More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Figure 4
Examples of domain architectures of false-positive HMM hits caused by TM helices in the fragment-mode search.
We show illustrative examples for six Pfam release 23 models: Herpes_glycop_D (PF01537.9), CDC50 (PF03381.7), Cation_ATPase_N (PF00690.18), GSPII_F (PF00482.11), PAP2 (PF01569.13) and HCV_NS4b (PF01001.11). The black boxes denote the problematic domain annotations in the respective sequences. Additional material such as hmmpfam outputs and alignments are available at the associated BII WWW site for this work. Domain architecture illustrations were created with DOG 1.5 [98].