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. 2019 Jul 24;2(4):e201900421. doi: 10.26508/lsa.201900421

Figure 1. Bioinformatics-based identification and features of putative trypanosomatid Pex3 proteins.

Figure 1.

(A) The secondary structure-based homology program HHpred was used to search a database of T. brucei gambiense with the known HsPex3 sequence. The uncharacterized target (T) protein XP_011780297.1 encoded by the Tbg972.11.11520 gene was identified with greater than 95% probability as having a similar predicted secondary structure (ss pred) as the query (Q), HsPex3. HHpred output includes a prediction of helices (H, h) and coils (C, c) (capitals represent a more reliable prediction), of conserved consensus residues (capitals represent a more reliable prediction) calculated from the query (Q) or Target (T), and a strength of alignment of amino acids according to their biophysical properties (“|” very good, “+” good, “·” neutral, “‒” bad, and “=” very bad) (Söding et al, 2005). (B) Alignment of the putative trypanosomatid Pex3 sequences from Leishmania major (Lm; Accession no. XP_001686984.1) and T. brucei (Tb; Accession no. XP_829090.1) with known Pex3 sequences from human (Hs; Accession no. NP_003621.1), the plant A. thaliana (At; Accession no. NP_001154410.1), the yeast S. cerevisiae (Sc; Accession no. NP_010616.3), the amoeba P. fungivorum (Pf; Accession no. PRP89031.1), and the stramenopile N. gaditana (Ng; Accession no. EWM25801.1). Sequences were aligned using Kalign(https://www.ebi.ac.uk/Tools/msa/kalign/). An amino acid that is identical to its corresponding amino acid in TbPex3 is highlighted in blue. An amino acid that is similar to its corresponding amino acid in TbPex3 is highlighted in yellow. Groupings of similar amino acids are as follows: (G, A, S), (A, V), (V, I, L, M), (I, L, M, F, Y, W), (K, R, H), (D, E, Q, N), and (S, T, Q, N). Dashes represent gaps. The conserved aromatic residues W/F of Pex3 required for interaction with Pex19 are shown in red and boxed. Other conserved residues that were mutated to evaluate the effect on the interaction between TbPex3 and TbPex19 in comparison with the interaction between ScPex3 and ScPex19 are boxed. See also Fig 2.