Fig. 5.

Alignment and phylogeny of LIPT2. (A) Alignment of LIPT2 with the enzymatically characterized LipB and LipM proteins. Unweighted sequence alignments were performed using T-Coffee (69) at the European Bioinformatics Institute website (https://www.ebi.ac.uk) using the default settings and displayed using Jalview. The sequence name indicates the enzyme type, the Uniprot code indicates the organism of origin, and the numbers indicate the amino acid residues displayed. Positions having 50% or greater identity are highlighted in blue. The catalytic cysteine residues of the LIPT2, LipB, and LipM are boxed and highlighted in black, as is the conserved lysine residue. The leucine-to-arginine mutations found in the human LIPT2 patients (27) are given in red. The edges of the alignment were trimmed using Jalview (70), so only the catalytic domain is shown. (B) Phylogeny of the LipB_LplA_LipM family (PF03099) was determined with sequences retrieved from the Pfam database (71). Multiple sequence alignments was done using ClustalW (72). The poorly conserved LplA N and C termini were removed. The phylogenetic tree was constructed using the maximum-likelihood method with the PhyML program (73, 74). PHYLIP Interleaved was used for alignment. Bootstrap analysis was set to 1,000 replicates.