Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH

[1]  Kai Blin,et al.  The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters , 2018, Nucleic Acids Res..

[2]  J. Imhoff,et al.  Lysoquinone-TH1, a New Polyphenolic Tridecaketide Produced by Expressing the Lysolipin Minimal PKS II in Streptomyces albus , 2018, Antibiotics.

[3]  Michael A. Skinnider,et al.  PRISM 3: expanded prediction of natural product chemical structures from microbial genomes , 2017, Nucleic Acids Res..

[4]  Kai Blin,et al.  antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification , 2017, Nucleic Acids Res..

[5]  G. Tang,et al.  New insights into bacterial type II polyketide biosynthesis , 2017, F1000Research.

[6]  I-Min A. Chen,et al.  IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes , 2016, Nucleic Acids Res..

[7]  Renzo Kottmann,et al.  The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters , 2016, Nucleic Acids Res..

[8]  Tilmann Weber,et al.  The evolution of genome mining in microbes - a review. , 2016, Natural product reports.

[9]  T. Kawasaki,et al.  Cloning and identification of saprolmycin biosynthetic gene cluster from Streptomyces sp. TK08046 , 2016, Bioscience, biotechnology, and biochemistry.

[10]  D. Newman,et al.  Natural Products as Sources of New Drugs from 1981 to 2014. , 2016, Journal of natural products.

[11]  Richard H. Baltz,et al.  Natural product discovery: past, present, and future , 2016, Journal of Industrial Microbiology & Biotechnology.

[12]  Michael A. Skinnider,et al.  Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM) , 2015, Nucleic acids research.

[13]  Michael A Fischbach,et al.  Computational approaches to natural product discovery. , 2015, Nature chemical biology.

[14]  Carla S. Jones,et al.  Minimum Information about a Biosynthetic Gene cluster. , 2015, Nature chemical biology.

[15]  Kai Blin,et al.  antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters , 2015, Nucleic Acids Res..

[16]  Hai-Xue Pan,et al.  Biosynthesis of trioxacarcin revealing a different starter unit and complex tailoring steps for type II polyketide synthase† †Electronic supplementary information (ESI) available: The experimental procedures, strains, plasmids and PCR primers, and compound characterization. See DOI: 10.1039/c5sc0011 , 2015, Chemical science.

[17]  H. Petković,et al.  Identification of the chelocardin biosynthetic gene cluster from Amycolatopsis sulphurea: a platform for producing novel tetracycline antibiotics. , 2013, Microbiology.

[18]  Zixin Deng,et al.  Deciphering and engineering of the final step halogenase for improved chlortetracycline biosynthesis in industrial Streptomyces aureofaciens. , 2013, Metabolic engineering.

[19]  Kai Blin,et al.  antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..

[20]  Nobuyuki Fujita,et al.  DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters , 2012, Nucleic Acids Res..

[21]  Gwan-Su Yi,et al.  PKMiner: a database for exploring type II polyketide synthases , 2012, BMC Microbiology.

[22]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[23]  S. Brady,et al.  Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites , 2011, Proceedings of the National Academy of Sciences.

[24]  Kai Blin,et al.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..

[25]  T. Weber,et al.  Isolation of the lysolipin gene cluster of Streptomyces tendae Tü 4042. , 2010, Gene.

[26]  Yi Tang,et al.  Oxytetracycline Biosynthesis* , 2010, The Journal of Biological Chemistry.

[27]  Yanran Li,et al.  Cyclization of aromatic polyketides from bacteria and fungi. , 2010, Natural product reports.

[28]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[29]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[30]  Yi Tang,et al.  Decoding and engineering tetracycline biosynthesis. , 2009, Metabolic engineering.

[31]  Jeroen S. Dickschat,et al.  A Type II polyketide synthase from the gram-negative Bacterium Stigmatella aurantiaca is involved in Aurachin alkaloid biosynthesis. , 2007, Angewandte Chemie.

[32]  Andriy Luzhetskyy,et al.  Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. , 2007, Natural product reports.

[33]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[34]  Shiou-Chuan Tsai,et al.  Polyketide chain length control by chain length factor. , 2003, Journal of the American Chemical Society.

[35]  C. Walsh,et al.  The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases. , 1999, Chemistry & biology.

[36]  B K Shoichet,et al.  Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. , 1999, Chemistry & biology.

[37]  D. Hopwood,et al.  Nucleotide sequence and deduced functions of a set of cotranscribed genes of Streptomyces coelicolor A3(2) including the polyketide synthase for the antibiotic actinorhodin. , 1992, The Journal of biological chemistry.

[38]  C. Hutchinson,et al.  Cloning and expression of daunorubicin biosynthesis genes from Streptomyces peucetius and S. peucetius subsp. caesius , 1990, Journal of bacteriology.