Table 4.

Summary of FINDMAP and visual mappings of epitopes of the selected anti-rhodopsin antibodies

The "Substitution score" is the degree to which the epitope sequence resembles the rhodopsin sequence to which it was mapped. Table 3 was used to score residue relatedness. An exact amino acid match (green letters in the table) scores 1.0, mapping to a closely related residue scores 0.50 (purple letters), mapping to a less related residue scores 0.25 (orange letters), and mapping to a "forbidden" residue (red letters) scores 0.0. The sum score is divided by the epitope length and converted to a percentage. Residues in black in some epitope mappings were forced to a particular residue before FINDMAP was run. All the FINDMAP results shown were obtained with a gap penalty of 0.5 and a maximum gap width penalty of 1.5 (Mumey et al. 2002). Mappings with a FINDMAP score labeled N/A were done by manual inspection. The constraint codes for different mappings are as follows. (1) most stringent restrictions for mapping to the rhodopsin sequence using rhodopsin residues limited to the cytoplasmic face (65–70, 140–150, 226–253, 306–348); (2) a wider range of rhodopsin sequence was made accessible for mapping, including rhodopsin residues (61–77, 133–152, 216–254, 301–348); (3) the least stringent restrictions on the rhodopsin residues used for mapping (51–90, 116–164, 211–264, 291–348); (4) for mapping the extracellular face of rhodopsin, allowed regions are 1–36, 91–109, 171–199, 277–289; and (5) similar to mapping the extracellular face of rhodopsin except slightly less stringently constrained to the extracellular; rhodopsin residues 37–45 and 200–205 were also allowed. The "ROYGBIV" rainbow color scheme under "epitope sequences" corresponds to the colors used in Figures 5 ▶–7. Red denotes position 1 of the consensus and violet in position 9. Tabulations of additional mapping are included in the Supplemental Material.