Multiple sequence alignment for A. thaliana trans-PTs, listed in Table 1. N-terminal sequences are omitted according to prediction by TargetP-2.0 [21] (http://www.cbs.dtu.dk/services/TargetP). Highly conserved regions are highlighted in gray. Only regions II and III are present in small subunit (SSU). Motifs essential for catalysis and binding of allylic substrate (first aspartate-rich motif (FARM), second aspartate-rich motif (SARM), and +5 and +6 arginines (RR)) are highlighted in black [19,20]. Basal residues active in IPP binding are marked with arrows [22]. The CXXXC motif highlighted in blue is critical for physical interaction between the large subunit (LSU) and the SSU [9]. The floor 1, 2, and 3 residues of the three-floor model [23] are indicated in green, red, and yellow, respectively. Blocking residues are boxed.