A one-dimensional (1D) motif usually comprises conserved essential residues involved in catalysis, ligand binding, or maintaining a specific structure. However, it cannot be easily detected in proteins with low sequence identity because it is difficult to (1) identify protein sequences suspected to contain the motif, and (2) align sequences with little sequence identity to spot the conserved residues. Here, we present a strategy for discovering phosphate-binding ID motifs in NAD(P)-binding proteins sharing low sequence identity that overcomes these two hurdles by determining all distinct locally conserved pyrophosphate-binding structures and aligning the same-length sequences comprising each of these structures to identify the conserved residues. We show that the sequence motifs derived from the distinct pyrophosphate-binding structures yield different numbers/spacing of conserved Gly residues. We also show that they depend on the side chain orientations and cofactor type (NAD or NADP). Thus, sequence motifs derived from local similarity of backbone structures without consideration of the cofactor type and/or side chain orientations would reduce their reliability in annotating protein function from sequence alone. The three-dimensional (3D) and 1D motifs comprising conserved residues in nonredundant proteins reveal hidden relationships between the protein structure/function and sequence as well as protein-cofactor interactions.