Cloing and Bioinformatics Analysis of ndk Gene from Vibrio alginolyticus

Yujia Zhang, Shi Wang, Jian Zhong, Weijie Zhang, Xing Xiao, Zhiqing Wei, Huanying Pang and Na Wang

Asian Agricultural Research, 2023, vol. 15, issue 07

Abstract: [Objectives] The paper was to clone and analyze bioinformatics of ndk gene from Vibrio alginolyticus. [Methods] A pair of specific primers was designed based on the ndk gene sequence of V. alginolyticus HY9901. The full length of ndk gene was amplified by PCR and bioinformatics analysis was performed. MEGA 5.0 software was used to construct NDK phylogenetic tree by neighbor-joining method. SWISS-MODEL program was used to obtain the three-dimensional structural model of single subunit from NDK protein. [Results] The ndk gene, molecular structural formula C702H1094N192O214S7, was 426 bp in total, encoding 141 amino acids, with the theoretical molecular weight of 15.871 99 kD and the theoretical pI value of 5.13. The prediction results of protein subcellular localization, SignalP 5.0, TMHMM Server 2.0 and SoftBerry-Psite showed that NDK mainly existed in the cytoplasm, and the protein was unstable and hydrophobic. There was neither signal peptide cleavage site, nor transmembrane region and KEGG metabolic pathway. The amino acid sequence had two protein kinase C phosphorylation sites, a casein kinase II phosphorylation site, a N-myristoylation site, three microbody C-terminal target signal sites, and a nucleoside diphosphate kinase active site. Homology analysis showed that the NDK of V. alginolyticus had high homology with that of V. diabolicus, with a similarity of 98.58%. Analysis of the structural functional domain revealed that the protein had one NDK structural functional domain. The prediction results of secondary structure showed that the α-helix, random coil, β-sheet and extended strand accounted for 53.19%, 28.37%, 7.09% and 11.35%, respectively. Analysis of NDK protein via STRING database demonstrated that the proteins interacting with NDK protein were NrdA, NrdB, GmK, CmK, TmK, PyrG, PyrH, RelA, FolE and SpoT. [Conclusions] The study plays a positive role in the prevention and control of vibriosis and the improvement of the current aquaculture environment.

Keywords: Agribusiness (search for similar items in EconPapers)
Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:ags:asagre:341851

DOI: 10.22004/ag.econ.341851

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