When we were performing BLAST homology searches with
the cannabinoid receptor against the Swissprot database, we
found at least 11 cannabinoid receptor proteins in the
database. These were divided up into two groups, the type I
and the type II receptors. There were two type I genes (A
and B) for Fugu (which has been postulated to have undergone
a recent genome duplication). We are going to align these
eleven sequences, and see where the two Fugu genes fit in.
First use SRS to retrieve all eleven cannabinoid receptor entries.
Go to the SRS home page,
click on the Library Page tab, and select the
Swissprot database, and type 'cannabinoid receptor' into the top
text-entry box, and click on 'Quick Search'.
Show SRS QUICK SEARCH image
Leaving the button
at 'unselected results only', click on 'Save'.
Show SRS OPERATIONS image
On the next page, change
the view from
'SeqSimpleView' to 'FastaSeqs'. Click on 'Save'.
Show SRS SAVE SEQUENCES image
The eleven
sequences are presented as plain text in FASTA format on our browser, so
we can now select them all, and copy them.
Now go to to the
ClustalW home page, and paste the sequences
which we have just copied into the main text-entry box. We can
leave all the default settings (although you may prefer to choose
a color alignment), so just click on 'Run ClustalW'.
Show CLUSTALW QUERY FORM image
The result
will come up in the same browser window shortly.
The first part of the output tells us how long our input sequences
were,
Show CLUSTALW RESULTS SECTION 1 image
and what the pairwise scores between each
pair of sequences were (the higher the score, the more similar
the sequences)
Show CLUSTALW RESULTS SECTION 2 image
and finally, it tells us that it has created a guide
tree (a rough phylogenetic tree, based on sequence similarities).
Show CLUSTALW RESULTS SECTION 3 image
It then uses this tree to form the multiple alignment.
When we look at the alignment, we can see that the last three
sequences are all more similar to each other than they are to any
of the other sequences, and where stretches of amino acid
residues are absent in one, then they will also be absent from
the other two sequences. Looking at this alignment, we can see
that the two Fugu sequences, albeit slightly different from each
other, are both nevertheless more similar to the type I cannabinoid
receptors than either of them are to the type II receptors, thus
confirming that they are indeed both type I receptors, and that
they have been correctly identified as such.
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