Fig. 2

Top structural similarities. Found by the DALI program in the 90% non-redundant PDB (PDB-90) using the full length foamy virus capsid as a query (145 residues). The columns are: the ranked number of the hit (No.), marked by a ’|’ for a capsid protein, otherwise ’:’; the PDB entry identifier (Chain, with the chain designation after the dash); the DALI Z-score (Z) (significance estimate); the root-mean-square-deviation (rmsd) over aligned α-carbon positions; the number of aligned positions (lali); the number of residues in the matched structure (nres); the percentage sequence identity of the match (%id) followed by a description of the molecule. It can be seen from the number of matched positions (lali) that most matches are partial, covering typically less than half the query structure