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SeMPI: a genome-based secondary metabolite prediction and identification web server

Paul F. Zierep, Natàlia Padilla, Dimitar G. Yonchev, Kiran K. Telukunta, Dennis Klementz, Stefan Günther
2017 Nucleic Acids Research  
The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters,
more » ... tructural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceuticalbioinformatics.de/sempi.
doi:10.1093/nar/gkx289 pmid:28453782 pmcid:PMC5570227 fatcat:kr5tzd2rdjawvax6jjtrmpureq

StreptomeDB 2.0—an extended resource of natural products produced by streptomycetes

Dennis Klementz, Kersten Döring, Xavier Lucas, Kiran K. Telukunta, Anika Erxleben, Denise Deubel, Astrid Erber, Irene Santillana, Oliver S. Thomas, Andreas Bechthold, Stefan Günther
2015 Nucleic Acids Research  
Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bacterial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, Strep-tomeDB was the first database focusing on compounds produced by streptomycetes. The new version presented herein represents a major step forward: its
more » ... content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA sequences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of compounds and scaffolds in an evolutionary context. Additionally, we have included predicted MS-and NMRspectra of thousands of compounds for assignment of experimental data. The database is freely accessible via http://www.pharmaceutical-bioinformatics. org/streptomedb.
doi:10.1093/nar/gkv1319 pmid:26615197 pmcid:PMC4702922 fatcat:u7svsg52wbcutnipkbzzzz6hom