The molecular phylogeny of the protein kinases upon which Kinomer is based was first described by Hanks and Hunter. In their classification scheme the eukaryotic protein kinase superfamily is broadly split into two groups: 'conventional' (ePK) and 'atypical' protein kinases (aPKs). ePKs are the largest group, and have been sub-classified into 8 groups by examining sequence similarity between catalytic domains, the presence of accessory domains, and by considering any known modes of regulation.

The 8 ePK groups are:

• AGC
• CAMK
• CK1
• CMGC
• RGC
• STE
• TK
• TKL

The aPKs are a small set of protein kinases that do not share clear sequence similarity with ePKs. To date, four groups of aPKs have been shown to display protein kinase activity and are regarded as bona fide aPKs. These comprise the following groups:

• Alpha
• PIKK
• PDHK
• RIO

There is, however, insufficient evidence to support the putative protein kinase catalytic activity for the remaining aPK groups.