Supplemental data for Rules of Coexistence: RiPP Recognition Elements Evolved to Prevent Pathway Interference through Leader Peptide Discrimination

NMR titration data of the 15N labeled RRE of PbaB1, with different peptides in 800_PbaB1 folder Series 1-5 PbaA peptide Series 101-107 LppA peptide Series 201-205 PbaA W-15Ypeptide Series 301-305 LppA Y-16W peptide ######################################################### Phylogenetic data in the Phylogenetic data folder: #........................................................... # rre.3024.FASTA Alignment of 3024 RRE domains with consensus sequence and sites, containing >95% gaps removed. Sequence deflines include RRE classification (RRE_LPP/RRE_PAEN/RRE_LASSO for LPP, paeninodins and other lasso). Aligned FASTA format. #........................................................... # rre.3024.ftx.tre Approximate ML tree, reconstructed using "FastTree -gamma -wag" command options. Leaves indicate protein GenBank IDs and RRE classification (RRE_LPP/RRE_PAEN/RRE_LASSO). Newick format. #........................................................... # Prok2311.rre.genes.tab Mapping of RREs to a collection of completely sequenced prokaryotic genomes (see https://doi.org/10.1038/s41564-025-02180-8). Columns: 1. Gene ID | NCBI locus tag 2. Genome assembly ID 3. Protein id in the assembly (WP_013528114_1 = WP_013528114.1) 4. GenBank ID of the closest relative in the rre.3024 set 5. RRE classification (RRE_LPP/RRE_PAEN/RRE_LASSO) 6. NCBI taxonomic lineage for the genome assembly ASCII tab-delimited text file. #........................................................... # Prok2311.Bacilli.uxr.tre Approximate ML tree for genomes in the Bacilli clade, reconstructed using 54 nearly universal bacterial COGs. Leaves indicate abbreviated taxonomy of the genome, Genome assembly ID, and, when approproate, classification of RRE genes, present in this genome (RRE_LPP/RRE_PAEN/RRE_LASSO). Internal nodes of the tree have numerical labels. Newick format. #........................................................... # Prok2311.Bacilli.pars.tab Equal-weight maximum parsimony reconstriuction of RRE_LPP and RRE_PAEN genes in Bacilli. Columns: 1. RRE classification (RRE_LPP/RRE_PAEN) 2. Tree node (___N5709 = node #5709 in the Prok2311.Bacilli.uxr.tre or Genome assembly ID for leaves) 3. Gene presence or absence (1/0) 4. Gain, loss or no change (1/-1/0) on the tree edge, leading to the node Only the nodes where the gene(s) are present or lost are shown. ASCII tab-delimited text file.