Comments (3)
Thank you for providing such a detailed report. It seems that through the cutting, the last 3di state changes from V to D. D and V have a negative substitution score (-3); therefore the last residue is not aligned. The first residue changed from A to D. However, this substitution score is positive (1) and is therefore aligned. I would recommend cutting the 3di sequences instead of truncating the PDB structure.
Here is the full query and target 3di sequence overlapped:
t_3di ----------------DEEALAEPPLCQVLVCVVCVVLVFFEDEPLVCVVFVLPLLVLLLVLLCDPPPPDPPDHHDALVSCCVNQVVGPYYDYPPRSLCVVRVCRNCVPHFYEHRDDDLVVRLVVCVVPLLVCLPDVVLVVCLVPDSGHSNSVSSSSCSSCCSQQVNDSDSVSNSVSSVVSVVVCVVPDDPLRYHYHGPPVDAQCSVCVSVVHDRDPDGRDDDPPPDPD-------------------------------------
q_3di DDQPLVPQPFFAPDAAAEEALAEPPLCQVLVCVVCVVLVFFEDEPLVCVVFVLNLLRLLLSLLCDPPPPDPPDHHDALGSCRSNQRVGNYYDYPPRSLCVVRVCRNRVNHFYEHRDDDLVVRLVVCVVPLLVCLPDVVLVVCLVPDSGHSNSVSSSSCSSCCSQQVNDSDSVSNSVSSVVSVVVCVVPDDPLRYHYHGPPVDAQCSVCVSSVHDRDPDGRDDDPPDDPVVVVVVVVVVVVVVSVVVVVVVVVVVVVVVVVVVVVVD
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Thanks for your reply.
I have the fasta file of the protein sequences and 3Di sequences ready.
How can I make a database starting from these 2 files?
@martin-steinegger
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I substituted each sequence of DB_ss with the sequence cut from the 3Di transformation of the whole structure, and it worked.
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