torchcell.metabolism.betaxanthin.build_betaxanthin_pathway

build_betaxanthin_pathway(model: Model, *, partners: dict[str, str] | None = None, include_oxidase_branch: bool = True) → HeterologousPathway[source]

Build the cassette as a pathway object against one genome-scale model.

Parameters:

  • model – The base model, read to check which partners it actually carries.

  • partners – Metabolite id to short name for the condensation partners. Defaults to DEFAULT_PARTNERS, filtered to those present in model.

  • include_oxidase_branch – Include the DOPA oxidase side activity and the betanidin branch. Cachera’s cassette carries wild-type CYP76AD1, verified by translating the pBTX002 open reading frame, which is tryptophan at 13 and phenylalanine at 309, so neither the W13L nor the F309L mutation that suppresses this activity is present. The branch is therefore chemically live in that screen, though its magnitude there is unmeasured, since DeLoache quantified it only under ascorbic acid, which stabilizes the otherwise self-polymerizing betanidin.

Returns:

The pathway, ready for torchcell.metabolism.pathway.apply_pathway().