Methionine (S-adenosylmethionine) cycle module

A taxon-neutral decomposition of the methionine / S-adenosylmethionine (SAM) cycle, the core methyl-group-cycling pathway that interconverts methionine, S-adenosyl-L-methionine, S-adenosyl-L-homocysteine, and homocysteine, with exits to transsulfuration (via cystathionine beta-synthase) and remethylation inputs from folate (via methionine synthase) and choline/betaine (via BHMT). This module is intentionally structured in two layers. The CATALYTIC layer (enzymatic steps) grounds each step to a GO molecular-function term, the same EC <-> GO MF alignment used by the gluconeogenesis module. The REGULATORY layer is captured as connections of type POSITIVELY_REGULATES / NEGATIVELY_REGULATES whose predicate is grounded to a Systems Biology Ontology (SBO) term that distinguishes the MECHANISM (competitive vs allosteric), with the effector represented as a ChEBI-grounded metabolite-pool node. This regulatory wiring (small-molecule effector -> enzyme, with mechanism and sign) is information GO cannot express: GO annotations attach to gene products, the effectors here are metabolites, and GO has no competitive-vs-allosteric distinction. The regulatory structure is transcribed from the biosustain Maud kinetic model `data/methionine/methionine_cycle.toml`. A notable showcase is METAT, where two isozyme forms of methionine adenosyltransferase catalyse the SAME reaction but are OPPOSITELY regulated by SAM: MAT-I is competitively product-inhibited by SAM, whereas MAT-III is allosterically activated by SAM. Isozyme-specific regulation of this kind is the central thing GO flattens away.