Recurrent evolution of penicillin-binding proteins across global Treponema pallidum populations: reproducibility data

Data supporting “Recurrent evolution of penicillin-binding proteins across global Treponema pallidum populations”. The study analyses 1,861 genomes from 31 countries; genomes with collection-year metadata span 1912–2023. The deposit contains sample metadata, variant callability and 40 observed PBP amino-acid substitutions; ancestral-state reconstructions and stochastic maps; FUBAR selection results; molecular-clock inputs and summaries; mrcA protein types; structural coordinates and annotations; and 49,286 ESM-2 substitution scores for mrcA, pbp1, pbp2 and tp47. ESM-2 reference proteins are translated from annotated Nichols coding sequences using bacterial genetic code 11, with initiating methionine. Reference sequences and annotations, five assembly genomes, collection dates and read-accession lists are included.