Why do PFAM alignments contain 'X'?

Question

[traviata]

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?

Answer 1

[mbens]

The nomenclature for amino acids includes 'X' for 'unknown amino acid' (IUPAC). According to Uniprot, second amino acid of G1N5G7_MELGA is unknown.