Structural predictions and sequences for VirB6-like and VirB2-like proteins in plasmids of gram-positive origin

PLSDB_conjugative_gp_reps_esmfold.zip ESMFold predictions for all representative PLSDB proteins from G+ and conjugative origin PLSDB_AF3_reps_VirB6_pentamers.zip AlphaFold 3 predictions for pentamers of all 174 representative VirB6-like proteins PLSDB_AF3_reps_VirB6_VirB2_multimers.zip AlphaFold 3 predictions for multimer predictions of all 174 representative VirB6-like proteins (pentamer) together with their VirB2-like candidate proteins (decamer), 320 predictions total. AF3_gram_positive_reference_plasmids.zip AlphaFold 3 predictions from AlphaFold server for G+ example plasmids with VirB6-like proteins (pentamer) together with their VirB2-like candidate proteins (decamer). Also contains custom PAE plots. Includes the following plasmids: pAD1 pAMB1 pCER270 pCF10 pCLJ pCP13 pCW3 pGO1 pIP501 pKAPB2 pMG1 pSK41 pXO1 pXO2 Gram-positive_reference_plasmids.zip Contains genomic information for each gram-positive reference plasmid Plasmid nucleotide fasta Plasmid protein fasta (as annotated by Prokka) Plasmid GenBank data (as annotated by Prokka) DeepTMHMM predictions in 3line format PLSDB_sequences.zip PLSDB_2024_05_31_v2_proteins.fasta PLSDB protein sequences for the PLSDB release used in this study conjugative_gp_proteins.fasta Subset of the PLSDB protein sequences with G+ and conjugative origin, as annotated by PLSDB conjugative_gp_proteins_cluster_cluster.tsv MMseqs2 clusters (90% identity and 90% coverage) of conjugative G+ proteins conjugative_gp_proteins_cluster_rep_seq.fasta Representative protein sequences of the MMseqs2 clusters conjugative_gp_proteins_cluster_all_seqs.fasta All protein sequences (all representatives and members)