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Table 5 Sites identified as divergently evolving by Bayes empirical Bayes inference under the ‘CmC αβ MVR & β T ’ Clade model

From: Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

Site PP Location Notes on Opsin Structure–Function
22 0.90 N-term  
24 0.81 N-term  
27 0.91 N-term  
31 0.75 N-term  
36 0.86 N-term / TM1 RH2 spectral tuning site [80]. Situated on edge of retinal uptake/release channel [76].
56 0.90 TM1  
99 0.91 TM2  
107 0.96 E1 Adjacent to RH2 spectral tuning site (site 108) [80].
109 0.86 E1 / TM3 Adjacent to RH2 spectral tuning site (site 108) [80]. Adjacent to cysteine bond site (site 110) [82].
112 0.80 TM3 RH2 spectral tuning site [80]. Adjacent to opsin counterion (site 113) [83].
122 0.85 TM3 Major RH2 spectral tuning site [78]. Also influences G protein activation efficiency, active-state decay rate, and visual pigment regeneration rate [84].
149 0.77 C2 / TM4 Possible phosphorylation site [85, 86].
158 0.86 TM4  
162 0.94 TM4  
165 0.79 TM4 Possible RH2 spectral tuning site [80].
179 0.88 E2  
213 0.75 TM5 RH2 spectral tuning site [80].
214 0.89 TM5 Adjacent to RH2 spectral tuning site (site 213) [80].
218 0.86 TM5 RH2 spectral tuning site [80].
263 0.90 TM6  
273 0.85 TM6 Role in retinal uptake [76, 81].
277 0.90 TM6 / E3  
282 0.80 E3  
284 0.75 E3  
290 0.93 TM7  
304 0.97 TM7  
335 0.79 C-term Possible phosphorylation site [85, 86].
  1. NOTE— Site numbering follows bovine RH1 opsin. Approximate location follows Sakmar et al. [34]. Abbreviations: N-term N-terminal tail, TM Transmembrane helix, E, Extracellular loop, C Cytoplasmic loop, C-term C-terminal tail.
  2. Only sites with posterior probability (PP) > 0.75 are shown. Underlined sites are those which substituted along branches within the Lake Tanganyikan cichlid RH2aβ partition of the phylogeny.