I am interested in a group of bacteria highly conserved on the 16s gene. Therefore, I will like to use recA for taxonomic assignment of the metagenomic data. Are there any publically available databases of recA? Thank you!
you probably can use the Fungene database, the database contain RecA and several other phylogenetic marker genes, both sequences and associated hmm motifs. Fungene can use hmm method for taxonomic classification.
We've also developed MetAnnotate for this purpose. One can do taxonomic profiling using recA or any other protein family / HMM. https://bitbucket.org/doxeylab/metannotateinstaller