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A prokaryotic protein sorting system is a special case of protein processing system that may control not only what modifications occur to a protein, but also where the mature protein appears. The bioinformatics grammar usually features a many-to-one relationship between sorting targets and their sorting machinery, although a dedicated system may occur in which the processing machiney exists for only single target protein only. Type I signal peptide, lipoprotein signal peptide, and twin-arginine translocation (TAT) are examples of N-terminal signals that include a hydrophobic transmembrane (TM) segment.

A number of C-terminal homology domains share the same tripartite architectural grammar, featuring a signature motif by which the domain can be named, a hydrophobic TM segment, and a cluster of basic residues at the C-terminus on the cytosolic face. These include:

  • LPXTG, acted on by sortase A
  • PEP-CTERM, acted on by exosortase
  • PGF-CTERM, acted on by archaeosortase A
  • GlyGly-CTERM, acted on by rhombosortase

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