{PDOC00291}
{PS00950; BACTERIAL_OPSIN_1}
{PS00327; BACTERIAL_OPSIN_RET}
{BEGIN}
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* Bacterial rhodopsins signatures *
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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.

-Consensus pattern: R-Y-x-[DT]-W-x-[LIVMF]-[ST]-[TV]-P-[LIVM]-[LIVMNQ]-[LIVM]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [FYIV]-{ND}-[FYVG]-[LIVM]-D-[LIVMF]-x-[STA]-K-x-{K}-[FY]
                    [K is the retinal binding site]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: 4.

-Last update: December 2004 / Patterns and text revised.

[ 1] Osterhelt D., Tittor J.
     Trends Biochem. Sci. 14:57-61(1989).
[ 2] Soppa J., Duschl J., Oesterhelt D.
     "Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial
     isolate Halobacterium sp. strain SG1: three new members of a growing
     family."
     J. Bacteriol. 175:2720-2726(1993).
     PubMed=8478333
[ 3] Kuan G., Saier M.H. Jr.
     "Phylogenetic relationships among bacteriorhodopsins."
     Res. Microbiol. 145:273-285(1994).
     PubMed=7997641

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