Figure 1.

Protein structure and associated sequence alignment. The structure of proclavaminate amidino hydrolase [PDB:1gq6] and the seed alignment from Pfam [33] for its family. Only a portion of the alignment is depicted. One chain of the trimer, shown as a ribbon, is associated with the first sequence in the alignment. The other two chains are shown as light blue backbone traces. The ribbon is colored from blue to pink to yellow with increasing conservation. Gray ribbon segments represent residues in columns for which conservation was not calculated due to a high proportion of gaps (0.5 or higher). Conservation values, also shown as histogram bars above the alignment, were obtained with the entropy-based measure in AL2CO [8] and "independent counts" weighting. Active site ions are shown in cyan. Residues in the structure that are completely conserved in the alignment have their side chains displayed and are indicated with blue boxes on the alignment. The part of the alignment that is shown includes conserved (boxed) ion-binding residues in a loop to the lower right of the ions. Highly conserved residues are primarily involved in the active site or inter-subunit interactions. Residues in the protein core are moderately conserved. In the sequence alignment, Clustal X coloring is used for the residue one-letter codes. The alignment part of the figure was exported directly from Multalign Viewer as Encapsulated PostScript.

Meng et al. BMC Bioinformatics 2006 7:339   doi:10.1186/1471-2105-7-339
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