Hi It depends on the software you’re using for the alignment. Some does a “better” job than others (e.g. I’d expect a strictly sequence based alignment like Blast to do a “good” job, but I’ve seen occasional misalignments [that are obvious to the eye!] with some of the HMM-based software like HHAlign - I have no idea why this might happen because the group that produces HH-suite doesn’t appear to be active enough to address issues on their github; I know that many of the authors are no longer working on the project).
So, my follow-up question would be “which software are you using for this?”. Harry > On 11 Feb 2026, at 05:27, Thripthi Shenoy > <[email protected]> wrote: > > Greetings to all, > > I am currently working on understanding the structure-based sequence > alignment of the crystal structure of NOXA BH3 domain and the complete > protein structure obtained from AlphaFold. According to my understanding, the > BH3 binding domain from the crystal structure should get aligned with the BH3 > domain in the entire protein structure. However, this is not the case and the > identical amino acids of the BH3 domains are not getting aligned. I would be > grateful to know if this is a correct approach to proceed with the structure > based protein alignment. > > Thanking you in advance > With regards, > Thripthi S. > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
