Computational protocol: Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

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Protocol publication

[…] After a plausible reaction was proposed by BioPath.Design, a list of candidate enzymes which might catalyze the reaction was prepared on the basis of the reference reaction in the BioPath.Database or by inference from the transformation rule of the predicted reaction . Detailed enzyme information, including literature references and sequence information when available, was obtained from the BRENDA database by searching with the EC number or the enzyme name.We used our previously described comparative genomics approach to predict putative enzymes for reactions . In brief, sequences of the target enzymes, which had been characterized experimentally, were obtained from the UniProt/Swiss-Prot database (http://www.uniprot.org/). The genomes of the sequenced LAB and other microorganisms used in this study were obtained from the non-redundant genome databases, the NCBI microbial genome database (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and/or the ERGO database . The retrieved protein sequence was used as a seed to perform a BLAST search against the microbial genomes to obtain their homologs. Multiple sequence alignments (MSAs) were created by MUSCLE , based on the homologous sequences of the target enzymes, as well as the sequences of the experimentally characterized enzymes from literature. Bootstrapped neighbor-joining phylogenetic trees were constructed within ClustalW based on the MSAs and visualized by LOFT . Orthologs of the putative enzymes in LAB genomes were proposed by phylogenetic analysis. The resulting enzymatic information was integrated into the retrosynthesized reactions and pathways for further analyses or applications. The outcome of a comparative genomics analysis was also used to verify the predicted reaction. For example, if no ortholog was found in the target organism, the selected reaction was regarded less likely to be correct. […]

Pipeline specifications

Software tools Clustal W, LOFT
Applications Genome annotation, Phylogenetics
Chemicals Lactic Acid