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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

Nakai, Kenta, Horton, Paul·1999·Trends in Biochemical Sciences

DOI 10.1016/s0968-0004(98)01336-x

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A new method for predicting signal sequence cleavage sites
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Horton, 1996, Intelligent Systems for Molecular Biology, 4, 109
Horton, 1997, Intelligent Systems for Molecular Biology, 5, 147
Nakai, K.(1996) in Genome Informatics 1996 (Vol. 7) (Akutsu, T. et al.., eds), pp. 72-81, Universal Academy Press
Bairoch, 1997, Nucleic Acids Res., 25, 217, 10.1093/nar/25.1.217 · DOI

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“de/) (11) and PSORT (http://psort.nibb.ac.jp/) ( 12 ).”
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“The peptides encoded by SYV46, SYV55, SYS7, and SYS56 were all predicted to be extracellular by PSORT II analysis, which is designed to predict the subcellular localiza- Vol. 14, No. 4, 2001 / 539 tion sites of proteins (Nakai and Horton 1999).”
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“We performed a PSORT II analysis, which is based on a pattern recognition algorithm called the k-nearest-neighbor method.(42) The predictive accuracy of PSORT II had been assessed by 10-fold crossvalidation using 1531 S.”
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Method
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Background
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“0 [49]), and localisation information (psortII [50]).”
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“The nuclear localization signals in ataxin-3 homologues were discovered with help of the prediction server PSORT II [29].”
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A Nitrite Transporter Associated with Nitrite Uptake by Higher Plant Chloroplasts
Sugiura, M., Georgescu, M. N., & Takahashi, M. (2007) · Plant and Cell Physiology · doi:10.1093/pcp/pcm073 · Cited by 138
“…0.640 for plasma membranes, 0.460 for the Golgi apparatus, 0.370 for endoplasmic reticulum membranes and 0.100 for the endoplasmic reticulum lumen; Nakai and Horton 1999), we introduced CsNitr1-S cDNA into respiration-deficient S. cerevisiae r0 cells to reduce the undesirable incorporation of…”
BackgroundMethodInfluential
The Hsp40 proteins of Plasmodium falciparum and other apicomplexa: Regulating chaperone power in the parasite and the host
Botha, M., Pesce, E.-., & Blatch, G. L. (2007) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2007.02.011 · Cited by 138
Evolutionary recruitment of a flavin-dependent monooxygenase for the detoxification of host plant-acquired pyrrolizidine alkaloids in the alkaloid-defended arctiid moth Tyria jacobaeae
Naumann, C., Hartmann, T., & Ober, D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082674499 · Cited by 138
Subcellular proteomics
Dreger, M. (2003) · Mass Spectrometry Reviews · doi:10.1002/mas.10047 · Cited by 139
Purification and Characterization of Enzymes Exhibiting β- d -Xylosidase Activities in Stem Tissues of Arabidopsis
Minić, Z., Rihouey, C., Trung, C., Lerouge, P., & Jouanin, L. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.041269 · Cited by 137
“Cleavage and glycosidase sites of deduced proteins were studied using PSORT and NetNGlyc software (Nielsen et al., 1997; Nakai and Horton, 1999) at http://psort.nibb.ac.jp/form.html and http://www.cbs.dtu.dk/services/NetNGlyc/.”
Method
A detergent‐ and cyanogen bromide‐free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome
Blonder, J., Conrads, T. P., Yu, L., Terunuma, A., Janini, G. M., Issaq, H. J., Vogel, J. C., & Veenstra, T. D. (2004) · PROTEOMICS · doi:10.1002/pmic.200300543 · Cited by 137
Molecular Cloning of Mouse Ganglioside Sialidase and Its Increased Expression in Neuro2a Cell Differentiation
Hasegawa, T., Yamaguchi, K., Wada, T., Takeda, A., Itoyama, Y., & Miyagi, T. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.11.8007 · Cited by 136
The HD‐GYP domain of RpfG mediates a direct linkage between the Rpf quorum‐sensing pathway and a subset of diguanylate cyclase proteins in the phytopathogen Xanthomonas axonopodis pv citri
Andrade, M. O., Alegria, M. C., Guzzo, C. R., Docena, C., Rosa, M. C. P., Ramos, C. H. I., & Farah, C. S. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05386.x · Cited by 135
Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
Settles, A. M., Holding, D. R., Tan, B. C., Latshaw, S. P., Liu, J., Suzuki, M., Li, L., O’Brien, B., Fajardo, D. S., Wroclawska, E., et al. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-116 · Cited by 136
“Furthermore, the PGD3 protein is predicted to be targeted to the chloroplast by the protein localization programs: TargetP, PSORT, and Predotar [35-37].”
Method
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins
Guda, C., Fahy, E., & Subramaniam, S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth171 · Cited by 136
“The PSORT program exploits comprehensive knowledge of protein sorting for prediction of subcellular localization (Nakai and Horton, 1999), but the sensitivity of the program is low.”
Method
Coronavirus Gene 7 Counteracts Host Defenses and Modulates Virus Virulence
Cruz, J. L. G., Sola, I., Bécares, M., Alberca, B., Plana, J., Enjuanes, L., & Zúñiga, S. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002090 · Cited by 133
“The predicted topology of TGEV protein 7 is also represented in lower panel [PSORTII [139]].”
Background
Using the concept of Chou’s pseudo amino acid composition to predict protein subcellular localization: an approach by incorporating evolutionary information and von Neumann entropies
Zhang, S., Zhang, Y., Yang, H.-F., Zhao, C.-H., & Pan, Q. (2007) · Amino Acids · doi:10.1007/s00726-007-0010-9 · Cited by 135
“During the last decade, many theoretical and computational methods were developed in an attempt to predict protein subcellular localization (Cedano et al. 1997; Chou and Elord 1999; Nakai and Horton 1999; Chou 2000, 2001; Chou and Cai 2002, 2003a, b; Cai and Chou 2003, 2004; Cui et al. 2004; Gao et al. 2005; Pan et al…”
Background
SeqNLS: Nuclear Localization Signal Prediction Based on Frequent Pattern Mining and Linear Motif Scoring
Lin, J.-R., & Hu, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076864 · Cited by 135
“Several NLS prediction methods have been developed such as PSORT II [1], PredictNLS [2], NLStradamus [3], cNLS Mapper [4], and NucImport [5].”
Method
Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses
Dugat‐Bony, É., Straub, C., Teissandier, A., Onésime, D., Loux, V., Monnet, C., Irlinger, F., Landaud, S., Leclercq-Perlat, M.-N., Bento, P., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124360 · Cited by 135
“candidum, only one predicted CDS encoding a putative protease contains a signal sequence indicating a possible extracellular localization according to SignalP [51] and the PSORT server [52].”
Method
Screening and characterization of a novel esterase from a metagenomic library
Kim, Y., Kim, Y., Choi, G.-S., et al. (2005) · Protein Expression and Purification · doi:10.1016/j.pep.2005.06.008 · Cited by 135
“No potential secretion signal sequence was found in Est25 by analysis using the PSORT program [ 24 ], suggesting the ester-hydrolyzing activity around the colonies was caused mainly by cell lysis [10,13,25].”
Method
The hydrophobic proteome of mitochondrial membranes from Arabidopsis cell suspensions
Brugière, S., Kowalski, S., Ferro, M., Seigneurin‐Berny, D., Miras, S., Salvi, D., Ravanel, S., d'Hérin, P., Garin, J., Bourguignon, J., et al. (2004) · Phytochemistry · doi:10.1016/j.phytochem.2004.03.028 · Cited by 134
The Bacillus subtilisσW anti‐sigma factor RsiW is degraded by intramembrane proteolysis through YluC
Schöbel, S., Zellmeier, S., Schumann, W., et al. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04031.x · Cited by 133
“These are RsrA of S. coelicolor inactivating sR (Kang et al., 1999) and ChrR of Rhodobacter sphaeroides inactivating sE (Newman et al., 2001).”
Background
Osmotic Stress Tolerance of Transgenic Tobacco Expressing a Gene Encoding a Membrane-Located Receptor-Like Protein from Tobacco Plants
Tamura, T., Hara, K., Yamaguchi, Y., et al. (2003) · PLANT PHYSIOLOGY · doi:10.1104/pp.102.011007 · Cited by 133
“Analysis using PSORT, a computer program for the prediction of protein localization sites in cells (Nakai and Horton, 1999), indicated that the N-terminal region is likely to serve as a signal peptide, cleaved at amino acid positions between 23 and 24 (A/Q; Fig.”
Method
Large-Scale Predictions of Gram-Negative Bacterial Protein Subcellular Locations
Chou, K., & Shen, H. (2006) · Journal of Proteome Research · doi:10.1021/pr060404b · Cited by 132
“( 6 ) Those subcellular locations (subsets) which contain less than 7 protein sequences were left out.”
Background
The Phycomyces madA gene encodes a blue-light photoreceptor for phototropism and other light responses
Idnurm, A., Rodríguez‐Romero, J., Corrochano, L. M., Sanz, C., Iturriaga, E. A., Eslava, A. P., & Heitman, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0600633103 · Cited by 131
DISC1: Structure, Function, and Therapeutic Potential for Major Mental Illness
Soares, D. C., Carlyle, B. C., Bradshaw, N. J., & Porteous, D. J. (2011) · ACS Chemical Neuroscience · doi:10.1021/cn200062k · Cited by 129
Cytoplasmic Degradation of the Arabidopsis Transcription Factor ABSCISIC ACID INSENSITIVE 5 Is Mediated by the RING-type E3 Ligase KEEP ON GOING
Liu, H., & Stone, S. L. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.465369 · Cited by 129
“Sequence Analysis and Alignment—To identify potential nuclear localization and export signal, the complete amino acid sequence of ABI5 was examined by using the WoLF PSORT computer program (16).”
Method
Reverse vaccinology
Mora, M., Veggi, D., Santini, L., Pizza, M., & Rappuoli, R. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02689-8 · Cited by 129
Selenoprotein H Is a Nucleolar Thioredoxin-like Protein with a Unique Expression Pattern
Novoselov, S. V., Kryukov, G. V., Xu, X., Carlson, B. A., Hatfield, D. L., & Gladyshev, V. N. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m701605200 · Cited by 129
Identification and Characterization of Mammalian Mitochondrial tRNA nucleotidyltransferases
Nagaike, T., Suzuki, T., Tomari, Y., Takemoto‐Hori, C., Negayama, F., Watanabe, K., & Ueda, T. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m106202200 · Cited by 128
Host invasion during rice‐blast disease requires carnitine‐dependent transport of peroxisomal acetyl‐CoA
Ramos‐Pamplona, M., & Naqvi, N. I. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05194.x · Cited by 128
“In silico analysis of Crat1 using subcellular localization prediction programs (PSORTII and TARGETP; Nakai and Horton, 1999; Emanuelsson et al., 2000) failed to reveal any canonical mitochondrial localization motif.”
Method
Computer aided selection of candidate vaccine antigens
Flower, D. R., Macdonald, I. K., Ramakrishnan, K., Davies, M. N., & Doytchinova, I. A. (2010) · Immunome Research · doi:10.1186/1745-7580-6-s2-s1 · Cited by 128
“PSORT is a well-known, well-used example; it is knowledge-based, multicategory prediction method, composed of several programs [43-46].”
Method
DNA‐binding proteins of the Whirly family in Arabidopsis thaliana are targeted to the organelles
Krause, K., Kilbienski, I., Mulisch, M., et al. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.05.059 · Cited by 127
“0 [5,6], PSORT and iPSORT [7] were employed.”
Method
Bioinformatic characterization of the SynCAM family of immunoglobulin-like domain-containing adhesion molecules
Biederer, T. (2005) · Genomics · doi:10.1016/j.ygeno.2005.08.017 · Cited by 127
“jp/) [43].”
Identification of a novel protein interacting with RPGR
Boylan, J. P. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.14.2085 · Cited by 127
“The PIX suite of protein prediction programs was used (HGMP-RC; http://www.hgmp.mrc.ac.uk/Registered/Webapp/ pix/ ) which includes prediction of cell localization [Psort ( 44 )], solubility analysis [SOSUI (33)], BLAST searches against domain databases [SBASE (45) and PRODOM (46)], searches against motif and domain da…”
Method
A defensin from tomato with dual function in defense and development
Stotz, H. U., Spence, B., & Wang, Y. (2009) · Plant Molecular Biology · doi:10.1007/s11103-009-9512-z · Cited by 126
“subcellular localization, assigned DEF2 to the cell wall (Nakai and Horton 1999).”
BackgroundMethod
Subcellular fractionation methods and strategies for proteomics
Lee, Y. H., Tan, H. T., & Chung, M. C. M. (2010) · PROTEOMICS · doi:10.1002/pmic.201000289 · Cited by 127
“Besides targeting motifs, many computational techniques [80, 133] are based on sequence homology with proteins of known localization derived from the database.”
Method
Thctf1 transcription factor of Trichoderma harzianum is involved in 6-pentyl-2H-pyran-2-one production and antifungal activity
RUBIO, M., Hermosa, R., Reino, J. L., et al. (2008) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2008.10.008 · Cited by 125
“The most probable cellular fate of THCTF1 was simulated using the PSORT II program (Nakai and Horton, 1999), which assigned the protein a nuclear location with 78.”
Method
Genome-defence small RNAs exapted for epigenetic mating-type inheritance
Singh, D. P., Saudemont, B., Guglielmi, G., Arnaiz, O., Goût, J.-F., Prajer, M., Potekhin, A. A., Przyboś, E., Fleury‐Aubusson, A., Bhullar, S., et al. (2014) · Nature · doi:10.1038/nature13318 · Cited by 132
Expanding the Definition of the Classical Bipartite Nuclear Localization Signal
Lange, A., McLane, L. M., Mills, R. E., Devine, S. E., & Corbett, A. H. (2009) · Traffic · doi:10.1111/j.1600-0854.2009.01028.x · Cited by 124
“The linker of the bipartite cNLS has traditionally been limited to 10 amino acids based on historical characterization of the nucleoplasmin cNLS (12,17) and, importantly, freely available NLS prediction programs such as PSORT II and PredictNLS restrict the bipartite linker to between 9 and 12 residues (21,22).”
BackgroundMethodInfluential
Mechanisms Underlying the Dual-Mode Regulation of Microtubule Dynamics by Kip3/Kinesin-8
Su, X., Qiu, W., Gupta, M. L., Pereira‐Leal, J. B., Reck‐Peterson, S. L., & Pellman, D. S. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.027 · Cited by 127
“jp/) (Nakai and Horton, 1999) to contain nuclear localization sequences in both the motor and tail domains.”
Background
Arabidopsis TOBAMOVIRUS MULTIPLICATION (TOM) 2 locus encodes a transmembrane protein that interacts with TOM1
Tsujimoto, Y., Numaga, T., Ohshima, K., et al. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg034 · Cited by 123
Ptr ToxA Interacts with a Chloroplast-Localized Protein
Manning, V. A., Hardison, L. K., & Ciuffetti, L. M. (2007) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-20-2-0168 · Cited by 123

Authors: Nakai, K., & Horton, P.
Affiliations: The University of Osaka (JP)
Corresponding author: Nakai, Kenta
ORCID: Nakai, Kenta
Horton, Paul
Venue: Trends in Biochemical Sciences
Publisher: Elsevier BV
Published: 1999-01
Volume: 24
Issue: 1
Pages: 34-35
ISSN: 0968-0004 (ISSN-L)
DOI: 10.1016/s0968-0004(98)01336-x
OpenAlex: W2006211612
Cited by: 2,181
References: 13
Citations by year: 2026: 25 · 2025: 26 · 2024: 43 · 2023: 33 · 2022: 23 · 2021: 31 · 2020: 36 · 2019: 53 · 2018: 59 · 2017: 46 · 2016: 59 · 2015: 69 · 2014: 76 · 2013: 89 · 2012: 105
FWCI: 27.84
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
Locations: Trends in Biochemical Sciences (publishedVersion)
PubMed (publishedVersion)
Funders: Ministry of Education, Culture, Sports, Science and Technology
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: protein sorting signals, subcellular localization prediction, protein localization, signal peptide, amino acid composition, protein function prediction
MeSH terms: Algorithms, Proteins, Software, Subcellular Fractions, Protein Sorting Signals

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PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization

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