1. Simplified neighbor-joining tree of ABC domains.
Simplified neighbor-joining tree of ABC domains. For clarity, only the main branches that point to ABC families are drawn. The major subdivisions of the tree correspond to the three classes of ABC systems, whose schematic structural representations are given in the right part of the figure. ABC domains are shown with green circles, and IM domains are shown with differently colored rectangles. For the sake of simplicity, accessory proteins (BPs, MFPs, and OMFs) are omitted. Class 1 (red branches) systems have fused ABC and IM domains, corresponding mainly to exporters. IM domains shown in purple represent ABC transporters with the IM domain at the N terminus, corresponding to IM-ABC and (IM-ABC)2 topologies. N- and C-terminal domains are symbolized by N and C, respectively. IM domains shown in orange represent ABC transporters with the IM domain at the C terminus, corresponding to ABC-IM and (ABC-IM)2 topologies. Class 1 contains two atypical families of systems, CCM and MCM, with a different structural organization. Class 2 (blue branches) systems have tandemly repeated ABC domains and no known TM domains (ABC2 topology), corresponding to proteins involved in nontransport processes. The UVR family was omitted during the generation of the tree because large domain insertions within the ABC domains prevent the establishment of the multiple sequence alignment. However, binary comparisons established the relationship between UVR proteins and class 2 systems. Class 3 (green branches) systems have IM (red rectangles) and ABC (green circles) domains carried by independent polypeptide chains, corresponding mainly to importers. For class 3, systems that could be exporters are shown in boxes. Family names are abbreviated according to the conventions used in Table 1 and throughout the text. See Table 1 for the abbreviations of family names and for functional descriptions. OPN-D, OPN-F, HAA-F, and HAA-G correspond to the two different ABC subunits of the OPN and HAA systems, respectively. MOS-N and MOS-C correspond to the N- and C-terminal ABC domains of MOS family ATPases. The scale at the top of the figure corresponds to 5% divergence per site between sequences.
Amy L. Davidson et al. Microbiol. Mol. Biol. Rev. 2008; doi: /MMBR