Phylogenetic analysis of the trypsins. A neighbour-joining tree based on an alignment of the trypsin protease domain generated with ClustalW , was inferred using the PHYLIP package  and drawn using the MEGA program  (see text for details). The various taxonomic lineages encountered in the analysis are represented in the different colours. For clarity, the protein identifiers are suffixed with the abbreviated species IDs (see Additional file 2). Only the protein clusters supported by significant bootstrap values (> 50%) are highlighted with the colour scheme. For the rest only the gene (and species) identifiers are highlighted with the colour scheme. The primary branches in the clusters populated by the representatives from non-identical lineage (taxa) are shaded in grey. Atypical members in an otherwise strong cluster are highlighted in the colour of their corresponding lineage. The phylogenetic clade corresponding to the trypsin-like proteins that carry the Colicin_V-S1 domain architecture is shaded pink. The colour schemes for the various lineages are as follows: Actinobacteria- Magenta; Alphaproteobacteria- Orange; Archaea- Red; Betaproteobacteria- Brown; Chlorobi- Olive green; Cyanobacteria- Green; Deltaproteobacteria- Yellow; Firmicutes- Cyan; Gammaprot- Gammaproteobacteria- Blue; Others- Black.