Automated Bioinformatic Annotation of Biosynthetic Domains

KS and C domains were extracted from select PKS and NRPS genes associated with experimentally characterized biosynthetic pathways using the online program NRPS-PKS (http://www.nii.res.in/searchall.html) [19] (link), [21] (link). The pathways selected include representatives of the currently known enzyme architectures and functions associated with type I and II PKSs and NRPSs and thus this database is not meant to be comprehensive. The biochemical function and enzyme architecture of each domain was manually confirmed by analysis of the associated domain string and secondary metabolic product. Based on these results, each sequence was preliminarily assigned to a domain class. The compound produced by the associated pathway, the literature reference including PubMed ID, and the gene accession number was also recorded for each domain.

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Ziemert N., Podell S., Penn K., Badger J.H., Allen E, & Jensen P.R. (2012). The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. PLoS ONE, 7(3), e34064.

Publication 2012

Biosynthetic pathways Enzyme Gene Secondary metabolic

Corresponding Organization :

Other organizations : Scripps Institution of Oceanography, University of California, San Diego, J. Craig Venter Institute

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Variable analysis

independent variables

KS and C domains extracted from select PKS and NRPS genes associated with experimentally characterized biosynthetic pathways

dependent variables

Biochemical function and enzyme architecture of each domain

control variables

The pathways selected include representatives of the currently known enzyme architectures and functions associated with type I and II PKSs and NRPSs

Annotations

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