SHARK enables homology assessment in unalignable anddisordered sequences
Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite comprising [~]21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment in assessing homology in unalignable sequences, and correctly identified dissimilar IDRs capable of functional rescue in IDR-replacement experiments reported in the literature. SHARK-dive not only predicts functionally similar IDRs, but also identifies cryptic sequence properties and motifs that drive remote homology, thereby facilitating systematic analysis and functional annotation of the unalignable protein universe.