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GapMind for Carbon Sources: Automated annotations of catabolic pathways

View ORCID ProfileMorgan N. Price, View ORCID ProfileAdam M. Deutschbauer, View ORCID ProfileAdam P. Arkin
doi: https://doi.org/10.1101/2021.11.02.466981
Morgan N. Price
Lawrence Berkeley National Laboratory, Berkeley CA, USA
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  • For correspondence: morgannprice@yahoo.com
Adam M. Deutschbauer
Lawrence Berkeley National Laboratory, Berkeley CA, USA
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Adam P. Arkin
Lawrence Berkeley National Laboratory, Berkeley CA, USA
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Abstract

GapMind for carbon sources is an automated tool for annotating catabolic pathways in bacterial and archaeal genomes. GapMind includes 62 compounds and identifies potential transporters and enzymes by their similarity to experimentally-characterized proteins. To improve GapMind’s coverage, we used high-throughput genetic data from 29 bacteria and systematically examined the gaps. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.6084/m9.figshare.16913530.v1

  • https://doi.org/10.6084/m9.figshare.16906993.v1

Copyright 
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 November 02, 2021.
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GapMind for Carbon Sources: Automated annotations of catabolic pathways
Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 2021.11.02.466981; doi: https://doi.org/10.1101/2021.11.02.466981
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GapMind for Carbon Sources: Automated annotations of catabolic pathways
Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
bioRxiv 2021.11.02.466981; doi: https://doi.org/10.1101/2021.11.02.466981

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