Fig. 5

A summary of NarJ subfamily member motifs determined in this study. For all motifs, residues with 60-74 % (normal font) sequence identity and >75 % (bold font) sequence identity are shown. Dashes in each motif indicate unalignable or missing residue gaps within the alignment. The overall NarJ subfamily motif is provided in the top box and was determined from the overall alignment of 324 sequences (Additional file 5: Figure S5); NarJ subfamily motif numbering is according to aligned E. coli TorD positions; red residues indicate newly determined amino acids as determined from this study. Motifs determined from sub-alignments of 82 NarJ, 6 NarW, 74 DmsD, 13 YcdY and 97 TorD sequences are listed below the overall NarJ subfamily motif. In NarJ motifs, differences between Gram- negative (Gm-; red font) and Gram- positive (Gm+; blue font) sequences are highlighted in addition to overall NarJ motif (black font) and both motifs are numbered according to E. coli NarJ (b1226). The NarJ motif alignment included Gammaproteobacterial NarW motifs (light blue font) which are numbered according to E. coli NarJ. The DmsD motif represents sequences with loci found in dmsABC operons and is numbered according to its alignment to E. coli DmsD (b1591). The YcdY motifs for members linked to ycdX operons is aligned with DmsD and numbered according to E. coli YcdY (b1035). Starred YcdY motif residues indicate positions that differ in YcdYb sequence motifs (K37G/N, A62Q, S80A, E88V/I, L95R, G99N, L102E, Q123N, W143C, T157S/A, A170L/M/I). Both TorD motifs shown indicate members that associated with torAC operons (green font) and fdhGHI operons (purple font) in addition to the overall TorD motif (black font) that is numbered according to E. coli TorD (b0998). Residues with known experimental functional/ structural significance are highlighted with coloured bars or arrows (refer to panel legend for details)