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AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixat...

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Autores principales: Singh, Abhijeet, Müller, Bettina, Fuxelius, Hans-Henrik, Schnürer, Anna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908459/
https://www.ncbi.nlm.nih.gov/pubmed/31832668
http://dx.doi.org/10.1093/database/baz142
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author Singh, Abhijeet
Müller, Bettina
Fuxelius, Hans-Henrik
Schnürer, Anna
author_facet Singh, Abhijeet
Müller, Bettina
Fuxelius, Hans-Henrik
Schnürer, Anna
author_sort Singh, Abhijeet
collection PubMed
description Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.
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spelling pubmed-69084592019-12-17 AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences Singh, Abhijeet Müller, Bettina Fuxelius, Hans-Henrik Schnürer, Anna Database (Oxford) Database Tool Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se. Oxford University Press 2019-12-12 /pmc/articles/PMC6908459/ /pubmed/31832668 http://dx.doi.org/10.1093/database/baz142 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Tool
Singh, Abhijeet
Müller, Bettina
Fuxelius, Hans-Henrik
Schnürer, Anna
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title_full AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title_fullStr AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title_full_unstemmed AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title_short AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
title_sort acetobase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
topic Database Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908459/
https://www.ncbi.nlm.nih.gov/pubmed/31832668
http://dx.doi.org/10.1093/database/baz142
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