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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

open this section3.Cluster information

open this section4.CDS list

close this section5.CDS information

It shows integrated information about CDS encoded in the biosynthesis cluster. This page has 6 sections; Location, Annotation, Genomic map, PKS/NRPS modules, Sequence and Features.
5.1. Location section
Location section displays basic information about the CDS. The name of organism, strain and contig that the CDS are displayed.
5.2. Annotation section
Annotation section displays various functional information assigned by annotators manually. Functional category, product name (in standardized vocabulary), substrate assignment and other notes are displayed. Annotation assigned in original genbank entry is also displayed.
Related reference and corresponding Uniprot entry are represented as the evidence of the annotation. Reference digest is written in Japanese as comment.
5.3. Genomic map section
Same as the genomic map section in Cluster information. See the cluster information page.
5.4. PKS/NRPS modules section
Same as the genomic map section in Cluster information. See the cluster information page.
5.5. Sequence section
Sequence section displays the nucleotide/amino acid sequence of the CDS. Displayed sequence can be switched each other by tab button. In the case of PKS/NRPS, each domain region highlighted inn different colors. Signature sequence the substrate is also represented in different color.
5.6. Feature section
Feature section displays search results of functional inference. °»Show BLAST table°… button has a hyperlink to the result of homology search (BLASTP) executed against Uniprot database. Domain signature search result against Interpro are also displayed.

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

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