FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring

Abstract

A glycosylphosphatidylinositol (GPI) anchor is a common but complex C-terminal post-translational modification of extracellular proteins in eukaryotes. Here we investigate the problem of correctly annotating GPI-anchored proteins for the growing number of sequences in public databases. We developed a computational system, called FragAnchor, based on the tandem use of a neural network (NN) and a hidden Markov model (HMM). Firstly, NN selects potential GPI-anchored proteins in a dataset, then HMM parses these potential GPI signals and refines the prediction by qualitative scoring. FragAnchor correctly predicted 91% of all the GPI-anchored proteins annotated in the Swiss-Prot database. In a large-scale analysis of 29 eukaryote proteomes, FragAnchor predicted that the percentage of highly probable GPI-anchored proteins is between 0.21% and 2.01%. The distinctive feature of FragAnchor, compared with other systems, is that it targets only the C-terminus of a protein, making it less sensitive to the background noise found in databases and possible incomplete protein sequences. Moreover, FragAnchor can be used to predict GPI-anchored proteins in all eukaryotes. Finally, by using qualitative scoring, the predictions combine both sensitivity and information content. The predictor is publicly available at http://navet.ics.hawaii.edu/~fraganchor/NNHMM/NNHMM.html.

Efficient Glycosylphosphatidylinositol (GPI) Modification of Membrane Proteins Requires a C-terminal Anchoring Signal of Marginal Hydrophobicity

“…Natural GPI-anchoring Signals Have Marginal Hydrophobicity-We first used the ⌬G predictor software to analyze a sequence dataset comprising 87 GPI-anchored proteins (14). The prediction program was fed the C-terminal 40 amino acids of each sequence and yielded the predicted ⌬G app for the most hydrophobic stretch.…”

“…-To study the relationship between GPI addition and the hydrophobicity of the GPI signal, we chose a representative set of 15 putative or verified GPI signals (14) with ⌬G app values spanning from Ϫ4 to 4 kcal mol Ϫ1 (Table 1), and engineered Lep-GPI fusions as in Fig. 2A.…”

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

“…TLPs are induced in plants in response to various biotic and abiotic stresses and have been thought to play a role in plant defense systems, particularly in systemically acquired resistance (1295). TLPs are known to accumulate in plants in response to infection by a pathogen, and some are known to have antifungal properties (1294,(1296)(1297)(1298)(1299). Some TLPs hydrolyze crude fungal walls, and one barley TL enzyme even lyses fungal spores (1295).…”

Field-Evolved Mode 1 Resistance of the Fall Armyworm to Transgenic Cry1Fa-Expressing Corn Associated with Reduced Cry1Fa Toxin Binding and Midgut Alkaline Phosphatase Expression

“…The resulting amplicons were ligated into pCR2.1-TOPO and transformed into E. coli for sequencing to confirm the open reading frames. Three full-length ALP isoforms were obtained, and the presence of glycosylphosphatidylinositol (GPI) anchor signals in the deduced protein sequences was evaluated using the big-Pi predictor (39), PredGPI (40), FragAnchor (41), and GPI-SOM (http://gpi.unibe.ch/) programs. All four programs predicted GPI anchors in two ALPs, which were named SfmALP1 and SfmALP2 for S. frugiperda membrane-bound ALP1 and -2, respectively.…”