Table 1 Known HXB2 N-linked glycosylation site conservation by different alignment methods in HIV-1 protein B sequences (Bold value denotes equally maximum score and ^a when unique for our method)

88 NVT

C1

100

100

98.72

100

100

100

136 NDT

V1

44.23

23.08

15.38

52.56

23.08

23.08

141 NSS

V1

55.13^a

17.95

26.28

7.05

6.41

20.51

156 NCS

V1

97.44

97.44

97.44

97.44

97.44

97.44

160 NIS

V2

89.1

89.1

89.1

89.1

89.1

89.1

186 NDT

V2

28.85^a

15.38

12.82

15.38

13.46

14.74

197 NTS

V2

98.08

98.08

98.08

98.08

98.08

98.08

230 NKT

C2

26.28

26.28

26.28

26.28

26.28

26.28

234 NGT

C2

74.36

74.36

74.36

74.36

74.36

74.36

241 NVS

C2

97.44

97.44

97.44

97.44

97.44

97.44

262 NGS

C2

100

100

100

100

100

100

276 NFT

C2

98.08

98.08

98.08

98.08

98.08

98.08

289 NTS

C2

69.23

69.23

69.23

69.23

69.23

69.23

295 NCT

C2

78.85

78.85

78.85

78.85

78.85

78.85

301 NNT

V3

92.95

92.95

92.95

92.95

92.95

92.95

332 NIS

C3

87.18

87.18

87.18

87.18

87.18

87.18

339 NNT

C3

77.56

77.56

77.56

77.56

77.56

78.21

356 NKT

C3

83.33

83.33

12.82

10.9

45.51

87.18

386 NST

V4

82.05

82.05

82.05

82.05

82.05

82.05

392 NST

V4

87.82

87.82

87.82

87.82

87.82

87.82

397 NST

V4

89.10^a

8.97

39.1

37.18

8.97

8.97

406 NNT

V4

32.05

20.51

17.31

50

8.97

16.03

448 NIT

C4

92.31

92.31

92.31

92.31

92.31

92.31

463 NES

V5

69.87^a

46.79

32.05

26.28

39.74

42.95

611 NAS

gp41

98.08

98.08

98.08

98.08

98.08

98.08

616 NKS

gp41

89.74

89.74

89.74

89.74

86.54

89.74

624 NHT

gp41

95.51

95.51

95.51

94.87

0.64

0.64

637 NYT

gp41

98.72

98.72

98.72

98.72

98.08

98.72

674 NIT

gp41

13.46

13.46

13.46

13.46

13.46

13.46

750 NGT

gp41

1.28

1.28

1.28

1.28

1.28

1.28

816 NAT

gp41

69.87

69.87

69.87

69.87

69.87

69.87

Combined score over N Sites

2317.95^a

2131.4

2069.87

2114.1

1962.82

2034.62