Extended Data Fig. 10: Identification of conserved motifs and distribution of VcSduA.
From: West African–South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems
(a-b) Sequence logos showing conservation of the identified GHKL ATPase motifs I-IV in the GHKL domain (a) and the identified PD-(D/E)xK nuclease motif in the DUF4263 domain (b) of the 543 VcSduA hits detected using MacSyFinder v.2.1.1, as compared to the equivalent residue number in V. cholerae A1552 VcSduA. Amino acids in logos are coloured according to chemical properties: polar (G, S, T, Y, C), green; neutral (Q, N), purple; basic (K, R, H), blue; acidic (D, E), red; and hydrophobic (A, V, L, I, P, W, F, M), black. (c) Location of the identified PD-(D/E)xK nuclease residues in the VcSduA structural prediction. (d) Western blot showing the protein levels of VcSduA, expressed in E. coli MG1655ΔaraCBAD from a chromosomally integrated transposon carrying the arabinose-inducible PBAD- promoter, induced by the addition of 0.2% arabinose, as compared to derivatives encoding the indicated site-directed variants. Sigma70 was used as a loading control. Blots are representative of the results of three independent experiments. (e) AlphaFold3 predicted structure of potential VcSduA tetramer. (f) Distribution of VcSduA hits detected using MacSyFinder v.2.1.1. The tree shows the order-level phylogeny of genera in the RefSeq database with more than 500 genomes (see methods). For the full list of 543 VcSduA hits see Supplementary Table 7.
