Maximum likelihood phylogeny of PAS domain protein sequences. 372 PAS domain sequences obtained from 28 Gram-positive bacterial genomes are included. As references, the phylogeny is shown in two color schemes: based on PDC/PAS domain architectures (A) and based on bacterial genera (B). Black and green circles at internal nodes represent those supported by bootstrap values greater than 60% and those supported by all three phylogenetic methods although bootstrap values were 60% or lower. Fourteen PAS domain sequences whose structures are known and used as the search queries were included in the phylogeny and they are labeled with black letters. One PDC domain sequence, 1P0Z (CitA, Klebsiella pneumoniae), was also included as the outgroup and is shown in black. See Table 1 and (Additional file 1: Table S1) and (Additional file 3: Table S2) for the species name abbreviations and protein IDs. Species abbreviations not listed in Table 1 are Av (Azotobacter vinelandii), Bj (Bradyrhizobium japonicum), Gs (Geobacter sulfurreducens), Hm (Haloarcula marismortui), Hh (Halorhodospira halophila), Rc (Rhodospirillum centenum), Rj (Rhodococcus jostii), Rm (Rhizobium meliloti), Tm (Thermotoga maritima), Vp (Vibrio parahaemolyticus).