IN CLASS DEMO (though we may just do the beginning and leave you to fend on your own and/or another time today) -
February 19, 2009: continuation of in-class Feb 5, 2009

What might be the function of LWPCN32?

PartII. A little bit of Jalview and a Phylogenetic Tree for the family.

For your recollection, so far we translated the DNA sequence "LWPCN32" into a hypothetical protein sequence previously:

>LWPCN32_protein
MAPAIKVLFLCTHNACRSILAEAIGRDLLIKLEDVTSAKWQFASAGSAPAGVVHPQTLLQ LAHRGYSTEGLSSKNWDVMADFTPDLVITVCDSAAGETCPLWLGHTLKLHWGLPDPTSTD PADMDAQFSSVIGTLEKRITALISLPLSAGIDAQKVSLQSIASQFPLT

Then we gathered homologous protein sequences in Swissprot and used the program MUSCLE from within Jalview to produce an alignment. For convenience you will find this MSA (in .aln format) here (note that I appended .txt to the file name here to ensure that your browsers display the file for you straightforwardly).

Open the .aln file in Jalview (use WebStart version + have the documentation open)
Add the query (protein) sequence
Realign, again using MUSCLE
Save your new MSA in .aln format
Try out the Jalview feature for removing redundancy, it's pretty cool. This can be helpful if you are interested in selecting a nicely representative subset of sequences, e.g. for a figure, or simply to decrease the number of sequences for palatability. Save a more representative set of aligned sequences if you like.
Generate a phylogenetic tree using the Genebee TreeTop server; select (only) the Cluster Algorithm, the bootstrapping option, generate a multiline Phylip format as an extra tree format, and (only) a Phylogram as the picture output format.
Note: This server is not really made for class-use, i.e. if you do not get any response leave it alone and try some other time, it's OK)
Finally, to show that there are more printable output formats for trees, copy-paste the Phylip formatted tree from Treetop (lots of parentheses - these indicate the sets specified by the branching) into the Phylodendron server (selecting a tree type that you like, and a GIF picture as output). Note that you are losing the bootstrap values generated by TreeTop (sadly) but retain some sort of scale (a small bar at the bottom of the figure).

According to this analysis, what would be the argument for that this protein may indeed function as an arsenate reductase? What else could we do to further corroborate this finding?