Generating MSAs for chimeric proteins

I'm attempting to generate predictions for multimeric complexes, where one chain is a chimeric/fusion protein and has components from different organisms. About ~85% of this chain is from one organism and the other ~15% is from another organism. The sequence coverage plot shows virtually 0 sequences aligning to the latter (and the predicted structure is very low confidence), likely due to this 15% component comprising such a small part of the overall protein that the sequences that align score very low in the search and are omitted. Is there any way to 'lock' segments of a single protein (especially chimeric proteins) to ensure diversity of sequences across that chain if the chain has components from different lineages?

Alternatively, if I need to create a custom MSA, is there a way to extract a .a3m file from ColabFold for the sequences that were used as the input (those shown in the sequence coverage plot)? All of the .a3m files that I can access seem to contain ~20k sequences, whereas the coverage plot only shows the final ~3k that went through the final seq diversity filtering.

Many thanks in advance!

Start with ColabFold's sequence coverage plot and the accessible .a3m outputs, comparing their ~20k sequences with the ~3k sequences retained after final sequence-diversity filtering. Determine whether segment locking for chimeric proteins or extraction of the filtered MSA is supported; done requires a documented, reproducible workflow or a clearly scoped implementation path.