Orthologs of acyl-CoA synthetases and AcAS identified for phylogenetic analysis.

The full amino acid sequences of PfACS9, PfACS10, PfACS11, and PfAcAS, and the partial amino acid sequence of PfACS12 (the first 664 amino acids, excluding the thiamin-diphosphate-binding fold domain) were used as query sequence (green) in an iterative search (jackhmmer) (5 iterations) for orthologs in the UniProtKB database [160]. E-values found in our jackhmmr search are reported, and hits were identified as genes that showed an E-value of −50 for at least 1 query sequence. The E-value of genes that were below the E-value cutoff for a query sequence are indicated in red. The following genes were excluded from phylogenetic analysis: genes that were not identified as hits as the E-value was below the cutoff for all query sequences (gray shading), genes that did not align using the partial deletion cutoff of 50% in our alignment using ClustalW (dark gray shading), and genes that did not cluster with other genes in the phylogenetic tree (blue shading). (XLSX)以PfACS9、PfACS10、PfACS11及PfAcAS的完整氨基酸序列，以及PfACS12的部分氨基酸序列（前664个氨基酸，剔除硫胺素二磷酸结合折叠结构域）作为查询序列（绿色标记），在通用蛋白知识库（UniProtKB）数据库中，通过迭代搜索工具jackhmmer进行5轮迭代的直系同源基因检索[160]。本次jackhmmer检索得到的期望值（E-value）已予以标注；当某基因对至少一条查询序列的E值达到10⁻⁵⁰时，即被认定为命中基因。对于在对应查询序列的E值阈值以下的基因，其E值以红色标注。系统发育分析将排除以下三类基因：一是对所有查询序列的E值均低于阈值、未被认定为命中基因的基因（灰色阴影标记）；二是在ClustalW序列比对中未通过50%局部缺失截断阈值的基因（深灰色阴影标记）；三是在系统发育树中未与其他基因形成聚类的基因（蓝色阴影标记）。（XLSX）