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.GapMind_Oct2024.tar.gz -- tarball of source code and compiled rules for the GapMind for amino acid biosynthesis. The compiled rules are in tmp/path.aa/orgsDef_206_ngaps.tsv -- table of prototrophic bacteria and archaea and the number of gaps in each genome (considering only steps on the best path that lacked even a medium-confidence step in either the protein annotation or the 6-frame translation)known_auxo.tsv -- table of known auxotrophies for bacteriaorgsDef_206.tar.gz -- GapMind analysis of the 206 prototroph genomes (tmp/orgsDef) and for the 6-frame translation (tmp/orgsDef.6f)orgsAuxo_28.tar.gz -- GapMind analysis of the 28 auxotroph genomesngaps.image -- R image including the ngaps table, the gaps table (one row per genome x pathway), and the best table (one row for each step on the best path for each genome x pathway)aa3.R -- R code for generating the tables in the R image