Alignment of multiple N-terminal amino acid sequences and phylogenetic tree reconstruction of plant CPRs. Deduced amino acids from the plants indicated were aligned using ClustalW software and further manually aligned by SeqPup software (Biology Department, Indiana University). A, Alignment of N termini of selected CPRs. Light-gray color indicates conserved amino acids (>60%) in all CPRs after 60th amino acid. Black and dark gray indicate conserved amino acids (>60%) within the N-terminal regions of CPR class I (above the horizontal line) and CPR class II (below the horizontal line), respectively. Underline designates the membrane-anchoring region. B, Maximum parsimony analysis of CPR amino acid sequences, excluding the first 59 positions. Tree reconstruction was performed with the tree-bisection-reconnection heuristic search algorithm using the Phylogenetic Analysis Using Parsimony software, version 4.0 (Sinaur Associates, Sunderland, MA). Branch lengths between nodes are drawn to scale to the number of evolutionary steps. Bootstrap values (percent of 1,000 replicates) for each cluster is shown at the nodes. Three mammalian CPR sequences were used as an out-group to root the tree. At, Arabidopsis; Cp, guinea pig (Cavia porcellus); Cr, Madagascar periwinkle; Ec, California poppy (Eschscholzia californica); Hs, human (Homo sapiens); Ht, Jerusalem artichoke; Mm, mouse (Mus musculus); Nt, tobacco (Nicotiana tabacum); Os, rice (Oryza sativa), Pc, parsley; Pm, Douglas fir (Pseudotsuga menziesii); Psa, pea (Pisum sativum); Pso, opium poppy; Ptd, hybrid poplar; Ta, bread wheat (Triticum aestivum); Vs, spring vetch (Vicia sativa); Vn, mung bean.