Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jan;41(Database issue):D408-14.
doi: 10.1093/nar/gks1177. Epub 2012 Nov 26.

DoBISCUIT: A Database of Secondary Metabolite Biosynthetic Gene Clusters

Affiliations
Free PMC article

DoBISCUIT: A Database of Secondary Metabolite Biosynthetic Gene Clusters

Natsuko Ichikawa et al. Nucleic Acids Res. .
Free PMC article

Abstract

This article introduces DoBISCUIT (Database of BIoSynthesis clusters CUrated and InTegrated, http://www.bio.nite.go.jp/pks/), a literature-based, manually curated database of gene clusters for secondary metabolite biosynthesis. Bacterial secondary metabolites often show pharmacologically important activities and can serve as lead compounds and/or candidates for drug development. Biosynthesis of each secondary metabolite is catalyzed by a number of enzymes, usually encoded by a gene cluster. Although many scientific papers describe such gene clusters, the gene information is not always described in a comprehensive manner and the related information is rarely integrated. DoBISCUIT integrates the latest literature information and provides standardized gene/module/domain descriptions related to the gene clusters.

Figures

Figure 1.
Figure 1.
(A) Default view of the cluster information page for the alpha-lipomycin biosynthetic gene cluster. Information related to chemical compound, producing organism, gene coordinates, domain/modules, related references and downloadable flat files are displayed. (B) CDS list view of the alpha-lipomycin biosynthetic cluster. The list page is reached via the cluster information page by clicking ‘CDS list’ tab. Relative coordinate of CDSs in the biosynthetic cluster, annotated gene descriptions and functional categories are listed.
Figure 2.
Figure 2.
Default view of the CDS information page for a gene in the tautomycetin biosynthetic cluster. A hyperlink to the CDS information page is provided on the cluster information page and the CDS list page. Manual curation results, such as annotated product name, original product name, gene name and functional category are displayed in the annotation section. Experimental evidence for this gene is also provided in the reference column of the annotation section. Functionally important domains for formation of the polyketide chain are displayed in the PKS/NRPS module section. In the sequence section, different domains are indicated by different colors.
Figure 3.
Figure 3.
Novelty chart view of the KS domain and the A domain. Number and similarity to known sequences of KS (left) and A (right) domain sequences amplified from NBRC strains are displayed as a bar chart. The width of the horizontal rectangle represents the number, and the color gradient of each rectangle represents the degree of similarity for each NBRC strain shown in the center.

Similar articles

See all similar articles

Cited by 33 articles

See all "Cited by" articles

References

    1. Newman DJ, Cragg GM. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J. Nat. Prod. 2012;75:311–335. - PMC - PubMed
    1. Park SR, Yoo YJ, Ban YH, Yoon YJ. Biosynthesis of rapamycin and its regulation: past achievements and recent progress. J. Antibiot. 2010;63:434–441. - PubMed
    1. Jenke-Kodama H, Borner T, Dittmann E. Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis. PLoS Comput. Biol. 2006;2:e132. - PMC - PubMed
    1. Khosla C, Kapur S, Cane DE. Revisiting the modularity of modular polyketide synthases. Curr. Opin. Chem. Biol. 2009;13:135–143. - PMC - PubMed
    1. Del Vecchio F, Petkovic H, Kendrew SG, Low L, Wilkinson B, Lill R, Cortes J, Rudd BA, Staunton J, Leadlay PF. Active-site residue, domain and module swaps in modular polyketide synthases. J. Ind. Microbiol. Biotechnol. 2003;30:489–494. - PubMed

Publication types

Feedback