Here is the CASP link for this target (which has the amino acid sequence):
Here is the sequence logo predicted by the SAM server.
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
For example, the Valine at residue 74 is predicted to be part of a helix. However, the Valine at residue 26 is highly predicted to be in a sheet.
Are these templates in pdb?
I will like to have the number, just to have a look on them.
I found the templates in the Protein Data Bank (pdb.org) by searching for the name of each template: 4d8k, 1Lck, and 2kym. The picture they give for 1Lck is not great; it fails to show how similar it is to 4d8k. Here are some images of the three templates from pyMOL that may help.
1Lck yellow 4d8k blue2kym
marie_s, any template that we will give you will be coming from the PDB. I will try to post a link to them in the puzzle comments.
Here are the ones from this puzzle (the same as Susume's screenshots):
and as Susume mentioned you can always grab the pdb ID for any template by toggling the Name/Score button (in the far right column of the Alignment Tool) and typing that ID into www.pdb.org
My thanks also to Susume. I find the pictures of the alignment folds very interesting.
Sometimes when we have been given 10 alignment prediction templates, I have been threading all 10 and saving them individually. That allows me to load them, or load them as guides. I can then use the "align guide" tool to align certain portions of the folds. Sometimes, I find shared solutions/guides easier to visualize than the ball and chain representation we get with the "show alignment" tool.
If 200 people were to make and save 10 local solutions, it would seem like a tremendous waste of time. Could each of the alignment templates be some type of global "Shared Solution" or "Shared Template" available for everyone?
In this puzzle, it would have been nice to be able to open a "Shared Solution" model for each of the 3 proteins that were given to us as templates.