Trouble deciphering a protein multiple sequence alignment. Any help?

Question

[RJY]

Hey, guys. I am having trouble deciphering this protein sequence alignment. I figure that the colors may be related to the conservation between the sequences but I'm not sure. I also thought that the color may be due to the different properties of the residues, but in some places Valine and Isoleucine are colored the same and in others they're not. I'm only in my second week of Bioinformatics and this paper is for a Cell Bio course, so I'm a little stuck.

Here is a link to the article. It's Figure 1A.

Thanks for any help!

Answer 1

[Ram]

I could give you the approach I'd take to solve this. Dig a little deeper and find which tool was used, then read its documentation. I could try and help you through it, if you like.

UPDATE:

So I took a deeper look but the sources lead nowhere. After applying some logic, I see the following pattern:

1. All 3 residues identical: Yellow font on red background
2. Mix of identical, similar and dissimilar, identical becomes white-on-green, similar becomes black-on-blue and dissimilar becomes black-on-white
3. All 3 dissimilar - black-on-white

Source for protein similarity lookup: http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html

[RJY]

Thank you. I went through the paper and I couldn't find that they mentioned what tool they used so I'm not really sure how to figure that out.

[Ram]

Hold on while I take a look at it.

[RJY]

Thank you. I really appreciate you taking the time.

[Ram]

Answer updated with my idea on the color coding. Hope it helps.

[RJY]

It helps a lot. Thank you again!