PSORT prediction tool uses amino acid sequence information to reliably predict protein localization sites, based on rules derived from experimental observations. For example, gram negative bacteria have four localization sites: cytoplasm, inner membrane, periplasm and the outer membrane.
- Inner membrane proteins are recognized by the presence of either a hydrophobic stretch in the predicted mature protein or an uncleavable N-terminal signal sequence.
- Lipoproteins are first recognized by a consensus pattern and then assumed present at either the inner or outer membrane. These two possibilities are further dissected by examining an acidic residue in the mature N-terminal portion.
- Periplasmic and outer membrane proteins can be successfully differentiated by their different amino acid compositions.
