Fig. 5
Top domain similarity alignments. The sequence alignments are shown for the top 12 capsid domain matches found by the DALI program using the foamy virus capsid N and C domains separately as a query over the full PDB. The sequence of the N-terminal domain (N-ter) is shown at the top of the first alignment block and the sequences of the C-terminal domain (C-ter) at the top of the second block. The sequences of the ortho-virsuses aligned below these all come from the “swapped” relationship of C and N terminal domains, respectively. These alignments, which are determined by structure not sequence, exhibit no specific similarity beyond what would be expected from aligning similar secondary structures from similar sized domains. (Amino acid identities are marked by a bar and similarities by a colon). The location of alpha helices is marked by the letter ‘a’, taken from the PDB entries of their adjacent proteins. A selection of other foamy virus sequences are aligned above the foamy virus sequence of known structure (human) which, from the top, are from: simian (orangutan), squirrel-monkey, cat, simian (unspecified) and horse. (NB. no alignment is implied between the two blocks of aligned domains)