Figure 2

Representative phylogram showing the relationship between intI genes. Genes colored in purple are putative pseudogenes, sequences in black are putative functional integron integrase genes, and genes colored in red have been shown to be functional in vivo. Circled genes are from mobile integrons. IntI proteins were aligned in MAFFT [58] and used to generate a DNA alignment. We used MrModelTest [60] to select the best-fit model of sequence evolution for MrBayes [59]. Rapid likelihood analysis trees where constructed in RAxML-VI-HPC [63]. PHYLIP [62] was used for constructing parsimony trees. Amino acid phylogenies also support the clades indicated (data not shown). The tree shown is the maximum likelihood estimation, and numbers for each clade indicate the maximum likelihood bootstrap, Bayesian posterior probability and maximum parsimony bootstrap values, respectively. The phyla names indicate the dominant organism type found within each clade. The tree was rooted with xerC and xerD genes from Escherichia coli and Thiobacillus denitrificans. Gene names and accession numbers are provided in Additional File 1.