Annotating conserved protein domains in bacterial assemblies
The first option. Using a pre-existing tool, such as PROKKA etc.

Diversity. Bacterial diversity is staggering and species such as E. coli and Salmonella, which are closely related diverged when mammals and dinosaurs/birds diverged, so searching nucleotide sequences is a bad idea as you will get nothing. Especially as you are hoping to find distant sequences that may be missed by the commonly used annotation tools.

Operons. Bacteria, especially thermophiles, often group their protein functionally in operons. Therefore, you can use the principle of guilt by association to guess what a mysterious protein does. It is extremely powerful. Say you have Voet &amp; Voet handy, a pathway with a hole and a mysterious protein you can guess easily what it does.

Note, if you have a protein that you are particularly interested in, I would suggest making your own PSI PSSM file. The automated system cannot read the literature or do some quick checks to see when to stop, so may be overly conservative with the clusters.