Synoptic view of the secretomics-based method for monoderm bacterium.

<p>Based on the biology of protein secretion, the coding sequences (CDS) are sequentially analysed in a workflow for (i) signal peptide (SP), (ii) secretory pathway, (iii) membrane retention, (iv) cell-wall retention, and (v) surface appendage. For each step, a combination of different tools allows defining different databases, as indicated in the detailed flowchart (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042982#pone-0042982-g002" target="_blank"><b>Figure 2</b></a>). From there, the resulting databases are analysed as depicted in the detailed decision trees (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042982#pone-0042982-g003" target="_blank"><b>Figure 3</b></a>). In the end, proteins are discriminated into different categories and different SCL are predicted. Sec-SP: Sec-dependent SP; Unc-SP: uncleaved SP; TMD: transmembrane domain; PGBD: peptidoglycan-binding domain; CWBD: cell-wall binding domain; SLHD: S-layer homology domain; SL-Prot: S-layer protein; Doc/Coh: dockerin/cohesin domain; IMP: integral membrane protein; GO: gene ontology.