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Database scope, entry explanation
Each MITE entry represents a single tailoring enzyme encoded by a single gene of a single organism (one entry per protein isoform, if applicable). Each MITE tailoring enzyme must have a UniProt (UniProtKB or UniParc) ID and/or an NCBI GenPept ID. MITE does not describe "ensembles" of enzymes or reference sequences. If an enzyme exists in multiple organisms and was described independently, each enzyme can be described independently.
The most relevant information of a MITE entry is the tailoring reaction information (Figure 1, 1). This depiction is the minimal, experimentally verified common substructure the enzyme needs for substrate recognition and reaction. Importantly, this "recognition pattern" does not have to be a full, valid structure; rather, it can encompass partial structures and wildcards (e.g. "any halogen"), expressed by the reaction SMARTS pattern language. These reaction patterns can range from highly promiscular to ultra-specific. In the MITE entry creation tutorial, we dedicate a section on how to summarize experimental evidence to arrive at the substructure pattern.
Besides the "hypothetical" reaction pattern, MITE entries also describe known substrate that are acted on by the tailoring enzymes, as well as their products (Figure 1, 2). Importantly, this is not an exhaustive list - but there is at least one example of a substrate-product pair that is described by the reaction pattern, for visual and data validation purposes.
Additionally, each MITE entry contains metadata (Figure 1, 3) that allow to classify the enzyme and its reactions, and cross-reference external data sources.
Figure 1: Overview of a MITE entry. Highlighted are the core information of a MITE entry: 1) the minimal chemical substructure for enzyme recognition and reaction; 2) one or more examples of experimentally verified substrate-product-pairs; 3) metadata and database cross-links.
Enzymes are within the scope of MITE if they directly partake in natural product biosynthesis but are not "core" or "gatekeeper" enzymes (for a detailed discussion, see Walsh. In a nutshell, any natural product-acting enzyme that is not shunting primary metabolite building blocks into the pathway can be considered a tailoring enzyme. This means that the "first step" of a biosynthetic pathway is excluded from MITE, e.g. non-ribosomal peptide synthetases. Edge cases are best discussed with the maintainers and are decided on a case-by-case basis.
MITE does not contain any enzymes of the primary metabolism, since there are several other resources available for this case. Should an enzyme find its way into MITE that is not a tailoring enzyme, it will be retired.
To stay true to its name (i.e. Minimal Information about a Tailoring Enzyme), MITE only supports a limited amount of data fields. Information that can be found elsewhere is usually cross-referenced. While we are open to amend our data schema, we try to keep it as compact as possible.
Author(s) of this page: Mitja M. Zdouc