Two sets of experimentally measured stability values were mapped to the latent space of Model 1. The first set consisted of six ancestral sequences from the previous ancestral campaign of the thoroughly characterized dehalogenases DbjA, DbeA, DhaA, DmxA, and DmmA . These sequences were realigned with the MSA profile of the original input sequences and only retained the corresponding columns that remained after the MSA processing procedure. The second set consisted of 24 previously engineered DhaA variants (the DhaA115 dataset) incorporating both evolutionary and energy-based mutations based on the FireProt method . Similarly, for the DhaA115 dataset, we performed individual sequence alignment with the query sequence P59336_S14, preserving the indices that were retained after the MSA preprocessing step.