Fig. 3: KKP modules are widespread in diverse Gram-negative organisms.

a Predicted structures of KKP_MP components by AlphaFold2. Conserved phosphatase motifs are shown in orange for PfpC. Conserved kinase motifs are shown in gray for PfkB and PfkA. b Distribution of triplet genes with a phosphatase domain (PF13672, PP2C) followed by two kinase domains (PF00069, Pkinase) before further filtering by CSD and FHA domain status. c Distribution of kinases (PF00069: Pkinase) fused with a CSD domain (PF00313: CSD). Left: taxonomic distribution. Right: proportion of bacterial kinases from left pie chart located in authentic KKP gene clusters. d Distribution of kinases (PF00069: Pkinase) fused with an FHA domain (PF00498: FHA). Left: taxonomic distribution. Right: proportion of bacterial kinases from left pie chart located in authentic KKP gene clusters. e Maximum likelihood tree of PfkA-like kinases. Colored bars around the tree indicate taxa. Filled circles indicate specific genera. Note that many Salmonella sequences were collapsed. f Genomic location distribution of KKP modules. g Representative KKP gene clusters with their genomic neighborhoods. KKP modules located in prophages and their co-resident prophages are indicated on the right, and other KKP-linked genes (transposons, TA systems, and restrictive modification systems) are indicated on the left. Gene names or conserved domains shown include: Psu, phage polarity suppression protein (PF07455); Phage_GPA, Bacteriophage replication gene A protein (GPA, PF05840); DNA_methylase, C-5 cytosine-specific DNA methylase (PF00145); RadC, DNA repair protein RadC (PF04002); DUF262 (PF03235); HNH, HNH endonuclease (PF01844); Ogr_Delta, viral family of phage zinc-binding transcriptional activators (PF04606); AplA, transcriptional regulator, AlpA family (PF05930); Phage_portal, Phage portal protein (PF04860); DUF1016, YhcG PDDEXK nuclease domain (PF06250); CI and CII, Bacteriophage repressor. The KKPs in prophages that were selected for follow-up are labeled in blue.