Computational protocol: A Tale of Two Reductases: Extending the Bacteriochlorophyll Biosynthetic Pathway in E. coli

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Protocol publication

[…] All protein alignments were performed in MEGA5.1 using the ClustalW algorithm . The protein sequences were identified using NCBI BLAST with RSBciA as the query and hit proteins limited those containing above 30% sequence identity. The phylogenetic tree was created in MEGA5.1 using the default parameters for the neighbor-joining algorithm with a bootstrap test of phylogeny (500 replicates) . Protein modelling was conducted using the automated mode in MODELLER v 9.12 and models were visualized using PyMOL v 1.6 (Schrödinger, LLC). […]

Pipeline specifications

Software tools MEGA, Clustal W, BLASTN, PyMOL
Application Phylogenetics
Organisms Rhodobacter sphaeroides, Escherichia coli, Chlorobaculum tepidum