I am having difficulties with an alignment on HHpred and was wondering if anyone had any answer to the following:

I am trying to align my protein (PDB 2VU9, a Botulinum Neurotoxin Type a) with one of the top hits generated from Vast.

I know that both my query protein and the other protein both have Glutamic acid as their active site. But, my protein has its active site on the 234th amino acid, whereas the other protein has the active site on its 230th amino acid.

So my question is: What would be the reasoning for which the top matches on Vast do not align at the active site with my protein, despite sharing the same amino acid at its active site?

Any response helps!


"HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD."

Söding et al. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue): W244–W248.


  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Apr 5, 2022 at 21:46


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