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      Biosynthesis of Chlorinated Lactylates in Sphaerospermopsis sp. LEGE 00249

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          Abstract

          Lactylates are an important group of molecules in the food and cosmetic industries. A series of natural halogenated 1-lactylates, chlorosphaerolactylates ( 14), were recently reported from Sphaerospermopsis sp. LEGE 00249. Here, we identify the cly biosynthetic gene cluster, containing all the necessary functionalities for the biosynthesis of the natural lactylates, based on in silico analyses. Using a combination of stable isotope incorporation experiments and bioinformatic analysis, we propose that dodecanoic acid and pyruvate are the key building blocks in the biosynthesis of 14. We additionally report minor analogues of these molecules with varying alkyl chains. This work paves the way to accessing industrially relevant lactylates through pathway engineering.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            SWISS-MODEL: homology modelling of protein structures and complexes

            Abstract Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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              antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

              Abstract Secondary metabolites produced by bacteria and fungi are an important source of antimicrobials and other bioactive compounds. In recent years, genome mining has seen broad applications in identifying and characterizing new compounds as well as in metabolic engineering. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ (https://antismash.secondarymetabolites.org) has assisted researchers in this, both as a web server and a standalone tool. It has established itself as the most widely used tool for identifying and analysing biosynthetic gene clusters (BGCs) in bacterial and fungal genome sequences. Here, we present an entirely redesigned and extended version 5 of antiSMASH. antiSMASH 5 adds detection rules for clusters encoding the biosynthesis of acyl-amino acids, β-lactones, fungal RiPPs, RaS-RiPPs, polybrominated diphenyl ethers, C-nucleosides, PPY-like ketones and lipolanthines. For type II polyketide synthase-encoding gene clusters, antiSMASH 5 now offers more detailed predictions. The HTML output visualization has been redesigned to improve the navigation and visual representation of annotations. We have again improved the runtime of analysis steps, making it possible to deliver comprehensive annotations for bacterial genomes within a few minutes. A new output file in the standard JavaScript object notation (JSON) format is aimed at downstream tools that process antiSMASH results programmatically.
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                Author and article information

                Journal
                J Nat Prod
                J Nat Prod
                np
                jnprdf
                Journal of Natural Products
                American Chemical Society and American Society of Pharmacognosy
                0163-3864
                1520-6025
                14 January 2021
                26 February 2021
                : 84
                : 2
                : 278-286
                Affiliations
                []Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto , Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
                []Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto , Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
                Author notes
                [* ]Email: pleao@ 123456ciimar.up.pt . Phone: +351 223 401 800. Fax: +351 223 401 800.
                Article
                10.1021/acs.jnatprod.0c00950
                7923214
                33444023
                b6e88cf2-fdfc-48df-910e-e1f2485b2aa1
                © 2021 American Chemical Society and American Society of Pharmacognosy

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                : 28 August 2020
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                np0c00950

                Organic & Biomolecular chemistry
                Organic & Biomolecular chemistry

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