I have a fasta file with a few hundreds of dissimilar protein sequences. Since they all come from homologous proteins, but outside of a conserved domain they all share, I was wondering if perhaps those dissimilarities in the regions outside of the conserved domain could have arisen by frameshift in their DNA sequences. I could probably find this out by making a bunch of tblastn queries, but I was wondering if there is an easier way to check for pairs of sequences which are dissimilar in their protein sequence, but would have a similar, but frame shifted, DNA sequence.
Frameshift mutations typically cause premature stop codons https://www.sciencedirect.com/topics/immunology-and-microbiology/frameshift-mutation
What you are seeing are likely in-frame Indels and missense variations.
You'll also see a lot of variations in the DNA that are not in the final protein due to "silent" changes in DNA.
I hope that helps!
Define your context: if your sequences derive from a homology search in a sequence database, they most likely are the result of evolution, which tends to build up protein to combine different functional domains, resulting in diverse sequences sharing specific domains.
Frameshift mutations generally either produce truncation due to premature stop codons, and/or result in a sticky, highly aggregation prone mess due to the inability of the new sequence to fold into a structure that shields most of the hydrophobic amino acids in its core. These aggregation-prone proteins are usually weeded out in the course of evolution, as aggregation impairs function.
For large divergent sequence stretches outside the conserved domain, the more likely explanation are splicing variants (in eucaryotic proteins) or genetic recombination, which in the evolution of the protein combined different functional domain into a single gene/peptide chain. You see this very frequently in proteins involved in signal transduction/regulation e.g. nuclear receptors, SH3-domain proteins, protein kinases etc. (see attached sample image for an example, taken from Article The Accessory Factor Nef Links HIV-1 to Tec/Btk Kinases in a...
)After clustering your sequences for similarity in the non-homologous regions, you can retrieve and compare the corresponding gene sequences of a few representative sequences from GenBank ( https://www.ncbi.nlm.nih.gov/genbank/about/ ) to confirm or rule out the hypothesis that frameshifts are responsible for the variations. Once this is ruled out, check out the UniProt ( https://www.uniprot.org ) record for the domain organisation of the protein and known splicing variants to distinguish between those two hypotheses.
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