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
unipathway_ontology
uniprot_super_pathway
true
true
UniProt super-pathway
synonym_type_property
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_synonym_type
id
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.
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'
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
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.
GO:0003824
reaction
UPa:UCR00000
reaction
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
KEGG:R00158
METACYC:RXN-12002
RHEA:24403
reaction
UPa:UCR00158
ATP + UMP = ADP + UDP
1
1
LR
1
LR
1
KEGG:R00158
KEGG reaction
METACYC:RXN-12002
MetaCyc
MetaCyc REACTION
RHEA:24403
Rhea reaction
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
KEGG:R00256
METACYC:GLUTAMIN-RXN
RHEA:15892
reaction
UPa:UCR00256
H(2)O + L-glutamine = L-glutamate + NH(3)
1
1
LR
2
LR
2
KEGG:R00256
KEGG reaction
METACYC:GLUTAMIN-RXN
MetaCyc
MetaCyc REACTION
RHEA:15892
Rhea reaction
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
KEGG:R00361
METACYC:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
RHEA:22559
reaction
UPa:UCR00361
(S)-malate + Quinone = Hydroquinone + oxaloacetate
1
KEGG:R00361
KEGG reaction
METACYC:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
MetaCyc
MetaCyc REACTION
RHEA:22559
Rhea reaction
LR
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
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
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
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
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
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
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
KEGG:R00410
METACYC:RXNI-2
RHEA:25483
reaction
UPa:UCR00410
acetoacetate + succinyl-CoA = acetoacetyl-CoA + succinate
1
1
LR
1
LR
1
KEGG:R00410
KEGG reaction
METACYC:RXNI-2
Rhea
MetaCyc REACTION
RHEA:25483
Rhea reaction
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
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
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
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
KEGG:R00428
reaction
UPa:UCR00428
GTP + H(2)O = formamidopyrimidine nucleoside triphosphate
1
LR
1
KEGG:R00428
KEGG reaction
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
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
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
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
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
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
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
KEGG:R00480
METACYC:ASPARTATEKIN-RXN
RHEA:23779
reaction
UPa:UCR00480
ATP + L-aspartate = 4-phospho-L-aspartate + ADP
1
1
1
LR
1
LR
1
LR
1
KEGG:R00480
KEGG reaction
METACYC:ASPARTATEKIN-RXN
Rhea
MetaCyc REACTION
RHEA:23779
Rhea reaction
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
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
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
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
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
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
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
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
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
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
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
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
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
KEGG:R00565
METACYC:GLYCINE-AMIDINOTRANSFERASE-RXN
RHEA:13204
reaction
UPa:UCR00565
L-arginine + glycine = L-ornithine + guanidinoacetate
1
LR
1
KEGG:R00565
KEGG reaction
METACYC:GLYCINE-AMIDINOTRANSFERASE-RXN
MetaCyc
MetaCyc REACTION
RHEA:13204
Rhea reaction
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
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
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
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
1
LR
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
KEGG:R00734
METACYC:TYROSINE-AMINOTRANSFERASE-RXN
RHEA:15096
reaction
UPa:UCR00734
2-oxoglutarate + L-tyrosine = (4-hydroxyphenyl)pyruvate + L-glutamate
1
1
LR
1
RL
1
KEGG:R00734
KEGG reaction
METACYC:TYROSINE-AMINOTRANSFERASE-RXN
Rhea
MetaCyc REACTION
RHEA:15096
Rhea reaction
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
KEGG:R00750
METACYC:MHPELY-RXN
RHEA:22627
reaction
UPa:UCR00750
acetaldehyde + pyruvate = 4-hydroxy-2-oxopentanoate
1
1
RL
1
RL
1
KEGG:R00750
KEGG reaction
METACYC:MHPELY-RXN
Rhea
MetaCyc REACTION
RHEA:22627
Rhea reaction
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
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
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
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
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
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
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
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