Improving the annotation of amino acid biosynthesis pathways: GapMind 2024

GapMind is an automated web-based tool for annotating amino acid biosynthesis pathways in bacterial and archaeal genomes. We updated GapMind to include recently identified enzymes, including new enzymes that we identified by using high-throughput genetics and comparative genomics. Across 206 prokaryotes that have high-quality genomes and are reported to grow in minimal media, the average number of unexplained missing steps or gaps dropped from 1.4 per genome to 0.8 per genome. The majority of the remaining gaps involve the gain or loss of phosphate groups.