Phylogeny of Arabidopsis eukaryotic kinases

Phylogeny of 942 eukaryotic kinase domains of Arabidopsis proteins. An alignment of 491 eukaryotic protein kinases was downloaded on Feb 9, 2012 from http://kinase.com/human/kinome/phylogeny.html, and this alignment was used to compute a profile Hidden Markov Model (HMM) using the software HMMer [12]. All representative gene models from Arabidopsis thaliana (TAIR10_pep) were searched against the profile HMM using HMMer. In total, 1,045 sequences generated hits with an E-value lower than 0.01. These sequences were then aligned to the profile HMM. Two sequences (AT1G11300.1 and AT2G32800.1) each had two distinct kinase domains and both domains per gene were therefore included as separate sequences in the alignment, resulting in an alignment of 1,047 distinct Arabidopsis kinase domains (additional File 5). All alignment positions not part of the profile HMM were removed from the alignment. In addition, all sequences covering less than 70% of the profileHMM were removed using the software REAP [13]. The cutoff value of 70% corresponded to a threshold value in sequence coverage distribution with sharp decline of sequence coverage for 111 kinase domains below coverage of 70% (additional File 8). The final alignment then consisted of 317 columns from 942 sequences (kinase domains) and was used to compute a maximum likelihood phylogeny and 100 bootstrap replicates using the PROTCATWAG model of the RAxML program [14]