Glycosylphosphatidylinositol (GPI) anchoring of proteins provides a potential mechanism for targeting to the plant plasma membrane and cell wall. However, relatively few such proteins have been identified. Here, we develop a procedure for database analysis to identify GPI-anchored proteins (GAP) based on their possession of common features. In a comprehensive search of the annotated Arabidopsis genome, we identified 167 novel putative GAP in addition to the 43 previously described candidates. Many of these 210 proteins show similarity to characterized cell surface proteins. The predicted GAP include homologs of -1,3-glucanases (16), metallo-and aspartyl proteases (13), glycerophosphodiesterases (6), phytocyanins (25), multi-copper oxidases (2), extensins (6), plasma membrane receptors (19), and lipid-transfer-proteins (18). Classical arabinogalactan (AG) proteins (13), AG peptides (9), fasciclin-like proteins (20), COBRA and 10 homologs, and novel potential signaling peptides that we name GAPEPs (8) were also identified. A further 34 proteins of unknown function were predicted to be GPI anchored. A surprising finding was that over 40% of the proteins identified here have probable AG glycosylation modules, suggesting that AG glycosylation of cell surface proteins is widespread. This analysis shows that GPI anchoring is likely to be a major modification in plants that is used to target a specific subset of proteins to the cell surface for extracellular matrix remodeling and signaling.Conventional membrane proteins possess one or more transmembrane domains that traverse the hydrophobic lipid bilayer. A glycosylphosphatidylinositol (GPI) anchor is an alternative means of attaching a protein to the membrane (for review, see Udenfriend and Kodukula, 1995), and it is found in all eukaryotic organisms. The C terminus of a GPIanchored protein (GAP) is covalently attached via phosphoethanolamine and a conserved glycan to phosphatidylinositol or a ceramide (Kinoshita and Inoue, 2000). GAPs have many features that distinguish them from proteins with transmembrane domains. The anchor can be removed by the action of specific phospholipases (Griffith and Ryan, 1999), converting the protein into a water-soluble form. In many organisms, they are found specifically at the outer leaflet of the plasma membrane (PM). It is important that GPI anchoring can target proteins to the PM in a polarized or localized manner, for example to the apical membrane of polarized mammalian epithelial cells (Le Gall et al., 1995) or the axon of neurons (Brown et al., 2000). As part of this targeting mechanism, GAPs are thought to associate with lipid rafts (Muniz and Riezman, 2000;Ikonen, 2001), and there is evidence for rafting of GAPs in plants ( Peskan et al., 2000). Therefore, this class of proteins forms a potentially important group of molecules involved in plant cell surface generation and remodeling (Sherrier et al., 1999).GAPs have only relatively recently been discovered in plants. Arabinogalactan (AG) proteins (AGPs), cell surface proteo...