The Conditionally Accepted PMN Pathway (CAPP) list contains pathways that are only accepted if they are predicted by the Pathologic program and meet additional criteria assigned to each pathway by PMN curators. Each CAPP can have criteria based on reactions and/or expected taxonomic range that are used to determine whether it should be accepted for a given species.
- CAPP Reactions: A CAPP pathway will be accepted if it has one or more enzymes predicted (by E2P2 v2.1) to catalyze one or more "key" reaction(s) assigned to the pathway. "Key" reactions are selected by curators based on a number of criteria including:
- Uniquely appears in a single pathway
- Differentiates a particular variant pathway from other related variants
- Appears as the final step in a biosynthetic pathway or as the first step in a degradation pathway
- The CAPP approval process also recognizes enzyme predictions linked to non-specific Enzyme Commission (EC) numbers (e.g.22.214.171.124) and does not use these for accepting any CAPP pathway.
- Please note: The acceptance of a pathway based on reaction criteria does not necessarily mean that the exact pathway depicted will be present in the given species, especially in the case of "specialized" or "secondary" metabolic pathways. The pathway is retained to allow users to see the metabolic context of the "key" reaction(s) in different organisms. These pathways have a computational evidence code to indicate that there is no experimental support for their existence in the given species. Moreover, if a published paper suggests that a pathway is likely only found in a very restricted taxonomic range or is excluded from a specific taxonomic range, a special warning comment is placed at the beginning of the pathway summary if this pathway is accepted for a species outside of its expected taxonomic range
- CAPP Taxonomic Range: A CAPP pathway will be accepted if it falls with an expected taxonomic range as described in a published manuscript. This range is typically only applied if this pathway is expected to be widespread in this taxon, e.g. a pathway that is very common to many legume species.
A CAPP taxonomic range criterion is usually added to avoid rejecting true positive pathways when key enzymes are missing due to genome or proteome annotation problems.
- Decision rules for CAPP pathways:
- If a pathway has more than one CAPP-Reaction and/or CAPP-taxonomic range associated with it, it will be accepted as long as one of the criteria is met for a given species. All criteria are treated as "OR" when the pathway is automatically evaluated during the SAVI pipeline.
- Reaction criteria are given first precedence and whenever possible, reaction criteria are used in addition to or instead of using expected taxonomic range, especially given the number of examples of scattered occurences of pathways and compounds throughout the plant lineage, particularly in the area of "specialized" or "secondary" metabolism.