Bacterial rhodopsins [1,2,3] are a family of retinal-containing proteins found in extremely halophilic bacteria which provide light-dependent ion transport and sensory functions for these organisms. Bacterial rhodopsins are integral membrane proteins with seven transmembrane regions. The retinal choromophore is covalently linked, via a Schiff's base, to the epsilon-amino group of a conserved lysine residue in the middle of the last transmembrane helix (called helix G). There are at least three types of bacterial rhodopsins:

• Bacteriorhodopsin (bop) , and archaerhodopsins 1 and 2, light-driven proton pumps.
• Halorhodopsin (hop), a light-driven chloride pump.
• Sensory rhodopsin (sop), which mediates both photoattractant (in the red) and photophobic (in the near UV) responses.

We developed two patterns which allow the specific detection of bacterial rhodopsins. The first pattern corresponds to the third transmembrane region (called helix C) and includes an arginine residue which seems involved in the release of a proteon from the Schiff's base to the extracellular medium. The second pattern includes the retinal binding lysine.