Supplementary Figure 1: Sequence alignment for modeling.
From: The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism
(a) Refined sequence alignment between the template (i.e., reordered X-ray crystal structure), and the normal sequence of VcINDY, which corresponds to the repeat-swapped model. The percentage of identical residues is ~24% for the full-length alignment, including peripheral elements; within the repeats, ~20% of the residues are identical. The sequence range of each repeat in the model is indicated by rectangles under the target sequences, colored as in Fig. 1a. The secondary structure (helix) assignment obtained with DSSP for the X-ray structure is indicated by dark blue rectangles. Amino acids are colored as followed: red for acidic (asp and glu), dark blue for basic (his, lys, and arg), cyan for polar (ser, thr, asn, and gln), yellow for aromatic (tyr, trp, and phe), pink for helix-breaking (pro and gly), and pale yellow for cysteine and aliphatic (ala, val, ile, leu, and met). (b) Schematic indicating which structural repeat segments (colored as in (a)) are modeled on which segments of the crystal structure template. The peripheral helices (TM 1) in the model and template are shown in gray.
