Table 1 Detection of TE-encoded sequences in PDB proteins. The number of PDB entries found with TE protein fragments (from autonomous TEs) by different search programs is shown. The percentage of total PDB entries is shown in the parenthesis. The square bracket indicates the number and the percentage of protein entries associated with sequences derived from TEs including the non-autonomous ones.

E-value ≤ 1

17543 (44.69%)

4924 (16.15%) [10890: 35.72%]

1558 (3.97%)

1643 (4.19%) [3343: 8.52%]

8662 (28.41%)

13107 (42.99%) [19891: 65.25%]

N/A

E-value ≤ 0.1

2757 (7.02%)

1531 (5.02%) [3076: 10.09%]

614 (1.56%)

764 (1.95%) [1207: 3.08%]

5671 (18.60%)

7721 (25.33%) [11474: 37.64%]

N/A

E-value ≤ 0.01

533 (1.36%)

778 (2.55%) [1453: 4.77%]

424 (1.08%)

586 (1.49%) [827: 2.11%]

3943 (12.93%)

5688 (18.66%) [8481: 27.82%]

N/A

E-value ≤ 0.001

256 (0.65%)

564 (1.85%) [917: 3.01%]

364 (0.93%)

530 (1.35%) [700: 1.78%]

3030 (9.94%)

4832 (15.85%) [6995: 22.94%]

N/A

E-value ≤ 0.0001

168 (0.43%)

423 (1.39%) [682: 2.24%]

308 (0.78%)

464 (1.18%) [552: 1.41%]

2266 (7.43%)

4057 (13.31%) [6033: 19.79%]

N/A

E-value ≤ 0.00001

148 (0.38%)

371 (1.22%) [555: 1.82%]

210 (0.54%)

388 (0.99%) [474: 1.21%]

1676 (5.50%)

3533 (11.59%) [5035: 16.52%]

N/A

GA (gathering threshold)

140 (0.36%)

N/A

N/A

N/A

N/A

N/A

N/A

TC (trusted cut offs)

140 (0.36%)

N/A

N/A

N/A

N/A

N/A

N/A

default value

N/A

N/A

N/A

N/A

N/A

N/A

465 (1.53%) [950: 3.12%]