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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.