Stereo view of the 3D structure of Aspergillus aculeatus rhamnogalacturonan acetylesterase (16) showing the localization in the structure of the annotated residues. The catalytic triad residues are shown in yellow stick representation, and the glycan structure bound at the two N-glycosylation sites is shown as red spheres (A). (B) The pairwise sequence alignment generated by the FeatureMap3D server. The catalytic residues are shown in yellow in the annotation line above the sequences and the two N-glycosylation sites are indicated in red.

Visualizing the underlying exon structure of Columba livia Alpha-A globin. This figure illustrates the mapping of the protein sequence and underlying exon structure of Columba livia (domestic pigeon) Alpha-A globin onto the PDB structure 1A4F [17], which contains the Alpha/Beta-globin dimer from Anser indicus (bar-headed goose). (A) Shows the coloring scheme when the exon structure annotation is not used. Here the coloring reflect the alignment between the query protein sequence and the PDB protein sequence. Color key—green: perfect match; brown: mismatch (low significance); violet: mismatch (high significance); blue: sequence gap in query sequence; light gray; unmatched chain(s)—in the case the Beta-globin chain. (B) Shows the coloring when the exon structure is taken into account. Color key—slate-blue: exon 1, red: exon 2, cyan: exon 3, light gray: unmatched chains(s). (C) Shows the pairwise alignment generated by the FeatureMap3D server (here it has been color-coded to highlight both the underlying exon structure and the sequence homology). The topmost sequence is the query sequence (Alpha-D), the sequence below is the PDB hit sequence (1A4F, chain a). The line above the query sequence holds the (optional) annotation information (here the numbers 1, 2 and 3—indicating the exon number). The line below the PDB sequence contains DSSP secondary structure information (inferred from the PDB entry).