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MyxoPortal：黏细菌基因组特征数据库。

MyxoPortal: a database of myxobacterial genomic features.

机构信息

School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore Campus, Tiruvalam Road, Katpadi, Vellore, Tamil Nadu 632 014, India.

School of Sports and Health Sciences, Cardiff Metropolitan University, Llandaff campus, Western Avenue, Cardiff CF5 2YB, UK.

出版信息

Database (Oxford). 2024 Jul 2;2024. doi: 10.1093/database/baae056.

DOI:10.1093/database/baae056
PMID:38958433
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11219305/
Abstract

Myxobacteria are predatory bacteria with antimicrobial activity, utilizing complex mechanisms to kill their prey and assimilate their macromolecules. Having large genomes encoding hundreds of secondary metabolites, hydrolytic enzymes and antimicrobial peptides, these organisms are widely studied for their antibiotic potential. MyxoPortal is a comprehensive genomic database hosting 262 genomes of myxobacterial strains. Datasets included provide genome annotations with gene locations, functions, amino acids and nucleotide sequences, allowing analysis of evolutionary and taxonomical relationships between strains and genes. Biosynthetic gene clusters are identified by AntiSMASH, and dbAMP-generated antimicrobial peptide sequences are included as a resource for novel antimicrobial discoveries, while curated datasets of CRISPR/Cas genes, regulatory protein sequences, and phage associated genes give useful insights into each strain's biological properties. MyxoPortal is an intuitive open-source database that brings together application-oriented genomic features that can be used in taxonomy, evolution, predation and antimicrobial research. MyxoPortal can be accessed at http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Database URL:  http://dicsoft1.physics.iisc.ac.in/MyxoPortal/. Graphical Abstract.

摘要

粘细菌是具有抗菌活性的捕食性细菌，利用复杂的机制来杀死猎物并吸收其大分子。这些生物体具有编码数百种次生代谢物、水解酶和抗菌肽的大型基因组，因此因其抗生素潜力而被广泛研究。MyxoPortal 是一个综合性的基因组数据库，包含 262 株粘细菌菌株的基因组。包含的数据集提供了基因组注释，包括基因位置、功能、氨基酸和核苷酸序列，允许分析菌株和基因之间的进化和分类关系。AntiSMASH 用于识别生物合成基因簇，并且包含 dbAMP 生成的抗菌肽序列作为新的抗菌发现的资源，而经过精心整理的 CRISPR/Cas 基因、调节蛋白序列和噬菌体相关基因数据集为每个菌株的生物学特性提供了有用的见解。MyxoPortal 是一个直观的开源数据库，汇集了可用于分类学、进化、捕食和抗菌研究的面向应用的基因组特征。可以在 http://dicsoft1.physics.iisc.ac.in/MyxoPortal/ 访问 MyxoPortal。数据库网址：http://dicsoft1.physics.iisc.ac.in/MyxoPortal/。图表摘要。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/8e91571c03b2/baae056f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/7e601247486d/baae056fa1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/936bf20e48bb/baae056f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/4629cb5c286f/baae056f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/8e91571c03b2/baae056f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/7e601247486d/baae056fa1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/936bf20e48bb/baae056f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/4629cb5c286f/baae056f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce85/11219305/8e91571c03b2/baae056f3.jpg

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本文引用的文献

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Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023.近年来从粘细菌中发现和生物合成天然产物的进展：2017 年至 2023 年概述。
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predation: an updated overview.捕食：最新综述
Front Microbiol. 2024 Jan 24;15:1339696. doi: 10.3389/fmicb.2024.1339696. eCollection 2024.
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Cell behaviors underlying aggregate dispersal.细胞行为是团聚体离散的基础。
mSystems. 2023 Oct 26;8(5):e0042523. doi: 10.1128/msystems.00425-23. Epub 2023 Sep 25.
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Myxobacteria: biology and bioactive secondary metabolites.黏细菌：生物学与生物活性次级代谢产物
Res Microbiol. 2023 Sep-Oct;174(7):104079. doi: 10.1016/j.resmic.2023.104079. Epub 2023 May 9.
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Genome-Guided Discovery of the Myxobacterial Thiolactone-Containing Sorangibactins.基于基因组的粘细菌硫内酯化合物索拉菌素的发现。
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Constructing a Myxobacterial Natural Product Database to Facilitate NMR-Based Metabolomics Bioprospecting of Myxobacteria.构建粘细菌天然产物数据库以促进基于核磁共振的粘细菌代谢组学生物勘探
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