Fig. 3

Conserved motif in bacterial rhodopsin sequences annotated by MetaCLADE in the MT dataset EPAC. a Conservation profile of the MetaCLADE CCM fragment generated by the Geodermatophilus obscurus (strain ATCC 25078/DSM 43160/JCM 3152/G-20; Actinobacteria) sequence of the rhodopsin-like domain used by MetaCLADE to annotate environmental sequences in EPAC [57]. An orange dot is located above all positions in the profile when one of the three top residues with the highest frequency appears as highest frequency residue in the corresponding position of the conservation profile in b. b Profile generated from the alignment of 371 environmental sequences annotated by MetaCLADE with CCMs of the rhodopsin-like domain and missed by HHMer. The letter height in the logo is proportional to the number of sequences in the alignment that contain the letter at a specific position, and the letter thickness is proportional to the number of gaps in the alignment at that position. c Rhodopsin fragment sequence from the dinoflagellate Prorocentrum donghaiense found in the NR database and matching, with E value 3e −22 and sequence identity 78%, the longest environmental sequence among the 371 annotated by MetaCLADE. Note that the fragment has been aligned to the profile in b for a visual inspection of conserved positions. d Conservation profile HMM of the Pfam bacterial rhodopsin domain PF01036 (fragment). As in c, positions are aligned with the profile in b for best visualisation. An orange dot is located above a position in the profile when one of the three top residues with the highest frequency appears as highest frequency residue in the corresponding position of the conservation profile in b