Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation

Detalhes bibliográficos
Autor(a) principal: Silveira, Melise Chaves
Data de Publicação: 2018
Outros Autores: Silva, Rangeline Azevedo da, Mota, Fábio Faria da, Catanho, Marcos, Jardim, Rodrigo, Guimarães, Ana Carolina R., Miranda, Antonio B. de
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/31608
Resumo: Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.
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spelling Silveira, Melise ChavesSilva, Rangeline Azevedo daMota, Fábio Faria daCatanho, MarcosJardim, RodrigoGuimarães, Ana Carolina R.Miranda, Antonio B. de2019-02-13T16:27:43Z2019-02-13T16:27:43Z2018SILVEIRA, Melise Chaves; et al. Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. Evolutionary Bioinformatics, v.14, p.1-11, 2018.1176-9343https://www.arca.fiocruz.br/handle/icict/3160810.1177/1169343118797351engSAGE Publicationsβ-lactamaseClasseSub-classeIdentificaçãoSemelhança de sequênciaβ-lactamaseClassSubclassIdentificationSequence similaritySystematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotationinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify βlactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology. The profiles HMM were improved for their specificity and sensitivity and then applied to fully assembled genomes. Five hierarchical classification levels are described, and a new class of β-lactamases with fused domains is proposed. Our profiles HMM provide a better annotation of β-lactamases, with classes and subclasses defined by objective criteria such as sequence similarity. This classification offers a solid base to the elaboration of studies on the diversity, dispersion, prevalence, and evolution of the different classes and subclasses of this critical enzymatic activity.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/31608/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALmelisechaves_rodrigojardim_etal_IOC_2018.pdfmelisechaves_rodrigojardim_etal_IOC_2018.pdfapplication/pdf1138253https://www.arca.fiocruz.br/bitstream/icict/31608/2/melisechaves_rodrigojardim_etal_IOC_2018.pdf92acf4cf6d1514d9e766eb559a51684dMD52TEXTmelisechaves_rodrigojardim_etal_IOC_2018.pdf.txtmelisechaves_rodrigojardim_etal_IOC_2018.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
title Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
spellingShingle Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
Silveira, Melise Chaves
β-lactamase
Classe
Sub-classe
Identificação
Semelhança de sequência
β-lactamase
Class
Subclass
Identification
Sequence similarity
title_short Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
title_full Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
title_fullStr Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
title_full_unstemmed Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
title_sort Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation
author Silveira, Melise Chaves
author_facet Silveira, Melise Chaves
Silva, Rangeline Azevedo da
Mota, Fábio Faria da
Catanho, Marcos
Jardim, Rodrigo
Guimarães, Ana Carolina R.
Miranda, Antonio B. de
author_role author
author2 Silva, Rangeline Azevedo da
Mota, Fábio Faria da
Catanho, Marcos
Jardim, Rodrigo
Guimarães, Ana Carolina R.
Miranda, Antonio B. de
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Silveira, Melise Chaves
Silva, Rangeline Azevedo da
Mota, Fábio Faria da
Catanho, Marcos
Jardim, Rodrigo
Guimarães, Ana Carolina R.
Miranda, Antonio B. de
dc.subject.other.pt_BR.fl_str_mv β-lactamase
Classe
Sub-classe
Identificação
Semelhança de sequência
topic β-lactamase
Classe
Sub-classe
Identificação
Semelhança de sequência
β-lactamase
Class
Subclass
Identification
Sequence similarity
dc.subject.en.pt_BR.fl_str_mv β-lactamase
Class
Subclass
Identification
Sequence similarity
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.
publishDate 2018
dc.date.issued.fl_str_mv 2018
dc.date.accessioned.fl_str_mv 2019-02-13T16:27:43Z
dc.date.available.fl_str_mv 2019-02-13T16:27:43Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv SILVEIRA, Melise Chaves; et al. Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. Evolutionary Bioinformatics, v.14, p.1-11, 2018.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/31608
dc.identifier.issn.pt_BR.fl_str_mv 1176-9343
dc.identifier.doi.none.fl_str_mv 10.1177/1169343118797351
identifier_str_mv SILVEIRA, Melise Chaves; et al. Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. Evolutionary Bioinformatics, v.14, p.1-11, 2018.
1176-9343
10.1177/1169343118797351
url https://www.arca.fiocruz.br/handle/icict/31608
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv SAGE Publications
publisher.none.fl_str_mv SAGE Publications
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/31608/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/31608/2/melisechaves_rodrigojardim_etal_IOC_2018.pdf
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