Table 1.

Peptide sequences selected by the K42-41L mAb from the J404 random peptide library

The "#" column indicates the number of phage clones with the same sequence that are independently isolated. Peptide sequences were ranked for antibody affinity by ELISA A₄₀₅, which was measured in quadruplicate for each page clone, and STD indicates the standard deviation of the ELISA absorbance. Positions in the aligned phage clone sequences were assigned a color (greens, reds, blues, and pinks) such that different colors corresponds to different approximate "motifs" of the TGALQERSK consensus sequence, when mapped to the rhodopsin sequence. Four motifs—GAL, QE, R, and T/KS—were common to many mappings of this sequence to rhodopsin (as shown later). "Identity scores" for each position in the consensus were calculated relative to the consensus sequence TGALQERSK, reflected the tightness of the consensus, and the scores are shown under the consensus near the bottom of the table. Exact amino acid matches scored "1.00" and the sum total score for all phage clones at each position was divided by the total number of clones with a residue aligned to that position. "Homology scores" for each position in the consensus are at the bottom of the table and were calculated in a similar manner to identity scores, except that chemically similar residues scored as "0.50" per occurrence for closely related residues (letters in medium-colored boxes under the identity scores), or "0.25" for other similar residues (letters in light-colored boxes under identity scores). The definitions for chemically similar residues are listed in Table 3.