Secondary metabolite biosynthetic databases | Chemical informatics data analysis
Production of secondary metabolites is one of the industrially important features of bacteria, such as actinomycetes and myxobacteria. Various secondary metabolites produced by bacteria have been developed as antibiotics, antitumor drugs and immunosuppressive drugs. Therefore, bacterial secondary metabolites have an important role in the development of novel medicines. Secondary metabolites usually comprise various chemical moieties, such as polyketide backbones, amino acid derivatives and sugars. Many enzymes are involved in the synthesis of secondary metabolites. Polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS), which catalyze the elongation of polyketides and synthesis of oligopeptides, respectively, are the major enzymes of secondary metabolite synthesis. Enzymes responsible for the synthesis of other constitutive compounds, such as sugars, are often encoded by genes adjacent to PKS and NRPS genes. Through further tailoring events, such as glycosylation, alkylation and oxidation, structurally diverse and complex metabolites are finally synthesized. In addition, the production and transportation of secondary metabolites are strictly regulated by transcriptional regulators and transporters.
Represents a bioinformatics resource concerning deciphering chemical structures of ribosomally synthesized and post-translationally modified peptides (RiPPs) through genome mining. The RiPPMiner supplies information regarding modification system, leader and core sequence, cross-links and gene cluster, precursor sequence and modified residues. This tool also contains a web app function allowing the distinction of RiPP precursors from other small proteins and the classification of precursors into 12 sub-classes of RiPPs. It can spot correct cross-link pattern in a core peptide into a large number of combinatorial possibilities.
Provides a collection of state-of the art annotated biosynthetic gene cluster (BGC) data. antiSMASH-DB enables researchers to perform cross-genome analyses by supplying complex queries on the data sets. It offers summary statistics about secondary metabolite types and taxa. This database can assist users in secondary metabolite genome mining projects. It can be useful for high quality secondary metabolite cluster predictions.
A database of microbial polyketide and non-ribosomal peptide gene clusters. ClusterMine360 takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files.
Offers experimentally verified and predicted biosynthetic gene clusters (BCs). IMG-ABC database contains more than 730000 BCs in 40034 isolate microbial genomes and more than 310000 BCs in 2416 metagenomes. BCs are predicted and annotated across all microbial isolate genomes and a set of metagenomes using a combination of Clusterfinder and antiSMASH. A set of experimentally verified BCs and their associated secondary metabolites are collected from the NCBI and imported into the database. IMG-ABC includes additional tools which enable fast exploration and analysis of BCs. These tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.
A literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.
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