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NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides

文献类型： 外文期刊

作者： Zhang, Zhihan 1 ; Zhou, Yuyang 4 ; Xie, Shengling 2 ; Liu, Run-Zhou 2 ; Huang, Zilei 2 ; Saravana Kumar, Pachaiyappan 2 ; Feng, Guozhong 7 ; Yuan, Fajie 5 ; Zhang, Lihan 2 ;

作者机构： 1.Zhejiang Univ, Dept Chem, Hangzhou 310058, Zhejiang, Peoples R China

2.Westlake Univ, Sch Sci, Dept Chem, Zhejiang Key Lab Precise Synth Funct Mol, Hangzhou 310030, Zhejiang, Peoples R China

3.Westlake Univ, Res Ctr Ind Future, Hangzhou 310030, Zhejiang, Peoples R China

4.Zhejiang Univ, Coll Comp Sci & Technol, Hangzhou 310027, Zhejiang, Peoples R China

5.Westlake Univ, Sch Engn, Hangzhou 310030, Peoples R China

6.Westlake Inst Adv Study, Inst Nat Sci, Hangzhou 310024, Zhejiang, Peoples R China

7.China Natl Rice Res Inst, State Key Lab Rice Biol & Breeding, Hangzhou 310006, Peoples R China

期刊名称：JOURNAL OF THE AMERICAN CHEMICAL SOCIETY （ 影响因子：15.6； 五年影响因子：15.5 ）

ISSN： 0002-7863

年卷期： 2025 年

页码：

收录情况： SCI

摘要： Nonribosomal peptides serve as pivotal sources for drug discovery. Accurate prediction of the substrate specificity of adenylation domains in nonribosomal peptide synthetases is crucial for genome mining of nonribosomal peptides, yet current prediction methods fall short in accuracy. In this work, we analyzed 4,100 adenylation domains from documented nonribosomal peptide synthetases and found that the flavodoxin-like subdomain universally governs substrate specificity in all bacterial adenylation domains and that its phylogenetic analysis can correlate the sequences of adenylation domains and their substrate specificity. Leveraging the sequences within the flavodoxin-like subdomain, we developed a substrate specificity prediction algorithm using a protein language model, achieving 92% overall prediction accuracy for 43 frequently observed amino acids, significantly improving the prediction reliability. The efficacy of our prediction tool was validated through targeted genome mining, which led to the discovery of novel antimicrobial peptides. Our work lays a foundation to understand the sequence-to-function relationship of the bacterial adenylation domain and will facilitate the exploitation of nonribosomal peptides. NRPStransformer is available at http://www.nrpstransformer.cn.

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