The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Journal Article · 13 November 2024 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkae1060 · OSTI ID:2481474

Udwary, Daniel W  ^[1]; Doering, Drew T ^[1]; Foster, Bryce ^[1]; Smirnova, Tatyana ^[1]; Kautsar, Satria A ^[1]; Mouncey, Nigel J  ^[1]

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1. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2481474
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 53; ISSN 0305-1048
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United States
• Language: English