria. SO:ke http://en.wikipedia.org/wiki/Bacteriophage wiki An attribute describing a feature that has either intra-genome or intracellular mobility. http://en.wikipedia.org/wiki/Mobile sequence SO:0001234 mobile An attribute describing a feature that has either intra-genome or intracellular mobility. RSC:cb http://en.wikipedia.org/wiki/Mobile wiki A region containing at least one unique origin of replication and a unique termination site. http://en.wikipedia.org/wiki/Replicon_(genetics) sequence SO:0001235 replicon A region containing at least one unique origin of replication and a unique termination site. ISBN:0716719207 http://en.wikipedia.org/wiki/Replicon_(genetics) wiki A region defined by its disposition to be involved in a biological process. INSDC_misc_feature INSDC_note:biological_region biological region sequence SO:0001411 biological_region A region defined by its disposition to be involved in a biological process. SO:cb A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping. topologically defined region sequence SO:0001412 topologically_defined_region A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping. PMID:32782014 SO:cb true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).