We added an additional nonproteomic classifier to our analysis using the protein domains found in chromosomal and nonchromosomal proteins (red/pink and green wedges in Figure 1D).
Using the protein domains as instructive identifiers of sequence homology and other bioinformatics tools, we have designed 1,820 immune-candidate probes, organized them into a M. galloprovincialis Immunochip and tested this new DNA microarray with haemolymph samples exemplifying the early and late response to live V. splendidus cells.
For identification of the PRRs we used the protein domain prediction tools (MyHits, HYPERLINK "http://hits.isb‐sib.ch/cgi‐bin/motif_scan" \o "http://hits.isb‐sib.ch/cgi‐bin/motif_scan"http://hits.isb‐sib.ch/cgi‐bin/motif_scan and Scansite, HYPERLINK "http://scansite.mit.edu" \o "http://scansite.mit.edu/" http://scansite.mit.edu).edu
Using the protein kinase domain of the yeast and Arabidopsis GCN2 and of the human PKR, PERK and HRI enzymes, we searched the Arabidopsis genome for the presence of additional eIF2α kinases.
However, amongst a clad of others, a FIKK- containing kinase was identified (cgd5_4390) which has been previously annotated as a R45-like orthologue (and named CpR45) by Schneider et al. from a tBLASTn search using the protein kinase domain of PFD1175w [ 46].
Each identified Dsh ortholog was analyzed for protein domains using the SMART protein domain analysis website (http://smart.embl-heidelberg.de), used in normal mode (Letunic et al. 2012).
The domain profiles used in the protein domain annotation are Pfam-A [ 21].
The domain profiles used in the protein domain annotation are from Pfam-A [ 26].
Proteins were then grouped according to the biological processes in which they operate; these details are available in Additional file 2. Finally, we limited the interactome prediction to the SCOP domains using the Protein Structural Interactome (PSI -Base data [ 10].
Protein set derived from genomic structural annotation was annotated using Blastp versus the NCBI/Genbank NR protein database [ 65], and using the protein domain/motif prediction program InterProScan [ 66].
