I am comparing multiple genomes via pan-genome analysis. I found that a gene cluster (of Histidine Kinase) have truncated CDS genes in some organisms. I am considering the truncations as one gene CDS is now divided into two or three CDS by the introduction of IS-sequence and nonsense mutations.
My question is:
Do all the truncations result in loss of function? (whether it is in mid or end?) because such protein will have the receiver part and the other will be phosphorylation part.
If not, then which website is suitable and easy to find out the functionality of such truncated CDS? I have tried a webserver to find the active sites/ligand binding (pocket sites) sites but still, I am not sure that is it sufficient or not?
Thanks in advance