(XLS 43 KB) Additional file 4: Figure S2: Predicted T7G translational

frameshift sites in Smp131 and closely related prophages from Xanthomoas and Stenotrophomonas. (A) T7G (enclosed by a rectangle) and the surrounding regions including genes p27, p27.1 and p28 of Smp131. Stop codons are denoted by three dots after the amino acids. Predicted start codon ATG of p27.1 is underlined, whereas ribosomal binding site AGAGG for gene p28 is in gray background. (B) DNA sequence alignment of the regions surrounding T7G translational frameshift sites (enclosed in rectangles) from Smp131 and the related prophages from X. campestris pv. campestris 33913, X. oryzae pv. oryzae strains KACC10331, EX 527 concentration MAFF311018 and PXO99A. An asterisk indicates identical nucleotides in all phages. (PPT 1 MB) Additional file 5: Figure S3: Comparison of tyrosine integrase of Smp131 and its homologues. Identical residues found in JNK-IN-8 datasheet more than 3 residues are highlighted. Active sites determined for XerD are indicated by downward arrowhead and the RKHRH pentad conserved

residues are indicated above. The α-helix (empty rectangle) and β-sheet (empty arrow) structural motifs under the alignments are based on the crystal structure of E. coli XerD. Abbreviations: Smp131, integrase deduced from Smp131 orf43; P2, integrase of Enterobacteria phage P2 (GenBank:P36932); 186, integrase of Enterobacteria phage 186 (GenBank:P06723); XerD, site-specific recombinase AC220 in vivo of E. coli (GenBank:1A0P_A). (PPT 2 MB) Additional file 6: Table S3: Identities of amino acid sequence shared between the proteins deduced from Smp131 and those from bacteriophages. (XLS 44 KB) Additional file 7: Table S4: Positions and sequences of att sites and tRNA of Smp131 and prophages in Xanthomonas and Stenotrophomonas. (XLS 26 KB) Additional file 8: Figure S4: Strategy for cloning the host-prophage junctions from Smp131-lysogenized S. maltophilia T13. (A) Sketch depicting the circular Smp131 filipin genome and genes near the predicted attP site. Arrows represent the genes and predicted attP site. (B) Sketch showing the host S. maltophilia

T13 chromosome and its attB site. (C) Map showing relative positions of genes after Smp131 integration into host S. maltophilia T13. Primers used in PCR were: L1; 5′-TGAAAGGTGCCATGACCACACG-3′; L2, 5′-GCGTTGCCAAGGTCAGATCGG-3′; L3; 5′-CGCATCGCACTCTAGGAAGTGAAG-3′; L4, 5′-AACTGCCAGAACCTCTGCAGTG-3′; R1, 5′-CTCTTGTCCTCGCTGTCGGT-3′; R2, 5′-TGATAGCCCTATTTTCAAGGGC-3′; R3, 5′-AGGCCCAGCAGCGCA-3′; R4, 5′-TGCCTGCCGCCAGCT-3′. S. maltophilia T13 chromosome containing prophage Smp131 was digested with HincII and NaeI. The fragments were self-ligated and the circularized DNA was then used as the templates for inverse PCR. Amplicons obtained were sequenced for comparison. (PPT 183 KB) References 1. Palleroni NJ, Bradbury JF: Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983.