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Sequence allignment questions

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Sequence allignment questions

Postby TToe » Fri Nov 23, 2012 3:51 pm

http://upload.wikimedia.org/wikipedia/c ... nment2.png

':' means Conservative amino acids. As we know it's the replacement of an amino acid residue with another one with similar properties, so why do the amino acids with the ':' below it have different properties (so different colours) (look at link above).

Are the absolutely crucial amino acids the amino acids that haven't be substituted with anything (so the are identical)?

What does this question mean:

1. Give an example (or highlight) of one position where the same amino acid is not found in all the sequences, but a small, hydrophobic amino acid is present in each sequence. Also give an example of a one position where a negatively-charged amino acid is found in all the sequences. (6 marks)

If you want me to understand better, could you answer the first part of the question? Here's the sequence alignment that is needed to answer the question (link below):

http://www.ebi.ac.uk/Tools/services/web ... olors=true
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Postby JackBean » Fri Nov 23, 2012 3:57 pm

The only problem I see is the K-E pair...

Yes, the crucial amino acids were (could) not be substituted, but not all identical amino acids are crucial.

Do you know, which amino acids belong to small hydrophobic AAs?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re:

Postby TToe » Fri Nov 23, 2012 4:07 pm

JackBean wrote:The only problem I see is the K-E pair...

Yes, the crucial amino acids were (could) not be substituted, but not all identical amino acids are crucial.

Do you know, which amino acids belong to small hydrophobic AAs?

No because it also appears on the link I gave you below (I'm really confused).

In the link below wouldn't all the amino acids be crucial?

According to the key is the red ones but the amino acids on the red columns have 2 or more amino acids that are the same.
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Re: Sequence allignment questions

Postby JackBean » Sat Nov 24, 2012 1:38 pm

No, there are only few amino acids marked with :

Trp is also red (W) and is not small amino acid.
http://www.biolib.cz/en/main/

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Re: Sequence allignment questions

Postby TToe » Sat Nov 24, 2012 3:46 pm

JackBean wrote:No, there are only few amino acids marked with :

Trp is also red (W) and is not small amino acid.

Are isoleucine and leucine small hydrophobic amino acids?
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Re: Sequence allignment questions

Postby TToe » Sat Nov 24, 2012 4:18 pm

JackBean wrote:No, there are only few amino acids marked with :

Trp is also red (W) and is not small amino acid.

Are alanine and valine small and hydrophobic?
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Postby JackBean » Sat Nov 24, 2012 8:43 pm

Yes, they are all hydrophobic and could be considered as small.
http://www.biolib.cz/en/main/

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