Computational protocol: An upstream sequence modulates phenazine production at the level of transcription and translation in the biological control strain Pseudomonas chlororaphis 30-84

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Protocol publication

[…] To obtain the nucleotide sequence upstream of phenazine biosynthetic operon, the 250 bp nucleotide sequence upstream of the translation start site of phzX were blasted against the Pseudomonas Genome Database (www.pseudomonas.com) and National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/). A total of 27 phenazine producing strains were retrieved and analyzed for the types of a phenazine modifying enzyme. The nucleotide sequences (250 bp flanking sequences from the translation start site of each strain’s phenazine biosynthetic operon) were aligned and edited using MUSCLE (MEGA7). MEGA7 was used to build a, Maximum Likelihood (ML) trees based on the Tamura-Nei Model [] []. ML bootstrapping was performed with 1,000 replicates to assess the relative stability of the branches. […]

Pipeline specifications

Software tools MUSCLE, MEGA
Databases Pseudomonas Genome Database
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Bacteria, Triticum aestivum, Fungi
Chemicals Phenazines