open all open/close all

DoBISCUIT (Database of BIoSynthesis cluster CUrated and InTegrated)

Secondary metabolites produced by actinomycetes are important as lead-compounds and/or candidates for drug development. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) have been attracting much attention for their roles in constructing complex compounds. Secondary metabolite biosynthesis gene clusters are often used in biotechnological applications such as heterologous expression and combinatorial biosynthesis. Many scientific papers are published describing biosynthesis gene clusters every year, but information about a particular gene cluster is often dispersed in many references and is not described in a comprehensive manner.

We constructed a literature-based database about known PKS and NRPS gene clusters. The database consists of biosynthesis cluster information, search menu, retrieve information menu and KS/A domain sequence menu. Our database enables easy access to a comprehensive information related to biosynthesis clusters and browsing standardized up-to-date gene descriptions. Our database will thus serve as a useful reference for the analysis of secondary metabolites. biosynthetic gene clusters.

open this section0.Interface overview

open this section1.Top page

open this section2.Compound list

close this section3.Cluster information

It shows integrated information about the biosynthesis cluster. This page has 6 sections;
Compound, Origin, Genomic map, PKS/NRPS modules, References and Data download.
3.1. Compound section
Compound section displays information about the compound produced. Chemical structure, activities and various attributes such as starter unit, sugar unit are displayed.
3.2. Origin section
Origin section displays the strain which produces the compound. You can follow the hyperlink and access the strain of NBRC. The original INSDC entries which report the sequence of the biosynthesis cluster are also displayed.
3.3. Genomic map section
Genomic map section displays the coordinates of genes encoded in the biosynthesis cluster.
If the original INSDC entries were divided in multiple entries, relative coordinates were re-constituted based on the description of the references. Each gene was colored based on its biological function.
3.4. PKS/NRPS modules section
PKS/NRPS modules section displays the domain composition of PKS/NRPS enzymes encoded in the biosynthesis cluster. Each module is displayed in a line. Deduced substrate of each AT or A domain is represented in the right column. Putative inactive domain is expressed in lower-case.
3.5. Reference section
Reference section displays related references about the biosynthesis cluster. We listed not only the paper reporting nucleotide sequence, but also functional analyses of tailoring enzymes published afterward are corrected.
3.6. Data download section
Data download section displays some kinds of data files that users can download. We are providing nucleotide sequence, CDS nucleotide/amino acid sequence and manual assigned annoations in CSV format or genbank format. Clicking each icon starts the download process.

open this section4.CDS list

open this section5.CDS information

open this section6.Simple text search

open this section7.Advanced text search

open this section8.Module search

open this section9.BLAST search

open this section10.Category list

open this section11.Get sequence

open this section12.Data download

open this section13.PCR amplified sequences

open this section14.Novelty chart

open this section15.PCR sequence BLAST

open this sectionXX.Other tips implemented in DoBISCUIT

Page top