Figure 1

Sequence analysis of CrVMP1. (A) Sequence alignment (ClustalW) of CrVMP1 and its six reported homologues from Dictyostelium discoideum (Dd), Homo sapiens (Hsa), Arabidopsis thaliana (Ath), Drosophila melanogaster (Dme), Caenorhabditis elegans (Cel), and Rattus norvegicus (Rno). Black shading denotes identical residues, grey shading—similar residues. Most of the homologue residues aligned before CrVMP1's first residue were omitted. Empty arrowheads point to the first and last residues of CrVMP1's SNARE domain. (B) A list of CrVMP1's six reported homologues, as well as its closest homologue (in Volvox carteri), along with their homology's Expect value (E), the percentage of identical/similar amino acids (I/S), and their length (L). (C) Phylogenetic tree of the seven reported VMP1 homologues. Sequences were first aligned with ClustalW, the tree then prepared with DNASTAR MegAlign using a bootstrap test with 1,000 iterations (bootstrap percentage values are indicated at each node. NA (not applicable) appears because MegAlign always generates rooted phylogenetic trees, whereas the Clustal algorithms produce un-rooted trees. In order for MegAlign to display the Clustal tree, it must first root the tree, which involves introducing a new node. When the tree is then re-rooted, if the new node lands on a branch within the rooted tree, it does not have a bootstrapping value because it was not included in the analysis). (D) Schematic representation of CrVMP's primary structure. Red areas represent transmembrane domains predicted by TMPred and TMHMM. One circle represents a domain absent from the Phobius prediction, two circles—absent from both the Phobius and the MINNOU predictions. The yellow area shows the predicted SNARE domain.