Lineage trees are shown in three places on the website:
- 3.Individual protein pages show lineage trees containing direct ancestors and descendents of a given protein.
Lineage trees on FPbase depict the historical, directed evolution of proteins, and are not phylogenies based on sequence similarity (though such phylogenies are straightforward to generate, and could be included as well). Nodes in the trees represent individual proteins, and hovering on a node (or tapping on mobile) shows the mutations to the parental protein sequence that yield the sequence of the child protein, along with the reference that introduced the protein. Clicking on a node brings you to the protein page. Node colors represent emission wavelength, and multi-state/photochromic proteins are colored with linear gradients representing each state.
On the lineage and organism pages, there is an additional search field with which one can search for specific mutations in the evolutionary tree. Mutations may be entered in HGVS format (e.g. A206K; 6), and any proteins matching the mutation query will be highlighted (Fig. S6). Note: for the lineage trees, amino acid numbering is always aligned to the root ancestral protein sequence, so “A206K” shows all monomeric avGFP derivatives, even though many of them have an added valine in the second position (making “A206” actually “A207”); this is in keeping with the convention usually followed in the literature. Partial mutation codes may be entered: for instance “A206” will show all proteins where alanine 206 was mutated, regardless of the resulting amino acid substitution, and “206K” reveals all proteins where the 206th amino acid was mutated to lysine, regardless of the initial amino acid. Multiple mutations may be entered to find proteins with “all” or “any” of the mutations (using the all/any toggle button). By default, all proteins with the mutation (relative to the root ancestral protein) will be highlighted; however, by selecting “relative to parent”, only proteins that possess the mutation(s) with respect to their direct parental protein will be highlighting.