Figure 1

Conserved sequence blocks in the rhodopsin superfamily. The conserved blocks are separated by numbers that indicate the length of less well conserved sequence segments which are not shown (see Additional File 1). The alignment columns are colored on the basis of the respective position conservation throughout the superfamily: yellow background indicates hydrophobic residues (ACFILMVWY), red letters indicate polar residues (DEHKNQR), and green background indicates small residues (ACGNPSTV). The transmembrane helices are indicated following transmembrane helix prediction for PGV sequence (helix A is not shown; see Additional File 2 for all 7 predicted transmembrane helices). The functionally important residues are numbered: 1, proton acceptor; 2, position important for spectral tuning; 3, proton donor; 4, retinal-binding amino acid residue. Each sequence is denoted by the corresponding taxon abbreviation followed by the species abbreviation and GenBank Identification (GI) number. Taxa abbreviations: A, Archaea; B, Bacteria; E, Eukaryota; Ae, Euryarchaeota; Ba, Actinobacteria; Bb, Bacteroidetes/Chlorobi group; Bc, Cyanobacteria; Bd, Deinococcus-Thermus; Bf, Firmicutes; Bh, Chloroflexi; Bo, Planctomycetes; Bp, Proteobacteria; E9, Viridiplantae; Ec, Alveolata; Eh, Cryptophyta; El, Opisthokonta; Em, Glaucocystophyceae; Ep, Haptophyceae. Species abbreviations: are listed in Additional File 3.