Gaps were closed by primer walking with PCR-amplification on Smp131 genomic DNA as the template using primers designed according to available sequences. Programs used for DNA sequence analysis and similarity search based on domain architecture were selected according to previous research [49]. Possible ORFs were searched in 6 reading frames on find more both strands of the Smp131 genomic DNA, which used ATG or GTG as the start codon, consisted of longer than 50 amino acid residues, and had a putative ribosomal

binding site in the upstream region. The 33,525-bp DNA sequence determined in this study for phage Smp131 has been deposited in GenBank under accession CA4P clinical trial number JQ809663. Cloning of the attL and attR regions flanking the Smp131 prophage To clone the junction regions containing attL and attR, an inverse PCR-based strategy was employed. The chromosome prepared from S. maltophilia T13, the Smp131 lysogenic strain, was cleaved SBE-��-CD order with NaeI and HincII separately and self-ligated to circularize the DNA molecules. Inverse PCR was performed using the circularized HincII and NaeI fragments as the templates with primer pairs L1/L2 (for amplification of the attL-containing region) and R1/R2

(for amplification of the attR-containing region), respectively. The amplicons obtained were sequenced for comparison. Separation of virion proteins by SDS-polyacrylamide gel electrophoresis Following dialysis, phage particles (approximately 1 × 108 PFU) purified by ultracentrifugation were boiled in a loading buffer

for 3 min and separated in SDS-PAGE (10% polyacrylamide and 0.1% SDS). Protein bands were visualized by staining the gel with Coomassie brilliant blue (Bio-Rad) [47]. Electron microscopy Phage Smp131 was examined by electron microscopy of negatively stained very preparations as described previously [4] using a JEM-1200 EX II transmission electron microscope (JEOL, Peabody, Mass) operated at 120 kV. Acknowledgements This work was supported by grant No. NSC101-2313-B-005-033 and NSC99-2321-B-005-010-MY3 from the National Science Council of the Republic of China. Electronic supplementary material Additional file 1: Table S1: Assignment of Smp131 genes. (XLS 30 KB) Additional file 2: Figure S1: Strategy employed to test whether Smp131 has a circular form of genome. Lines: 1, restriction map deduced from the Smp131 sequence determined in this study; 2, fragments E1-3 (2.5 kb) and E5B1 (0.7 kb) used as probes for Southern hybridization; 3 and 4, 4.7-kb AvaI fragment (A1) and 4.7-kb EcoRV fragment (B5), respectively, that would hybridize to probes EI-3 and E5BI should the genome be circular. (B) Southern hybridization of AvaI and EcoRV digests from Smp131 genome using E1-3 and E5B1 separately as probes.