| 引用本文: | 黄艳青,刘港彪,王 利.鮰爱德华菌外膜蛋白OmpLC基因的生物信息学分析[J].生物信息学,2016,14(2):61-70. |
| HUANG Yanqing,LIU Gangbiao,WANG li.Bioinformatics analysis of the Edwardsiella ictaluri OmpLCgene[J].Chinese Journal of Bioinformatics,2016,14(2):61-70. |
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| 摘要: |
| 采用PCR方法从鮰爱德华菌基因组中扩增出外膜蛋白OmpLC基因,利用生物信息学相关软件和网络数据库,预测该基因编码产物的基本理化性质、亲疏水性、信号肽、跨膜性、二级结构、结构域及基序、以及三级结构,同时构建OmpLC同源基因的系统发育进化树。结果表明:该蛋白由360个氨基酸组成,分子量为39.407 kD,理论等电点为4.98,不稳定系数为18.26,是一种稳定的强亲水性蛋白,有信号肽,成熟蛋白无跨膜螺区。其二级结构中α螺旋、β折叠和无规则卷曲分别占6.67%、45.28%和48.06%,其空间结构为β桶状,属于OM_channels superfamily的gram_neg_porins成员。蛋白质多重序列比对和聚类分析显示,该蛋白序列与OmpLC 蛋白(AEQ59632、AEQ59639)具有高度同源性,且在系统发育树上与二者聚为一簇。鮰爱德华菌OmpLC的生物信息学分析不仅为进一步探索该蛋白的功能提供参考资料,也为研究鮰爱德华菌的感染和致病机理,研制相关疫苗提供理论依据。 |
| 关键词: 鮰爱德华菌 外膜蛋白 结构预测 生物信息学 |
| DOI：10.3969/j.issn.1672-5565.2016.02.01 |
| 分类号:S968.25 |
| 文献标识码:A |
| 基金项目:国家自然基金面上项目(No.31172421)；四川省科技支撑项目(No.2016NZ0044);西南民族大学研究生学位点建设项目(No.2016XWD-SO71007)。 |
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| Bioinformatics analysis of the Edwardsiella ictaluri OmpLCgene |
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HUANG Yanqing1, LIU Gangbiao2, WANG li2
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(1. Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China;2. Key Laboratory of Animal Genetics and Breeding of State Ethnic Affairs Commission & Ministry of Education College of Life Science and Technology, Southwest University for Nationalities , Chengdu 610041, China)
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| Abstract: |
| The purpose of this study is to predict and analyze the structure and function of out membrane protein LC(OmpLC) of Edwardsiella ictaluri.The OmpLCgene was amplified by PCR method. The characteristics of physico-chemical parameters,hydropathy profile,signal peptide,transmembrane helices, secondary structure and tertiary structure were analyzed by bioinformatics softwares and web servers. The results showed that OmpLC protein of Edwardsiella ictaluri composed of 360 amino acids, the calculated molecular mass was 39.407 kD and the theoretical isoelectricpoint was 4.98, and the instability index was 18.26. OmpLC protein had signal peptide and strong hydrophilicity but without transmembrane helices in mature protein. In the second structure α-helix , β-sheet and random coil made up 6.67%, 45.28%, 48.06%, respectively. The three-dimensional structure was β-barrel, its main domain was classified to gram_neg_porins which belong to OM_channels superfamily. The multiple alignment and clustering analysis showed that OmpLCprotein of Edwardsiella ictalurihas high similarity to other OmpLC proteins (AEQ59632,AEQ59639).The properties of OmpLCobtained by bioinformatic analysis can provide reference for the prodiction of novel functional domain and the research on related pathogenesis and new vaccines. |
| Key words: Edwardsiella ictaluri OmpLC Structure prediction Bioinformatics |
