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      Complete Genome Sequence of Citrobacter freundii Myophage Maroon

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          Abstract

          Citrobacter freundii is a nosocomial opportunistic pathogen that can cause urinary and bloodstream infections. Phage therapies against C. freundii may prove useful in treating infections caused by this ubiquitous bacterium. Here, we report the complete genome of a T4-like myophage, Maroon, that infects C. freundii.

          ABSTRACT

          Citrobacter freundii is a nosocomial opportunistic pathogen that can cause urinary and bloodstream infections. Phage therapies against C. freundii may prove useful in treating infections caused by this ubiquitous bacterium. Here, we report the complete genome of a T4-like myophage, Maroon, that infects C. freundii.

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          Prediction of lipoprotein signal peptides in Gram-negative bacteria.

          Agnieszka S Juncker, Hanni Willenbrock, Gunnar von Heijne … (2003)
          A method to predict lipoprotein signal peptides in Gram-negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII-cleaved proteins), SPaseI-cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI-cleaved, cytoplasmic, and transmembrane proteins. The results obtained were significantly better than those of previously developed methods. Even though Gram-positive lipoprotein signal peptides differ from Gram-negatives, the HMM was able to identify 92.9% of the lipoproteins included in a Gram-positive test set. A genome search was carried out for 12 Gram-negative genomes and one Gram-positive genome. The results for Escherichia coli K12 were compared with new experimental data, and the predictions by the HMM agree well with the experimentally verified lipoproteins. A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/.
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            Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

            Peter Cock, Björn Grüning, Konrad H. Paszkiewicz … (2013)
            The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).
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              Citrobacter freundii bacteremia: Risk factors of mortality and prevalence of resistance genes

              Alice Wu, Nai-Yu Wang, Li-Hsiang Liu … (2018)
              Article 0 comments Cited 55 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Catherine Putonti: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                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): 24 October 2019
                Publication date Collection: October 2019
                Volume: 8
                Issue: 43
                Electronic Location Identifier: e01145-19
                Affiliations
                [a ]Center for Phage Technology, Texas A&M University, College Station, Texas, USA
                Loyola University Chicago
                Author notes
                Address correspondence to Mei Liu, meiliu@ 123456tamu.edu .

                Citation McDermott JR, Shao Q, O’Leary C, Kongari R, Liu M. 2019. Complete genome sequence of Citrobacter freundii myophage Maroon. Microbiol Resour Announc 8:e01145-19. https://doi.org/10.1128/MRA.01145-19.

                Author information
                https://orcid.org/0000-0002-6842-6214
                Article
                Publisher ID: MRA01145-19
                DOI: 10.1128/MRA.01145-19
                PMC ID: 6813397
                PubMed ID: 31649085
                SO-VID: 5b51c3ae-ee78-49fe-88ca-096d45ffb3ad
                Copyright © Copyright © 2019 McDermott et al.
                License:

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

                History
                Date received : 13 September 2019
                Date accepted : 5 October 2019
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 18, Pages: 2, Words: 1423
                Funding
                Funded by: National Science Foundation (NSF), https://doi.org/10.13039/100000001;
                Award ID: EF-0949351
                Award ID: DBI-1565146
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date October 2019

                Data availability:

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