After aligning a few proteins obtained from blast search I detected some sequences in the MSA which are exactly half of the alignment. It seems more likely that they are due to gene loss. Alternatively the protein might have evolved from the duplication of this gene. Is there any way to check it?
I think there are a lot of potential factors - if you go back and get the nucleotide sequence (for the longest version), you can try BLATing it to the appropriate reference genome to see if you get multiple, reasonable hits. Likewise, you can compare the nucleotide sequence to other genomes to see if the gene is conserved (for example, if you were studying human, perhaps see where the gene ends in chimp).
That said, I don't know if this is absolute evidence for a gene duplication. For example, I think there is a lot of shared homology between olfactory receptor genes. Although duplication events presumably took place at some point, the specific evolutionary history may be hard to derive (due to the fact that you aren't working with just one pair of duplicate genes).
Hi, I would say that in case the two halves look homologous (you can split the long gene in two and align the resulting sequences) than you can infer the existence of an ancestral half. In that case, both scenarios would be still possible (that is, either you would have had an ancestral duplication followed by a deletion or, alternatively, you would have had a duplication in a subclade of the gene family). Otherwise, I would simply reject the hypothesis of the existence of an ancestral half by Ockham's razor. Also, removing half of the protein does not necessary imply a complete loss of function: a physiological decoy activity, for example, could be still possible. I hope this helps.