Unknown ORFs were analysed using InterProScan http://www.ebi.ac.uk/InterProScan/, [71]] to locate motifs or domains where similarity with known proteins was low or absent. Size and total % GC content was determined using
the GC-Profile program [[72], http://tubic.tju.edu.cn/GC-Profile/]. Phylogenetic and molecular evolutionary analyses were conducted using genetic-distance-based neighbour-joining algorithms within MEGA version 4.0 [[73], http://www.megasoftware.net/] Nucleotide sequence accession numbers The DNA sequences described in this article have been assigned the accession numbers listed in Table 3. Acknowledgements MPR was funded was provided by a Postgraduate bursary from the Chemical and Environmental Science Department, Faculty of Science and Engineering, University of Limerick. We would like to thank the reviewers for their useful suggestions. Electronic see more Vorinostat nmr supplementary material Additional file 1: Alignment of the conserved domains
among the site-specific recombinases of the tyrosine integrase family. Alignment of the conserved domains among the site-specific recombinases of the tyrosine integrase family from phages, conjugative transposons, plasmids and other sources. R (Arginine) being in Domain I and H (Histidine)-R-Y (Tyrosine) in Domain II. (PDF 34 KB) Additional file 2: Phylogenetic tree of the Integrase proteins from Tn 4371 -like integrases available on the GenBank database and other Phage and ICE integrases. Phylogenetic tree of the Integrase proteins from available Tn4371-like integrases available on the GenBank database and other Phage and ICE integrases. Cluster analysis was based upon the neighbour joining method. Numbers at branch-points are Small molecule library manufacturer percentages
of 1000 bootstrap resamplings that support the topology of the tree. The scale bar represents 0.2 substitutions per nucleotide position. (PDF 42 KB) Additional file 3: Gene numbers for genes in the elements discovered in this study. The gene numbering for genes of the elements discovered in this study. Genes with yellow background are the scaffold genes of the element. (XLS 146 KB) Additional file 4: Alignment of Janus kinase (JAK) the first/last 200 bp of Tn 4371 -like ICEs using ClustalW. Fig S1a: Alignment of the first 200 bp of Tn4371-like ICEs using ClustalW. Fig S1b: Alignment of the last 200 bp of I Tn4371-like ICEs using ClustalW. (PDF 80 KB) References 1. Toussaint A, Merlin C: Mobile elements as a combination of functional modules. Plasmid 2002, 47:26–35.CrossRefPubMed 2. Burrus V, Pavlovic G, Decaris B, Guédon G: Conjugative transposons: the tip of the iceberg. Mol Microbiol 2002, 46:601–610.CrossRefPubMed 3. Churchward G: Conjugative transposons and related mobile elements. Mobile DNA II (Edited by: Craig NL, Craigie R, Gellert M, Lambowitz ML). Washington DC: American Society for Microbiology 2002, 177–191. 4.
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