Alignment of GH18 class III chitinase sequences. Forty sequences were selected from the one hundred fourteen class IIIa, IIIa-XIP, and IIIb sequences used to construct the GH18 family phylogenetic tree. The selected proteins include the experimentally verified wheat (Ta) and rice (Os) proteins. All of the Brachypodium (Bradi) class III proteins were included in the alignment along with sorghum (Sb) and rice proteins selected to represent branches of the class III clades. The sequences were aligned using the Clustal W method in MegAlign 5.05 (DNAStar software package). The region presented includes the DXXDXDXE motif (within the blue box) required for chitinolytic activity and two residues (within the red boxes) that in most of the IIIa-XIP sequences contain amino acids (R or K) capable of forming salt bridges with the E in the DXXDXDXE motif. The class IIIa-XIP protein Bradi4g09429 contains a large N-proximal deletion, and the first amino acid shown is at position 33 in the sequence. The position of the first amino acid shown ranges from positions 139 to 159 for the other class IIIa-XIP proteins, from positions 139 to150 for class IIIa, and from positions 125 to 149 for class IIIb.
Tyler et al. BMC Genomics 2010 11:600 doi:10.1186/1471-2164-11-600