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GapMind: Automated annotation of amino acid biosynthesis

Morgan Price, Adam M. Deutschbauer, Adam P. Arkin
doi: https://doi.org/10.1101/741918
Morgan Price
1Lawrence Berkeley Lab
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  • For correspondence: morgannprice@yahoo.com
Adam M. Deutschbauer
2Lawrence Berkeley National Laboratory
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Adam P. Arkin
3University of California
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Abstract

GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl/gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. If a potential gap in the genome of interest is also a gap in a related microbe that can grow in minimal media, GapMind marks the gap as “known.”

Footnotes

  • https://doi.org/10.6084/m9.figshare.9693689.v1

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 21, 2019.
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GapMind: Automated annotation of amino acid biosynthesis
Morgan Price, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 741918; doi: https://doi.org/10.1101/741918
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GapMind: Automated annotation of amino acid biosynthesis
Morgan Price, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 741918; doi: https://doi.org/10.1101/741918

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