Kinase Logos

We use sequence logos to show patterns of sequence conservation within each kinase class. Every kinase group, family, and subfamily is aligned to generate a HMM. From this, we use custom software to build a logo view. Here's a logo from the TK group kinase domain, showing the key HRD and DFG motifs:

Logo view of TK group

Each stack of letters is from a single position in the aligned sequences, and represents the popularity of those residues (in bits). For instance, H is almost universal at position 263, while the R at 264 is sometimes replaced by G, M or other (hard to see!) residues. If you compare this with the equivalent region in TKL group kinases:

Logo view of TKL group

you can see the same HRD and DFG motifs standing out, but also group-specific patterns, such as the TK consensus of HRDLAARN changing to HRDLKSxN in TKL. By comparing logos, we can detect both common shared motifs and residues and motifs that are specific to individual kinase classes.

You can access both the HMM profiles and logos for every kinase class in the class report pages. Here's an example from the PDK1 family:

Screenshot of PDK1 family report, highlighting links to logos and HMMs

You can dynamically compare logos for any kinase groups, families, or subfamilies using our Logo Aligner tool, based on LogoMat (Oct 7 update: changes in HMMer and our parsing module have caused an alignment bug, which we're working on, but beware that some pairs of logos may be misaligned).