Sequence motifs
Two sequence motifs were reported previously in 46 for the PURase from Pseudomonoas chlororaphis , PueA (Table 3 ). The occurrence of the serine hydrolase motif (GXSXG) and the secretion signal sequence motif (GGXGXDXXX) were confirmed for the vast majority of all 2054 sequence entries in a multiple sequence alignment for superfamily 11 of the LED. Most PURase homologues from superfamily 11 have a GHSLG motif flanking the catalytic serine and secretion motif GGKGNDYLE. For sequences from superfamily 11 in the LED, the catalytic triad is formed by serine, aspartate, and histidine. In addition, most sequences in superfamily 11 (2039 out of 2054) matched the profile HMM for a RTX calcium-binding nonapeptide repeat (PFAM PF00353), which supports the previous suggestion of a Type I secretion system for protein translocation 47.
Prominent amino acid positions in superfamily 13, which comprises homologues of the PURase PudA from Delftia acidovorans , include the GXSXG serine hydrolase motif, a catalytic triad of serine, aspartate, and histidine, and a putative PUR binding region at PudA positions 347 to 395 48. Many of these positions were found to be conserved within the sequences of superfamily 13 (Table 4 ). Most PURase homologues from superfamily 13 have the motif GES AG flanking the catalytic serine, the motif VPX3G[ST]X2DE at the catalytic glutamate, and the motif AXH X3[LI]XY flanking the catalytic histidine. In addition, several positions in the putative PUR binding region were found to be conserved, including mostly hydrophobic amino acids (Table S8 ).