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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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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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Background
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Method
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Method
Genome-Wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database
Rose, A., Manikantan, S., Schraegle, S. J., et al. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.103.035626 · Cited by 69
“…Claros et al. (1996) PredictNLS NLS http://maple.bioc.columbia.edu/predictNLS/ Cokol et al. (2000) PSORT NLS, TMH http://psort.nibb.ac.jp/ Nakai and Horton (1999) SignalP 2.0 HMM SP http://www.cbs.dtu.dk/services/SignalP-2.0/ Nielsen and Krogh (1998) SignalP 2.0 NN SP…”
Influential
Protein Annotation at Genomic Scale: The Current Status
Frishman, D. (2007) · Chemical Reviews · doi:10.1021/cr068303k · Cited by 68
The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer
van der Giezen, M., Cox, S. S. E., & Tovar, J. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-7 · Cited by 69
“, PSORT II [33], MitoProt [34], NNPSL [35]).”
Genomic Sequence and Structure of the Human ABCG1 (ABC8) Gene
Stefan Lorkowski, A., Rust, S., Engel, T., et al. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.4089 · Cited by 69
TmpL, a Transmembrane Protein Required for Intracellular Redox Homeostasis and Virulence in a Plant and an Animal Fungal Pathogen
Kim, K., Willger, S. D., Park, S.-W., Puttikamonkul, S., Grahl, N., Cho, Y., Mukhopadhyay, B., Cramer, R. A., & Lawrence, C. B. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000653 · Cited by 68
“First, in silico analyses were performed using WoLF PSORT, SHERLOC, TARGETP, TMHMM, PRED-TMR and SIGNALP [46,47,48,49,50,51].”
Method
fPoxDB: fungal peroxidase database for comparative genomics
Choi, J., Détry, N., Kim, K., et al. (2014) · BMC Microbiology · doi:10.1186/1471-2180-14-117 · Cited by 68
“1b [48], PSortII [49], ChloroP 1.”
Characterization and Heterologous Gene Expression of a Novel Esterase fromLactobacillus caseiCL96
Choi, Y. J., Míguez, C. B., & Lee, B. H. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.6.3213-3221.2004 · Cited by 69
“No potential signal sequence was found in estI, as revealed by the PSORT program (40).”
Background
Molecular Characterization and Origin of Novel Bipartite Cold-regulated Ice Recrystallization Inhibition Proteins from Cereals
Tremblay, K., Ouellet, F., Fournier, J., et al. (2005) · Plant and Cell Physiology · doi:10.1093/pcp/pci093 · Cited by 68
“Analysis of the TaIRI protein sequences using the PSORT, SignalP and TargetP programs (Nielsen et al. 1997, Nakai and Horton 1999, Emanuelsson et al. 2000) predicted a putative Nterminal cleavage site between amino acids 20 and 21.”
Method
The Isolation of FOS-1, a Gene Encoding a Putative Two-Component Histidine Kinase from Aspergillus fumigatus
Pott, G. B., Miller, T. K., Bartlett, J. A., et al. (2000) · Fungal Genetics and Biology · doi:10.1006/fgbi.2000.1225 · Cited by 68
Yeast Nop15p is an RNA‐binding protein required for pre‐rRNA processing and cytokinesis
Oeffinger, M., & Tollervey, D. W. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg616 · Cited by 68
Differential Enzyme Targeting As an Evolutionary Adaptation to Herbivory in Carnivora
Birdsey, G. M. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh054 · Cited by 68
Topology of Transmembrane Channel-like Gene 1 Protein
Labay, V., Weichert, R. M., Makishima, T., & Griffith, A. J. (2010) · Biochemistry · doi:10.1021/bi1004377 · Cited by 67
Structural Organization of the Human Glutathione Reductase Gene: Determination of Correct cDNA Sequence and Identification of a Mitochondrial Leader Sequence
Kelner, M. J., & Montoya, M. A. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.2267 · Cited by 67
Utility of the Trypanosoma cruzi Sequence Database for Identification of Potential Vaccine Candidates by In Silico and In Vitro Screening
Bhatia, V., Sinha, M., Luxon, B. A., et al. (2004) · Infection and Immunity · doi:10.1128/iai.72.11.6245-6254.2004 · Cited by 67
“Localization of the encoded products to plasma membrane (PM) and outside (OS) was determined by PSORT analysis (probability score, 0 to 1).”
MethodInfluential
Dual RNA‐seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants
Petitot, A., Dereeper, A., Agbessi, M. D. T., Silva, C. D., Guy, J., Ardisson, M., & Fernandez, D. (2015) · Molecular Plant Pathology · doi:10.1111/mpp.12334 · Cited by 72
Identification by suppression subtractive hybridization and expression analysis of Arabidopsis thaliana putative defence genes during Orobanche ramosa infection
Santos, C. V. D., Delavault, P. M., Letousey, P., & Thalouarn, P. A. (2003) · Physiological and Molecular Plant Pathology · doi:10.1016/s0885-5765(03)00073-0 · Cited by 66
AMPDB: the Arabidopsis Mitochondrial Protein Database
Heazlewood, J. L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki048 · Cited by 67
“MitoProt II (3), PSORT (4) and iPSORT (5) utilize predefined parameters of signal peptides to predict subcellular localization.”
Influential
Comparative Sequence Analysis of the Largest E1A Proteins of Human and Simian Adenoviruses
Avvakumov, N., Wheeler, R., D’Halluin, J. C., & Mymryk, J. S. (2002) · Journal of Virology · doi:10.1128/jvi.76.16.7968-7975.2002 · Cited by 68
“We used the program PSORT (51) to predict NLS sequences in each of the E1A proteins (Table 2).”
MethodInfluential
The Predicted Candidates of Arabidopsis Plastid Inner Envelope Membrane Proteins and Their Expression Profiles,
Koo, A. J., & Ohlrogge, J. B. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.008052 · Cited by 67
“%) to use for discrimination between the thylakoid and the envelope-localized proteins (Nakai and Horton, 1999).”
Background
Genome-Wide Survey and Expression Analysis of the Putative Non-Specific Lipid Transfer Proteins in Brassica rapa L
Li, J., Gao, G., Xu, K., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084556 · Cited by 66
“Subsequently, the proteins without NSSs (checked by the SignalP 4.0, http://www.cbs.dtu.dk/services/SignalP) [85] and with C-terminal GPI anchor signals (predicted by the big-PI Plant Predictor [86] and PSORT [87]), were also removed.”
BackgroundInfluential
Subcellular localization of adenosine kinase in mammalian cells: The long isoform of AdK is localized in the nucleus
Cui, X. A., Singh, B., Park, J., & Gupta, R. S. (2009) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2009.07.106 · Cited by 66
“PSORT, BaCelLo) reveal no specific localization of these isoforms and thus they are both assumed to be present in the cytoplasm [18,19].”
BackgroundMethodInfluential
Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants
Ottenhof, H. H., Ashurst, J. L., Whitney, H. M., Saldanha, S. A., Schmitzberger, F., Gweon, H. S., Blundell, T. L., Abell, C., & Smith, A. G. (2003) · The Plant Journal · doi:10.1046/j.1365-313x.2003.01940.x · Cited by 66
An expression analysis of the ascorbate biosynthesis enzyme VTC2
Müller-Moulé, P. (2008) · Plant Molecular Biology · doi:10.1007/s11103-008-9350-4 · Cited by 66
A Novel Effector Protein, MJ-NULG1a, Targeted to Giant Cell Nuclei Plays a Role inMeloidogyne javanicaParasitism
Lin, B., Zhuo, K., Wu, P., et al. (2012) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-05-12-0114-fi · Cited by 66
“Molecular mass and pI were predicted using ProtParam (Wilkins et al. 1998), while NLS domains were predicted through PSORT II (Nakai and Horton 1999) and WoLF PSORT (Horton et al. 2006).”
Method
ProLoc: Prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features
Huang, W.-L., Tung, C.-W., Huang, H.-L., et al. (2007) · Biosystems · doi:10.1016/j.biosystems.2007.01.001 · Cited by 66
“E-mail address: syho@mail.nctu.edu.tw (S.-Y. Ho).”
BackgroundMethodInfluential
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
Wilson, M. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.6.1352 · Cited by 66
“CIP1 is 100% identical to our putative cation-chloride cotransporter-like protein and is predicted by PSORT (58) to have 12 transmembrane helices.”
Background
Cytoplasmic localization of the interferon‐inducible protein that is encoded by the AIM2 (absent in melanoma) gene from the 200‐gene family
Choubey, D., Walter, S., Geng, Y., & Xin, H. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01571-4 · Cited by 65
Alternative translation initiation augments the human mitochondrial proteome
Kazak, L., Reyes, A., Duncan, A. L., Rorbach, J., Wood, S., Brea‐Calvo, G., Gammage, P. A., Robinson, A. J., Minczuk, M. A., & Holt, I. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1347 · Cited by 65
“(B) In silico mitochondrial targeting prediction scores from: Mitoprot, TargetP, Predotar (35), PSORTII (36) and iPSORT of human and mouse PIF1.”
Background
A Novel Functional Class I Lineage in Zebrafish (Danio rerio), Carp (Cyprinus carpio), and Large Barbus (Barbus intermedius) Showing an Unusual Conservation of the Peptide Binding Domains
Kruiswijk, C. P., Hermsen, T., Westphal, A. H., Savelkoul, H. F. J., & Stet, R. J. M. (2002) · The Journal of Immunology · doi:10.4049/jimmunol.169.4.1936 · Cited by 65
“Correspond to HLA-A*02011 (31) Peptide N terminus Peptide C terminus”
Background
Genome-Wide Analysis of Ruminant Staphylococcus aureus Reveals Diversification of the Core Genome
Zakour, N. L. B., Sturdevant, D. E., Even, S., Guinane, C. M., Barbey, C., Alves, P. D. D., Cochet, M., Gautier, M., Otto, M. J., Fitzgerald, J. R., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.01984-07 · Cited by 65
Identification and characterization of a novel Nogo‐interacting mitochondrial protein (NIMP)
Hu, W., Hausmann, O. N., Yan, M., et al. (2002) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2002.00788.x · Cited by 65
“Prediction analysis of protein sorting signals and localization sites using PROSORT (Nakai and Horton 1999) reveals that the N-terminal portion (residues 1–42) of both human and mouse NIMP contains a potential mitochondrial localization signal (MLS) with a predicted cleavage site at RS\TV.”
Method
Human Experimental Challenge With Enterotoxigenic Escherichia coli Elicits Immune Responses to Canonical and Novel Antigens Relevant to Vaccine Development
Chakraborty, S., Randall, A. Z., Vickers, T. J., Molina, D., Harro, C. D., DeNearing, B., Brubaker, J., Sack, D. A., Bourgeois, A. L., Felgner, P. L., et al. (2018) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiy312 · Cited by 64
Protein secretion systems in Fusobacterium nucleatum: Genomic identification of Type 4 piliation and complete Type V pathways brings new insight into mechanisms of pathogenesis
Desvaux, M., Khan, A., Beatson, S. A., Scott-Tucker, A., & Henderson, I. R. (2005) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2005.05.002 · Cited by 64
Assigning Functional Domains within the p101 Regulatory Subunit of Phosphoinositide 3-Kinase γ
Voigt, P., Brock, C., Nürnberg, B., et al. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m413104200 · Cited by 64
Functional characterisation of ganglioside-induced differentiation-associated protein 1 as a glutathione transferase
Shield, A., Murray, T. P., & Philip G. Board (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.06.189 · Cited by 64
Isolation and characterization of a rice mutant with narrow and rolled leaves
Wu, C., Fu, Y., Hu, G., Si, H., Cheng, S., & Liu, W. (2010) · Planta · doi:10.1007/s00425-010-1180-3 · Cited by 63
“The subcellular location of the NRL1 protein was predicted by Predotar and PSORT (Nakai and Horton 1999; Small et al. 2004) and the results suggested that the NRL1 protein could be imported into endoplasmic reticulum.”
Background
A Comparative Study of Lectin Affinity Based Plant N-Glycoproteome Profiling Using Tomato Fruit as a Model
Ruíz-May, E., Hucko, S. D., Howe, K. J., Zhang, S., Sherwood, R., Thannhauser, T. W., & Rose, J. K. C. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.028969 · Cited by 64
“We used PSORT and TargetP to predict the subcellular localization of all 578 putative N-glycoproteins and indeed 523 (90”
MethodInfluential
A Penicillium expansum Glucose Oxidase–Encoding Gene, GOX2, Is Essential for Gluconic Acid Production and Acidification During Colonization of Deciduous Fruit
Barad, S., Horowitz, S. B., Moscovitz, O., Lichter, A., Sherman, A., & Prusky, D. (2012) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-01-12-0002 · Cited by 64
“AUTHOR-RECOMMENDED INTERNET RESOURCES The National Center for Biotechnology Information BLAST webpage: blast.ncbi.nlm.nih.gov/Blast.cgi PSORTII protein prediction server: psort.ims.u-tokyo.ac.jp Center for Biological Sequence Analysis (CBS) SignalP-HMM server: www.cbs.dtu.dk/services/SignalP CBS TargetP server: www.cb…”
MethodInfluential

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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