A bioinformatics classifier and database for heme-copper oxygen reductases.

<h4>Background</h4>Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The n...

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Autores principales:	Filipa L Sousa, Renato J Alves, José B Pereira-Leal, Miguel Teixeira, Manuela M Pereira
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9df2416dbc5a481c96087da26c9fb21a
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spelling	oai:doaj.org-article:9df2416dbc5a481c96087da26c9fb21a2021-11-18T06:54:44ZA bioinformatics classifier and database for heme-copper oxygen reductases.1932-620310.1371/journal.pone.0019117https://doaj.org/article/9df2416dbc5a481c96087da26c9fb21a2011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21559461/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged.<h4>Methodology</h4>We reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes.<h4>Conclusions</h4>We concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco).Filipa L SousaRenato J AlvesJosé B Pereira-LealMiguel TeixeiraManuela M PereiraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e19117 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Filipa L Sousa Renato J Alves José B Pereira-Leal Miguel Teixeira Manuela M Pereira A bioinformatics classifier and database for heme-copper oxygen reductases.
description	<h4>Background</h4>Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged.<h4>Methodology</h4>We reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes.<h4>Conclusions</h4>We concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco).
format	article
author	Filipa L Sousa Renato J Alves José B Pereira-Leal Miguel Teixeira Manuela M Pereira
author_facet	Filipa L Sousa Renato J Alves José B Pereira-Leal Miguel Teixeira Manuela M Pereira
author_sort	Filipa L Sousa
title	A bioinformatics classifier and database for heme-copper oxygen reductases.
title_short	A bioinformatics classifier and database for heme-copper oxygen reductases.
title_full	A bioinformatics classifier and database for heme-copper oxygen reductases.
title_fullStr	A bioinformatics classifier and database for heme-copper oxygen reductases.
title_full_unstemmed	A bioinformatics classifier and database for heme-copper oxygen reductases.
title_sort	bioinformatics classifier and database for heme-copper oxygen reductases.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/9df2416dbc5a481c96087da26c9fb21a
work_keys_str_mv	AT filipalsousa abioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT renatojalves abioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT josebpereiraleal abioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT miguelteixeira abioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT manuelampereira abioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT filipalsousa bioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT renatojalves bioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT josebpereiraleal bioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT miguelteixeira bioinformaticsclassifieranddatabaseforhemecopperoxygenreductases AT manuelampereira bioinformaticsclassifieranddatabaseforhemecopperoxygenreductases
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A bioinformatics classifier and database for heme-copper oxygen reductases.

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