The extreme N-terminal region of FliH is very poorly conserved, but some sequence conservation is evident in the various bacterial groups (e.g. enterobacteria, epsilon proteobacteria),

but not the YscL protein family. A GxxxG segment of variable length follows, then a poorly conserved segment likely to be helical in structure, followed by a well-conserved C-terminal domain known to be responsible for Fostamatinib manufacturer the interaction with the N-terminus of the flagellar/Type III ATPase (Figures 1, 2 and 3). When we noticed the presence of conserved consecutive GxxxG repeats in FliH/YscL, we asked if this motif had been previously observed in other types of proteins. Lemmon et al. [22] first discovered that specific interactions are required for the transmembrane helix-helix dimerization of glycophorin A. It was later shown that dimerization was mediated by a GxxxG-containing motif [23]. The GxxxG motif has been identified as the dominant motif in the transmembrane regions of hundreds of proteins [24, 25], and appears to play a critical role in the stabilization of helix-helix interactions. Such motifs were subsequently observed in many soluble proteins [26]. The amino acid composition of the variable positions in the glycine repeats of soluble proteins is certain to be very different from that of transmembrane proteins; transmembrane proteins would contain mostly hydrophobic residues in the variable positions of the repeats, while the variable

positions in soluble proteins would contain mostly find more hydrophilic residues. As such, the only commonality between glycine repeats in transmembrane proteins and glycine repeats in soluble proteins is likely to be the glycines found

at every fourth residue. As glycine lacks a side chain, it is suitable for allowing the close packing of helices, and could hence facilitate helix-helix dimerization. Most annotated FliH sequences contain a segment of repeats of the form AxxxG(xxxG) m xxxA, where m can vary on average between 2 and 10 depending on the bacterial Rebamipide species. While there is some variation to this pattern, not all sequences contain the N-terminal-side Axxx or the C-terminal-side xxxA, and FliH proteins from some species have no GxxxG repeats at all. Nevertheless, a significant proportion (44% in our set of sequences) of FliH proteins extracted from the non-redundant sequence database (see Methods) do exhibit the AxxxG(xxxG)mxxxA pattern. In addition to this long AxxxG(xxxG) m xxxA repeat segment, most FliH proteins also contain one or more shorter repeat segments elsewhere in the primary sequence (Figures 1, 2 and 3), which usually contain just a single AxxxG, GxxxG, or GxxxA. These shorter repeat segments are very poorly conserved, do not contain an obvious preference for particular amino acids at any of the three middle non-glycine positions, and often contain proline. Hence, these non-conserved GxxxG segments are unlikely to be either helical or biologically significant.