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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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“The major open reading frames for consensus sequences were then predicted using MacVector (Oxford Molecular) and analyzed using PSORT (54) (http://psort.nibb.ac.jp/) to determine if the predicted amino acid sequence contained a potential secretory leader (SECL1).”
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Background
Prediction of protein subcellular location using a combined feature of sequence
Gao, Q.-B., Wang, Z., Yan, C. G., & Du, Y. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.05.021 · Cited by 85
“Subsequently, a computational program based on the same approach, called PSORT [5], was presented.”
Method
Glucose Transport and Transporters in the Endomembranes
Lizák, B., Szarka, A., Kim, Y., Choi, K.-S., Németh, C. E., Marcolongo, P., Benedetti, A., Bánhegyi, G., & Margittai, É. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20235898 · Cited by 92
“PSORTII uses the k-nearest-neighbor method to predict the subcellular localization of different proteins [68].”
Method
Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome
Chen, L., Tovar-Corona, J. M., & Urrutia, A. O. (2012) · International Journal of Evolutionary Biology · doi:10.1155/2012/596274 · Cited by 87
“PSORT II [21] was used to identify the likely subcellular localization of protein products.”
A family of proteins related to Spätzle, the toll receptor ligand, are encoded in the Drosophila genome
Parker, J., Mizuguchi, K., & Gay, N. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1125 · Cited by 99
sup-9, sup-10, andunc-93May Encode Components of a Two-Pore K+Channel that Coordinates Muscle Contraction inCaenorhabditis elegans
de la Cruz, I. P., Levin, J. Z., Cummins, C. M., et al. (2003) · Journal of Neuroscience · doi:10.1523/jneurosci.23-27-09133.2003 · Cited by 84
“The underlined residues represent the putative signal sequence (SS) and the transmembrane domain (TMD), which were determined using the PSORTII II program developed by Nakai and Horton (1999) (available at http://psort.nibb.ac.jp/).”
Method
Differential Detergent Fractionation for Non-electrophoretic Eukaryote Cell Proteomics
McCarthy, F., Burgess, S. C., van den Berg, B. H. J., et al. (2005) · Journal of Proteome Research · doi:10.1021/pr049842d · Cited by 84
Mitochondrial protein BmPAPI modulates the length of mature piRNAs
Honda, S., Kirino, Y., Maragkakis, M., Alexiou, P., Ohtaki, A., Murali, R., Mourelatos, Z., & Kirino, Y. (2013) · RNA · doi:10.1261/rna.040428.113 · Cited by 86
“2000) and Psort II (Nakai and Horton 1999) prediction programs identified a putativemitochondrial localization signal that encompassed the transmembrane helix domain of the BmPAPI N terminus.”
Background
GsLRPK, a novel cold-activated leucine-rich repeat receptor-like protein kinase from Glycine soja, is a positive regulator to cold stress tolerance
Yang, L., Wu, K., Gao, P., et al. (2013) · Plant Science · doi:10.1016/j.plantsci.2013.10.009 · Cited by 83
Expression pattern of LRR and Ig domain-containing protein (LRRIG protein) in the early mouse embryo
Homma, S., Shimada, T., Hikake, T., & Yaginuma, H. (2008) · Gene Expression Patterns · doi:10.1016/j.gep.2008.09.004 · Cited by 83
Is retinoic acid genetic machinery a chordate innovation?
Cañestro, C., Postlethwait, J. H., Gonzàlez‐Duarte, R., & Albalat, R. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00113.x · Cited by 83
“Subcellular localization prediction The PSORT-II program was used to predict from the amino acid sequence the subcellular localization of the deduced enzymes (Nakai and Horton 1999).”
Method
Is Catalase Activity One of the Factors Associated with Maize Resistance to Aspergillus flavus?
Magbanua, Z. V., Moraes, C. Μ. D., Brooks, T. D., et al. (2007) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-20-6-0697 · Cited by 83
“P-Sort bioinformatic analysis (Nakai and Horton 1999) was used to predict subcellular location of Cat3.”
Method
Prediction of dual protein targeting to plant organelles
Mitschke, J., Fuß, J., Blum, T., et al. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02832.x · Cited by 83
“Numerous approaches have been implemented and are available as prediction services ( Nakai & Horton, 1999; Emanuelsson et al., 2000; Guda et al., 2004; Small et al., 2004; Boden & Hawkins, 2005; Hoglund et al., 2006).”
Method
Molecular characterisation and expression of two venom allergen-like protein genes in Heterodera glycines
Gao, B., Allen, R., Maier, T. R., Davis, E., Baum, T. J., & HUSSEY, R. S. (2001) · International Journal for Parasitology · doi:10.1016/s0020-7519(01)00300-9 · Cited by 83
Discovery of differentially expressed genes in human breast cancer using subtracted cDNA libraries and cDNA microarrays
Jiang, Y., Harlocker, S. L., Molesh, D. A., et al. (2002) · Oncogene · doi:10.1038/sj.onc.1205278 · Cited by 83
“DNA homology database searches were performed using the BLAST program (Nakai and Horton, 1999). cDNA microarray cDNA microarray was performed as described previously (Xu et al., 2000).”
Method
MitoP2, an integrated database on mitochondrial proteins in yeast and man
Andréoli, C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh137 · Cited by 83
“9 1331 Computational predictions PSORT (15) 6125 MitoProt (score > 0.”
BackgroundMethod
Lsa63, a newly identified surface protein of Leptospira interrogans binds laminin and collagen IV
Vieira, M. L., de Morais, Z. M., Gonçales, A. P., et al. (2009) · Journal of Infection · doi:10.1016/j.jinf.2009.10.047 · Cited by 82
Functional analysis of glycoside hydrolase family 18 and 20 genes in Neurospora crassa
Tzelepis, G. D., Melin, P., Jensen, D. F., Stenlid, J., & Karlsson, M. (2012) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2012.06.013 · Cited by 83
“, 2000) and PSORT II (Nakai and Horton, 1999) were used to analyze subcellular localization, TMHMM 2.”
Method
The ATP-dependent Lon protease of Mus musculus is a DNA-binding protein that is functionally conserved between yeast and mammals
Lü, B., Liu, T., Crosby, J. A., Thomas-Wohlever, J. A., Lee, I., & Suzuki, C. K. (2003) · Gene · doi:10.1016/s0378-1119(03)00403-7 · Cited by 80
Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea
Tzelepis, G. D., Karlsson, M., Jensen, D. F., & Dubey, M. K. (2015) · Microbiology · doi:10.1099/mic.0.000096 · Cited by 82
“Target P v. 1.1 (Emanuelsson et al., 2000) and PSORT II (Nakai & Horton, 1999) were used to analyse subcellular localization.”
MethodInfluential
Topology of acyltransferase motifs and substrate specificity and accessibility in 1-acyl-sn-glycero-3-phosphate acyltransferase 1
Yamashita, A., Nakanishi, H., Suzuki, H. I., Kamata, R., Tanaka, K., Waku, K., & Sugiura, T. (2007) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2007.07.002 · Cited by 88
Different Domains of Phytophthora sojae Effector Avr4/6 Are Recognized by Soybean Resistance Genes Rps4 and Rps6
Dou, D., Kale, S. D., Liu, T., et al. (2010) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-23-4-0425 · Cited by 82
“P. megasperma f. sp. glycinea), is one of the most destructive soybean diseases and results in annual yield losses of up to 300 million dollars in North America (Wrather and Koenning 2006) and over 1 billion dollars worldwide (Nicholls 2004).”
Background
Biz1, a Zinc Finger Protein Required for Plant Invasion by Ustilago maydis , Regulates the Levels of a Mitotic Cyclin
Flor‐Parra, I., Vraneš, M., Kämper, J., et al. (2006) · The Plant Cell · doi:10.1105/tpc.106.042754 · Cited by 82
“PSORT (Nakai and Horton, 1999) predicts for Biz1 a high probability for nuclear localization (P ¼ 94.1).”
BackgroundMethodInfluential
Roles of aTrypanosoma brucei5′→3′ exoribonuclease homolog in mRNA degradation
Li, C.-H., Irmer, H., Gudjonsdottir-Planck, D., Freese, S., Salm, H., Haile, S., Estévez, A. M., & CLAYTON, C. E. (2006) · RNA · doi:10.1261/rna.291506 · Cited by 82
“A search for targeting signals using http://psort.nibb.ac.jp (Nakai and Horton 1999) showed weak nuclear localization signals for all four TbXRNs, but none of the proteins was unambiguously predicted to be nuclear.”
Background
Molecular and structural analyses of a novel temperature stress‐induced lipocalin from wheat and Arabidopsis
Charron, J.-B. F., Breton, G., Badawi, M. A., & Sarhan, F. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)02606-6 · Cited by 82
Affinity Labeling of Highly Hydrophobic Integral Membrane Proteins for Proteome-Wide Analysis
Goshe, M. B., Blonder, J., & Smith, R. D. (2003) · Journal of Proteome Research · doi:10.1021/pr0255607 · Cited by 82
DLC1 interacts with 14-3-3 proteins to inhibit RhoGAP activity and block nucleocytoplasmic shuttling
Scholz, R., Regner, J., Theil, A., Erlmann, P., Holeiter, G., Jähne, R., Schmid, S., Haußer, A., & Olayioye, M. A. (2008) · Journal of Cell Science · doi:10.1242/jcs.036251 · Cited by 82
“7A, highlighted in bold) (Nakai and Horton, 1999).”
Active uptake of cyst nematode parasitism proteins into the plant cell nucleus
Elling, A. A., Davis, E., HUSSEY, R. S., et al. (2007) · International Journal for Parasitology · doi:10.1016/j.ijpara.2007.03.012 · Cited by 81
“PSORT II ( Nakai and Horton, 1999 ) was used to determine the location of the putative NLS motifs within the protein sequence and to classify the NLS motifs into SV40 and bipartite-like groups (Table 3). These analyses were conducted using the parasitism protein sequences without the predicted N-terminal signal peptid…”
Method
Generating disulfides with the Quiescin-sulfhydryl oxidases
Heckler, E. J., Rancy, P. C., Kodali, V. K., & Thorpe, C. (2007) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2007.10.002 · Cited by 81
Cloning and characterization of a chitin synthase cDNA from the mosquito Aedes aegypti
Ibrahim, G. H., Smartt, C. T., Kiley, L. M., et al. (2000) · Insect Biochemistry and Molecular Biology · doi:10.1016/s0965-1748(00)00100-4 · Cited by 81
“Membrane topology predictions indicate that the N-terminal region of theAedesCS is oriented inside, facing the cytoplasm (PSORT prediction program- [Nakai and Horton, 1999]).”
Background
Better prediction of sub‐cellular localization by combining evolutionary and structural information
Nair, R. P., & Rost, B. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10507 · Cited by 81
“When comparing these methods on a data set of sequence-unique SWISS-PROT proteins of known localization that had been added be-tween release 40 and 41 (and were neither used in our development nor in that of the other methods tested), we got different results (Table IV): now SubLoc reached an…”
Method
The proteome of higher plant mitochondria
Rao, R. S. P., Salvato, F., Thal, B., Eubel, H., Thelen, J. J., & Møller, I. M. (2016) · Mitochondrion · doi:10.1016/j.mito.2016.07.002 · Cited by 78
“With the availability of more experimentally characterized protein sequences, PSORT was upgraded to PSORT II (http://psort.hgc.jp/form2.html), albeit only for yeast and animal sequences (Nakai and Horton, 1999).”
Background
Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo‐amino acid composition
Chou, K., & Cai, Y. (2004) · Journal of Cellular Biochemistry · doi:10.1002/jcb.10790 · Cited by 80
“For facilitating comparison, the rates obtained by the other predictors, such as TargetP [Emanuellson et al., 2000], and Psort [Nakai and Kanehisa, 1992; Nakai and Horton, 1999], are also listed in the same table.”
Result
Human polynucleotide phosphorylase, hPNPase, is localized in mitochondria.
Piwowarski, J., Grzechnik, P., Dziembowski, A., Dmochowska, A., Minczuk, M., & Stepien, P. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00528-x · Cited by 87
Therapy-induced senescent tumor cell-derived extracellular vesicles promote colorectal cancer progression through SERPINE1-mediated NF-κB p65 nuclear translocation
Zhang, D., Zhang, J., Xu, H., Chen, X., Gao, Y., Jiang, H.-G., Wang, Y., Wu, H., Yang, L., Wang, W., et al. (2024) · Molecular Cancer · doi:10.1186/s12943-024-01985-1 · Cited by 88
“But according to the PSORT II prediction software package (https://psort.hgc.jp/form2.html), SERPINE1 contains no currently identifiable NLS [52].”
Method
Ethylene in induced conifer defense: cDNA cloning, protein expression, and cellular and subcellular localization of 1-aminocyclopropane-1-carboxylate oxidase in resin duct and phenolic parenchyma cells
Hudgins, J. W., Ralph, S. G., Franceschi, V. R., et al. (2006) · Planta · doi:10.1007/s00425-006-0274-4 · Cited by 79
“The subcellular localization of ACO proteins was predicted using the TargetP v1.01 (Emanuelsson et al. 2000; http:// www.cbs.dtu.dk/services/TargetP/) and PSORT ( Nakai and Horton 1999; http://psort.nibb.ac.jp/) software programs.”
Method
INCREASED LEVEL OF POLYPLOIDY1, a Conserved Repressor of CYCLINA2 Transcription, Controls Endoreduplication in Arabidopsis
Yoshizumi, T., Tsumoto, Y., Takiguchi, T., et al. (2006) · The Plant Cell · doi:10.1105/tpc.106.043869 · Cited by 79
“In these two conserved regions, we found a putative nuclear localization signal (NLS) using the PSORT program (Nakai and Horton, 1999).”
Method
Putative phenoloxidases in the tunicate Ciona intestinalis and the origin of the arthropod hemocyanin superfamily
Immesberger, A., & Burmester, T. (2004) · Journal of Comparative Physiology B · doi:10.1007/s00360-003-0402-4 · Cited by 79
“Computer predictions using the PSORT II program (Nakai and Horton 1999) indicate that neither CinPO-1 nor CinPO-2 contain any signal peptide required for transmembrane transport and thus the proteins are most likely local-”
Identification of 12 New Yeast Mitochondrial Ribosomal Proteins Including 6 That Have No Prokaryotic Homologues
Saveanu, C., Fromont‐Racine, M., Harington, A., Ricard, F., Namane, A., & Jacquier, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m010864200 · Cited by 79

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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