Computational protocol: “Deadman” and “Passcode” microbial kill switches for bacterial containment

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Protocol publication

[…] ClustalW2 was used for protein sequence alignment of GalS, GalR, AscG, RbsR, PurR, GntR, LacI, and MalI from E. coli; CelR from T. fusca; ScrR from V. alginolyticus (ScrR-V); and ScrR from K. pneumonia (ScrR-K). Protein crystal structure analysis was performed with PyMol 1.5.x using Protein Data Bank (PDB) entries 1EFA, 1LBG, 1LBI, 1LBH, 1QPZ, and 1TLF–. […]

Pipeline specifications

Software tools Clustal W, PyMOL
Application Amino acid sequence alignment
Organisms Escherichia coli