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Fig. 5 | Biology Direct

Fig. 5

From: COGcollator: a web server for analysis of distant relationships between homologous protein families

Fig. 5

Phylogenetic tree for COG0055 (FOF1-type ATP synthase, the catalytic β-subunit), COG0056 (FOF1-type ATP synthase, the non-catalytic α-subunit), COG1155 (catalytic A-subunits, A/V-type ATPase), COG1156 (non-catalytic B-subunits, A/V-type ATPase), and COG1157 (flagellar biosynthesis ATPase). The tree was constructed by using the MEGA 5 software [34] with the neighbor-joining algorithm [35] and JTT matrix for calculation of the evolutionary distances [36], see also (Additional file 2: Figure S1) for the full version of the tree. The sequences were sampled from proteins belonging to the COG0055, COG0056, COG1155, COG1156 and COG1157 from the set of 124 genomes (see, Additional file 1: Table S1): totally 368 amino acid sequences were used. We also added sequences belonging to the short representative list of 27 eukaryotic genomes (see, Additional file 1: Table S2), totally 196 proteins (with isoforms excluded) were added. Abnormally short (less than 400 amino acids) and long (more than 800 amino acids) sequences were removed, as well as poorly aligned proteins, which resulted in a set of 541 sequences. Conserved blocks were used for the tree construction (totally 391 positions). The branch lengths are in the units of the number of amino acid substitutions per site. Eukaryotic sequences are colored according to the taxonomy of corresponding organisms: orange for animals, brown for fungi, green for plants and light orange for other species. The clades of early-branching N-ATPases [21] are indicated by arcs

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