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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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Research works printed but not linked: 4

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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“A surface localization motif was identified using three prediction algorithms: PSORT (62), TMHMM (63, 64), and signalP (65, 66).”
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“transmembrane domain. Amino acid sequences from multiple cloned R genes were subjected to the pSORTII subcellular localization predictor, which can determine the presence of bipartitite and monopartite NLSs ( Nakai and Horton, 1999 ).”
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“As for Rv1872c, no TMDs were predicted with TMHMM, and one TMD was predicted using PSORT.”
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“The remaining proteins were soluble cytoplasmic proteins, inner membrane proteins, and proteins of unknown localization (according to PSORT) that contaminated the envelope fraction.”
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“:}} www.cbs.dtu.dk}services}SignalP) and Tmpred (Hofmann & Stoffel, 1993 ; http :}}www.ch.embnet.org}software) and localization of predicted proteins was analysed by (Nakai & Horton, 1999 ; http :}}psort.nibb.ac.jp).”
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“molecular weight, isoelectric point) of the encoded protein, the prediction of its subcellular localization [PSort (14)], a search for motifs [e.”
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“The NLS (amino acids 670-673) was identified using the PSORT II programme (Nakai and Horton, 1999).”
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“Whenweused the programPSORT II (40) to search for NLS motifs, a potential NLS was identified in the TR 1 A/B domain.”
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“The PSORT II algorithm (50) predicts one potential transmembrane portion between residues 112 and 130, with the N-terminal portion of the protein predicted to be within the inner side of the IMV membrane.”
Method
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“The first approach is based on surface protein prediction by genome analysis using algorithms such as PSORT [18].”
Method
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“LOPP contains a putative nuclear localization signal, PQRRRDS (residues 39–45), as shown by the PSORT program (26).”
Method
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“The following domain structures are indicated: potentially sumoylated lysines with a [hydrophobic]-K-X-[ED] motif (red) predicted by the SUMOsp 1.0 program (85), predicted nuclear localization sequences (green) determined with the NUCDISC subprogram of PSORTII (56), a predicted mitochondrial targeting sequence in Ntg1…”
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Plane pollution.
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“In contrast to the predictions of SignalP and SecretomeP, PSORT [22] predicted 171 extracellular proteins, 7 cell wall-associated proteins, and 6 cytoplasmic proteins.”
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“PSORT analysis (Nakai and Horton, 1999) identifies a predicted Figure 1.”
Method
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“…discriminant algorithm (CD) in (2,27), and an augmented CD in (6)], an Artiﬁcial Neural Network approach in (15,20), a Nearest Neighbor approach in (1,11,17,23,26), a Markov Model (MM) in (21), a Bayesian Network (BN) approach in (24), and Support Vector Machines (SVMs) approach in (7,9,16,18,25).”
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“Proteins visualized in the 2-DE profile were also classified based on their functions using PSORT and TMpred.”
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“jp; [28]).”
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“ELISA plates were coated overnight in PBS at 4◦C with 100 μL of 10 μg/mL PLG. Plates were then blocked and increasing concentrations of the purified recombinant proteins (0-1 μM) were added (100 μL/well in PBS).”
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“Three prediction methods (TargetP[92], PSORT[93] and SubLoc[94]) and literature curation (Additional file 6) was performed, where possible, on the full-length sequence of the proteins in the entire dataset.”
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“In the same study, we used the ChloroP [10] and PSORT [11] algorithms that predict protein localization signals to examine the N-terminal amino acid sequence derived from the Arabidopsis FDH cDNA.”
Method
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Kihara, D., & Kanehisa, M. I. (2000) · Genome Research · doi:10.1101/gr.10.6.731 · Cited by 47
Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence
Tsujii, A., Miyamoto, Y., Moriyama, T., Tsuchiya, Y., Obuse, C., Mizuguchi, K., Oka, M., & Yoneda, Y. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.681908 · Cited by 42
“This is consistent with the fact that the cNLS mapper (30) and PSORTII (31) cNLS prediction algorithms did not detect any potential cNLS in the RBBP4 protein, indicating that there are no obvious cNLSs in the coding sequence of RBBP4.”
Result
The Q-soluble N-Ethylmaleimide-sensitive Factor Attachment Protein Receptor (Q-SNARE) SNAP-47 Regulates Trafficking of Selected Vesicle-associated Membrane Proteins (VAMPs)
Kuster, A., Nola, S., Dingli, F., Vacca, B., Gauchy, C., Beaujouan, J., Nunez, M., Moncion, T., Loew, D., Formstecher, É., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.666362 · Cited by 45
“For prediction of nuclear localization signals (NLS) and nuclear export signals (NES), PSORT II program (29) and NetNES 1.”
Method
Structurally divergent lysophosphatidic acid acyltransferases with high selectivity for saturated medium chain fatty acids from Cuphea seeds
Kim, H. J., Collins-Silva, J., Iskandarov, U., et al. (2015) · The Plant Journal · doi:10.1111/tpj.13063 · Cited by 46
CISD1 codifies a mitochondrial protein upregulated by the CFTR channel
Taminelli, G., Sotomayor, V., Valdivieso, Á. G., Teiber, M. L., Marín, M. C., & Santa-Coloma, T. A. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.11.076 · Cited by 46
RNA Splicing in a New Rhabdovirus from Culex Mosquitoes
Kuwata, R., Isawa, H., Hoshino, K., et al. (2011) · Journal of Virology · doi:10.1128/jvi.00040-11 · Cited by 46
A Meloidogyne graminicola C‐type lectin, Mg01965, is secreted into the host apoplast to suppress plant defence and promote parasitism
Zhuo, K., Naalden, D., Nowak, S., et al. (2018) · Molecular Plant Pathology · doi:10.1111/mpp.12759 · Cited by 46
Subcellular localization and lysophospholipase/transacylation activities of human group IVC phospholipase A2 (cPLA2γ)
Yamashita, A., Tanaka, K., Kamata, R., 司紗, 熊., Suzuki, N., Koga, H., Waku, K., & Sugiura, T. (2009) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2009.05.008 · Cited by 46
“Sequence-based analyses by PSORT II [26], SOSUI signal [27], and MitoProt II [28] predict that cPLA2γ does not have a signal sequence or a typical mitochondrial targeting signal.”
Method
Biochemical Characterization of a Membrane-bound Manganese-containing Superoxide Dismutase from the CyanobacteriumAnabaena PCC 7120
Regelsberger, G., Atzenhofer, W., Rüker, F., Peschek, G. A., Jakopitsch, C., Paumann, M., Furtmüller, P. G., & Obinger, C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207691200 · Cited by 46
Mitochondrial glycolate oxidation contributes to photorespiration in higher plants
Niessen, M., Thiruveedhi, K., Rosenkranz, R., Kebeish, R., Hirsch, H., Kreuzaler, F., & Peterhänsel, C. (2007) · Journal of Experimental Botany · doi:10.1093/jxb/erm131 · Cited by 45
“…by aminotransferases, and putative alanine:glyoxylate aminotransferases were localized to mitochondria by both bioinformatic prediction [At2g38400, At1g72330, and At1g17290 according to PSORT (Nakai and Horton, 1999)] and organelle proteome analyses (Millar et al., 2001; Ito et al., 2006).”
BackgroundMethodInfluential
γ‐BAR, a novel AP‐1‐interacting protein involved in post‐Golgi trafficking
Neubrand, V. E., Will, R. D., Möbius, W., Poustka, A., Wiemann, S., Schu, P. V., Dotti, C. G., Pepperkok, R., & Simpson, J. C. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600600 · Cited by 46
“quence analysis using the PSORT program (Nakai and Horton, 1999).”
Protein classification using probabilistic chain graphs and the Gene Ontology structure
Carroll, S., & Pavlović, V. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl187 · Cited by 46
Review: Prediction of in Vivo Fates of Proteins in the Era of Genomics and Proteomics
Nakai, K. (2001) · Journal of Structural Biology · doi:10.1006/jsbi.2001.4378 · Cited by 46
Self-citation
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Yudate, H. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.185 · Cited by 46
“(5) for prediction of signal sequences, cleavage sites, trans-”
Background
Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks
Vibin, J., Chamings, A., Klaassen, M., & Alexandersen, S. (2020) · Scientific Reports · doi:10.1038/s41598-020-79413-9 · Cited by 49
Predicting multisite protein subcellular locations: progress and challenges
Du, P.-F., & Xu, C. (2013) · Expert Review of Proteomics · doi:10.1586/epr.13.16 · Cited by 45
“PSORT servers were the first and the most successful practice in applying the protein sorting theory [4] .”
Method
Multiple Nuclear Localization Signals Mediate Nuclear Localization of the GATA Transcription Factor AreA
Hunter, C. C., Siebert, K. S., Downes, D. J., et al. (2014) · Eukaryotic Cell · doi:10.1128/ec.00040-14 · Cited by 45
“As the PSORTII algorithm does not include this noncanonical bipartite NLS, we identified by manual inspection an RRX33RXR motif within the AreA zinc finger domain at residues 685 to 722 as a sixth bipartite NLS (bip) (Fig.”
MethodInfluential
Microbial Eukaryote Globins
Vinogradov, S. N., Bailly, X., Smith, D. R., Tinajero‐Trejo, M., Poole, R. K., & Hoogewijs, D. (2013) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/b978-0-12-407693-8.00009-1 · Cited by 50
Cloning, genomic organization, and tissue-specific expression of the RASL11B gene
Stolle, K., Schnoor, M., Fuellen, G., Spitzer, M., Cullen, P., & Lorkowski, S. (2007) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/j.bbaexp.2007.05.005 · Cited by 45
“jp/) [26].”
The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana
Figueroa, P. M., León, G., Elorza, Á. A., Holuigue, L., Araya, A., & Jordana, X. (2002) · Plant Molecular Biology · doi:10.1023/a:1019926301981 · Cited by 46
“Computer analysis of the four Arabidopsis N-terminal extensions by PSORT (Nakai and Horton, 1999) and MITOPROT II (Claros and Vincens, 1996) predicts a mitochondrial localization for all of them.”
Background
Functionality of System Components: Conservation of Protein Function in Protein Feature SpacePreprint
Jensen, L. J., Ussery, D. W., & Brunak, S. (2003) · Genome Research · doi:10.1101/gr.1190803 · Cited by 45
“1999), PEST regions (Rechsteiner and Rogers 1996), PSIPRED (Jones 1999), PSORT (Nakai and Horton 1999), SEG filter (Wootton 1994), SignalP (Nielsen et al.”
BackgroundMethodInfluential
Fatty acid acylation regulates trafficking of the unusual Plasmodium falciparum calpain to the nucleolus
Russo, I., Oksman, A., & Goldberg, D. E. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06639.x · Cited by 44
“This was recognized by PSORT II (Nakai and Horton, 1999), which gave a nuclear prediction with a reliability of 94.”
MethodInfluential
The NS16 protein of aquareovirus-C is a fusion-associated small transmembrane (FAST) protein, and its activity can be enhanced by the nonstructural protein NS26
Guo, H., Sun, X., Yan, L., et al. (2012) · Virus Research · doi:10.1016/j.virusres.2012.11.011 · Cited by 44
SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus
Sharma, K., Åkerström, S., Sharma, A. K., Chow, V. T. K., Teow, S., Abrenica, B., Booth, S. A., Booth, T. F., Mirazimi, A., & Lal, S. K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019436 · Cited by 45
“org/) predicted absence of NLS in it and suggested its nuclear import to be passive [30].”
Background
Full-length genome sequence analysis of enzootic nasal tumor virus reveals an unusually high degree of genetic stability
Walsh, S. R., Linnerth-Petrik, N. M., Laporte, A. N., MENZIES, P. I., Foster, R. A., & Wootton, S. K. (2010) · Virus Research · doi:10.1016/j.virusres.2010.04.002 · Cited by 44
Mutational analysis of highly conserved aspartate residues essential to the catalytic core of the piggyBac transposase
Keith, J. H., Schaeper, C. A., Fraser, T. S., & Fraser, M. J. (2008) · BMC Molecular Biology · doi:10.1186/1471-2199-9-73 · Cited by 44
“In fact, this region is so rich with basic amino acids, that 4 PSORTII [57] predicted NLS matches exist in this short region: 2 monopartite at positions 551 and 563, and 2 bipartite signals at positions 554 and 555, respectively.”
Background
Epithelial-mesenchymal transition-associated secretory phenotype predicts survival in lung cancer patients
Reka, A. K., Chen, G., Jones, R. C., et al. (2014) · Carcinogenesis · doi:10.1093/carcin/bgu041 · Cited by 44
A pathway for assembling [4Fe‐4S]2+ clusters in mitochondrial iron–sulfur protein biogenesis
Nasta, V., Suraci, D., Gourdoupis, S., Ciofi‐Baffoni, S., & Banci, L. (2019) · FEBS Journal · doi:10.1111/febs.15140 · Cited by 43
Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case
Clemente, H. S., Pont‐Lezica, R., & Jamet, É. (2009) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s2065 · Cited by 44
A New Member of the Sorting Nexin Family Interacts with the C-Terminus of P-Selectin
Florian, V., Schlüter, T., & Bohnensack, R. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.4467 · Cited by 44
Microcephalin coordinates mitosis in the syncytialDrosophilaembryo
Brunk, K., Vernay, B., Griffith, E., Reynolds, N. L., Strutt, D. I., Ingham, P. W., & Jackson, A. P. (2007) · Journal of Cell Science · doi:10.1242/jcs.014290 · Cited by 46
“…a unique pattern of BRCT domains, with a single N-terminal and tandem C-terminal BRCT domains, and is predicted to be a nuclear protein (PSORT II) (Nakai and Horton, 1999). mcph1 splice variants mcph1 has two sites of alternative splicing at intron 1 and 7, potentially resulting in four processed…”
Background
The elongation defective1 mutant of Arabidopsis is impaired in the gene encoding a serine-rich secreted protein
Lertpiriyapong, K., & Sung, Z. R. (2003) · Plant Molecular Biology · doi:10.1023/b:plan.0000019067.05185.d6 · Cited by 44
“Analysis of the ELD1 amino acid sequence with the PSORT prediction program ( Nakai and Horton, 1999; http://psort.nibb.ac.jp) revealed, with a high probability score, that the ELD1 protein is a secreted extracellular protein (Table 2). Moreover, SignalP-HMM (Henriket al., 1997; Henrik and Krogh, 1998; www.cbs.dtu.dk/s…”
Method
A novel serine/threonine kinase gene, STK33 , on human chromosome 11p15.3
Mujica, A. O., Hankeln, T., & Schmidt, E. R. (2001) · Gene · doi:10.1016/s0378-1119(01)00780-6 · Cited by 44

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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