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. 2023 Mar 23;14:1624. doi: 10.1038/s41467-023-37287-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a General RRE-dependent RiPP biosynthetic pathway. b Stylized depiction for use of RRE-Finder to discover RiPP BGCs independent of known RiPP chemistry. c Daptide precursor peptide sequence logo (n = 184). d Frequency of common pHMM hits in daptide BGCs. Common best hit pHMMs were counted and grouped as follows: Aminotransferase – PF00202, TIGR00508, TIGR00707; RRE-peptidase – PF02163, Actino_DapP_RRE, Bacill_DapP_RRE; DUF-RRE – Actino_DapB_RRE, Bacill_DapB_RRE; Methyltransferase – PF13649, PF08241, PF13849, PF08242; Fe-dependent alcohol dehydrogenase (ADH) – PF00465, TIGR03405, PF13685; Short chain oxidoreductase – PF13561, TIGR01830, TIGR02638; YcaO – PF02624, TIGR01575; Azoline dehydrogenase – TIGR03605; Lanthipeptide dehydratase – PF00069, TIGR03897; Luciferase-like reductase – TIGR03564, PF00296; Acyltransferase – PF00583, TIGR01575. e Targeted BGC from Microbacterium paraoxydans DSM 15019 identified from the genome mining analysis of RREs.