Question

protein multiple alignment

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3.9 years ago

Mohammad Salehi ▴ 30

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

alignment • 943 views

ADD COMMENT • link 3.9 years ago by Mohammad Salehi ▴ 30

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

ADD REPLY • link 3.9 years ago by Mohammad Salehi ▴ 30

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exactly.

see @Joe answer for more details

ADD REPLY • link 3.9 years ago by lieven.sterck 15k

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

ADD REPLY • link 3.9 years ago by lieven.sterck 15k

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Thank you so much Joe.

ADD REPLY • link 3.9 years ago by Mohammad Salehi ▴ 30

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Is this a homework/assignment question?

ADD REPLY • link 3.9 years ago by Joe 21k

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

ADD REPLY • link 3.9 years ago by Mohammad Salehi ▴ 30

score 1 · Answer 1 · 2021-02-10

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