21:07:2015 00:00 unipathway_ontology 1.2 anne.morgat@isb-sib.ch UniPathway Release 2015_03 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 FORMULA InChI synonym_type_property database_cross_reference has_obo_format_version has_obo_namespace has_related_synonym has_synonym_type shorthand 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 unipathway_ontology 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 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 BFO:0000062 unipathway_ontology preceded_by preceded_by 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 occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process 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 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 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 A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand 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 process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall 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. Chris Mungall 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)". RO_0000053 some (RO_0000054 only ?Y) 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. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant Chris Mungall 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. Chris Mungall consumes RO:0002233 unipathway_ontology has_input_compound has_input_compound has input has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. Chris Mungall produces RO:0002234 unipathway_ontology has_output_compound has_output_compound has output has output 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 cjm 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 cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A mereological relationship or a topological relationship Chris Mungall 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 Chris Mungall 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. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall 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. Chris Mungall 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 Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by inverse of has input Chris Mungall input of inverse of has output Chris Mungall output of inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes 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. Chris Mungall 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 p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall 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 Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' 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. Chris Mungall 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/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations 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. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. Chris Mungall molecularly controls activity directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall inhibits molecularly decreases activity of activity directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall activates molecularly increases activity of activity directly positively regulates activity of Chris Mungall 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) p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall 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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall 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 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 Chris Mungall 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 entities Chris Mungall causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences Process(P1) directly regulates process(P2) 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. Chris Mungall 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 Chris Mungall 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. Chris Mungall 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 Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel produced by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 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 cjm 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 cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect unipathway_ontology has_connecting_compound has connecting compound unipathway_ontology uniprot_super_pathway UniProt super-pathway 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. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity molecular process molecular_function catalytic activity biological_process true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups A chemical reaction involved in a UniPathway pathway. reaction UPa:UCR00000 reaction 1 1 1 1 1 KEGG:R00005 METACYC:ALLOPHANATE-HYDROLASE-RXN RHEA:19032 reaction UPa:UCR00005 H(2)O + urea-1-carboxylate = 2 CO(2) + 2 NH(3) 1 LR 1 KEGG:R00005 KEGG reaction METACYC:ALLOPHANATE-HYDROLASE-RXN MetaCyc MetaCyc REACTION RHEA:19032 Rhea reaction 1 1 1 1 KEGG:R00010 METACYC:TREHALA-RXN RHEA:20871 RHEA:32678 reaction UPa:UCR00010 H(2)O + alpha,alpha-trehalose = 2 D-glucose 1 LR 1 KEGG:R00010 KEGG reaction METACYC:TREHALA-RXN MetaCyc MetaCyc REACTION RHEA:20871 Rhea reaction RHEA:32678 Rhea reaction 1 1 1 1 KEGG:R00013 METACYC:GLYOCARBOLIG-RXN RHEA:10139 reaction UPa:UCR00013 2 glyoxylate = 2-hydroxy-3-oxopropanoate + CO(2) 1 LR 1 KEGG:R00013 KEGG reaction METACYC:GLYOCARBOLIG-RXN MetaCyc MetaCyc REACTION RHEA:10139 Rhea reaction 1 1 1 1 1 KEGG:R00014 METACYC:RXN-12583 reaction UPa:UCR00014 pyruvate + thiamine diphosphate = 2-hydroxyethyl-ThPP + CO(2) 1 LR 1 KEGG:R00014 KEGG reaction METACYC:RXN-12583 MetaCyc MetaCyc REACTION 1 1 1 1 1 1 1 KEGG:R00021 METACYC:GLUTAMATE-SYNTHASE-FERREDOXIN-RXN RHEA:12131 reaction UPa:UCR00021 2 L-glutamate + 2 oxidized ferredoxin = 2-oxoglutarate + 2 H(+) + L-glutamine + 2 reduced ferredoxin 1 RL 1 KEGG:R00021 KEGG reaction METACYC:GLUTAMATE-SYNTHASE-FERREDOXIN-RXN MetaCyc MetaCyc REACTION RHEA:12131 Rhea reaction 1 1 1 1 KEGG:R00036 METACYC:PORPHOBILSYNTH-RXN RHEA:24067 reaction UPa:UCR00036 2 5-aminolevulinate = 2 H(2)O + porphobilinogen 1 LR 1 KEGG:R00036 KEGG reaction METACYC:PORPHOBILSYNTH-RXN Rhea MetaCyc REACTION RHEA:24067 Rhea reaction 1 1 1 1 KEGG:R00066 METACYC:RIBOFLAVIN-SYN-RXN RHEA:20775 reaction UPa:UCR00066 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = 5-amino-6-(D-ribitylamino)uracil + riboflavin 1 LR 1 KEGG:R00066 KEGG reaction METACYC:RIBOFLAVIN-SYN-RXN MetaCyc MetaCyc REACTION RHEA:20775 Rhea reaction 1 1 1 1 1 KEGG:R00084 METACYC:OHMETHYLBILANESYN-RXN RHEA:13188 reaction UPa:UCR00084 H(2)O + 4 porphobilinogen = 4 NH(3) + hydroxymethylbilane 1 LR 1 KEGG:R00084 KEGG reaction METACYC:OHMETHYLBILANESYN-RXN Rhea MetaCyc REACTION RHEA:13188 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00093 METACYC:GLUTAMATE-SYNTHASE-NADH-RXN RHEA:13756 reaction UPa:UCR00093 2 L-glutamate + NAD(+) = 2-oxoglutarate + H(+) + L-glutamine + NADH 1 RL 1 KEGG:R00093 KEGG reaction METACYC:GLUTAMATE-SYNTHASE-NADH-RXN MetaCyc MetaCyc REACTION RHEA:13756 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00114 METACYC:GLUTAMATESYN-RXN RHEA:15504 reaction UPa:UCR00114 2 L-glutamate + NADP(+) = 2-oxoglutarate + H(+) + L-glutamine + NADPH 1 RL 1 KEGG:R00114 KEGG reaction METACYC:GLUTAMATESYN-RXN MetaCyc MetaCyc REACTION RHEA:15504 Rhea reaction 1 1 1 1 KEGG:R00127 METACYC:ADENYL-KIN-RXN RHEA:12976 reaction UPa:UCR00127 AMP + ATP = 2 ADP 1 RL 1 KEGG:R00127 KEGG reaction METACYC:ADENYL-KIN-RXN Rhea MetaCyc REACTION RHEA:12976 Rhea reaction 1 1 1 1 1 KEGG:R00130 METACYC:DEPHOSPHOCOAKIN-RXN RHEA:18248 reaction UPa:UCR00130 3'-dephospho-CoA + ATP = ADP + CoA 1 LR 1 KEGG:R00130 KEGG reaction METACYC:DEPHOSPHOCOAKIN-RXN MetaCyc MetaCyc REACTION RHEA:18248 Rhea reaction 1 1 1 1 1 KEGG:R00131 METACYC:UREASE-RXN RHEA:20560 reaction UPa:UCR00131 H(2)O + urea = CO(2) + 2 NH(3) 1 LR 1 KEGG:R00131 KEGG reaction METACYC:UREASE-RXN MetaCyc MetaCyc REACTION RHEA:20560 Rhea reaction 1 1 1 1 1 KEGG:R00137 METACYC:2.7.7.1-RXN RHEA:21363 reaction UPa:UCR00137 ATP + nicotinamide D-ribonucleotide = NAD(+) + diphosphate 1 LR 1 KEGG:R00137 KEGG reaction METACYC:2.7.7.1-RXN MetaCyc MetaCyc REACTION RHEA:21363 Rhea reaction 1 1 1 1 1 1 KEGG:R00150 METACYC:CARBAMATE-KINASE-RXN RHEA:10155 reaction UPa:UCR00150 ATP + CO(2) + NH(3) = ADP + carbamoyl phosphate 1 RL 1 KEGG:R00150 KEGG reaction METACYC:CARBAMATE-KINASE-RXN Rhea MetaCyc REACTION RHEA:10155 Rhea reaction 1 1 1 1 1 KEGG:R00156 METACYC:UDPKIN-RXN RHEA:25101 reaction UPa:UCR00156 ATP + UDP = ADP + UTP 1 LR 1 KEGG:R00156 KEGG reaction METACYC:UDPKIN-RXN MetaCyc MetaCyc REACTION RHEA:25101 Rhea reaction 1 1 1 1 1 1 KEGG:R00158 METACYC:RXN-12002 RHEA:24403 reaction UPa:UCR00158 ATP + UMP = ADP + UDP 1 LR 1 1 LR 1 KEGG:R00158 KEGG reaction METACYC:RXN-12002 MetaCyc MetaCyc REACTION RHEA:24403 Rhea reaction 1 1 1 1 1 KEGG:R00161 METACYC:FADSYN-RXN RHEA:17240 reaction UPa:UCR00161 ATP + FMN = FAD + diphosphate 1 LR 1 KEGG:R00161 KEGG reaction METACYC:FADSYN-RXN MetaCyc MetaCyc REACTION RHEA:17240 Rhea reaction 1 1 1 1 1 KEGG:R00173 METACYC:3.1.3.74-RXN RHEA:20536 reaction UPa:UCR00173 H(2)O + pyridoxal 5'-phosphate = phosphate + pyridoxal 1 LR 1 KEGG:R00173 KEGG reaction METACYC:3.1.3.74-RXN MetaCyc MetaCyc REACTION RHEA:20536 Rhea reaction 1 1 1 1 1 KEGG:R00174 METACYC:PYRIDOXKIN-RXN RHEA:10227 reaction UPa:UCR00174 ATP + pyridoxal = ADP + pyridoxal 5'-phosphate 1 LR 1 KEGG:R00174 KEGG reaction METACYC:PYRIDOXKIN-RXN MetaCyc MetaCyc REACTION RHEA:10227 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00177 METACYC:S-ADENMETSYN-RXN RHEA:21083 reaction UPa:UCR00177 S-adenosyl-L-methionine + diphosphate + phosphate = ATP + H(2)O + L-methionine 1 RL 1 KEGG:R00177 KEGG reaction METACYC:S-ADENMETSYN-RXN MetaCyc MetaCyc REACTION RHEA:21083 Rhea reaction 1 1 1 1 1 KEGG:R00178 METACYC:SAMDECARB-RXN RHEA:15984 reaction UPa:UCR00178 H(+) + S-adenosyl-L-methionine = CO(2) + S-adenosylmethioninamine 1 LR 1 KEGG:R00178 KEGG reaction METACYC:SAMDECARB-RXN MetaCyc MetaCyc REACTION RHEA:15984 Rhea reaction 1 1 1 1 KEGG:R00179 METACYC:4.4.1.14-RXN RHEA:21747 reaction UPa:UCR00179 S-adenosyl-L-methionine = 1-aminocyclopropanecarboxylate + S-methyl-5'-thioadenosine 1 LR 1 KEGG:R00179 KEGG reaction METACYC:4.4.1.14-RXN MetaCyc MetaCyc REACTION RHEA:21747 Rhea reaction 1 1 1 1 1 KEGG:R00181 METACYC:AMP-DEAMINASE-RXN RHEA:14780 reaction UPa:UCR00181 AMP + H(2)O = IMP + NH(3) 1 LR 1 KEGG:R00181 KEGG reaction METACYC:AMP-DEAMINASE-RXN MetaCyc MetaCyc REACTION RHEA:14780 Rhea reaction 1 1 1 1 1 KEGG:R00185 METACYC:ADENOSINE-KINASE-RXN RHEA:20827 reaction UPa:UCR00185 ATP + adenosine = ADP + AMP 1 LR 1 KEGG:R00185 KEGG reaction METACYC:ADENOSINE-KINASE-RXN MetaCyc MetaCyc REACTION RHEA:20827 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00189 METACYC:NAD-SYNTH-NH3-RXN RHEA:21191 reaction UPa:UCR00189 ATP + NH(3) + deamido-NAD(+) = AMP + NAD(+) + diphosphate 1 LR 1 KEGG:R00189 KEGG reaction METACYC:NAD-SYNTH-NH3-RXN MetaCyc MetaCyc REACTION RHEA:21191 Rhea reaction 1 1 1 1 1 KEGG:R00190 METACYC:ADENPRIBOSYLTRAN-RXN RHEA:16612 reaction UPa:UCR00190 AMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + adenine 1 RL 1 KEGG:R00190 KEGG reaction METACYC:ADENPRIBOSYLTRAN-RXN Rhea MetaCyc REACTION RHEA:16612 Rhea reaction 1 1 1 1 KEGG:R00191 METACYC:RXN0-5038 RHEA:25280 reaction UPa:UCR00191 3',5'-cyclic AMP + H(2)O = AMP 1 LR 1 KEGG:R00191 KEGG reaction METACYC:RXN0-5038 MetaCyc MetaCyc REACTION RHEA:25280 Rhea reaction 1 1 1 1 1 KEGG:R00192 METACYC:ADENOSYLHOMOCYSTEINASE-RXN RHEA:21711 reaction UPa:UCR00192 H(2)O + S-adenosyl-L-homocysteine = L-homocysteine + adenosine 1 LR 1 KEGG:R00192 KEGG reaction METACYC:ADENOSYLHOMOCYSTEINASE-RXN Rhea MetaCyc REACTION RHEA:21711 Rhea reaction 1 1 1 1 1 KEGG:R00200 METACYC:PEPDEPHOS-RXN RHEA:18160 reaction UPa:UCR00200 ATP + pyruvate = ADP + phosphoenolpyruvate 1 RL 1 KEGG:R00200 KEGG reaction METACYC:PEPDEPHOS-RXN Rhea MetaCyc REACTION RHEA:18160 Rhea reaction 1 1 1 1 1 KEGG:R00212 METACYC:PYRUVFORMLY-RXN RHEA:11847 reaction UPa:UCR00212 acetyl-CoA + formate = CoA + pyruvate 1 RL 1 KEGG:R00212 KEGG reaction METACYC:PYRUVFORMLY-RXN Rhea MetaCyc REACTION RHEA:11847 Rhea reaction 1 1 1 1 KEGG:R00226 METACYC:ACETOLACTSYN-RXN RHEA:25252 reaction UPa:UCR00226 (S)-2-acetolactate + CO(2) = 2 pyruvate 1 RL 1 KEGG:R00226 KEGG reaction METACYC:ACETOLACTSYN-RXN Rhea MetaCyc REACTION RHEA:25252 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00228 METACYC:ACETALD-DEHYDROG-RXN RHEA:23291 reaction UPa:UCR00228 CoA + NAD(+) + acetaldehyde = H(+) + NADH + acetyl-CoA 1 LR 1 KEGG:R00228 KEGG reaction METACYC:ACETALD-DEHYDROG-RXN Rhea MetaCyc REACTION RHEA:23291 Rhea reaction 1 1 1 1 1 KEGG:R00230 METACYC:PHOSACETYLTRANS-RXN RHEA:19524 reaction UPa:UCR00230 acetyl-CoA + phosphate = CoA + acetyl phosphate 1 RL 1 KEGG:R00230 KEGG reaction METACYC:PHOSACETYLTRANS-RXN Rhea MetaCyc REACTION RHEA:19524 Rhea reaction 1 1 1 1 KEGG:R00233 METACYC:MALONYL-COA-DECARBOXYLASE-RXN RHEA:18784 reaction UPa:UCR00233 malonyl-CoA = CO(2) + acetyl-CoA 1 LR 1 KEGG:R00233 KEGG reaction METACYC:MALONYL-COA-DECARBOXYLASE-RXN MetaCyc MetaCyc REACTION RHEA:18784 Rhea reaction 1 1 1 1 KEGG:R00238 METACYC:ACETYL-COA-ACETYLTRANSFER-RXN RHEA:21039 reaction UPa:UCR00238 2 acetyl-CoA = CoA + acetoacetyl-CoA 1 LR 1 KEGG:R00238 KEGG reaction METACYC:ACETYL-COA-ACETYLTRANSFER-RXN Rhea MetaCyc REACTION RHEA:21039 Rhea reaction 1 1 1 1 1 KEGG:R00239 METACYC:GLUTKIN-RXN RHEA:14880 reaction UPa:UCR00239 ATP + L-glutamate = ADP + L-glutamyl 5-phosphate 1 LR 1 KEGG:R00239 KEGG reaction METACYC:GLUTKIN-RXN MetaCyc MetaCyc REACTION RHEA:14880 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00243 METACYC:GLUTAMATE-DEHYDROGENASE-RXN RHEA:15136 reaction UPa:UCR00243 H(2)O + L-glutamate + NAD(+) = 2-oxoglutarate + H(+) + NADH + NH(3) 1 LR 1 KEGG:R00243 KEGG reaction METACYC:GLUTAMATE-DEHYDROGENASE-RXN Rhea MetaCyc REACTION RHEA:15136 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00253 METACYC:GLUTAMINESYN-RXN RHEA:16172 reaction UPa:UCR00253 ATP + L-glutamate + NH(3) = ADP + L-glutamine + phosphate 1 LR 1 KEGG:R00253 KEGG reaction METACYC:GLUTAMINESYN-RXN Rhea MetaCyc REACTION RHEA:16172 Rhea reaction 1 1 1 1 1 1 KEGG:R00256 METACYC:GLUTAMIN-RXN RHEA:15892 reaction UPa:UCR00256 H(2)O + L-glutamine = L-glutamate + NH(3) 1 LR 2 1 LR 2 KEGG:R00256 KEGG reaction METACYC:GLUTAMIN-RXN MetaCyc MetaCyc REACTION RHEA:15892 Rhea reaction 1 1 1 1 1 1 1 1 1 KEGG:R00257 METACYC:NAD-SYNTH-GLN-RXN RHEA:24387 reaction UPa:UCR00257 ATP + H(2)O + L-glutamine + deamido-NAD(+) = AMP + L-glutamate + NAD(+) + diphosphate 1 LR 1 KEGG:R00257 KEGG reaction METACYC:NAD-SYNTH-GLN-RXN MetaCyc MetaCyc REACTION RHEA:24387 Rhea reaction 1 1 1 1 1 KEGG:R00258 METACYC:ALANINE-AMINOTRANSFERASE-RXN RHEA:19456 reaction UPa:UCR00258 2-oxoglutarate + L-alanine = L-glutamate + pyruvate 1 LR 1 KEGG:R00258 KEGG reaction METACYC:ALANINE-AMINOTRANSFERASE-RXN Rhea MetaCyc REACTION RHEA:19456 Rhea reaction 1 1 1 1 1 KEGG:R00259 METACYC:N-ACETYLTRANSFER-RXN RHEA:24295 reaction UPa:UCR00259 L-glutamate + acetyl-CoA = CoA + N-acetyl-L-glutamate 1 LR 1 KEGG:R00259 KEGG reaction METACYC:N-ACETYLTRANSFER-RXN Rhea MetaCyc REACTION RHEA:24295 Rhea reaction 1 1 1 KEGG:R00262 METACYC:METHYLASPARTATE-MUTASE-RXN RHEA:12860 reaction UPa:UCR00262 (2S,3S)-3-methyl-L-aspartate = L-glutamate 1 RL 1 KEGG:R00262 KEGG reaction METACYC:METHYLASPARTATE-MUTASE-RXN MetaCyc MetaCyc REACTION RHEA:12860 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00264 METACYC:25-DIOXOVALERATE-DEHYDROGENASE-RXN RHEA:11299 reaction UPa:UCR00264 2,5-dioxopentanoate + H(2)O + NADP(+) = 2-oxoglutarate + H(+) + NADPH 1 LR 1 KEGG:R00264 KEGG reaction METACYC:25-DIOXOVALERATE-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:11299 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00267 METACYC:ISOCITDEH-RXN METACYC:RXN-8642 RHEA:19632 reaction UPa:UCR00267 NADP(+) + isocitrate = 2-oxoglutarate + CO(2) + H(+) + NADPH 1 LR 1 KEGG:R00267 KEGG reaction METACYC:ISOCITDEH-RXN MetaCyc MetaCyc REACTION METACYC:RXN-8642 MetaCyc Rhea MetaCyc REACTION RHEA:19632 Rhea reaction 1 1 1 1 1 1 KEGG:R00271 METACYC:HOMOCITRATE-SYNTHASE-RXN RHEA:12932 reaction UPa:UCR00271 2-oxoglutarate + H(2)O + acetyl-CoA = (R)-homocitrate + CoA 1 LR 1 KEGG:R00271 KEGG reaction METACYC:HOMOCITRATE-SYNTHASE-RXN Rhea MetaCyc REACTION RHEA:12932 Rhea reaction 1 1 1 1 KEGG:R00272 METACYC:RXN-7774 RHEA:10527 reaction UPa:UCR00272 2-oxoglutarate = CO(2) + succinate semialdehyde 1 LR 1 KEGG:R00272 KEGG reaction METACYC:RXN-7774 MetaCyc MetaCyc REACTION RHEA:10527 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00277 METACYC:PMPOXI-RXN RHEA:15820 reaction UPa:UCR00277 H(2)O + O(2) + pyridoxamine 5'-phosphate = H(2)O(2) + NH(3) + pyridoxal 5'-phosphate 1 LR 1 KEGG:R00277 KEGG reaction METACYC:PMPOXI-RXN MetaCyc MetaCyc REACTION RHEA:15820 Rhea reaction 1 1 1 1 1 KEGG:R00278 METACYC:PNPOXI-RXN RHEA:15152 reaction UPa:UCR00278 O(2) + pyridoxine 5'-phosphate = H(2)O(2) + pyridoxal 5'-phosphate 1 LR 1 KEGG:R00278 KEGG reaction METACYC:PNPOXI-RXN MetaCyc MetaCyc REACTION RHEA:15152 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00286 METACYC:UGD-RXN RHEA:23599 reaction UPa:UCR00286 H(2)O + 2 NAD(+) + UDP-alpha-D-glucose = 2 H(+) + 2 NADH + UDP-alpha-D-glucuronate 1 LR 1 KEGG:R00286 KEGG reaction METACYC:UGD-RXN MetaCyc MetaCyc REACTION RHEA:23599 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00294 METACYC:NITRIC-OXIDE-REDUCTASE-RXN RHEA:10991 RHEA:30214 reaction UPa:UCR00294 2 H(+) + 2 ferrocytochrome c + 2 nitric oxide = H(2)O + 2 ferricytochrome c + nitrous oxide 1 LR 1 KEGG:R00294 KEGG reaction METACYC:NITRIC-OXIDE-REDUCTASE-RXN Rhea MetaCyc REACTION RHEA:10991 Rhea reaction RHEA:30214 Rhea reaction 1 1 1 1 1 KEGG:R00299 METACYC:GLUCOKIN-RXN RHEA:17828 reaction UPa:UCR00299 ATP + D-glucose = ADP + D-glucose 6-phosphate 1 LR 1 KEGG:R00299 KEGG reaction METACYC:GLUCOKIN-RXN Rhea MetaCyc REACTION RHEA:17828 Rhea reaction 1 1 1 1 1 KEGG:R00310 METACYC:PROTOHEMEFERROCHELAT-RXN RHEA:22587 reaction UPa:UCR00310 Fe2+ + protoporphyrin-IX = 2 H(+) + protoheme 1 LR 1 KEGG:R00310 KEGG reaction METACYC:PROTOHEMEFERROCHELAT-RXN MetaCyc MetaCyc REACTION RHEA:22587 Rhea reaction 1 1 1 1 1 KEGG:R00315 METACYC:ACETATEKIN-RXN RHEA:11355 reaction UPa:UCR00315 ATP + acetate = ADP + acetyl phosphate 1 LR 1 KEGG:R00315 KEGG reaction METACYC:ACETATEKIN-RXN Rhea MetaCyc REACTION RHEA:11355 Rhea reaction 1 1 1 1 KEGG:R00325 METACYC:CITRAMALATE-LYASE-RXN RHEA:15548 reaction UPa:UCR00325 L-citramalate = acetate + pyruvate 1 LR 1 KEGG:R00325 KEGG reaction METACYC:CITRAMALATE-LYASE-RXN Rhea MetaCyc REACTION RHEA:15548 Rhea reaction 1 1 1 1 1 KEGG:R00336 METACYC:PPGPPSYN-RXN RHEA:14256 reaction UPa:UCR00336 H(2)O + ppGpp = GDP + diphosphate 1 RL 1 KEGG:R00336 KEGG reaction METACYC:PPGPPSYN-RXN MetaCyc MetaCyc REACTION RHEA:14256 Rhea reaction 1 1 1 1 1 1 KEGG:R00342 METACYC:MALATE-DEH-RXN RHEA:21435 reaction UPa:UCR00342 (S)-malate + NAD(+) = H(+) + NADH + oxaloacetate 1 LR 1 KEGG:R00342 KEGG reaction METACYC:MALATE-DEH-RXN Rhea MetaCyc REACTION RHEA:21435 Rhea reaction 1 1 1 1 1 1 KEGG:R00351 METACYC:CITSYN-RXN RHEA:16848 reaction UPa:UCR00351 CoA + citrate = H(2)O + acetyl-CoA + oxaloacetate 1 RL 1 KEGG:R00351 KEGG reaction METACYC:CITSYN-RXN MetaCyc MetaCyc REACTION RHEA:16848 Rhea reaction 1 1 1 1 1 KEGG:R00355 METACYC:ASPAMINOTRANS-RXN RHEA:21827 reaction UPa:UCR00355 2-oxoglutarate + L-aspartate = L-glutamate + oxaloacetate 1 RL 1 KEGG:R00355 KEGG reaction METACYC:ASPAMINOTRANS-RXN Rhea MetaCyc REACTION RHEA:21827 Rhea reaction 1 1 1 1 1 KEGG:R00361 METACYC:MALATE-DEHYDROGENASE-ACCEPTOR-RXN RHEA:22559 reaction UPa:UCR00361 (S)-malate + Quinone = Hydroquinone + oxaloacetate 1 LR 1 KEGG:R00361 KEGG reaction METACYC:MALATE-DEHYDROGENASE-ACCEPTOR-RXN MetaCyc MetaCyc REACTION RHEA:22559 Rhea reaction 1 1 1 1 1 KEGG:R00367 METACYC:GLYCINE-N-METHYLTRANSFERASE-RXN RHEA:19940 reaction UPa:UCR00367 S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine 1 LR 1 KEGG:R00367 KEGG reaction METACYC:GLYCINE-N-METHYLTRANSFERASE-RXN MetaCyc MetaCyc REACTION RHEA:19940 Rhea reaction 1 1 1 1 1 KEGG:R00369 METACYC:ALANINE--GLYOXYLATE-AMINOTRANSFERASE-RXN RHEA:24251 reaction UPa:UCR00369 L-alanine + glyoxylate = glycine + pyruvate 1 LR 1 KEGG:R00369 KEGG reaction METACYC:ALANINE--GLYOXYLATE-AMINOTRANSFERASE-RXN MetaCyc MetaCyc REACTION RHEA:24251 Rhea reaction 1 1 1 1 1 KEGG:R00371 METACYC:AKBLIG-RXN RHEA:20739 reaction UPa:UCR00371 acetyl-CoA + glycine = CoA + L-2-amino-3-oxobutanoic acid 1 RL 1 KEGG:R00371 KEGG reaction METACYC:AKBLIG-RXN MetaCyc Rhea MetaCyc REACTION RHEA:20739 Rhea reaction 1 1 1 1 1 KEGG:R00372 METACYC:GLYCINE-AMINOTRANSFERASE-RXN RHEA:14092 reaction UPa:UCR00372 2-oxoglutarate + glycine = L-glutamate + glyoxylate 1 RL 1 KEGG:R00372 KEGG reaction METACYC:GLYCINE-AMINOTRANSFERASE-RXN MetaCyc MetaCyc REACTION RHEA:14092 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00396 METACYC:ALANINE-DEHYDROGENASE-RXN RHEA:18408 reaction UPa:UCR00396 H(2)O + L-alanine + NAD(+) = H(+) + NADH + NH(3) + pyruvate 1 LR 1 KEGG:R00396 KEGG reaction METACYC:ALANINE-DEHYDROGENASE-RXN Rhea MetaCyc REACTION RHEA:18408 Rhea reaction 1 1 1 KEGG:R00401 METACYC:ALARACECAT-RXN RHEA:20252 reaction UPa:UCR00401 L-alanine = D-alanine 1 LR 1 KEGG:R00401 KEGG reaction METACYC:ALARACECAT-RXN Rhea MetaCyc REACTION RHEA:20252 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00405 METACYC:SUCCCOASYN-RXN RHEA:17664 reaction UPa:UCR00405 ATP + CoA + succinate = ADP + phosphate + succinyl-CoA 1 RL 1 KEGG:R00405 KEGG reaction METACYC:SUCCCOASYN-RXN Rhea MetaCyc REACTION RHEA:17664 Rhea reaction 1 1 1 1 1 1 KEGG:R00410 METACYC:RXNI-2 RHEA:25483 reaction UPa:UCR00410 acetoacetate + succinyl-CoA = acetoacetyl-CoA + succinate 1 LR 1 1 LR 1 KEGG:R00410 KEGG reaction METACYC:RXNI-2 Rhea MetaCyc REACTION RHEA:25483 Rhea reaction 1 1 1 1 1 KEGG:R00411 METACYC:SUCCGLUDESUCC-RXN RHEA:15172 reaction UPa:UCR00411 H(2)O + N(2)-succinyl-L-glutamic acid = L-glutamate + succinate 1 LR 1 KEGG:R00411 KEGG reaction METACYC:SUCCGLUDESUCC-RXN Rhea MetaCyc REACTION RHEA:15172 Rhea reaction 1 1 1 1 1 KEGG:R00412 RHEA:16360 reaction UPa:UCR00412 acceptor + succinate = fumarate + reduced acceptor 1 LR 1 KEGG:R00412 KEGG reaction RHEA:16360 Rhea reaction 1 1 1 1 1 KEGG:R00416 METACYC:NAG1P-URIDYLTRANS-RXN RHEA:13512 reaction UPa:UCR00416 N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = UDP-N-acetyl-alpha-D-glucosamine + diphosphate 1 LR 1 KEGG:R00416 KEGG reaction METACYC:NAG1P-URIDYLTRANS-RXN MetaCyc MetaCyc REACTION RHEA:13512 Rhea reaction 1 1 1 1 1 1 KEGG:R00425 METACYC:GTP-CYCLOHYDRO-II-RXN RHEA:23707 reaction UPa:UCR00425 GTP + 3 H(2)O = 2,5-diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine + diphosphate + formate 1 LR 1 KEGG:R00425 KEGG reaction METACYC:GTP-CYCLOHYDRO-II-RXN MetaCyc MetaCyc REACTION RHEA:23707 Rhea reaction 1 1 1 1 KEGG:R00428 reaction UPa:UCR00428 GTP + H(2)O = formamidopyrimidine nucleoside triphosphate 1 LR 1 KEGG:R00428 KEGG reaction 1 1 1 1 1 KEGG:R00429 METACYC:GTPPYPHOSKIN-RXN RHEA:22091 reaction UPa:UCR00429 ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate 1 LR 1 KEGG:R00429 KEGG reaction METACYC:GTPPYPHOSKIN-RXN MetaCyc MetaCyc REACTION RHEA:22091 Rhea reaction 1 1 1 1 KEGG:R00451 METACYC:DIAMINOPIMDECARB-RXN RHEA:15104 reaction UPa:UCR00451 DL-2,6-diaminopimelate = CO(2) + L-lysine 1 LR 1 KEGG:R00451 KEGG reaction METACYC:DIAMINOPIMDECARB-RXN MetaCyc MetaCyc REACTION RHEA:15104 Rhea reaction 1 1 1 1 1 1 KEGG:R00469 METACYC:UREIDOGLYCOLATE-HYDROLASE-RXN RHEA:19812 reaction UPa:UCR00469 (S)-ureidoglycolate + H(2)O = CO(2) + 2 NH(3) + glyoxylate 1 LR 1 KEGG:R00469 KEGG reaction METACYC:UREIDOGLYCOLATE-HYDROLASE-RXN MetaCyc MetaCyc REACTION RHEA:19812 Rhea reaction 1 1 1 1 1 1 KEGG:R00472 METACYC:MALSYN-RXN RHEA:18184 reaction UPa:UCR00472 (S)-malate + CoA = H(2)O + acetyl-CoA + glyoxylate 1 RL 1 KEGG:R00472 KEGG reaction METACYC:MALSYN-RXN MetaCyc MetaCyc REACTION RHEA:18184 Rhea reaction 1 1 1 1 1 KEGG:R00475 METACYC:RXN-969 RHEA:25314 reaction UPa:UCR00475 O(2) + glycolate = H(2)O(2) + glyoxylate 1 LR 1 KEGG:R00475 KEGG reaction METACYC:RXN-969 MetaCyc MetaCyc REACTION RHEA:25314 Rhea reaction 1 1 1 1 1 KEGG:R00476 METACYC:GLYCOLATEDEHYDRO-RXN RHEA:21267 reaction UPa:UCR00476 acceptor + glycolate = glyoxylate + reduced acceptor 1 LR 1 KEGG:R00476 KEGG reaction METACYC:GLYCOLATEDEHYDRO-RXN Rhea MetaCyc REACTION RHEA:21267 Rhea reaction 1 1 1 1 KEGG:R00479 METACYC:ISOCIT-CLEAV-RXN RHEA:13248 reaction UPa:UCR00479 isocitrate = glyoxylate + succinate 1 LR 1 KEGG:R00479 KEGG reaction METACYC:ISOCIT-CLEAV-RXN Rhea MetaCyc REACTION RHEA:13248 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00480 METACYC:ASPARTATEKIN-RXN RHEA:23779 reaction UPa:UCR00480 ATP + L-aspartate = 4-phospho-L-aspartate + ADP 1 LR 1 1 LR 1 1 LR 1 KEGG:R00480 KEGG reaction METACYC:ASPARTATEKIN-RXN Rhea MetaCyc REACTION RHEA:23779 Rhea reaction 1 1 1 1 1 KEGG:R00481 RHEA:25879 reaction UPa:UCR00481 L-aspartate + O(2) = H(2)O(2) + iminoaspartate 1 LR 1 KEGG:R00481 KEGG reaction RHEA:25879 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00483 METACYC:ASNSYNA-RXN RHEA:11375 reaction UPa:UCR00483 ATP + L-aspartate + NH(3) = AMP + L-asparagine + diphosphate 1 LR 1 KEGG:R00483 KEGG reaction METACYC:ASNSYNA-RXN MetaCyc MetaCyc REACTION RHEA:11375 Rhea reaction 1 1 1 1 KEGG:R00489 METACYC:ASPDECARBOX-RXN RHEA:19500 reaction UPa:UCR00489 L-aspartate = CO(2) + beta-alanine 1 LR 1 KEGG:R00489 KEGG reaction METACYC:ASPDECARBOX-RXN MetaCyc MetaCyc REACTION RHEA:19500 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00497 METACYC:GLUTATHIONE-SYN-RXN RHEA:13560 reaction UPa:UCR00497 ATP + L-gamma-glutamyl-L-cysteine + glycine = ADP + glutathione + phosphate 1 LR 1 KEGG:R00497 KEGG reaction METACYC:GLUTATHIONE-SYN-RXN MetaCyc MetaCyc REACTION RHEA:13560 Rhea reaction 1 1 1 1 1 KEGG:R00509 METACYC:ADENYLYLSULFKIN-RXN RHEA:24155 reaction UPa:UCR00509 5'-adenylyl sulfate + ATP = 3'-phospho-5'-adenylyl sulfate + ADP 1 LR 1 KEGG:R00509 KEGG reaction METACYC:ADENYLYLSULFKIN-RXN Rhea MetaCyc REACTION RHEA:24155 Rhea reaction 1 1 1 1 1 KEGG:R00512 METACYC:RXN-11832 RHEA:11603 reaction UPa:UCR00512 ATP + CMP = ADP + CDP 1 LR 1 KEGG:R00512 KEGG reaction METACYC:RXN-11832 Rhea MetaCyc REACTION RHEA:11603 Rhea reaction 1 1 1 1 1 KEGG:R00513 METACYC:CYTIKIN-RXN RHEA:24677 reaction UPa:UCR00513 ATP + cytidine = ADP + CMP 1 LR 1 KEGG:R00513 KEGG reaction METACYC:CYTIKIN-RXN Rhea MetaCyc REACTION RHEA:24677 Rhea reaction 1 1 1 1 1 KEGG:R00525 METACYC:N-FORMYLGLUTAMATE-DEFORMYLASE-RXN RHEA:12479 reaction UPa:UCR00525 H(2)O + N-formyl-L-glutamate = L-glutamate + formate 1 LR 1 KEGG:R00525 KEGG reaction METACYC:N-FORMYLGLUTAMATE-DEFORMYLASE-RXN MetaCyc MetaCyc REACTION RHEA:12479 Rhea reaction 1 1 1 1 1 KEGG:R00527 METACYC:S-FORMYLGLUTATHIONE-HYDROLASE-RXN RHEA:14964 reaction UPa:UCR00527 H(2)O + S-formylglutathione = formate + glutathione 1 LR 1 KEGG:R00527 KEGG reaction METACYC:S-FORMYLGLUTATHIONE-HYDROLASE-RXN MetaCyc MetaCyc REACTION RHEA:14964 Rhea reaction 1 1 1 1 1 KEGG:R00529 METACYC:SULFATE-ADENYLYLTRANS-RXN RHEA:18136 reaction UPa:UCR00529 ATP + sulfate = 5'-adenylyl sulfate + diphosphate 1 LR 1 KEGG:R00529 KEGG reaction METACYC:SULFATE-ADENYLYLTRANS-RXN Rhea MetaCyc REACTION RHEA:18136 Rhea reaction 1 1 1 1 1 KEGG:R00549 METACYC:RIBOFLAVINKIN-RXN RHEA:14360 reaction UPa:UCR00549 ATP + riboflavin = ADP + FMN 1 LR 1 KEGG:R00549 KEGG reaction METACYC:RIBOFLAVINKIN-RXN MetaCyc MetaCyc REACTION RHEA:14360 Rhea reaction 1 1 1 1 1 KEGG:R00551 METACYC:ARGINASE-RXN RHEA:20572 reaction UPa:UCR00551 H(2)O + L-arginine = L-ornithine + urea 1 LR 1 KEGG:R00551 KEGG reaction METACYC:ARGINASE-RXN Rhea MetaCyc REACTION RHEA:20572 Rhea reaction 1 1 1 1 1 KEGG:R00552 METACYC:ARGININE-DEIMINASE-RXN RHEA:19600 reaction UPa:UCR00552 H(2)O + L-arginine = L-citrulline + NH(3) 1 LR 1 KEGG:R00552 KEGG reaction METACYC:ARGININE-DEIMINASE-RXN Rhea MetaCyc REACTION RHEA:19600 Rhea reaction 1 1 1 1 1 KEGG:R00565 METACYC:GLYCINE-AMIDINOTRANSFERASE-RXN RHEA:13204 reaction UPa:UCR00565 L-arginine + glycine = L-ornithine + guanidinoacetate RHEA:13204 Rhea reaction 1 LR 1 KEGG:R00565 KEGG reaction METACYC:GLYCINE-AMIDINOTRANSFERASE-RXN MetaCyc MetaCyc REACTION 1 1 1 1 KEGG:R00566 METACYC:ARGDECARBOX-RXN RHEA:17644 reaction UPa:UCR00566 L-arginine = CO(2) + agmatine 1 LR 1 KEGG:R00566 KEGG reaction METACYC:ARGDECARBOX-RXN Rhea MetaCyc REACTION RHEA:17644 Rhea reaction 1 1 1 1 1 KEGG:R00570 METACYC:CDPKIN-RXN RHEA:25240 reaction UPa:UCR00570 ATP + CDP = ADP + CTP 1 LR 1 KEGG:R00570 KEGG reaction METACYC:CDPKIN-RXN MetaCyc MetaCyc REACTION RHEA:25240 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00571 RHEA:16600 reaction UPa:UCR00571 ATP + NH(3) + UTP = ADP + CTP + phosphate 1 LR 1 KEGG:R00571 KEGG reaction RHEA:16600 Rhea reaction 1 1 1 1 1 1 1 1 1 1 KEGG:R00575 METACYC:CARBPSYN-RXN RHEA:18636 reaction UPa:UCR00575 2 ATP + H(2)O + L-glutamine + bicarbonate = 2 ADP + L-glutamate + carbamoyl phosphate + phosphate 1 LR 1 1 LR 1 KEGG:R00575 KEGG reaction METACYC:CARBPSYN-RXN Rhea MetaCyc REACTION RHEA:18636 Rhea reaction 1 1 1 1 1 1 1 1 1 KEGG:R00578 METACYC:ASNSYNB-RXN RHEA:12231 reaction UPa:UCR00578 ATP + H(2)O + L-aspartate + L-glutamine = AMP + L-asparagine + L-glutamate + diphosphate 1 LR 1 KEGG:R00578 KEGG reaction METACYC:ASNSYNB-RXN MetaCyc MetaCyc REACTION RHEA:12231 Rhea reaction 1 1 1 1 1 KEGG:R00582 METACYC:RXN0-5114 RHEA:21211 reaction UPa:UCR00582 H(2)O + O-phospho-L-serine = L-serine + phosphate 1 LR 1 KEGG:R00582 KEGG reaction METACYC:RXN0-5114 MetaCyc MetaCyc REACTION RHEA:21211 Rhea reaction 1 1 1 1 1 KEGG:R00585 METACYC:SERINE--PYRUVATE-AMINOTRANSFERASE-RXN RHEA:22855 reaction UPa:UCR00585 L-serine + pyruvate = 3-hydroxypyruvate + L-alanine 1 LR 1 KEGG:R00585 KEGG reaction METACYC:SERINE--PYRUVATE-AMINOTRANSFERASE-RXN Rhea MetaCyc REACTION RHEA:22855 Rhea reaction 1 1 1 1 1 KEGG:R00586 METACYC:SERINE-O-ACETTRAN-RXN RHEA:24563 reaction UPa:UCR00586 L-serine + acetyl-CoA = CoA + O-acetyl-L-serine 1 LR 1 KEGG:R00586 KEGG reaction METACYC:SERINE-O-ACETTRAN-RXN Rhea MetaCyc REACTION RHEA:24563 Rhea reaction 1 1 1 1 1 1 KEGG:R00605 METACYC:METHANOL-DEHYDROGENASE-RXN RHEA:19404 reaction UPa:UCR00605 NAD(+) + methanol = H(+) + NADH + formaldehyde 1 LR 1 KEGG:R00605 KEGG reaction METACYC:METHANOL-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:19404 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00606 METACYC:RXN-2841 RHEA:30210 reaction UPa:UCR00606 H(2)O + amicyanin + methylamine = 2 H(+) + NH(3) + formaldehyde + reduced amicyanin 1 LR 1 KEGG:R00606 KEGG reaction METACYC:RXN-2841 MetaCyc MetaCyc REACTION RHEA:30210 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00611 METACYC:SARCOSINE-DEHYDROGENASE-RXN RHEA:19796 reaction UPa:UCR00611 H(2)O + electron-transferring flavoprotein + sarcosine = formaldehyde + glycine + reduced electron-transferring flavoprotein 1 LR 1 KEGG:R00611 KEGG reaction METACYC:SARCOSINE-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:19796 Rhea reaction 1 1 1 1 1 KEGG:R00617 METACYC:THI-P-KIN-RXN RHEA:15916 reaction UPa:UCR00617 ATP + thiamine phosphate = ADP + thiamine diphosphate 1 LR 1 KEGG:R00617 KEGG reaction METACYC:THI-P-KIN-RXN MetaCyc MetaCyc REACTION RHEA:15916 Rhea reaction 1 1 1 1 1 KEGG:R00619 METACYC:THIAMIN-PYROPHOSPHOKINASE-RXN RHEA:11579 reaction UPa:UCR00619 ATP + thiamine = AMP + thiamine diphosphate 1 LR 1 KEGG:R00619 KEGG reaction METACYC:THIAMIN-PYROPHOSPHOKINASE-RXN MetaCyc MetaCyc REACTION RHEA:11579 Rhea reaction 1 1 1 1 1 1 KEGG:R00640 METACYC:GALACTONOLACTONE-DEHYDROGENASE-RXN RHEA:14760 reaction UPa:UCR00640 L-Galactono-1,4-lactone + 2 ferricytochrome c = 2 H(+) + L-ascorbate + 2 ferrocytochrome c 1 LR 1 KEGG:R00640 KEGG reaction METACYC:GALACTONOLACTONE-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:14760 Rhea reaction 1 1 1 KEGG:R00647 METACYC:RXN-8784 RHEA:15272 reaction UPa:UCR00647 L-ascorbate = L-xylo-hexulonolactone 1 RL 2 KEGG:R00647 KEGG reaction METACYC:RXN-8784 MetaCyc MetaCyc REACTION RHEA:15272 Rhea reaction 1 1 1 1 KEGG:R00658 METACYC:2PGADEHYDRAT-RXN RHEA:10167 reaction UPa:UCR00658 2-phospho-D-glycerate = H(2)O + phosphoenolpyruvate 1 LR 1 KEGG:R00658 KEGG reaction METACYC:2PGADEHYDRAT-RXN Rhea MetaCyc REACTION RHEA:10167 Rhea reaction 1 1 1 1 1 KEGG:R00667 METACYC:ORNITHINE-GLU-AMINOTRANSFORASE-RXN RHEA:25163 reaction UPa:UCR00667 2-oxoglutarate + L-ornithine = L-glutamate + L-glutamate 5-semialdehyde 1 LR 1 KEGG:R00667 KEGG reaction METACYC:ORNITHINE-GLU-AMINOTRANSFORASE-RXN Rhea MetaCyc REACTION RHEA:25163 Rhea reaction 1 1 1 1 1 KEGG:R00669 METACYC:ACETYLORNDEACET-RXN RHEA:15944 reaction UPa:UCR00669 H(2)O + N(2)-acetyl-L-ornithine = L-ornithine + acetate 1 LR 1 KEGG:R00669 KEGG reaction METACYC:ACETYLORNDEACET-RXN Rhea MetaCyc REACTION RHEA:15944 Rhea reaction 1 1 1 1 KEGG:R00670 METACYC:ORNDECARBOX-RXN RHEA:22967 reaction UPa:UCR00670 L-ornithine = CO(2) + putrescine 1 LR 1 KEGG:R00670 KEGG reaction METACYC:ORNDECARBOX-RXN MetaCyc MetaCyc REACTION RHEA:22967 Rhea reaction 1 1 1 1 KEGG:R00671 METACYC:ORNITHINE-CYCLODEAMINASE-RXN RHEA:24371 reaction UPa:UCR00671 L-ornithine = L-proline + NH(3) 1 LR 1 KEGG:R00671 KEGG reaction METACYC:ORNITHINE-CYCLODEAMINASE-RXN MetaCyc MetaCyc REACTION RHEA:24371 Rhea reaction 1 1 1 1 1 1 KEGG:R00673 METACYC:TRYPTOPHAN-RXN RHEA:19556 reaction UPa:UCR00673 H(2)O + L-tryptophan = NH(3) + indole + pyruvate 1 LR 1 KEGG:R00673 KEGG reaction METACYC:TRYPTOPHAN-RXN Rhea MetaCyc REACTION RHEA:19556 Rhea reaction 1 1 1 1 1 KEGG:R00674 METACYC:RXN0-2382 RHEA:26437 reaction UPa:UCR00674 L-serine + indole = H(2)O + L-tryptophan 1 LR 2 KEGG:R00674 KEGG reaction METACYC:RXN0-2382 MetaCyc MetaCyc REACTION RHEA:26437 Rhea reaction 1 1 1 1 KEGG:R00678 METACYC:RXN-8665 RHEA:24539 reaction UPa:UCR00678 L-tryptophan + O(2) = N-formyl-N-kynurenine 1 LR 1 KEGG:R00678 KEGG reaction METACYC:RXN-8665 MetaCyc MetaCyc REACTION RHEA:24539 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00688 METACYC:PHENYLALANINE-DEHYDROGENASE-RXN RHEA:21411 reaction UPa:UCR00688 H(2)O + L-phenylalanine + NAD(+) = H(+) + NADH + NH(3) + phenylpyruvate 1 RL 1 KEGG:R00688 KEGG reaction METACYC:PHENYLALANINE-DEHYDROGENASE-RXN Rhea MetaCyc REACTION RHEA:21411 Rhea reaction 1 1 1 1 1 KEGG:R00691 METACYC:CARBOXYCYCLOHEXADIENYL-DEHYDRATASE-RXN RHEA:12539 reaction UPa:UCR00691 L-arogenate = CO(2) + H(2)O + L-phenylalanine 1 LR 1 KEGG:R00691 KEGG reaction METACYC:CARBOXYCYCLOHEXADIENYL-DEHYDRATASE-RXN MetaCyc MetaCyc REACTION RHEA:12539 Rhea reaction 1 1 1 1 1 KEGG:R00694 METACYC:PHEAMINOTRANS-RXN RHEA:25155 reaction UPa:UCR00694 2-oxoglutarate + L-phenylalanine = L-glutamate + phenylpyruvate 1 RL 1 KEGG:R00694 KEGG reaction METACYC:PHEAMINOTRANS-RXN Rhea MetaCyc REACTION RHEA:25155 Rhea reaction 1 1 1 1 KEGG:R00697 METACYC:PHENYLALANINE-AMMONIA-LYASE-RXN RHEA:21387 reaction UPa:UCR00697 L-phenylalanine = NH(3) + trans-cinnamate 1 LR 1 KEGG:R00697 KEGG reaction METACYC:PHENYLALANINE-AMMONIA-LYASE-RXN MetaCyc MetaCyc REACTION RHEA:21387 Rhea reaction 1 1 1 1 KEGG:R00699 METACYC:PHENYLALANINE-DECARBOXYLASE-RXN RHEA:19720 reaction UPa:UCR00699 L-phenylalanine = 2-phenylethylamine + CO(2) 1 LR 1 KEGG:R00699 KEGG reaction METACYC:PHENYLALANINE-DECARBOXYLASE-RXN MetaCyc MetaCyc REACTION RHEA:19720 Rhea reaction 1 1 1 1 1 1 KEGG:R00703 METACYC:L-LACTATE-DEHYDROGENASE-RXN RHEA:23447 reaction UPa:UCR00703 (S)-lactate + NAD(+) = H(+) + NADH + pyruvate 1 RL 1 KEGG:R00703 KEGG reaction METACYC:L-LACTATE-DEHYDROGENASE-RXN Rhea MetaCyc REACTION RHEA:23447 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00705 METACYC:RXN-2902 RHEA:22995 reaction UPa:UCR00705 3-oxopropanoate + CoA + NAD(+) = CO(2) + H(+) + NADH + acetyl-CoA 1 LR 1 KEGG:R00705 KEGG reaction METACYC:RXN-2902 MetaCyc MetaCyc REACTION RHEA:22995 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00706 METACYC:1.2.1.18-RXN RHEA:22991 reaction UPa:UCR00706 3-oxopropanoate + CoA + NADP(+) = CO(2) + H(+) + NADPH + acetyl-CoA 1 LR 1 KEGG:R00706 KEGG reaction METACYC:1.2.1.18-RXN Rhea MetaCyc REACTION RHEA:22991 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00707 METACYC:PYRROLINECARBDEHYDROG-RXN METACYC:RXN-11632 RHEA:16420 RHEA:24893 reaction UPa:UCR00707 (S)-1-pyrroline-5-carboxylic acid + 2 H(2)O + NAD(+) = H(+) + L-glutamate + NADH 1 LR 1 KEGG:R00707 KEGG reaction METACYC:PYRROLINECARBDEHYDROG-RXN MetaCyc MetaCyc REACTION METACYC:RXN-11632 MetaCyc Rhea MetaCyc REACTION RHEA:16420 Rhea reaction RHEA:24893 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00709 METACYC:ISOCITRATE-DEHYDROGENASE-NAD+-RXN METACYC:RXN-7969 RHEA:23635 reaction UPa:UCR00709 NAD(+) + isocitrate = 2-oxoglutarate + CO(2) + H(+) + NADH 1 LR 1 KEGG:R00709 KEGG reaction METACYC:ISOCITRATE-DEHYDROGENASE-NAD+-RXN MetaCyc MetaCyc REACTION METACYC:RXN-7969 MetaCyc Rhea MetaCyc REACTION RHEA:23635 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00710 METACYC:RXN66-3 RHEA:25297 reaction UPa:UCR00710 H(2)O + NAD(+) + acetaldehyde = H(+) + NADH + acetate 1 LR 1 KEGG:R00710 KEGG reaction METACYC:RXN66-3 MetaCyc MetaCyc REACTION RHEA:25297 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00713 METACYC:SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN RHEA:13220 reaction UPa:UCR00713 H(2)O + NAD(+) + succinate semialdehyde = H(+) + NADH + succinate 1 LR 1 KEGG:R00713 KEGG reaction METACYC:SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:13220 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00714 METACYC:SUCCSEMIALDDEHYDROG-RXN RHEA:13216 reaction UPa:UCR00714 H(2)O + NADP(+) + succinate semialdehyde = H(+) + NADPH + succinate 1 LR 1 KEGG:R00714 KEGG reaction METACYC:SUCCSEMIALDDEHYDROG-RXN MetaCyc MetaCyc REACTION RHEA:13216 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00715 METACYC:1.5.1.7-RXN RHEA:12443 reaction UPa:UCR00715 H(2)O + NAD(+) + saccharopine = 2-oxoglutarate + H(+) + L-lysine + NADH 1 LR 1 KEGG:R00715 KEGG reaction METACYC:1.5.1.7-RXN MetaCyc MetaCyc REACTION RHEA:12443 Rhea reaction 1 1 1 1 1 1 1 1 KEGG:R00716 METACYC:1.5.1.8-RXN RHEA:19376 reaction UPa:UCR00716 H(2)O + NADP(+) + saccharopine = 2-oxoglutarate + H(+) + L-lysine + NADPH 1 RL 1 KEGG:R00716 KEGG reaction METACYC:1.5.1.8-RXN MetaCyc MetaCyc REACTION RHEA:19376 Rhea reaction 1 1 1 1 1 KEGG:R00731 RHEA:34286 reaction UPa:UCR00731 L-tyrosine + O(2) = H(2)O + L-dopa 1 LR 1 KEGG:R00731 KEGG reaction RHEA:34286 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00732 METACYC:CYCLOHEXADIENYL-DEHYDROGENASE-RXN RHEA:12259 reaction UPa:UCR00732 L-arogenate + NAD(+) = CO(2) + H(+) + L-tyrosine + NADH 1 LR 1 KEGG:R00732 KEGG reaction METACYC:CYCLOHEXADIENYL-DEHYDROGENASE-RXN MetaCyc MetaCyc REACTION RHEA:12259 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00733 METACYC:RXN-5682 RHEA:15420 reaction UPa:UCR00733 L-arogenate + NADP(+) = CO(2) + H(+) + L-tyrosine + NADPH 1 LR 1 KEGG:R00733 KEGG reaction METACYC:RXN-5682 MetaCyc MetaCyc REACTION RHEA:15420 Rhea reaction 1 1 1 1 1 1 KEGG:R00734 METACYC:TYROSINE-AMINOTRANSFERASE-RXN RHEA:15096 reaction UPa:UCR00734 2-oxoglutarate + L-tyrosine = (4-hydroxyphenyl)pyruvate + L-glutamate 1 LR 1 1 RL 1 KEGG:R00734 KEGG reaction METACYC:TYROSINE-AMINOTRANSFERASE-RXN Rhea MetaCyc REACTION RHEA:15096 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00742 METACYC:ACETYL-COA-CARBOXYLTRANSFER-RXN RHEA:11311 reaction UPa:UCR00742 ATP + acetyl-CoA + bicarbonate = ADP + malonyl-CoA + phosphate 1 LR 1 KEGG:R00742 KEGG reaction METACYC:ACETYL-COA-CARBOXYLTRANSFER-RXN MetaCyc MetaCyc REACTION RHEA:11311 Rhea reaction 1 1 1 1 1 KEGG:R00750 METACYC:MHPELY-RXN RHEA:22627 reaction UPa:UCR00750 acetaldehyde + pyruvate = 4-hydroxy-2-oxopentanoate 1 RL 1 1 RL 1 KEGG:R00750 KEGG reaction METACYC:MHPELY-RXN Rhea MetaCyc REACTION RHEA:22627 Rhea reaction 1 1 1 1 KEGG:R00751 METACYC:THREONINE-ALDOLASE-RXN RHEA:19628 reaction UPa:UCR00751 L-threonine = acetaldehyde + glycine 1 LR 1 KEGG:R00751 KEGG reaction METACYC:THREONINE-ALDOLASE-RXN MetaCyc MetaCyc REACTION RHEA:19628 Rhea reaction 1 1 1 1 1 1 KEGG:R00754 METACYC:ALCOHOL-DEHYDROG-RXN RHEA:25293 reaction UPa:UCR00754 NAD(+) + ethanol = H(+) + NADH + acetaldehyde 1 LR 1 KEGG:R00754 KEGG reaction METACYC:ALCOHOL-DEHYDROG-RXN Rhea MetaCyc REACTION RHEA:25293 Rhea reaction 1 1 1 1 1 KEGG:R00756 METACYC:6PFRUCTPHOS-RXN RHEA:16112 reaction UPa:UCR00756 ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate 1 LR 1 KEGG:R00756 KEGG reaction METACYC:6PFRUCTPHOS-RXN MetaCyc MetaCyc REACTION RHEA:16112 Rhea reaction 1 1 1 1 1 KEGG:R00765 METACYC:GLUCOSAMINE-6-P-DEAMIN-RXN RHEA:12175 reaction UPa:UCR00765 H(2)O + alpha-D-glucosamine 6-phosphate = D-fructose 6-phosphate + NH(3) 1 LR 1 KEGG:R00765 KEGG reaction METACYC:GLUCOSAMINE-6-P-DEAMIN-RXN Rhea MetaCyc REACTION RHEA:12175 Rhea reaction 1 1 1 1 1 KEGG:R00766 METACYC:SUCROSE-PHOSPHATE-SYNTHASE-RXN RHEA:22175 reaction UPa:UCR00766 D-fructose 6-phosphate + UDP-alpha-D-glucose = UDP + sucrose 6-phosphate 1 LR 1 KEGG:R00766 KEGG reaction METACYC:SUCROSE-PHOSPHATE-SYNTHASE-RXN MetaCyc MetaCyc REACTION RHEA:22175 Rhea reaction 1 1 1 1 1 KEGG:R00768 METACYC:L-GLN-FRUCT-6-P-AMINOTRANS-RXN RHEA:13240 reaction UPa:UCR00768 D-fructose 6-phosphate + L-glutamine = L-glutamate + alpha-D-glucosamine 6-phosphate 1 LR 1 KEGG:R00768 KEGG reaction METACYC:L-GLN-FRUCT-6-P-AMINOTRANS-RXN MetaCyc MetaCyc REACTION RHEA:13240 Rhea reaction 1 1 1 KEGG:R00771 METACYC:PGLUCISOM-RXN METACYC:RXN-6182 RHEA:11819 reaction UPa:UCR00771 D-glucose 6-phosphate = D-fructose 6-phosphate 1 LR 1 KEGG:R00771 KEGG reaction METACYC:PGLUCISOM-RXN Rhea MetaCyc REACTION METACYC:RXN-6182 MetaCyc Rhea MetaCyc REACTION RHEA:11819 Rhea reaction 1 1 1 KEGG:R00772 METACYC:MANNPISOM-RXN RHEA:12359 reaction UPa:UCR00772 D-mannose 6-phosphate = D-fructose 6-phosphate 1 RL 1 KEGG:R00772 KEGG reaction METACYC:MANNPISOM-RXN Rhea MetaCyc REACTION RHEA:12359 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00774 METACYC:UREA-CARBOXYLASE-RXN RHEA:20899 reaction UPa:UCR00774 ATP + bicarbonate + urea = ADP + phosphate + urea-1-carboxylate 1 LR 1 KEGG:R00774 KEGG reaction METACYC:UREA-CARBOXYLASE-RXN MetaCyc MetaCyc REACTION RHEA:20899 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00783 METACYC:NITRITE-REDUCTASE-CYTOCHROME-RXN RHEA:15236 reaction UPa:UCR00783 H(2)O + ferricytochrome c + nitric oxide = H(+) + ferrocytochrome c + nitrite 1 RL 1 KEGG:R00783 KEGG reaction METACYC:NITRITE-REDUCTASE-CYTOCHROME-RXN MetaCyc Rhea MetaCyc REACTION RHEA:15236 Rhea reaction 1 1 1 1 1 1 KEGG:R00798 METACYC:NITRATREDUCT-RXN RHEA:21071 reaction UPa:UCR00798 H(2)O + acceptor + nitrite = nitrate + reduced acceptor 1 RL 1 KEGG:R00798 KEGG reaction METACYC:NITRATREDUCT-RXN Rhea MetaCyc REACTION RHEA:21071 Rhea reaction 1 1 1 1 1 KEGG:R00805 METACYC:SUCROSE-PHOSPHATASE-RXN RHEA:19292 reaction UPa:UCR00805 H(2)O + sucrose 6-phosphate = phosphate + sucrose 1 LR 1 KEGG:R00805 KEGG reaction METACYC:SUCROSE-PHOSPHATASE-RXN MetaCyc MetaCyc REACTION RHEA:19292 Rhea reaction 1 1 1 1 1 1 KEGG:R00812 METACYC:1.3.1.19-RXN RHEA:15460 reaction UPa:UCR00812 NAD(+) + cis-1,2-dihydrobenzene-1,2-diol = H(+) + NADH + catechol 1 LR 1 KEGG:R00812 KEGG reaction METACYC:1.3.1.19-RXN MetaCyc MetaCyc REACTION RHEA:15460 Rhea reaction 1 1 1 1 1 1 1 KEGG:R00813 METACYC:1.3.1.25-RXN RHEA:11563 reaction UPa:UCR00813 (1R,6S)-1,6-dihydroxycyclohexa-2,4-dienecarboxylic acid + NAD(+) = CO(2) + H(+) + NADH + catechol 1 LR 1 KEGG:R00813 KEGG reaction METACYC:1.3.1.25-RXN MetaCyc MetaCyc REACTION RHEA:11563 Rhea reaction 1 1 1 1 KEGG:R00817 METACYC:CATECHOL-12-DIOXYGENASE-RXN RHEA:23855 reaction UPa:UCR00817 O(2) + catechol = cis,cis-muconate 1 LR 1 KEGG:R00817 KEGG reaction METACYC:CATECHOL-12-DIOXYGENASE-RXN MetaCyc MetaCyc REACTION RHEA:23855 Rhea reaction 1 1 1 1 1 1 1 1 1 KEGG:R00823 RHEA:11079 reaction UPa:UCR00823 H(+) + NADH + O(2) + anthranilate = CO(2) + NAD(+) + NH(3) + catechol 1 LR 1 KEGG:R00823 KEGG reaction RHEA:11079 Rhea reaction 1 1 1 1 1 KEGG:R00829 METACYC:RXN-3641 RHEA:19484 reaction UPa:UCR00829 acetyl-CoA + succinyl-CoA = 3-oxoadipyl-CoA + CoA 1 RL 1 KEGG:R00829 KEGG reaction METACYC:RXN-3641 MetaCyc MetaCyc REACTION RHEA:19484 Rhea reaction 1 1 1 1 1 1 KEGG:R00830 METACYC:5-AMINOLEVULINIC-ACID-SYNTHASE-RXN RHEA:12924 reaction UPa:UCR00830 glycine + succinyl-CoA = 5-aminolevulinate + CO(2) + CoA 1 LR 1 KEGG:R00830 KEGG reaction METACYC:5-AMINOLEVULINIC-ACID-SYNTHASE-RXN MetaCyc MetaCyc REACTION RHEA:12924 Rhea reaction 1 1 1 1 1 KEGG:R00832 METACYC:ARGININE-N-SUCCINYLTRANSFERASE-RXN RHEA:15188 reaction UPa:UCR00832 L-arginine + succinyl-CoA = CoA + N(2)-succinyl-L-arginine 1 LR 1 KEGG:R00832 KEGG reaction METACYC:ARGININE-N-SUCCINYLTRANSFERASE-RXN Rhea MetaCyc REACTION RHEA:15188 Rhea reaction 1 1 1 KEGG:R00833 METACYC:METHYLMALONYL-COA-MUT-RXN RHEA:22891 reaction UPa:UCR00833 (R)-methylmalonyl-CoA = succinyl-CoA 1 LR 1 KEGG:R00833 KEGG reaction METACYC:METHYLMALONYL-COA-MUT-RXN Rhea MetaCyc REACTION RHEA:22891 Rhea reaction 1 1 1 1 1 1 KEGG:R00835 METACYC:RXN-14819 RHEA:15844 reaction UPa:UCR00835 D-glucose 6-phosphate + NADP(+) = D-glucono-1,5-lactone 6-phosphate + H(+) + NADPH 1 LR 1 KEGG:R00835 KEGG reaction METACYC:RXN-14819 MetaCyc Rhea MetaCyc REACTION RHEA:15844 Rhea reaction 1 1 1 1 1 KEGG:R00847 METACYC:GLYCEROL-KIN-RXN RHEA:21647 reaction UPa:UCR00847 ATP + glycerol = ADP + sn-glycerol 3-phosphate 1 LR 1 KEGG:R00847 KEGG reaction METACYC:GLYCEROL-KIN-RXN Rhea MetaCyc REACTION RHEA:21647 Rhea reaction 1 1 1 1 1