The Potyviridae family is a major group of plant viruses including nearly 200 species distributed in seven genera [E1]. The viral RNA genome is translated into large polyproteins that are further processed into functional peptides by virus-encoded endopeptidases. Amongst these are P1 proteins, chymotrypsin-like serine proteases located at the beginning of viral polyproteins. Generally present in one copy, some potyvirids code for two P1 proteins with different proteolytic specificities. P1 proteins can be classified as Type A or Type B on the basis, amongst other things, of their dependence or not on a host factor to develop their protease activity. The protease activity of Type B proteins, such as P1b from Cucumber vein yellowing virus (CVYV), has no host factor requirements. Type A proteins, which include PPV P1, depend on as yet unknown host factor(s) for processing. Of the mature proteins encoded by the potyviral genomes, P1 presents the greatest variability in length and in amino acid sequence. Despite this significant variability, the P1 C-terminal region is relatively well conserved. It harbours a serine protease domain responsible for cis-cleavage at its own C-terminal end, and thus P1 self-releases from the polyprotein. The hypervariable N-terminal region that precedes the protease domain is predicted as intrinsically disordered and behaves as a negative regulator of P1 proteolytic activity in Type A P1s [1,2,3,4,5].

The potyviral P1 protease domain bears the catalytic triad formed by histidine, aspartic acid and serine that is characteristic of the serine protease family. It constitutes the peptidase family C30 that belongs to subclan S of clan PA [3,4,E2].

The profile we developed covers the entire potyviral P1 protease domain.