Table 4.

Classification of proteins containing TE-associated Pfam domains detected by the GA and TC cut-offs of HMMER. The categories of hits are described in the text and the number (percentage) for each category is shown for searches against the PDB and SwissProt data sets.

Category	PDB	Swiss-Prot
Potential TE-related proteins	11 (7.86%)	3 (21.43%)
Viral proteins	14 (10.00%)	0 (0%)
TE-encoded proteins	18 (12.86%)	7 (50.00%)
Synthetic construct	47 (33.57%)	0 (0%)
non-specific TE-related protein domains	50 (35.71%)	4 (28.57%)