In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [1]. Some of the proteins known to undergo such processing currently include (for recent listings see [1,2,3]):

• Major outer membrane lipoprotein (murein-lipoproteins) (gene lpp).
• Escherichia coli lipoprotein-28 (gene nlpA).
• Escherichia coli lipoprotein-34 (gene nlpB).
• Escherichia coli lipoprotein nlpC.
• Escherichia coli lipoprotein nlpD.
• Escherichia coli osmotically inducible lipoprotein B (gene osmB).
• Escherichia coli osmotically inducible lipoprotein E (gene osmE).
• Escherichia coli peptidoglycan-associated lipoprotein (gene pal).
• Escherichia coli rare lipoproteins A and B (genes rplA and rplB).
• Escherichia coli copper homeostasis protein cutF (or nlpE).
• Escherichia coli plasmids traT proteins.
• Escherichia coli Col plasmids lysis proteins.
• A number of Bacillus β-lactamases.
• Bacillus subtilis periplasmic oligopeptide-binding protein (gene oppA).
• Borrelia burgdorferi outer surface proteins A and B (genes ospA and ospB).
• Borrelia hermsii variable major protein 21 (gene vmp21) and 7 (gene vmp7).
• Chlamydia trachomatis outer membrane protein 3 (gene omp3).
• Fibrobacter succinogenes endoglucanase cel-3.
• Haemophilus influenzae proteins Pal and Pcp.
• Klebsiella pullulunase (gene pulA).
• Klebsiella pullulunase secretion protein pulS.
• Mycoplasma hyorhinis protein p37.
• Mycoplasma hyorhinis variant surface antigens A, B, and C (genes vlpABC).
• Neisseria outer membrane protein H.8.
• Pseudomonas aeruginosa lipopeptide (gene lppL).
• Pseudomonas solanacearum endoglucanase egl.
• Rhodopseudomonas viridis reaction center cytochrome subunit (gene cytC).
• Rickettsia 17 Kd antigen.
• Shigella flexneri invasion plasmid proteins mxiJ and mxiM.
• Streptococcus pneumoniae oligopeptide transport protein A (gene amiA).
• Treponema pallidium 34 Kd antigen.
• Treponema pallidium membrane protein A (gene tmpA).
• Vibrio harveyi chitobiase (gene chb).
• Yersinia virulence plasmid protein yscJ.
• Halocyanin from Natrobacterium pharaonis [4], a membrane associated copper- binding protein. This is the first archaebacterial protein known to be modified in such a fashion).

From the precursor sequences of all these proteins, we derived a profile that starts at the beginning of the sequence and ends after the post-translationally modified cysteine.