Computational protocol: Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene

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Protocol publication

[…] The nucleotide sequences of aciI were compared with GenBank databases using BLASTX program available from NCBI website. Ten LuxI homologues with identities of ∼95% to AciI in terms of amino acid sequence were selected from the protein database. Redundant sequences or bacteria strain with ambiguities were omitted. All parameters were set at default and BLOSUM62 was employed in the scoring matrix. Searches for ORF and prediction of nucleotide translational products were performed using the ORF Finder tool while the fundamental properties of the proteins were predicted using by ExPASy. Multiple sequence alignments of the amino acid sequences were carried out using Clustal OMEGA tool with its default parameter settings. A phylogenetic tree of the aciI gene was then constructed using molecular evolutionary genetics analysis (MEGA) version 5 () using Neighbor-Joining strategy as described previously (). Glucose dehydrogenase enzyme (GI: 729809030) from E. coli was chosen as the outgroup for comparison. Bootstrap analyses for 1,000 re-samplings were applied to provide confidence estimates for tree topologies while other parameters were maintained as default. [...] From the draft genome of strain GG2, gene prediction was performed using Prodigal (v2.60; ) and gene annotation was performed using Blast2GO (). Further annotation was obtained using the SEED-based automated annotation system provided by the rapid annotations using subsystems technology (RAST) server (version 4.0; ). Comparative analysis of the GG2 genome with the closest related species, A. baumannii AB0057 genome was performed using Mauve software (), an online Java-based tool for ordering contigs and inspecting assembly statistic. BRIG (BLAST Ring Image Generator; ) software was used for the circular representation of multiple genome comparison among strain GG2 and other closely related species. The genome of strain GG2 was used as the reference genome and was compared with genome of A. baumannii AB0057 (CP001182), A. baumannii AYE (NC_010410), A. baumannii ACICU (CP000863), and A. baumannii ATCC 19606 (NZ_ACQB00000000.1) which were obtained from NCBI database. […]

Pipeline specifications

Software tools BLASTX, Open Reading Frame Finder, Clustal Omega, MEGA, Prodigal, Blast2GO, RAST, Mauve, BRIG
Databases ExPASy
Applications Phylogenetics, Nucleotide sequence alignment, Genome data visualization
Organisms Escherichia coli BL21(DE3), Escherichia coli