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Table 1 Alignment of the year 2009 consensus sequences of the V3 loop.

From: Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties

Subtype

Sequence

Charge

 

123456789012345678901234567890123456

 

2B4C

CTRPNQNTRKSIHIGPGRAFYTTG-EIIGDIRQAHC

3

2QAD

CTRPNNNTRKSINIGPGRALYTTG-EIIGDIRQAHC

3

A

CTRPNNNTRKSVRIGPGQAFYATG-DIIGDIRQAHC

3

AB

CIRPGNNTRTSIRIGPGQTFYATG-DVIGDIRQAHC

2

AE

CTRPSNNTRTSITIGPGQVFYRTG-DIIGDIRKAYC

3

AG

CTRPNNNTRKSVRIGPGQTFYATG-DIIGDIRQAHC

3

B

CTRPNNNTRKSIHIGPGRAFYATG-DIIGDIRQAHC

3

C

CTRPNNNTRKSIRIGPGQTFYATG-DIIGDIRQAHC

3

CPX

CTRPNNNTRKSIHIGPGQAFYATG-DIIGDIRQAHC

2

D

CTRPYNNTRQSTHIGPGQALYTT---IIGDIRQAHC

2

D35

CTRPYNNTRQSTHIGPGQALYTTK-NIIGDIRQAHC

3

F

CTRPNNNTRKSIHLGPGQAFYATG-DIIGDIRKAHC

3

G

CTRPNNNTRKSIRIGPGQAFYATG-DIIGDIRQAHC

3

H

CTRPNNNTRKSIHIGPGQAFYATG-DIIGDIRQAHC

2

J

CIRPANNTRKGIHIGPGQVLYATG-EIIGDIRQAHC

2

K

CTRPNNNTRKSIHIGPGRAFYATG-DIIGDIRQAHC

3

N

CTRPGNNTGGQVQIGPAMTFYNIE-KIVGDIRQAHC

1

O

CERPGNNTVQEIKIGP-MAWYSMGLEENNNSRAAYC

-1

  1. V3 loop subtype consensus sequences were obtained using the tools available within the Los Alamos National Laboratory Database ([23]; http://www.hiv.lanl.gov), except for sequences 2B4C and 2QAD, which are from the crystal structures deposited at the PDB. Some subtype consensus sequences were identical: CPX with H, and B with K. Subtypes AB, AE, AG, and CPX are circulating recombinant forms (CRFs). The construction of D35 from D is described in Methods. Gaps are introduced by the alignment.