To account for proteins targeted to some of the common bacterial hyperstructures and host-destined SCLs, new subcategory localizations have been introduced in PSORTb 3.0, as listed in Table 1 . This represents, to our knowledge, the first implementation of subcategories for primary SCL localizations, for an SCL predictor. These subcategory localizations for a protein were identified using the SCL-BLAST module, which infers localization by homology using criteria that are of measured high precision (Nair and Rost, 2002 (link)). Proteins detected to have a secondary localization are also predicted as one of the four main categories for Gram-positive bacteria or one of five main compartments for Gram-negative bacteria (or similarly for those bacteria with atypical cell structures). Any protein exported past the outer-most layer of the bacterial cell is considered as extracellular, whereas proteins localized to one of the membranes that are part of a hyperstructure (such as the flagellum) are identified both as an inner or outer membrane protein as well as a protein of that hyperstructure. The basal components of the flagellum are not annotated as such, since they are often homologous to proteins that are not part of the flagellar apparatus (for example, a general ATPase).
New subcategory SCLs predicted by PSORTb 3.0
| SCL subcategories | Description |
|---|---|
| Host-associated | Any proteins destined to the host cell cytoplasm, cell membrane or nucleus by any of the bacterial secretion systems |
| Type III secretion | Components of the Type III secretion apparatus |
| Fimbrial | Components of a bacterial or archaeal fimbrium or pilus |
| Flagellar | Components of a bacterial or archaeal flagellum |
| Spore | Components of a spore |
