CHAIN alignment of the CDK subfamily activation loop. CHAIN alignment of the activation loop in the Pfcrk-5-like CDK subfamily ("Foreground") compared to the corresponding region in a large set of diverse eukaryotic CDK sequences ("Background"). The kinase-conserved DFG and APE motifs bordering the activation loop are indicated at the top, along with the subfamily-conserved PTxC motif. An asterisk indicates the position of the threonine observed to be phosphorylated in other CDKs, conserved in both the foreground and background. The histogram above each sequence set represents the differential levels of conservation between the two sets at each position, using logarithmic scaling. Dots above each alignment column indicate the contrasting conservation pattern determined by CHAIN. Note that the Apicomplexa (foreground, top) and Eukaryota (background, bottom) sets have different conservation patterns. In the sequence alignment itself, columns of the conserved pattern are colored according to the consensus residue type. The consensus residue types are listed below the alignment. Weighted residue frequencies are shown in the following rows, in units of integer tenths (e.g. "9" indicates conservation of 90-100%). The number of sequences in each set are shown in parentheses. A complete CHAIN alignment of these sequences is provided in Additional File 4.
Talevich et al. BMC Evolutionary Biology 2011 11:321 doi:10.1186/1471-2148-11-321