Computational protocol: Evolution of the SpoIISABC Toxin Antitoxin Antitoxin System in Bacilli

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Protocol publication

[…] The amino acid sequences of the SpoIISA, SpoIISB and SpoIISC proteins from various bacterial species were obtained using protein BLAST [] against the non-redundant database. Amino acid sequences of the characterized SpoIISA (NCBI-Protein ID: AHA77284), SpoIISBsub (NCBI-Protein ID: AHA77283) [,] and SpoIISCsub (NCBI-Protein ID: AHA77282) proteins from B. subtilis PY79 and the SpoIISA (NCBI-Protein ID: AAP09399) and SpoIISCcer (NCBI-Protein ID: AAP09400) proteins from B. cereus ATCC 14579 [] were used as queries. Since the amino acid sequence of SpoIISBcer from B. cereus ATCC 14579 is not found in the NCBI protein database, it was translated directly from the genomic sequence [] and then used as the BLAST search query. If the amino acid sequences of the SpoIIS proteins from a given bacterial species were not found using BLAST, they were produced by translating from the appropriate genomic sequence. The resulting amino acid sequences were then aligned using ClustalX []. Nucleic acid sequences of particular spoIIS genes were obtained from the bacterial genomes available in GenBank []. A neighbor-joining (NJ) tree [] was calculated using ClustalX using default parameters, and the tree topology reliability was evaluated using the bootstrap test [] with 1000 replications. Selection pressure was estimated using the SELECTON tool [] using the M8 codon-substitution model [] and a neighbor-joining tree. For calculating selection pressure, the sequences listed in were used. Sequence similarities were estimated using MatGAT [] using the BLOSUM62 matrix. […]

Pipeline specifications

Software tools DELTA-BLAST, Clustal W, Selecton, MatGAT
Databases NCBI Protein
Applications Population genetic analysis, Amino acid sequence alignment
Organisms Escherichia coli, Bacillus subtilis, Firmicutes, Bacillus subtilis BEST7003, Bacillus cereus
Diseases Drug-Related Side Effects and Adverse Reactions