Conservation scoring 1: mapping conservation onto a protein sequence
For the impatient: click here to go straight to the results page.
Take HPPD as an example. Download the folder with the input files for this example by clicking here (right click, save and unzip). Find the file with the sequences homologous to HPPD (refseq_animals.fasta) and upload. You can leave the Reference Sequence field empty for the moment. Click submit.
Admire the conservation map produced. You can download it by right clicking on it, and selecting "Save image." HPPD is an enzyme, and a tel binding one, for that matter. Where do you think the residues belonging to the catalytic pocket are?
The conservation was mapped to the human sequence - the first one in the uploaded file. Now try mapping the conservation onto the sequence of D. rerio. One of D. rerio sequences in the test alignment (check with the text editor) is 51230599 (the full id is gi|51230599|ref|NP_001003742.1|, but you can use the shortened version). paste the name 51230599 into the field "The name of the reference sequence" and repat your search.
Do not have your own set of sequences?
Not happy with the alignment produced by the server? Read here about re-aligning sequences by yourself.