Building blocks and blueprints for bacterial autolysins
Fig 1
For each organism of interest, the user provides as input a set of “seed” proteins, here based on GO terms indicative of peptidoglycan recognition and catalysis. The LEDGOs data collection pipeline then gathers organism-specific homologs of the seed proteins by repeated PSI-BLAST searches. The LEDGOs pipeline further annotates the catalytic and cell-wall binding domains within the collected sequences according to Pfam families, and catalogs the domain architectures of the proteins. Note that the identified homologs can extend (past the marked “||”) to include additional domains beyond those in the seeds. There can also be uncharacterized sequence regions (marked “?”) between the annotated domains. The domain sequences, annotations, and architectures within full enzymes are stored in the LEDGOs database. The LEDGOs data analysis tools then query this database to characterize and compare/contrast the lysin domain building blocks and architectures employed by the different organisms.