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

Singh, Abhijeet and Müller, Bettina and Fuxelius, Hans-Henrik and Schnürer, Anna (2019). AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences. Database. 2019 , baz142 , 1-14
[Journal article]

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Official URL: https://acetobase.molbio.slu.se/

Abstract

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.

Authors/Creators:Singh, Abhijeet and Müller, Bettina and Fuxelius, Hans-Henrik and Schnürer, Anna
Title:AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
Year of publishing :2019
Volume:2019
Article number:baz142
Number of Pages:14
Publisher:Oxford University Press
ISSN:1758-0463
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Keywords:Acetogenic bacteria, formyltetrahydrofolate synthetase (FTHFS), FTHFS sequences, database, repository
URN:NBN:urn:nbn:se:slu:epsilon-p-105822
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105822
Additional ID:
Type of IDID
DOI10.1093/database/baz142
ID Code:17147
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Molecular Sciences
Deposited By: SLUpub Connector
Deposited On:29 Jun 2020 07:04
Metadata Last Modified:29 Jun 2020 07:04

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