Computational protocol: The LacI–Family Transcription Factor, RbsR, Is a Pleiotropic Regulator of Motility, Virulence, Siderophore and Antibiotic Production, Gas Vesicle Morphogenesis and Flotation in Serratia

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Protocol publication

[…] The rbsR sequence was compared to those available in Genbank (Benson et al., ) using Basic Local Alignment Search Tool (BLAST) (Altschul et al., ). Conserved protein domains were analyzed using pfam (Bateman et al., ) and Conserved Domain Database (CCD) (Marchler-Bauer et al., ). The binding motifs of RbsR were predicted using the MEME suite (Bailey et al., ). The amino acid sequences of rbsR from Serratia and closely related strains were used to construct the phylogenetic tree using Molecular Evolutionary Genetic Analysis (MEGA) version 7.0 (Kumar et al., ). The evolution history was inferred by the Maximum Likelihood method based on the JTT matrix-based model (Jones et al., ). All positions containing gaps and missing data were eliminated. Bootstrap trials were replicated 1,000 times to estimate confidence values of the phylogenetic tree. […]

Pipeline specifications

Software tools BLASTN, MEME Suite, MEGA
Databases Pfam CDD
Application Phylogenetics
Diseases Deficiency Diseases
Chemicals Ribose