A number of bacteria express filamentous adhesins known as pili. The pili are polar flexible filaments of about 5.4 nm diameter and 2500 nm average length; they consist of a single polypeptide chain (called pilin or fimbrial protein) arranged in a helical configuration of five subunits per turn in the assembled pilus. Gram-negative bacteria produce pilin which are characterized by the presence of a very short leader peptide of 6 to 7 residues, followed by a methylated N-terminal phenylalanine residue and by a highly conserved sequence of about 24 hydrophobic residues. This class of pilin is often referred to as NMePhe or type-4 pili [1,2].

Recently a number of bacterial proteins have been sequenced which share the following structural characteristics with type-4 pili [3]:

 a) The N-terminal residue, which  is  methylated, is hydrophobic (generally a
    phenylalanine or a methionine);
 b) The leader peptide is hydrophilic, consists of 5 to  10 residues (with two
    exceptions, see below) and ends with a glycine;
 c) The fifth residue of the mature  sequence is a glutamate which seems to be
    required for the methylation step;
 d) The first twenty residues of the mature sequence are highly hydrophobic.

These proteins are listed below:

• Four proteins in an operon involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) [4]. These proteins have been assigned a different gene name in each of the species where they have been sequenced: Species Gene names ------------------------ ------------------------- Aeromonas hydrophila exeG exeH exeI exeJ Erwinia chrysanthemi outG outH outI outJ Escherichia coli hofG hofH yheH yheI Klebsiella pneumoniae pulG pulH pulI pulJ Pseudomonase aeruginosa xcpT xcpU xcpV xcpW Vibrio cholerae epsG epsH epsI epsJ Xanthomonas campestris xpsG xpsH xpsI xpsJ
• Vibrio cholerae toxin co-regulated pilin (gene tcpA). This pilin has a much longer putative leader peptide (25 residues).
• Bacillus subtilis comG competence operon proteins 3, 4, and 5 which are involved for the uptake of DNA by competent Bacillus subtilis cells.
• ppdA, ppdB and ppdC, three Escherichia coli hypothetical proteins found in the thyA-recC intergenic region.
• ppdA, a hypothetical protein near the groeLS operon of Clostridium perfringens. The putative leader peptide is 23 residues long.

We developed a signature pattern based on the N-terminal conserved region of all these proteins.