Dubey Amit Kumar, Yadav Sangeeta, Kumar Manish, Singh Vinay Kumar, Sarangi Bijaya Ketan, Yadav Dinesh
Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur 273 009, India.
Enzyme Res. 2010 Sep 19;2010:950230. doi: 10.4061/2010/950230.
A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439-467, 715-816, and 829-910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.
总共121个果胶酸裂解酶的蛋白质序列接受了同源性搜索、多序列比对、系统发育树构建和基序分析。构建的系统发育树显示，基于代表细菌、真菌、植物和线虫果胶酸裂解酶的不同来源生物体，形成了不同的聚类。细菌、真菌、线虫和植物果胶酸裂解酶蛋白质序列的多个登录号紧密排列，显示出序列水平的相似性。来自不同来源生物体的这些果胶酸裂解酶蛋白质序列的多序列比对显示，在不同片段存在保守区域，氨基酸残基439 - 467、715 - 816和829 - 910具有最大同源性，可用于设计针对果胶酸裂解酶的简并引物或探针。基序分析揭示了一个保守的Pec_Lyase_C结构域，在所有果胶酸裂解酶中均能一致观察到，无论来源如何变化，这表明其在结构和酶功能中可能发挥作用。
