Computational protocol: Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation

Similar protocols

Protocol publication

[…] The sequences were aligned using CLUSTALW v2.0.9 using the default parameters. Larkin et al. [] Phylogenetic tree reconstruction for the sphingolipid metabolism was done using MEGA 5 program by the Neighbour-Joining method with 10000 bootstrap resampling’s. Saitou and Nei [,]. The evolutionary distances (Number of amino acid substitutions/site) were computed using the Poisson correction method. [...] To evaluate the potential functional divergence and to predict the amino acid residues accounting for the functional differences among the three enzymes, Type I functional divergence was estimated using DIVERGE 2.0. Gaucher et al. [] Sequences were classified into three different groups (IPCS, SPL and SPT) using the P-distance method (Additional file : Table S2). For each pairwise comparison, the coefficient of evolutionary functional divergence (θ) and standard error were determined. Utilizing the coefficient of evolutionary functional divergence (θ) the sequences were subjected to significant functional divergence and likelihood ratio test (LRT). Based on the site-specific posterior probabilities, sites experiencing functional divergence in the subgroups were identified [],[]. [...] SDP’s determine the differences in functional specificity within the protein family [,]. The input set of sequences was divided into 4 groups (IPCS, SMS, SPL and SPT) containing 34, 20, 40 and 78 sequences respectively. SDP’S were predicted by SDPfox and SDPpred and the Z scores were calculated for each alignment column. […]

Pipeline specifications

Software tools Clustal W, MEGA, DIVERGE, SDPfox, SDPpred
Applications Phylogenetics, Protein sequence analysis
Chemicals Sphingosine