I'm working with the PFAM family RNA_pol_Rpb2_1 (PF04563). I've discovered that some of the sequences in the full alignment I downloaded, including
>G1N5G7_MELGA/1-331, contain the character
X even though
X is not a valid protein character.
Why is this? Is it related to some sequences being low-quality or are some sequences using an entirely different alphabet?