Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1.
Many posttranslational modifications (N-myristoylation or glycosylphosphatidylinositol (GPI) lipid anchoring) and localization signals (the peroxisomal targeting signal PTS1) are encoded in short, partly compositionally biased regions at the N- or C-terminus of the protein sequence. These sequence signals are not well defined in terms of amino acid type preferences but they have significant interpositional correlations. Although the number of verified protein examples is small, the quantification of several physical conditions necessary for productive protein binding with the enzyme complexes executing the respective transformations can lead to predictors that recognize the signals from the amino acid sequence of queries alone. Taxon-specific prediction functions are required due to the divergent evolution of the active complexes. The big-Pi tool for the prediction of the C-terminal signal for GPI lipid anchor attachment is available for metazoan, protozoan and plant sequences. The myristoyl transferase (NMT) predictor recognizes glycine N-myristoylation sites (at the N-terminus and for fragments after processing) of higher eukaryotes (including their viruses) and fungi. The PTS1 signal predictor finds proteins with a C-terminus appropriate for peroxisomal import (for metazoa and fungi). Guidelines for application of the three WWW-based predictors (http://mendel.imp.univie.ac.at/) and for the interpretation of their output are described.
Eisenhaber
Frank
F
Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Republic of Austria. frank.eisenhaber@imp.univie.ac.at
Eisenhaber
Birgit
B
Kubina
Werner
W
Maurer-Stroh
Sebastian
S
Neuberger
Georg
G
Schneider
Georg
G
Wildpaner
Michael
M
D000217:Acyltransferases / Q000378:metabolism; D020816:Amino Acid Motifs; D000818:Animals; D005057:Eukaryotic Cells / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D005998:Glycine / Q000378:metabolism; D017261:Glycosylphosphatidylinositols / Q000378:metabolism; D020407:Internet; D050356:Lipid Metabolism; D008969:Molecular Sequence Data; D009227:Myristic Acids / Q000378:metabolism; D020675:Peroxisomes / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D021382:Protein Sorting Signals; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D015800:Protozoan Proteins / Q000737:chemistry / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism
D005656:Fungal Proteins; D017261:Glycosylphosphatidylinositols; D009227:Myristic Acids; D010940:Plant Proteins; D021382:Protein Sorting Signals; D011506:Proteins; D015800:Protozoan Proteins; D014764:Viral Proteins; D000217:Acyltransferases; C050480:glycylpeptide N-tetradecanoyltransferase; D005998:Glycine