RT Journal Article
SR Electronic
T1 Improving the annotation of amino acid biosynthesis pathways: GapMind 2024
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.10.14.618325
DO 10.1101/2024.10.14.618325
A1 Price, Morgan N.
A1 Shiver, Anthony L.
A1 Day, Leslie A.
A1 Torres, Marta
A1 Lesea, Hira P.
A1 Owens, Trenton K.
A1 Deutschbauer, Adam M.
A1 Arkin, Adam P.
YR 2024
UL http://biorxiv.org/content/early/2024/10/14/2024.10.14.618325.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.