D’Auria et al. BMC Genomics 2010, 11:181 http://www.biomedcentral.com/1471-2164/11/181 Page 5 of 13 Figure 3 Functional analysis. Functional analysis. COGs distribution within the core and dispensable compartments of L. pneumophila pangenome. Finally, the island ends with three hypothetical proteins and an IS4-family transposase (lpp0083). Several genes such as the TraK, the LvrA-related protein and the phage-related integrases are also maintained in the same positions in the Alcoy, Corby, Lens and Philadelphia strains. A similar system (R2), was also found in the Lens strain. It is a small region containing transposases as well as two homologs of a stability system StbDE (lpl1587, lpl1588). This island was originally associated with plasmids [25], but it has also been found on the chromosomes of other pathogenic bacteria [26]. Transport/secretion systems (TS) Only one TS island has been found in the Lpa and Lpc genomes. TS1 in the Alcoy strain is composed of 16 ORFs (lpa01590 to lpa01614). Three of these ORFs, lpa01601, lpa01599 and lpa01598, are related to the cobalt/zinc/cadmium efflux HelABC transport system that provides resistance against these heavy metals [27]. They are followed by lpa01604, which codes for the metallo-regulator ArsR that, in the presence of metals, derepresses the operator/promotor DNA, thereby acti- vating the transcription of downstream genes [28]. As happens in other islands, this ends with a phage inte- grase and three transposase-related ORFs, indicating a possible exogenous origin in Legionella. It is worth men- tioning that all five genomes carry a HelABC operon belonging to the core genome, while Alcoy and Corby strains also possess the two additional above-mentioned systems. In the Corby strain, TS1 is bigger than in the Alcoy, spanning about 50 kb. It contains the previously men- tioned HelABC operon (LPC_1847- LPC_1849), in addi- tion to the HelABC systems present as part of the core genome (LPC_02269, LPC_02270, LPC_02271), a trans- posase (LPC_1856) and a phage repressor protein (LPC_1857). The first 9 ORFs of the TS1c island (mainly hypothetical proteins and one transposase) are syntenic with the Paris ND9 island (see below). The island continues for about 19 kb with apparently no syn- teny with other genomes and then regains synteny with the Paris ND10 island. Interestingly, the TS1a-HelABC genes seem to be more similar to the core Lpl operon than to that of Lpc TS1 while TS1c-HelABC genes are more similar to