Figure 6

Examples of false negative domain assignments. a) Ribbon diagrams of unmapped domain (left) transcription factor Ndt80 (PDB: 1mnn[33]) and library representative (right) p52 subunit of NF-kappa B, N-terminal domain (PDB: 1a3q[49], residues A37-A226). β-strands that belong to the Ig fold core are yellow, and additional structural elements are grey. Dashed lines indicate breaks in the chain. b) Ribbon diagrams of unmapped domain (left) E. coli adaptor protein ClpS (PDB: 1lzw[34], chain A) and library representative (right) ribosomal protein L7/12 from E. coli, C-terminal domain (PDB: 1ctf[50]). Dashed lines indicate breaks in the chain. c) Cα traces of unmapped domain (left) δ-conotoxin TxVIA from Conus textile (PDB: 1fu3[35]) and library representative (right) ω-conotoxin TXVII from Conus textile (PDB: 1f3k[51]). These two conotoxin domains share ~40% sequence identity. Disulfide bonds are shown in ball-and-stick format.