Predicting Pathogenicity Through Bioinformatics

The pathogenicity of isolates was predicted by the Pathogen-Host Interactions database (PHI) and the Virulence Factors of Pathogenic Bacteria (VFDB). Amino acid sequences were compared in the databases by the program DIAMOND (cutoff: 40% identity). When the annotation results were over one, the best annotation was selected by ensuring the biological functions. The arrangement and similarities of gene clusters were illustrated with Easyfig (Version 2.2.2). The amino acid similarities of type VI secretion system effector genes were compared through BlastP on the NCBI website (https://blast.ncbi.nlm.nih.gov/Blast.cgi).

Free full text: Click here

Tao Y., Ge Y., Yang J., Song W., Jin D., Lin H., Zheng H., Lu S., Luo W., Huang Y., Zhuang Z, & Xu J. (2023). A novel phytopathogen Erwinia sorbitola sp. nov., isolated from the feces of ruddy shelducks. Frontiers in Cellular and Infection Microbiology, 13, 1109634.

Publication 2023

Amino acid Amino acid sequences Bacteria Biological functions Diamond Gene clusters Genes Pathogen host interactions Pathogenic factors Pathogenicity Type vi secretion system Virulence

Corresponding Organization : Nankai University

Other organizations : Gansu University of Traditional Chinese Medicine

Top 5 similar protocols

Variable analysis

independent variables

Amino acid sequences compared in the databases by the program DIAMOND (cutoff: 40% identity)

dependent variables

Pathogenicity of isolates predicted by the Pathogen-Host Interactions database (PHI) and the Virulence Factors of Pathogenic Bacteria (VFDB)
Amino acid similarities of type VI secretion system effector genes compared through BlastP on the NCBI website

control variables

Arrangement and similarities of gene clusters illustrated with Easyfig (Version 2.2.2)

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!