Figure 3. Enhanced Sequence Alignment Derived from the Structural Alignment of Kinase Representatives.

Abbreviated names of kinase representatives are provided with the gray box at the left-hand side of the figure (see Table 1 for more information on structures). The name is followed by the PDB ID [18] for the structure used in the alignment. The number in parenthesis following the PDB ID is the residue number of the first residue shown in the alignment. The sequences of the six AKs are clustered at the top of the alignment, followed by the sequence of PKA, which is highlighted. The alignment is annotated for key structural features using the JOY software [78]. Secondary structure is represented using the following conventions: light-gray box, β-strand; medium-gray box, 3–10 helix; dark-gray box, α-helix. Residue characteristics are represented using the following conventions: uppercase, solvent inaccessible; lowercase, solvent accessible; bold, hydrogen bond to main chain amide; underline, hydrogen bond to main chain carbonyl; tilde, hydrogen bond to other side-chain; italic, positive Φ; breve, cis-peptide. Residues that are highly conserved within the TPK family and some AKs are highlighted in boxes for the sequences where the conservation applies. The residue(s) seen at these positions are shown in uppercase above the boxes. The letter O stands for general hydrophobicity, but not a specific residue type. Residues that are more weakly conserved in the TPKs but are also conserved in many other AK families are noted with a lowercase letter above the appropriate alignment columns. Selected residues of interest that are conserved only within the TPKs are depicted using the same conventions above, but with gray lettering (depiction of residues conserved only in the TPKs is not exhaustive, i.e., only residues discussed in the text are highlighted above the alignment. Generally, this is done in structural regions unique to the TPKs). Secondary structures are labeled with the nomenclature used for PKA [12]. Sequence representing unresolved portions of the structure is not shown by JOY. In key portions of the alignment, this sequence is added back in and shown in light gray.