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. 2014 Jul 22;6(7):1894–1910. doi: 10.1093/gbe/evu147

Fig. 3.—

Fig. 3.—

Domain search strategy and homology clustering. Homologous sequences of the N- and C-terminal region of cyt b (COB_n) and (COB_c) were detected by HMMER3 (Eddy 2011) from the NCBI RefSeq database (Pruitt et al. 2007). Colors of the N- and C-terminal regions are identical to figure 2, and the striped box denotes the C-terminal region below the inclusion threshold of HMMER3, whereas its Qo motif was identified by multiple sequence alignment (COB_NC’). Entries from COB_n and COB_c were sorted according to their structural compositions as COB_NC, COB_NC’, COB_N, and COB_C (see Materials and Methods), with incomplete sequences removed. The latter two groups represent cyt b with split N- and C-terminal regions and were further paired according to their gene locus tags to represent their full-length form (COB_N//C). Representative sequences were obtained by clustering all sequences with 50–100% identity by CD-HIT (Li and Godzik 2006).