Fig. 1 Schematic diagram of the integration sites and Prophage-induced primer amplification region in CR-HMKP K2-ST375 The four different colors indicate the four prophages, respectively. F1 - F4 are the forward primers for Prophage-1 - Prophage-4 induced identification, respectively; R1 - R4 are the reverse primers for Prophage-1 - Prophage-4 induced identification, respectively

Fig. 2 Induction and verification of circularization structure of Prophage-4 A: Prophage-4 induction by mitomycin C; M: DNA marker DL2000; lane 1: the Prophage-4-induction primers were used to amplify the bacterial supernatant; lane 2: the primer of phoE were used to amplify the bacterial supernatant; lane 3: negative control. B: Identification of circularization structure of Prophage-4; M: DNA marker DL2000; lane 1: the Prophage-4-cyclization primer were used to amplify the bacterial supernatant; lane 2: the primer of phoE were used to amplify the bacterial supernatant; lane 3: negative control

Fig. 3 Schematic diagram of Prophage-4 circular structure formation The first diagram shows the integration of Prophage-4 into the Kp0179 chromosome, where blue indicates the Prophage-4 genome, red and yellow respectively indicate the 40 bp homologous repeats sequences HR1 and HR2; the adjacent attL is the left attachment site, and attR is the right attachment site. The middle diagram shows the Kp0179 chromosome with the 40 bp homologous repeats sequences present in the Prophage-4 genome. The diagram on the right shows Prophage-4 being excised from the Kp0179 chromosome to form phage-4, with the large green circle representing the Kp0179 chromosome after excision. In the dotted box is an amplified region of the cyclization primer for Prophage-4

Fig. 4 Genetic structure of Prophage-4 in the chromosome of CR-HMKP K2-ST375 From the inside to the outside: the first layer refers to the genome length of Prophage-4; the second layer refers to the GC content; the third layer refers to the GC skew; and the outermost layer refers to the coding genes of Prophage-4

Fig. 5 Prediction of signal peptides in endolysin by SignalP 4.1 The horizontal axis of the curve indicates the sequence, and the vertical axis indicates the score. Purple, green, and blue colors indicate the cleavage site score（C-score）, signal peptide score（S-score）, and the combined score of C-score and S-score（Y-score）, respectively. In the text output results, “NO” indicates that the endolysin does not contain a signal peptide sequence

Fig. 6 Transmembrane domains prediction of endolysin by DeepTMHMM The horizontal axis of the curve represents the sequence, and the vertical axis represents the probabilitity. Blue indicates the probability of the protein being outside the membrane, while yellow indicates the probability of signal peptides

Fig. 7 Analysis of the phosphorylation sites in endolysin using NetPhos-3.1 The horizontal axis refers to the sequence, while the vertical axis refers to the probability of phosphorylation. The four colors, red, green, blue, and pink, indicate serine, threonine, tyrosine, and the threshold, respectively. When the threshold exceeds 0.5, it indicates that the amino acid at that position is a phosphorylation site

Fig. 8 Prediction of the secondary structure of the endolysin using Phyre2 The first line indicates the sequence positions: Yellow indicates polar amino acids: A（Alanine）, S（Serine）, T（Threonine）, G（Glycine）, and P（Proline）; green indicates hydrophobic amino acids: M（Methionine）, I（Isoleucine）, L（Leucine）, and V（Valine）; red indicates charged amino acids: K（Lysine）, R（Arginine）, E（Glutamic acid）, N（Asparagine）, D（Aspartic acid）, H（Histidine）, and Q（Glutamine）; purple indicates aromatic amino acids: W（Tryptophan）, Y（Tyrosine）, F（Phenylalanine）, and C（Cysteine）. The second line indicates the secondary structure, with green for α-helices and blue for β-sheets. The third and fourth lines are for confidence assessment: red indicates high confidence 9, blue indicates low confidence 0, with a total of 10 levels divided in between

Fig. 9 Prediction the three-dimensional structure of the endolysin by SWISS-MODEL Helices indicate alpha helices, sheet-like arrows indicate beta sheets, and lines indicate random coils

Fig. 10 Conserved structural domains prediction of endolysin by CD Search The first line indicates the sequence position; the blue region indicates that this amino acid sequence completely matches with the lysozyme superfamily proteins, where the dark blue parts have a higher degree of match with endolysin R21-like; the blue triangles indicate that the amino acid is an annotated functional sites

Fig. 11 Phylogenetic tree of Prophage-4 based on the terminase large subunit The maximum likelihood method was used to construct the CR-HMKP K2-ST375 Prophage-4 phylogenetic tree, and the numbers on the branches were the bootstrap value

Fig. 12 Phylogenetic tree of Prophage-4 based on the endolysin The maximum likelihood method was used to construct the endolysin phylogenetic tree encoded by CR-HMKP K2-ST375 Prophage-4, and the numbers on the branches were the bootstrap value