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Table 4 Radical amino acid sites under positive selection detected by Datamonkey, Branch-site model and TreeSAAP Simultaneously

From: Molecular evolution of globin genes in Gymnotiform electric fishes: relation to hypoxia tolerance

Gene

Positiona

Cladeb

AA Changes

Radical Changes in AA Propertiesc

Total

Hba

18

w

I-A

pK’, R a ,

2

 

35

k

T-A

P α

1

  

s

T-V

N s , R a

2

  

n

T-P

K o, H t

2

  

o

T-I

N s , B r , pK’ , R a , H p , H t

6

 

46

w

H-S

F, E t

2

 

73

h, s

S-A

P α , P c , P

3

  

w

A-G

P α , P c , P

3

 

79

o, w

A-T

P α

1

  

p, q

A-C

P α , N s , c , K o , pK’ , α n

6

 

83

k, q

A-S

P α , P c , P

3

Hbb

15

p

M-I

pK’

1

 

20

o

S-H

F

1

 

29

o

L-I

pK’

1

 

81

s

N-A

P α , P c , P

3

 

113

o

V-T

N s , R a

2

 

114

o

C-T

N s , B r , c

3

 

123

m, w

V-G

P β , B l , P c , F , R a , P

6

  

o, q

V-A

P β

1

 

132

o

W-I

pK’

1

 

133

a

Q-C

N s , B r , c , h , p , E t

6

  

h

C-S

N s , B r , μ

3

  

w

S-A

P α , P c , P

3

  

q

C-Q

N s , B r , c , h , p , E t

6

  

m

C-T

N s , B r , c

3

  

o

C-E

P α , N s , B r , c , h , E l , P r , p , α c , H p , E t

11

Mb

9

o

K-A

E t , B r , K o, h, E sm

5

 

12

a

G-P

B l , α c , H t

3

 

27

w

T-G

B l ,

1

  

l

T-V

N s , R a

2

  

o

S-W

B l , R F , P c , C a , E l , F , M v , M w , V 0 , u , R a , H t

12

 

37

w

Q-I

N s , B r , pK’ , h , F , p , E t , E l , R a , H p , H t

11

 

92

w, f

K-Q

Ph i

1

  

g

K-I

N s , P β , B r , R F , pK’ , h , E l , F , H nc , P r , p , R a , H p , E t

14

  

t

I-V

pK’

1

  

d

K-T

Ph i , E t

2

 

98

a

N-A

P α , P c , P

3

  

w

A-I

pK’, R a

2

  

d

A-G

P α , P c , P

3

  

m

G-V

P β , B l , P c , F , R a , P

6

  

o

A-N

P α , P c , P

3

 

106

w

V-C

pK’, C, R a , P

4

 

108

w

V-C

pK’, C, R a , P

4

 

109

w

K-V

N s , B r , h , E l , F , p , R a , H p , H nc , E t

10

  

o

K-S

E t

1

 

122

o

Q-A

K o, E t

2

 

134

o

N-A

P α , P c , P

3

  1. aRelative to Zebrafish (Danio rerio) protein sequences, i.e., Mb (Q6VN46), Hba (Q90487), and Hbb (Q90486) in UniProtKB. Codons identified as under positive selection more than one ML methods. Positively selected sites detected by Datamonkey are represented in underlined letters
  2. bAmino acid substitution occurred along clades, with detailed information marked in Fig. 1
  3. cRadical changes in amino acid properties under category 6–8 were detected in TreeSAAP. Amino acid sites that belong to the Type II class (greater than 6 property changes) are represented in bold. Physicochemical amino acid properties available in TreeSAAP are as following: α c : Power to be - C-term., α-helix; α n : Power to be in the N-terminal of an α-helix; B r : Buriedness; c: Composition; C a : Helical contact energy; E l : Long-range non-bonded energy; E sm : Short and medium range non-bonded energy; E t : Total non-bonding Energy; F: Mean r.m.s. fluctuation displacement; h: Hydropathy; H nc : Normal consensus hydrophobicity; H p : Surrounding hydrophobicity; H t : Thermodynamic transfer hydrophobicity; K o: Compressibility; μ: Refractive index; M v : Molecular volume; M w : Molecular weight; N s : Average number of surrounding residues; P α : α- helical tendencies; P β : β-structure tendencies; P c : Coil tendencies; P: Turn tendencies; p: Polarity; pH i : Isoelectric point; pK’: Equilibrium Constant of ionization for COOH; P r : Polar requirement; R a : Solvent accessible reduction ratio; R F : Chromatographic index; V 0: Partial specific volume
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BMC Ecology and Evolution

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