The following Gram-negative outer membrane proteins share a domain of about 150 residues [1,2]:

• Outer membrane protein ompA from enterobacteria such as Escherichia coli.
• Outer membrane protein P5 from Haemophilus influenzae.
• Outer membrane protein P.III/class IV from Neisseria.
• Outer membrane porin F (gene oprF) from Pseudomonas.
• Protein TpN50 from Treponema pallidum.
• Peptidoglycan-associated lipoprotein (gene pal) from Escherichia coli, Haemophilus influenzae, Legionella pneumophila and Pseudomonas putida.
• Outer membrane lipoprotein P6 from Haemophilus influenzae.
• Escherichia coli hypothetical lipoprotein yiaD.
• Vibrio parahaemolyticus sodium-type flagellar protein motY.

This domain is found in the C-terminal section of the above proteins. Apart from this domain, these proteins are not structurally related. Most of them are porin-like integral membrane proteins (such as ompA), but some are small lipid-anchored proteins (such as pal). In addition to being attached to the outer membrane, OmpA-like domains are also found attached to the inner membrane: MotB proteins, part of the flagellar motor/stator complex in Gram-positive and Gram-negative bacteria, span the inner membrane and contain OmpA-like domains in their periplasmic regions [3].

The OmpA-like domain is thought to be responsible for non-covalent interactions with peptidoglycan [3].

The OmpA-like domain adopts a β-α-β-α-β-β fold (see <PDB:1R1M>). The core OmpA-like domain consists of a mixed β-sheet formed from parallel and antiparallel β-strands (β1 to β4), which are flanked by two long α helices (α2 and α3). A short helix α1 is part of the segment connecting β1 to α2. An extension formed by two antiparallel α helices (α4 and α5), is stabilized by a disulphide bond. The domain fold creates a hydrophilic groove which could accomodate a glycan chain [3].

The signature pattern that we developed spans the central part of the OmpA-like domain. We also developed a profile which covers the entire domain.