Figure 1 Genetic organization and the predicted primary structure of CB-839 chemical structure PnxIIIA in P. pneumotropica ATCC 35149. (A) AR-13324 molecular weight Schematic representation of the pnxIII operon genetic map and the functions of each gene. Circles represent potential transcriptional termination loops. Predicted functions determined by the protein database are indicated below the gray boxes. (B) Schematic representation of probable domains that were identified by comparing with the HMM database. The numbers represent the regions containing a large repeat sequence.

Arrowheads below the number box represent the position of sequence alignment in Additional file 1. The pnxIIIE gene product contains the OmpA domain (Pfam reference: accession no. PF00691) in the selleck compound C-terminus and is 54% similar to the OM protein A of Cardiobacterium hominis ATCC 15826 (ZP_05705729), with 84% coverage. Although the protein BLAST search yielded no highly similar proteins, the deduced amino

acid sequence of pnxIIIA was partially similar (46%) to the RTX family exoprotein of uropathogenic E. coli (UPEC) CFT073 [29] (NP_752300), i.e., 59% coverage. PnxIIIA is believed to be an essential cytotoxic protein of the structural RTX toxin. Figure 1B shows the putative domains and repeat sequence in the primary structure of PnxIIIA. PnxIIIA did not have any significant identical conserved domains in the Pfam database; however, several partial sequences that

were not significantly similar to conserved domains were identified in the HMM database. In brief, several groups of bacterial immunoglobulin (Ig)-like domains (Pfam reference: accession no. PF05345, PF02369, PF02368, PF07532, and PF10648) and a hemagglutinin repeat (PF05594) were scattered in the primary sequence of PnxIIIA, and a hemolysin-type calcium-binding PIK3C2G repeat (PF00353) identical to nonapeptides of the RTX repeat sequence in the C-terminal half was present (Figure 1B). In particular, only 1 copy of amino acid residues in position 2319-2327 (LDGGDGNDT) was found to be identical to the RTX sequence; otherwise, 2 RTX-like sequences were found in positions 2114-2122 (NFGGMGVSN; alternate amino acid residues are italicized) and 2377-2384 (IKGGT-NDT; the missing amino acid residue is indicated with a hyphen). PnxIIIA was also found to have a unique feature: 3 regions with large repeat sequences existed, and the amino acid sequences in these regions were similar to the repeat sequences of the extracellular protein toxin identified in various prokaryotes, including important pathogens (see multiple alignments in Additional file 1). Of these, except for the unknown function of the RTX exoprotein and hemolysin-type calcium-binding protein, almost similar proteins were predicted to be localized in the OM fraction and to function as adhesive proteins.