Evolutionarily Conserved Fragments reveal modular architecture and expand functional coverage in bacteriophage proteins

Evolutionarily Conserved Fragments (ECFs) built from 5,396 RefSeq bacteriophage genomes annotate 50% of phage representative proteins, expanding functional coverage beyond ECOD and Pfam.

• Why it matters: Classical domains only partially capture phage protein evolutionary modules, leaving conserved sequence units and functional organization underdefined.
• What they did: Using large-scale HMM-HMM comparisons, the study constructed 13,035 ECFs grouped into 3,167 families without predefined domain boundaries, then compared them to ECOD and Pfam and tested replication in independent metagenomic data.
• The result: ECFs overlapped ECOD/Pfam yet included nested, multi-scale modules and fragments absent from both resources, enabling functional associations for 23,925 protein families lacking detectable Pfam or ECOD domains.

AI summary of the abstract · may contain errors · not medical advice · read the paper.