Predicting metabolic pathways of plant enzymes without using sequence similarity: Models from machine learning

The Plant Genome
Rodrigo de Oliveira Almeida, Guilherme Targino Valente

Abstract

Most of the bioinformatics tools for enzyme annotation focus on enzymatic function assignments. Sequence similarity to well-characterized enzymes is often used for functional annotation and to assign metabolic pathways. However, these approaches are not feasible for all sequences leading to inaccurate annotations or lack of metabolic pathway information. Here we present the mApLe (metabolic pathway predictor of plant enzymes), a high-performance machine learning-based tool with models to label the metabolic pathway of enzymes rather than specifying enzymes' reactions. The mApLe uses molecular descriptors of the enzyme sequences to perform predictions without considering sequence similarities with reference sequences. Hence, mApLe can classify a diversity of enzymes, even the ones without any homolog or with incomplete EC numbers. This tool can be used to improve the quality of genomic annotation of plants or to narrow down the number of candidate genes for metabolic engineering researches. The mApLe tool is available online, and the GUI can be locally installed.

References

Dec 11, 1999·Nucleic Acids Research·A Bairoch
Feb 24, 2001·Genome Biology·J A Gerlt, P C Babbitt
Aug 4, 2001·Trends in Genetics : TIG·D Devos, A Valencia
Jun 8, 2002·Journal of Molecular Biology·Burkhard Rost
Dec 20, 2002·Bioinformatics·Walter R GilksChristos A Ouzounis
Mar 6, 2003·Genome Research·José Manuel Peregrin-AlvarezChristos A Ouzounis
Nov 7, 2003·Nucleic Acids Research·Clotilde Claudel-RenardDaniel Kahn
May 18, 2005·Journal of Molecular Biology·Shiri FreilichJanet M Thornton
Jun 15, 2006·Briefings in Bioinformatics·Iddo Friedberg
Jul 18, 2006·Nucleic Acids Research·Luca PiredduRussell Greiner
Aug 29, 2006·Current Opinion in Chemical Biology·Margaret E GlasnerPatricia C Babbitt
Dec 15, 2006·BMC Genomics·Adrian K ArakakiJeffrey Skolnick
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Aug 28, 2007·Bioinformatics·Yvan SaeysPedro Larrañaga
Mar 8, 2008·BMC Bioinformatics·Kwangmin Choi, Sun Kim
Apr 14, 2009·BMC Bioinformatics·Adrian K ArakakiJeffrey Skolnick
Jul 22, 2009·Nature Chemical Biology·Nicholas FurnhamJanet M Thornton
Feb 24, 2010·BMC Genomics·Kingsley J L LiewPreiser R Peter
May 1, 2010·Microbiology·Maria S Poptsova, J Peter Gogarten
Sep 3, 2011·Microbial Biotechnology·Praveen Kaul, Yasuhisa Asano
Apr 19, 2012·Nature Reviews. Genetics·Mark Yandell, Daniel Ence
Aug 28, 2012·Bioinformatics·Narendra Kumar, Jeffrey Skolnick
Apr 20, 2014·Nature Chemical Biology·Jens NielsenBernhard Palsson
Jan 1, 2012·Biology·Manuel Gonzalo ClarosNoé Fernández-Pozo
Jul 28, 2017·PloS One·Christian-Alexander DudekDietmar Schomburg
Oct 25, 2017·Synthetic and Systems Biotechnology·Hironori TaniguchiKohsuke Honda
May 8, 2018·Applications in Plant Sciences·Fay-Wei Li, Alex Harkess
Jun 20, 2019·International Journal of Molecular Sciences·Ruibo GaoJunlan Nie
Jun 22, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jae Yong RyuSang Yup Lee

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Citations

Aug 20, 2021·Frontiers in Bioengineering and Biotechnology·Kunal DuttaIbrahim Khalifa

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