Phylogenetic tree showing relationship between serine protease homologues and serine proteases from the same snakes.

<p>65 amino acid sequences from 10 snakes were included together with bovine α-chymotrypsinogen (NCBI accession number: P00766) which was used as an outgroup. The alignment was generated using ClustalW <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021532#pone.0021532-Larkin1" target="_blank">[12]</a> within MEGA 4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021532#pone.0021532-Kumar1" target="_blank">[16]</a> using a gap opening penalty of 10 and a gap extension penalty of 0.1 for the initial pairwise alignment, gap opening penalty of 3 and gap extension penalty of 1.8 for the multiple alignment and the Gonnet protein weight matrix. The phylogenetic tree was generated from this within MEGA 4 using the neighbour-joining method and the Jones-Taylor-Thornton substitution model. The bootstrap test was done using 2000 replications. In the diagram sequences are identified using a code which consists of up to 3 characters representing the snake name, (TG: <i>Trimeresurus gramineus</i>; VS: <i>Viridovipera stejnegeri</i>; TJ: <i>Trimeresurus jerdonii;</i> BJu: <i>Bothrops jararacussu</i> ; ML: <i>Macrovipera lebetina</i>; EO: <i>Echis ocellatus</i>; BG: <i>Bitis gabonica</i>; Bja: <i>Bothrops jararaca</i>; TF: <i>Trimeresurus flavoviridis;</i> BAs: <i>Bothrops asper</i>) followed by a dash and then up to 5 characters representing the protein name. Where possible NCBI accession numbers are also included. ML-P3 and ML-P4 sequences were obtained directly from the sequences named VLP3 and VLP4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021532#pone.0021532-Siigur1" target="_blank">[5]</a>. Red circles indicate the sequences with mutations to the catalytic triad.