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. 2014 Jun 2;15:166. doi: 10.1186/1471-2105-15-166

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Copyright © 2014 Wong et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Structural alignments between representative structures of domain model and hit sequence for the 3 true (false-negative) hits. The original E-values of these 3 hits (A. CHLI_PORPU,B. HEM1_METKA, C. TIP12_MAIZE) were insignificant against the Pfam domain models (PF00004.24 AAA, PF00106.20 adh_short, PF01226.12 Form_Nir_trans). However, their structural E-values were nevertheless significant (E < 0.1). Indeed, the structural alignments of representative structures between domain models and hits showed that their RMSD values were between 3.2 to 3.91 and over their full-length sequences. This indicated that the domain model and the associated hit sequences were indeed homologous to each other.