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what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to prove this many thanks

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At first it only means that these sequences share a similarity (sorry, but its not more). This can mean that they are smaller parts of a bigger protein which has been broken up, it can mean that you aligned different proteins which are only partly similiar and so on. To go over this, you have to provide some more information. And/or show an image of the alignment if possible. –  Chris Dec 16 '13 at 19:21
    
Just curious @user5182 are you currently doing a Bioinformatics MSc at ICL? –  hello_there_andy Dec 17 '13 at 1:39
    
@chris yes i think that one of the sequences is the "real sequences" and the other 3 are bits of it rearranged, i am working with toxins specifically if this helps, i tried to post the sequence earlier but unfortunately as it was not in frame people complained about how it was unclear. please let me know if there is anywhere in specific i should be looking. many thanks –  user5182 Dec 17 '13 at 23:50
    
@hello_there_andy no im doing an MSc in pharmacy my dissertation is on toxin diversification in a coral reef –  user5182 Dec 17 '13 at 23:52
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2 Answers 2

up vote 3 down vote accepted

Expanding on the comment by @Chris:

Short Answer

Overlapping sequences imply evolutionarily conserved regions, i.e. preserved by evolution through time due to theirs having some important function.

Long Answer

Assuming the sequences are homologous, overlapping regions of similarity reveal "evolutionarily conserved regions".

These are regions in the protein sequence that are shared by the ancestors through ancestral history due to that shared sequence bearing some important function at the phenotypic level. Evolution acts to "preserve" the sequence through natural selection if that function was important for fitness (see Negative selection).

E.g. Perhaps the shared sequence codes for an active site for an enzyme that is shared by all the ancestors you are using in the multiple sequence alignment - natural selection will then prevent changes to that sequence from occurring.

Look at this online lecture for finer detail.

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one more little piece of information: with proteins there are always short but good overlaps which in most cases indicates similarity of domains.. –  WYSIWYG Dec 26 '13 at 15:48
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it means those region are conserved if you compare two sequence and find similarity one example is the hox coding region which is conserved and it shows similarity

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Go on to add information on how one goes on proving this –  AndroidPenguin Dec 17 '13 at 14:59
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