A call for a more comprehensive SARS-CoV-2 sequence database for Brazil

Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy

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FarRRegulates the farAB-Encoded Efflux Pump of Neisseriagonorrhoeae via an MtrR RegulatoryMechanism

Journal of Bacteriology ◽

10.1128/jb.185.24.7145-7152.2003 ◽

2003 ◽

Vol 185 (24) ◽

pp. 7145-7152 ◽

Cited By ~ 53

Author(s):

E.-H. Lee ◽

C. Rouquette-Loughlin ◽

J. P. Folster ◽

W. M. Shafer

Keyword(s):

Regulatory Mechanism ◽

Efflux Pump ◽

Regulatory Protein ◽

Transcriptional Repressors ◽

Sequence Database ◽

Mobility Shift ◽

Pump System ◽

Regulatory Cascade ◽

Genome Sequence Database ◽

Gel Mobility Shift

ABSTRACT The farAB operon of Neisseria gonorrhoeae encodes an efflux pump which mediates gonococcal resistance to antibacterial fatty acids. It was previously observed that expression of the farAB operon was positively regulated by MtrR, which is a repressor of the mtrCDE-encoded efflux pump system (E.-H. Lee and W. M. Shafer, Mol. Microbiol. 33:839-845, 1999). This regulation was believed to be indirect since MtrR did not bind to the farAB promoter. In this study, computer analysis of the gonococcal genome sequence database, lacZ reporter fusions, and gel mobility shift assays were used to elucidate the regulatory mechanism by which expression of the farAB operon is modulated by MtrR in gonococci. We identified a regulatory protein belonging to the MarR family of transcriptional repressors and found that it negatively controls expression of farAB by directly binding to the farAB promoter. We designated this regulator FarR to signify its role in regulating the farAB operon. We found that MtrR binds to the farR promoter, thereby repressing farR expression. Hence, MtrR regulates farAB in a positive fashion by modulating farR expression. This MtrR regulatory cascade seems to play an important role in adjusting levels of the FarAB and MtrCDE efflux pumps to prevent their excess expression in gonococci.

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The EMBL Nucleotide Sequence Database

Nucleic Acids Research ◽

10.1093/nar/gkh120 ◽

2004 ◽

Vol 32 (90001) ◽

pp. 27D-30 ◽

Cited By ~ 85

Author(s):

T. Kulikova

Keyword(s):

Nucleotide Sequence ◽

Sequence Database ◽

Embl Nucleotide Sequence Database ◽

Nucleotide Sequence Database

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FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification

Plant Disease ◽

10.1094/pdis-09-21-2105-sr ◽

2021 ◽

Author(s):

Terry Torres-Cruz ◽

Briana Whitaker ◽

Robert Proctor ◽

Kirk Broders ◽

Imane Laraba ◽

...

Keyword(s):

Sequence Data ◽

Safety Concern ◽

Fusarium Species ◽

Elongation Factor ◽

Sequence Database ◽

Accurate Identification ◽

Dna Sequence Data ◽

Species Complexes ◽

Marker Loci ◽

Feed Safety

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680 bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely-available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

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