About

ATP2 is a prediction tool trained with sequences of plant proteins dually (ambiguously) targeted to plastids and mitochondria, to predict such localization in plant proteins.
GTP_Pp is a prediction tool trained with sequences from Physcomitrella patens to predict subcellular targeting of P. patens/plant proteins.
GTP_Ref is a prediction tool trained mainly with seed plant sequences from the TargetP training set to predict subcellular targeting of plant proteins.
Fuss J., Liegmann O., Krause K., Rensing S.A. (2013) Green Targeting Predictor and Ambiguous Targeting Predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems. New Phytol 200:1022

Four subcellular localizations are supported:

  • CHL: Chloroplast
  • MIT: Mitochondria
  • SEC: Secretory Pathway
  • NUCCYT: Nucleo-cytoplasm ("without N-terminal signal")

Description of output:

  • Sequence: Description of your input sequence
  • Prediction: Predicted localization (by best score)
  • Score: Likelihood for the sequence to be targeted to the predicted localization (Values between 0 and 1, the higher the better). The suggested cutoffs balancing sensitivity and specificity are 0.5 for GTP_Pp, 0.7 for GTP_Ref and 0.5 for ATP2.
  • Confidence (GTP only): Confidence for prediction to be correct (Values between 0 and 1, the higher the better); the confidence value is the difference between the scores for the first localization and for the second localization.
  • CHL/MIT/SEC/NUCCYT: Scores for the respective compartment



HowTo

Please insert protein sequences in FASTA format. You can enter them directly into the input field or upload them as a file. The input sequences need to be at least 71 amino acids long. All shorter sequences will be disregarded. You can predict at most 50 sequences at a time. If you like to predict a large number of sequences, please contact us at stefan.rensing@cup.uni-freiburg.de.

For proteins with low GTP values for MIT or CHL and/or low confidence scores we suggest to check by ATP2 whether the protein might be ambiguously targeted to these two compartments.



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