Figure 5

Two examples for interpreting DDBP (domain/domain boundary prediction) method. A: According to the prediction of Interpro/InterProScan, 3-H6 (NP_508026), a 431-amino-acid protein that has no TM region or the signal peptide, possibly contained three domains: Domain1 (24–118), Domain 2 (141–234), and Domain 3 (254–370). a, b, c, d on the right of horizontal lines mark four separate alignment results between protein 3-H6 and Protein Data Bank (PDB) database. a: the region 4–131 of 3-H6 is homology with the region 20–147 of 1ROU with 60% identity; b: the region 4–244 of 3-H6 was similar to the region 41–280 of 1Q1C with 48% identity; c: the region 7–408 of 3-H6 was similar to the region 24-422 of a 1KTO/A with 40% identity; d: the region 128–428 of 3-H6 was similar to the region 22–330 of 1P5Q/A with 35% identity. By combining the results of Interpro/InterProScan and alignments, three protein fragments (1–131, 128–244, and 245–431) were selected for 3-H6 as stable domains/fragments. B: 11020-H6 (corresponding to the region 299–792 of protein NP_493412), a 494-amino-acid protein that has no TM regions or the signal peptide, was predicted to have three possible domains/fragments (Fragment1: 53–225; Fragment2: 236–494; Fragment3: 337–475) by InterPro/InterProScan (shown on top). DLF results showed that protein 11020-H6 may contain five possible domain linkers (DL1: 19–52; DL2: 106–145; DL3: 215–241; DL4: 325–330; DL5, 373–383) (shown at the bottom). The stable domains/fragments of 11020-H6 were predicted as 53–225, 236–494 and 331–494 by the DDBP method (shown as the conclusion in the box at right).