Table 1.
Predicted signal peptide cleavage sites for all HA subtypes.
Figure 1.
Sequence alignment of HA for known sub-types.
Alignment of mature HA sequence for all known HA sub-types. Additional strains have been included for sub-types which show variation in the length of HA. Sequences are ordered according to their phylogenetic classification as group 1 (magenta bar) or group 2 (orange bar) HA. The protein secondary structure elements, α-helices and β-strands, are highlighted with red bars and cyan arrows, respectively. A blue box highlights regions which have high structural variation across all subtypes. Amino acids within these regions should not be defined as equivalent between all sub-types. Each amino acid is coloured according to clustalx2 rules [11]. Briefly, glycine and proline are coloured orange and yellow, respectively. Conserved positively charged residues and negatively charged residues are coloured red and magenta, respectively. Conserved cysteines are coloured pink while conserved serine or threonine residues are in green. The remaining amino acids, if conserved are coloured blue. The sequences representative of each subtype are as follows: H1(A/United Kingdom/1/1933); H1pdm(A/California/04/2009); H2(A/Singapore/1/1957); H3(A/Aichi/2/1968); H4(A/swine/Ontario/01911/2/1999); H5(A/Vietnam/1203/2004); H5c221(A/chicken/Egypt/0915-NLQP/2009); H6(A/chicken/Taiwan/0705/1999); H7(A/Netherlands/219/2003); H8(A/turkey/Ontario/6118/1968); H9(A/swine/HongKong/9/1998); H10(A/mallard/bavaria/3/2006); H11(A/duck/England/1/1956); H12(A/duck/Alberta/60/1976); H13(A/gull/Maryland/704/1977); H14(A/mallard/Astrakhan/263/1982); H15(A/duck/Australia/341/1983); H16(A/black-headed-gull/Turkmenistan/13/1976); H17(A/little-yellow-shouldered-bat/Guatemala/060/2010); H18(A/flat-facedbat/Peru/033/2010).
Table 2.
Equivalent amino acid numbering for subtypes currently circulating in humans or have pandemic potential.