Rv1025 (DUF501) reproducibility bundle for: "A strictly conserved cysteine-histidine-glutamate metal site defines the bacterial family DUF501: evolutionary inference of function for a protein family with no structural relative" (version 2)

Version 2 (2026-11-02). Analysis scripts, curated DUF501 (Pfam PF04417) family data, cached AlphaFold3/Boltz-2 structural predictions, figures and supplementary materials reproducing every figure, table and reported statistic of the manuscript "A strictly conserved cysteine-histidine-glutamate metal site defines the bacterial family DUF501: evolutionary inference of function for a protein family with no structural relative" (Guyeux C., submitted to the Journal of Molecular Evolution; preprint bioRxiv 10.64898/2026.08.31.746906). Compared with version 1, this version adds the scripts phase40 to phase46 (maximum-likelihood tree of the family, protein-level audit of the eukaryotic losses of the metal site, three-state mapping on the tree, figure 4, Online Resources 10 and 14), their outputs, and the recomputed Henikoff effective sequence number. Contents: analyses/ (45 Python scripts, PyMOL scenes and shell scripts), data/, resultats/, figures/, supplementary_materials/ (Online Resources 1 to 14 of the manuscript). Companion code repository: https://github.com/cguyeux/rv1025-duf501-mtbc.