To illustrate how MITE entries for the enzymes in a given NP pathway would be annotated, we analyzed one specific pathway in detail. The antimicrobial peptide microcin J25 is a strong inhibitor of the RNA-polymerase of Gram-negative bacteria . Belonging to the lasso peptide subclass of ribosomally synthesized and post-translationally modified peptides , the biosynthesis of microcin J25 is governed by four plasmid-encoded genes (37): mcjA, which encodes the 58 amino acid precursor peptide; mcjB, encoding a cysteine protease responsible for removal of the leader and folding of the core peptide; mcjC, the product of which introduces the characteristic macrolactam isopeptide bond (the lariat fold); and mcjD, encoding Given that (reaction) SMARTS do not preserve hydrogens, ambiguous hydrogens must also be stated explicitly to prevent mismatches. Therefore, explicit hydrogens of the N-terminal secondary amine, the C-terminal secondary amide, and the C-terminal glycine are specified (MITE0000004, ).