(last modified December 18, 2002)
go to the NCBI homepage - alternatives EBI (Europe), DDBJ (Japan)
under "SEARCH" select "LocusLink"
search for syntrophin (query "syntrophin")
open the human alpha1 syntrophin link (locus 6640)
under "NCBI Reference Sequences (RefSeq), Protein" select the link to the protein sequence (NP_003089)
under "Display" change "Default View" to "FASTA" and click "Display"
select (highlight) the protein sequence and copy it (right mouse button, "Copy")
go to the NCBI homepage ("Back" button or "NCBI" top left corner)
select "BLAST" (middle blue line)
under "Protein BLAST" select "Standard protein-protein BLAST [blastp]
"Paste" the human alpha-syntrophin protein sequence into the "Search"-window (right mouse button, "Paste")
perform two searches
under "Choose database" select "swissprot" and under "Now:" press "BLAST!" and finally on the new page select "FORMAT!"
return to the NCBI blast window, go one page back, under "Choose database" select "nr" and under "Now:" press "BLAST!" and finally on the new page select "FORMAT!"
analyse the search results and note that;
NOTE - for details on the database hits detected select the
accession number (left, start of line); to see the alignment of a hit select
the figure in the "Score (bits)" column
NOTE - for a better overview it might be helpful to change the
display of the results page; go to the "formatting BLAST"
page, under "Alignment view" select "query-anchored with
identities" and press the "FORMAT!" button. The display of
the results page will now change
a syntrophin contains two known protein domains (PDZ and PH)
the SwissProt database does not yet contain syntrophin sequences
alpha-syntrophin is part of a protein family (alpha 1, beta 1, beta 2, gamma, ...)
(SwissProt result) the PDZ domain is found in many other proteins
syntrophins are present in a range of other organisms
NOTE - on the "results of BLAST" page
click on "Taxonomy reports" (directly top left of the
graphical view)
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J.T. den Dunnen