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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,doi:10.1093/nar/gkx289 pmid:28453782 pmcid:PMC5570227 fatcat:kr5tzd2rdjawvax6jjtrmpureq
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.
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: itsdoi:10.1093/nar/gkv1319 pmid:26615197 pmcid:PMC4702922 fatcat:u7svsg52wbcutnipkbzzzz6hom