FIG 3.
Cooccurrence of DUF1127 proteins with LsrB and cuckoo sRNAs. The tree shows the phylogenetic relations of a selection of alpha- (α-proteo.) and gammaproteobacteria (γ-proteo.). For each strain, the numbers of SDPs, YjiS-like proteins, and LDPs are given. BLAST searches identified the proteins with the highest similarity to LsrB from A. tumefaciens (A9CI74, B5ZXG9, A0A068SS95, A0A081MRV5, C3MD12, W8I232, G7D4X2, Q2YRP4, Q3J274, Q9I1F9, A1JKA5, A0A0H2UWZ6, A0A0H3GNP2, P30864, and Q8ZRM6). Red and blue colors represent proteins with higher and lower sequence identity than 40%, respectively A genomic neighborhood to a trxB homolog is indicated by a check mark. Putative cuckoo sRNA sequences were extracted from each genome by searching for the pattern (CCTCCTCCC-N20–50)≥1-CCTCCTCCC. The numbers of sequences encoding two, three, or four CCUCCUCCC motifs are given.