What is the best approach to identify TFs in a non-model organism with limited homology to the closest model organism? Is predicting DNA-binding domains and assuming that most proteins containing DBDs are TFs a valid strategy?
This doesn't directly answer your question but have you considered protein clustering with MMseqs2?
An example where it was used to identify homologs across very distantly related organisms: https://www.nature.com/articles/s41586-020-2762-2
In deed in case of expected low homology I would focus on TF's Domains. I would suppose that These are still more or less conserved.
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