Identification of CKX proteins in Brassica genome

To identify CKX proteins, BLASTP and HMM searches were performed using AtCKX proteins as query sequences to identify the putative CKX proteins in B. juncea genome database (chromosome V2.0, http://brassicadb.org/brad/), with set parameters as Evalue 1e-10, identity > 70%, query coverage > 95%, and other parameters as normal. The AtCKX sequences were submitted to Pfam database and CK-binding and FAD-binding domains were identified (accession numbers PF09265 and PF01565, respectively). Then, using these domains as queries, the HMM searches were performed using HMMER toolkit. The identified CKX proteins were further filtered for the presence of marker FAD-binding and CK-binding domains by using Pfam database, NCBI Conserved Domain Database (CDD) (http://pfam.janelia.org/), and InterProScan (http://www.ebi.ac.uk/interpro/). Based on BLASTN and BLASTP searches, a total of 24 BjCKX candidate gene sequences were identified.