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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

Figure 3

Phylogenetic tree derived from 44 IRK AA sequences. Forty-four sequences included 3 Halocynthia roretzi IRKs, 4 Ciona IRKs, 15 human IRKs, 3 Caenorhabditis elegans IRKs, 3 Caenorhabditis briggsae IRKs, 4 Drosophila melanogaster IRKs, and 5 Anopheles gambiae IRKs. These amino acid (AA) sequences were referred from JGI Ciona genome database, from NCBI GenBank and Genome database, or from Ensembl database. The obtained AA sequences from the seven taxa were aligned using ClustalX1.83 program. The gaps within nonpreserved regions were carefully deleted manually by the BioEdit program. Then the phylogenetic tree derived from the aligned data was made by the Neighbor Joining Method in the Mega3 v3.1 program, using the Amino Poisson correction model with Gamma-distributed Rates among sites (Gamma parameter 2.0) and Bootstrap as the test of inferred branches (Repetition 500), including 295 sites with a pair-wise deletion of Gap/Missing Data. As an outgroup, the seven bacterial IRK-like proteins were chosen, including KirBAC1.1, of which the molecular structure was recently determined by X-ray [32]. Those bacterial AA sequences were also referred from an NCBI microbial genome database. The scale for tree-branch length is 0.2 mutation per AA site and is illustrated at the lowermost part of the figure. Abbreviations: IRK, elementary IRK; IRK/G, G-protein-activated IRK; IRK/AR, ATP-regulated IRK; IRK/AS, ATP-sensitive IRK like SU-receptor-coupled IRK. Nossp, Nostoc sp.; Nospc, Nostoc punctiforme; Magn, Magnetospirillum magnetotacticum; Chrom, Chromobacterium violaceum; Buhpd, Burkholderia pseudomallei; Buhfg, Burkholderia fungorum; Rals, Ralstonia solanacearum. Kef-type K+ transport system. Prob-ATPsenIRK, Probable ATP-sensitive IRK. Put-ATPsenIRK, Putative ATP-sensitive IRK. The scale and abbreviations are applied in this and the following figures.

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