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The olfactory system is a highly-specialised chemical recognition system
that, like the immune system, is capable of discriminating with tremendous
sensitivity between numerous foreign molecules in the environment.
Olfactory transduction is believed to be initiated by the binding of
odorants to specific receptor proteins in the cilia of olfactory receptor
cells. Although little is known about the precise mechanism by which
odorant binding might initiate membrane depolarisation, it is believed
that cyclic AMP may serve as an intracellular messenger for olfactory
The olfactory receptors are integral membrane proteins that belong to a
superfamily of G protein-coupled receptors. The activating ligands of the
different superfamily members vary widely in structure and character, yet
the proteins appear faithfully to have conserved a basic structural frame-
work, believed to consist of 7 transmembrane (TM) helices. Although the
sequences of these proteins are very diverse, reflecting to some extent
this broad range of activating ligands, nevertheless, motifs have been
identified in the TM regions that are characteristic of virtually the
entire superfamily [7,8]. Amongst the exceptions are the olfactory
receptors, which cluster together in a subfamily that lacks significant
matches with domains 2, 4 and 6 .
OLFACTORYR is a 5-element fingerprint that provides a signature for the
olfactory receptors. The fingerprint was derived from an initial alignment
of 19 sequences: the motifs were drawn from conserved regions spanning
virtually the full alignment length - motif 1 lies in the first external
loop; motif 2 spans the second cytoplasmic loop, leading into TM domain 4;
motif 3 lies in the second external loop; motif 4 lies in the third
cytoplasmic loop; and motif 5 spans the C-terminal portion of TM domain 7,
leading into the C-terminus. Fourteen iterations on SPTR39_14f were
required to reach convergence, at which point a true set comprising 186
sequences was identified. Several partial matches were found, all of which
are olfactory receptors that fail to make significant matches with one or