Annotation, comparative genomic analysis, and multiple alignments Preliminary annotations were generated using a combination of the RAST [22] algorithm (rast.nmpdr.org). Loci containing mutations were used to query the non-redundant (nr) databases and Refseq protein databases at NCBI using directed BLASTx and BLASTp. The comparative BLAST tool from RAST was utilized for genome-wide protein sequence comparisons to B. subtilis. Results were filtered for bidirectional hits. Multiple alignments were generated by MegAlign from the LaserGene software package using the CUSTALW algorithm.