Secondary structure alignments. Alignment of the secondary structures of cyanobacterial (green letters) and known E. coli (black letters) hydrogenase maturating endopeptidases. The secondary structures, except for the top sequence 1CFZ (bold letters), were determined from the deduced amino acid sequences using NNPREDICT . The secondary structure features from the crystal structure of E. coli HydD (1CFZ)  were extracted using DSSP and used as reference (top sequence). Boxes are drawn and named according to the nomenclature used by Fritsche et al. . The stars mark the position of nickel ligating amino acid residues. The right column indicates amino acid counting. H: alpha helix, S: beta sheet, x6803: HoxW from Synechocystis PCC 6803, x7120: HoxW from Anabaena PCC 7120, p7120: HupW from Anabaena PCC 7120, p73102: HupW from Nostoc punctiforme ATCC 29133/PCC 73102, HyaD, HybD, and HycI: sequences from Escherichia coli. – Note that the same amino acid sequence underlies 1CFZ and HybD. Thus, their secondary structure comparison reflects the accuracy of NNPREDICT.