Computational protocol: Manganese Homeostasis in Group A Streptococcus Is Critical for Resistance to Oxidative Stress and Virulence

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Protocol publication

[…] Phylogenetic analyses of 59 cation diffusion facilitator family protein sequences, selected on the basis of BLAST (NCBI) analysis against functionally characterized CDF family proteins, CzcD, EmfA, and MntE, were used to determine the clustering of the different CDF families. An amino acid alignment was generated using Clustal Omega v1.2.1 (). A best-fit phylogenetic tree was estimated using PhyML v3.0 () based on the WAG substitution model with gamma correction of among-site rate variation. One hundred nonparametric bootstraps were applied. […]

Pipeline specifications

Software tools Clustal Omega, PhyML
Application Phylogenetics
Organisms Streptococcus pyogenes, Homo sapiens
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Hydrogen Peroxide, Iron, Manganese, Zinc