Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed. Using N-terminal sequence information only, it discriminates between proteins destined for the mitochondrion, the chloroplast, the secretory pathway, and "other" localizations with a success rate of 85% (plant) or 90% (non-plant) on redundancy-reduced test sets. From a TargetP analysis of the recently sequenced Arabidopsis thaliana chromosomes 2 and 4 and the Ensembl Homo sapiens protein set, we estimate that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%. TargetP also predicts cleavage sites with levels of correctly predicted sites ranging from approximately 40% to 50% (chloroplastic and mitochondrial presequences) to above 70% (secretory signal peptides). TargetP is available as a web-server at http://www.cbs.dtu.dk/services/TargetP/.
Emanuelsson
O
O
Stockholm Bioinformatics Center, Department of Biochemistry, Stockholm University, Stockholm, S-106 91, Sweden.
Nielsen
H
H
Brunak
S
S
von Heijne
G
G
D000595:Amino Acid Sequence; D017360:Arabidopsis; D001692:Biological Transport; D002736:Chloroplasts / Q000737:chemistry / Q000378:metabolism; D003593:Cytoplasm / Q000737:chemistry / Q000378:metabolism; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D008928:Mitochondria / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D021382:Protein Sorting Signals / Q000737:chemistry / Q000502:physiology*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
D009687:Nuclear Proteins; D010940:Plant Proteins; D021382:Protein Sorting Signals; D011506:Proteins