What Does Each Element in a Protein Alignment Represent?

[megga124]

Need Help on school project quick!

I am trying to do this protein alignment assignment for my Biotech class and I'm having trouble interpreting the results. I used the Blast program at www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html[/URL] and have to answer the following questions: What are "Query" and "Sbjct"?, What do the letters of the middle row signify?, What do the "+" signs of the middle row signify?, What does "conservation" mean when referring to proteins?, and Why does actin's ability to bind many other proteins cause its sequence to be highly conserved?

I don't really have a clue as to the answers to these questions, so any help at all would be grately appreciated! The project is due tomorrow (Thursday) at 1pm.

Thanks.

 

[Another God]

Sounds like you should ahve asked earlier. I should know the answers to these questions... but I am not sure that I do. Let's see what I can offer:

Conservation means that the Amino Acid sequence hasn't been changed. Thanks to redundancy in the Genetic code (ie: More than one combination of the 3 base codon refers to a single amino acid) it is possible for there to be mutations in the DNA which don't change the Amino Acid sequence. Conservation of proteins doesn't have anything to do with this, it is only concerned with the fact that the A.A's are the same. It is 'Highly COnserved' because not all A.A's play functional roles, nor have any real influence on the function of the Protein, so those A.A's can change and it doesn't matter. As long as there is a function being served by a protein, and that function is achieved by a particular AA, a particular combination of AA's or a particular consequence of a class of AA's, those AA's would be conserved, or at least limited (ie: Sometimes the function may be 'To be hydrophobic' (so it can reside within the membrane for example), so any AA which has a hydrophoic side chain would be possible, but any AA which wasn't hydrophobic would be selected against.)

Actin would be conserved because for every other molecule that it binds to, the Amino Acids at the site of binding need to be the AA's that are there, or at least similar AA's...that is, they play a distinct functional role, and if something else was there, that role couldn't be fulfilled. If that role wasn't fulfilled, Actin wouldn't be doing its Job, and without actin, the animal in question would probably end up dying (Natural selection in process). So, wherever there is a functional part of actin, the Amino Acids in that area need to be conserved (to maintain its functionality), and since it binds to so many different molecules, there are probably many areas in the protein which play functional roles, so most of it is conserved.

As for the Blast Stufff... I can't helo you because I don't know to what Query sbject, middle row, and + you refer to. I assume you are talking about the screen after the search where the results are displayed, but I don't know what you searched for, and I can't figure out how to make up a search.

obviously sbjct = Subject

I would guess: Query = The code you entered ie: Your query which is it searching to align.
sbjct = The result of the search is that you sequence belong to organism/gene X. X = the subject.
no idea what middle row u are talking about, so can't help.

give me more clues, or give me the sequence and I might be able to help more.

 

[iansmith]

Originally posted by megga124
What do the letters of the middle row signify?, What do the "+" signs of the middle row signify

The middle tells you if the a.a. is conserve. "|" means that it is the same a.a. whereas a "+" means that the a.a. are equivalent and have more or less the same property. if its a space than the a.a. are not the same and are not equivalent.

 

[Another God]

Originally posted by iansmith
a "+" means that the a.a. are equivalent and have more or less the same property.

Cool. Now I know.

Thats what I was talking about too of course, when I mentioned the 'Hydrophobicity' etc in reference to AA's being confined to having the same properties.

Some amino acids are hydrophobic, some are hydrophilic (or perhaps it would be more accurate to say they have Hydrophobic/philic side chains), some are polar, some are not etc.