Genome and characteristics of <i>Arthrobacter globiformis</i> AZ cluster phage London

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ABSTRACT

London is a predicted temperate bacteriophage with siphovirus morphology infecting Arthrobacter globiformis NRRL strain B-2880. Sequencing of the genome revealed a length of 43,599 bp comprising 69 predicted open-reading frames and no tRNA genes. It is categorized as a cluster AZ1 phage along with closely related actinobacteriophages Elezi, Eraser, and Niobe.

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Most cited references 16

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Basic local alignment search tool.

Stephen F Altschul, Warren Gish, Webb Miller … (1990)

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

Dean Laslett, Björn Canbäck (2004)

A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.

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The HHpred interactive server for protein homology detection and structure prediction

Johannes Söding, Andreas Biegert, Andrei Lupas (2005)

HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in a user-friendly format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at .

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Author and article information

Contributors

Andrea R. Beyer:

ORCID: https://orcid.org/0000-0002-8773-348X

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review and editing

Hannah L. Hatke Hughes: Role: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draft

Jasmae S. Flowers: Role: Data curationRole: Formal analysisRole: Methodology

Jacquelin Bullock: Role: Data curationRole: Formal analysisRole: Methodology

Demesha T. Daniels: Role: Data curationRole: Formal analysisRole: Methodology

Makayla Drew: Role: Data curationRole: Formal analysisRole: Methodology

Queen Lee-Mayes: Role: Data curationRole: Formal analysisRole: Methodology

Brianna M. Marshall: Role: Data curationRole: Formal analysisRole: Methodology

Vivica Remson: Role: Data curationRole: Formal analysisRole: Methodology

Micaelah Thomas: Role: Data curationRole: Formal analysisRole: Methodology

Simon Roux: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, collection): November 2023

Publication date (Electronic, pub): 31 October 2023

Publication date PMC-release: 31 October 2023

Volume: 12

Issue: 11

Electronic Location Identifier: e00819-23

Affiliations

[1 ] Department of Biology, Virginia State University; , Petersburg, Virginia, USA

DOE Joint Genome Institute; , Berkeley, California, USA

Author notes

Address correspondence to Andrea R. Beyer, abeyer@ 123456vsu.edu

The authors declare no conflict of interest.

Author information

Andrea R. Beyer https://orcid.org/0000-0002-8773-348X

Article

Publisher ID: 00819-23 Publisher ID: MRA.00819-23

DOI: 10.1128/MRA.00819-23

PMC ID: 10652945

PubMed ID: 37906022

SO-VID: 7161cd3f-d1c5-4396-b9d2-0c9f37e41bb6

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 31 August 2023

Date accepted : 27 September 2023

Page count

supplementary-material: 0, authors: 10, Figures: 1, References: 16, Pages: 3, Words: 1393

Funding

Funded by: Virginia State University Biology Department;

Award Recipient : Andrea R. Beyer

Custom metadata

cover-date November 2023

Keywords: bacteriophages,arthrobacter,genomes

Data availability:

Keywords: bacteriophages, arthrobacter, genomes

Genome and characteristics of Arthrobacter globiformis AZ cluster phage London

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ABSTRACT

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Most cited references 16

Basic local alignment search tool.

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

The HHpred interactive server for protein homology detection and structure prediction

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