protein multiple alignment
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8 weeks ago

In protein multiple alignments some columns have the same colour but contain different amino acids. Why?

alignment • 108 views
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I think they might share the same physiological properties such as being nonpolar, polar (Having charge or not).

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exactly.

see @Joe answer for more details

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if you needed to guess, what would you think it means? :)

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Thank you so much Joe.

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Is this a homework/assignment question?

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No, I saw it when I was doing a protein alignment on MEGA with clustal w method.

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8 weeks ago
Joe 19k

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:

http://www.jalview.org/help/html/colourSchemes/clustal.html

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