Figure_2_cysDN_phylogeny

Figure 2 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"
Files included:Fig2_cysN_ef_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation FactorFig2_cysD_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysD_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysD_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation Factor
Figure 2. Phylogeny of heterodimeric ATP sulfurylase subunits (CysDN). (a) Bayesian phylogeny of 416 amino acid residues of sulfate adenylyltransferase subunit 1 (CysN) and elongation factor 1 alpha (EF-1A) or elongation factor thermo unstable (EF-Tu) proteins. CysN, in green, formed a separate phylogenetic cluster from the homologous EF-1A and EF-Tu in blue. ANME proteins are bolded in red. The phylogenetic analysis distinguished CysN from their homologous elongation factor in ANME. (b) Bayesian phylogeny of 270 amino acid residues of sulfate adenylyltransferase subunit 2 (CysD) in green. They are found in ANME genomes next to CysN confirming that they are the heterodimeric ATP sulfurylase subunits. Asterisks (*) indicate proteins that have been studied biochemically or structurally (Andersen et al., 2000; Kobayashi et al., 2010; Liu et al., 1994; Mougous et al., 2006; Schmeing et al., 2009; Thirup et al., 2015; Vitagliano et al., 2001). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.

本数据集对应手稿《厌氧产甲烷古菌（Anaerobic methanotrophic archaea, ANME）同化性硫酸盐还原通路的比较基因组学与蛋白质组学分析》的图2，所包含的文件如下：
1. Fig2_cysN_ef_clustalo_alignment.faa：经ClustalO比对得到的蛋白质序列比对文件
2. Fig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa：用于系统发育分析的过滤后蛋白质序列文件（共包含416个氨基酸残基）
3. Fig2_cysN_ef_clustalo_tree.png：CysN与延伸因子的最终贝叶斯系统发育树图
4. Fig2_cysD_clustalo_alignment.faa：经ClustalO比对得到的CysD蛋白质序列比对文件
5. Fig2_cysD_clustalo_alignment_filtered_for_tree.faa：用于系统发育分析的过滤后蛋白质序列文件
6. Fig2_cysD_clustalo_tree.png：CysD的最终贝叶斯系统发育树图

图2 异二聚体ATP硫酸化酶（ATP sulfurylase）亚基（CysDN）的系统发育分析：
(a) 硫酸盐腺苷转移酶（sulfate adenylyltransferase）亚基1（CysN）与延伸因子1α（elongation factor 1 alpha, EF-1A）或热不稳定延伸因子（elongation factor thermo unstable, EF-Tu）共416个氨基酸残基的贝叶斯系统发育树。其中CysN以绿色标注，与蓝色标注的同源EF-1A和EF-Tu形成独立的系统发育簇。ANME来源的蛋白以红色粗体标注。本系统发育分析可区分ANME中的CysN与其同源延伸因子。
(b) 硫酸盐腺苷转移酶亚基2（CysD，绿色标注）共270个氨基酸残基的贝叶斯系统发育树。该蛋白在ANME基因组中与CysN相邻分布，证实二者为异二聚体ATP硫酸化酶的两个亚基。星号（*）表示经生化或结构研究验证的蛋白（Andersen等，2000；Kobayashi等，2010；Liu等，1994；Mougous等，2006；Schmeing等，2009；Thirup等，2015；Vitagliano等，2001）。蛋白登录号取自NCBI（National Center for Biotechnology Information）数据库，基因ID取自IMG（Integrated Microbial Genomes）数据库，均标注于括号内。分支上的黑色圆点代表贝叶斯后验概率大于90%，标尺表示每一位点的氨基酸替换数。