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CusProSe：一种可定制的蛋白质注释软件，应用于预测真菌次生代谢基因。

CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes.

机构信息

Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.

Orphanet-INSERM, US14, Plateforme des Maladies Rares, Paris, France.

出版信息

Sci Rep. 2023 Jan 25;13(1):1417. doi: 10.1038/s41598-023-27813-y.

DOI:10.1038/s41598-023-27813-y
PMID:36697464
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9876896/
Abstract

We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.

摘要

我们在此报告一个新的应用程序，CustomProteinSearch（CusProSe），其目的是帮助用户根据其结构域组成搜索感兴趣的蛋白质。该应用程序是可定制的。它由两个独立的工具组成，即 IterHMMBuild 和 ProSeCDA。IterHMMBuild 允许为选定蛋白质序列的保守结构域迭代构建隐马尔可夫模型（HMM）轮廓，而 ProSeCDA 则针对 HMM 轮廓数据库扫描感兴趣的蛋白质组，并使用用户定义的规则对鉴定的蛋白质进行注释。CusProSe 成功地用于鉴定真菌基因组中参与次生代谢的关键酶家族的基因，如聚酮合酶（PKS）、非核糖体肽合酶（NRPS）、混合 PKS-NRPS 和二甲基烯丙基色氨酸合酶（DMATS），以及描述不同萜烯合酶（TS）亚家族。该应用程序的高度可配置特性使其成为一种通用工具，允许用户细化预测蛋白质的功能，将检测扩展到新的酶家族，并且也可以应用于真菌以外的生物系统和参与次生代谢以外的蛋白质。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/035cf4e628e6/41598_2023_27813_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/2a30c8dc9cec/41598_2023_27813_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/1c18c6d54b34/41598_2023_27813_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/42480a206206/41598_2023_27813_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/29f14aa2222f/41598_2023_27813_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/035cf4e628e6/41598_2023_27813_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/2a30c8dc9cec/41598_2023_27813_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/1c18c6d54b34/41598_2023_27813_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/42480a206206/41598_2023_27813_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/29f14aa2222f/41598_2023_27813_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6de6/9876896/035cf4e628e6/41598_2023_27813_Fig5_HTML.jpg

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