protein multiple alignment
In protein multiple alignments some columns have the same colour but contain different amino acids. Why?
• 1,519 views
•
link
1 answer
Amino acids can be similar, but not the same (e.g. positively or negatively charged). This has implications for the effect on the structure of the protein when they are substituted. CLUSTAL implements a colourscheme to depict this (as do many other tools).
You can find information about CLUSTAL's colouring online:
• 0 views
•
link
Log in to answer this question.
Is this a homework/assignment question?
No, I saw it when I was doing a protein alignment on MEGA with clustal w method.
if you needed to guess, what would you think it means? :)
I think they might share the same physiological properties such as being nonpolar, polar (Having charge or not).
exactly.
see @Joe answer for more details
Thank you so much Joe.