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Protein Science (2003), 12:2360-2366.
Copyright © 2003 The Protein Society

LumenP—A neural network predictor for protein localization in the thylakoid lumen

Isabelle Westerlund, Gunnar von Heijne and Olof Emanuelsson

Stockholm Bioinformatics Center, and Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden

Reprint requests to: Gunnar von Heijne, Stockholm Bioinformatics Center, and Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; e-mail: gunnar{at}dbb.su.se; fax: 46-8-15 36 79.

We report the development of LumenP, a new neural network-based predictor for the identification of proteins targeted to the thylakoid lumen of plant chloroplasts and prediction of their cleavage sites. When used together with the previously developed TargetP predictor, LumenP reaches a significantly better performance than what has been recorded for previous attempts at predicting thylakoid lumen location, mostly due to a lower false positive rate. The combination of TargetP and LumenP predicts around 1.5%–3% of all proteins encoded in the genomes of Arabidopsis thaliana and Oryza sativa to be located in the lumen of the thylakoid.

Keywords: Thylakoid lumen; protein sorting; chloroplast; prediction


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