Recent releases of libbio-perl-perl have decoupled a few modules to their own packages, libbio-searchio-hmmer-perl is one of them:
gbp clone git@salsa.debian.org:med-team/libbio-searchio-hmmer-perl.git
This module is needed by prokka (even the currently packaged version)
I just pushed updates to prokka that add an autopkgtest which revealed this issue.
Thanks!