Figures and Supplemental figures.

Table II. Identifiers to discriminate between the different ABC families and domains.

Figure 1. Domain arrangements in the ABC families. The transmembrane (TM) domains are indicated by 6 connected hatched segments. ATP Binding Cassettes are indicated by ovals marked ABC. The phosphorylatable regulatory region of ABCA members is marked R. The order of the domains in the various proteins is given but the intervening distances are not to scale. These proteins range in size from 300 amino acids to 2,000 amino acids.

Figure 2. Clustering of the ABC domains of Dictyostelium proteins. The amino acid sequences of 103 Dictyostelium ABC domains were aligned and related to each other. An unrooted tree with bootstrap values is presented with the values for the separation of the families given in bold. With a single exception (ABCG.20) domains from members of the same family clustered together. The first and second ABC domains in full transporters are marked with a bar to the right and clustered together. The single ABC domains found in members of the A, B and G families also clustered together within their respective families. ABCA.10 and ABCA.11 have only a single ABC domain but may be the first and second ABC domains of a full transporter, respectively. They cluster with the ABC domains of other full transporters of this family.

Figure 3.A) Tree of the ABCA family. The complete amino acid sequences of the ABCs were aligned and related to each other and homologs from other species. In this and other figures the bootstrap values are presented for unrooted trees. Full transporters with 2 TM/ABC domains formed a single group that clustered with homologs in Trypanosoma crusi (Tc), Homo sapiens (Hs) and Arabidopsis thaliana (At). These species designations are used throughout this study. Two half transporters clustered with other genes from these organisms as well as one from Entamoeba histolytica (Eh).

Figure 3.B) Proposed order of gene loss in the ABCA family. The common ancestor of animals, plants, fungi and Dictyostelium is presumed to have carried a gene encoding a half tranporter as well as one encoding a full transporter. The half transporter was lost in the line leading to animals and fungi before these two kingdoms diverged. The full transporter was subsequently lost from the progenitor of fungi. Gene losses are indicated by an X.

Figure 4. Two possible routes by which the ABCG genes may have arisen. It has been assumed that the original gene in which the ABC domain precedes the TM domain was formed by the fusion of independent regions encoding such domains. Alternatively, a copy of the central region of a pre-existing ABC gene generated a functional half-transporter. Tandem duplication and fusion of this gene could have generated the full transporters.

Figure sup 1 - ABCB Family Tree. The two full transporters of this family grouped together and clustered with human MDR1, an Entaboeba gene and a rice gene (Os). The half transporters clustered with other human homologs and a fly gene from Drosophila melanogaster (Dm). Three of the genes that carry a serine-protease domain, Tag B,C and D, grouped together and more distantly with another such gene, TagA.

Figure sup 2 - ABCC Family Tree. Members of this family formed two groups, one of which is homologous to an Arabidopsis gene, MRP.4, and the other to Arabidopsis genes MRP.1 and MRP.2. There is a human homolog to the second group, Hs ABCC.5. A different human gene, Hs ABCC.2, as well as a gene of Saccharomyces cerevisiae, Sc YCF1, cluster with the remaining Dictyostelium member of this family, ABCC.8.

Figure sup 3 - ABCD Family Tree. The three members of this family clustered with distinct homologs.

Figure sup 4 - ABCE Family Tree. Members of this family do not have transmembrane domains. The single Dictyostelium gene of this family clusters with human and plant genes that encode RNase L inhibitors. The closest homologs in yeast are more distantly related. Homologs present in archae bacteria form a separate group (not shown).

Figure sup 5 - ABCF Family Tree. Members of this family do not have transmembrane domains. ABCF.1 and ABCF.4 cluster with the yeast translational regulator GCN20

Figure sup 6 - ABCG Family Tree. A) The full transporters form two groups. Homologs of one are only found in the plant Arabidopsis, AtPDR5like being only one example of this clustering, while homologs of the other are only found in fungi. B). The half-transporters form a group with two outlyers. Homologs are found in the human, Arabidopsis and Drosophila genomes but not in those of yeast.

Figure sup 7 - ABCH Family Tree. A) The Dictyostelium member of the ArsA family clusters with plant and animal homologs more closely than do yeast genes. B) No eukaryotic homologs of ABCH.1 and ABCH.2 were recognizable which are both closely related to the Escherichia coli gene Ec YbbA and to bacterial genes involved in the uptake of polar amino acids.

Figure sup 8. Alignment of concensus domains from the family groups of ABC genes. Positions where more than half the entries showed a conserved amino acid were used to generate concensus domains. Alignment of these 14 domains allowed us to recognize identifier motifs unique to each family group shown in red within the shaded boxes. A list of the identifiers is given in Table 2. The position of the Walker A, B and ABC signature are indicated by the white boxes. Download Figure 8.