Early Evolutionary Origin of Major Homeodomain Sequence Classes

We have analyzed the relationships of 337 homeodomain and related sequences using a distance matrix approach. Based on our results, homeodomain sequences can be classified into at least 30 distinguishable classes. Sequences belonging to the same class are highly similar to each other but there are no obvious close relationships between the separate classes. Since many of these classes each contain sequences from quite diverged organisms, we conclude that these separate classes of homeodomain sequences were established early during evolution.