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I want to model a protein using only one template,because i have obtained significant sequence similarity with our query sequence. But i am having a different question. In the template there are three residues between two cosicutive structurally conserved region, where in the query sequence the gaps are inserted due to proper alignment. I am assigning coordinates to the structurally conserved region, thus there is a gap in my model protein. how can i solve this problem? can any one help me?
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