In a bacteria genome I´ve found several ORF for Surface layer protein, and I suspect some are truncated copies of the gene. I would like to find if all of them have promoters.
We have had success using BPROM by Softberry (http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb) for the alphaproteobacterium Rhodobacter capsulatus.