Fig. 2

Site-specific amino-acid preferences for β-lactamase. The height of each letter is proportional to the preference for that amino acid at that site, and letters are colored by amino-acid hydrophobicity. These are the preferences experimentally measured in [14] for TEM-1 β-lactamase under selection with 2.5 mg/ml ampicillin, re-scaled by the stringency parameter β= 1.01 from Table 2. The re-scaling is done so that if the experimentally measured preference for amino-acid a at site r is π _r,a , then the rescaled preference is proportional to (π _r,a )^β. The β-lactamase sequence is numbered using the Ambler scheme [82], meaning that residue numbers 239 and 253 are skipped. Comparable data for Gal4, NP, and HA are shown in Additional files 2, 3 and 4, respectively