When doing pair-wise and multiple sequence alignment, in the end we end up with some bit of gaps. I really don't understand how the gaps come about. Could that be as a result of one of the sequences not having a given amino acid at a given position after alignment? Kindly explain with some clear examples if possible.
Yes, there are sequences missing some residues which creates gaps. There are parts of proteins that are less sensitive to residue subtractions or additions, and others that are more sensitive.
Think about a human hand. All human hands have the same basic functionality even though our fingers are not of the same length or shape. Neither are our nails. That means we can add or subtract to finger length without compromising the basic function. There is also a relative order of importance in which these changes can be made. While losing any part of any finger wouldn't be fun, it would be more detrimental to lose half a thumb or index finger than half a pinkie.
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