Extended Worked Examples for The Vavilov–Zwicky Framework: A Provable Compression Principle in Modular Protein Design

Detailed step-by-step application of the Vavilov–Zwicky framework to three modular protein systems — DEBS-type polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and Class-2 CRISPR-Cas effectors. These extended worked examples demonstrate the full workflow (parameterisation, attribute definition, morphological matrix construction, Vavilov homology constraints, and output ranking) and serve as supplementary material to the main manuscript "The Vavilov–Zwicky Framework: A Provable Compression Principle in Modular Protein Design". All values are literature-derived ranges consistent with published data (MIBiG 3.0, Pfam, metagenomic surveys, etc.) and are provided solely to illustrate the scale of compression achievable under biologically realistic assumptions. They do not represent outputs from actual algorithm runs on full sequence databases.