GapMind: Automated Annotation of Amino Acid Biosynthesis

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 s. To avoid error-prone transitive annotations, GapMi...

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Autores principales:	Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	amino acid biosynthesis gene annotation high-throughput genetics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/5b04ad84b3da4cc58c6076cb78d08a2b
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spelling	oai:doaj.org-article:5b04ad84b3da4cc58c6076cb78d08a2b2021-12-02T18:44:35ZGapMind: Automated Annotation of Amino Acid Biosynthesis10.1128/mSystems.00291-202379-5077https://doaj.org/article/5b04ad84b3da4cc58c6076cb78d08a2b2020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00291-20https://doaj.org/toc/2379-5077ABSTRACT 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 s. 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 defined media without amino acids, 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. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements. IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.Morgan N. PriceAdam M. DeutschbauerAdam P. ArkinAmerican Society for Microbiologyarticleamino acid biosynthesisgene annotationhigh-throughput geneticsMicrobiologyQR1-502ENmSystems, Vol 5, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	amino acid biosynthesis gene annotation high-throughput genetics Microbiology QR1-502
spellingShingle	amino acid biosynthesis gene annotation high-throughput genetics Microbiology QR1-502 Morgan N. Price Adam M. Deutschbauer Adam P. Arkin GapMind: Automated Annotation of Amino Acid Biosynthesis
description	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 s. 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 defined media without amino acids, 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. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements. IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.
format	article
author	Morgan N. Price Adam M. Deutschbauer Adam P. Arkin
author_facet	Morgan N. Price Adam M. Deutschbauer Adam P. Arkin
author_sort	Morgan N. Price
title	GapMind: Automated Annotation of Amino Acid Biosynthesis
title_short	GapMind: Automated Annotation of Amino Acid Biosynthesis
title_full	GapMind: Automated Annotation of Amino Acid Biosynthesis
title_fullStr	GapMind: Automated Annotation of Amino Acid Biosynthesis
title_full_unstemmed	GapMind: Automated Annotation of Amino Acid Biosynthesis
title_sort	gapmind: automated annotation of amino acid biosynthesis
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/5b04ad84b3da4cc58c6076cb78d08a2b
work_keys_str_mv	AT morgannprice gapmindautomatedannotationofaminoacidbiosynthesis AT adammdeutschbauer gapmindautomatedannotationofaminoacidbiosynthesis AT adamparkin gapmindautomatedannotationofaminoacidbiosynthesis
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GapMind: Automated Annotation of Amino Acid Biosynthesis

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