**7. Comparison with other secretory systems: T2SS, T4SS and T6SS**

To compare with T3SS, earlier analyses for T2SS and T4SS were updated and an analysis of T6SS protein sequences was performed. Coiled-coil predictions and disorder analysis were carried out for *Helicobacter pylori* (T4SS), *Legionella pneumophila* (T2SS and T4SS), the Type-4 pili (T4P) of *L. pneumophila* and *Pseudomonas aeruginosa* and *P. aeruginosa* strain PA14 (T6SS). For 2878 proteins encoded in the *L. pneumophila* genome (GenBank accession number NC\_006369), the predicted coiled-coil content is 4%.

Using the Virulence Factor Database (Yang et al., 2008) for the classification of *L. pneumophila* proteins, a coiled-coil content of 14% is predicted for T2SS (11 proteins), 19% for T4SS (50 proteins), and 13% for T4P (3 proteins). For 1573 proteins of *H. pylori* (NC\_000915) a coiled-coil content of 3% is predicted, with 26% for T4SS (24 proteins). For 5571 proteins of *P. aeruginosa* (NC\_002516) the predicted content is 4%, 8% for T2SS (11 proteins) and 10% for T4P (32 proteins). A high coiled-coil content is predicted for the T4SS of *H. pylori* and the T4SS effectors of *L. pneumophila*. The latter (Table 3) exhibit a particularly high propensity for structural disorder (on the average 46% disordered regions) and coiled-coil content (30%), thus strongly resembling T3SS effectors. The analysis of T6SS protein sequences retrieved from the KEGG database is in Table 4. Hcp and Vgr proteins are proposed effectors (Mougous, et al., 2006), although they may also act as T6SS machine components (Zheng &Leung, 2007). Non-secreted components include ClpV an AAA+ Clp-like ATPase(Cascales, 2008) and various other core components. The analysis suggests a low coiled-coil content for most secreted proteins (on the average 6%) and a higher one (12% on the average) for core proteins. Interestingly, the mean overall disorder of secreted T6SS components is very high (41%) and comparable to T3SS effectors or to T4SS effectors of *L. pneumophila*. Core components of T6SS display a significantly lower degree disorder (28%).


Table 3. Predictions (using MATCHER ) of the heptad repeats content and disorder analysis (using FOLDINDEX) for effectors from the T4SS of *L. pneumophila* strain Philadelphia 1.


Table 4. T6SS proteins (T6S system HSI-I, HSI-III) of the *P. aeruginosa* strain PA14.
