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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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“[11] Nakai, K., Horton, P., PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization.”
Method
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“The PROSITE database (Bairoch et al., 1997) was searched to identify known protein motifs, and PSORT II analysis (Nakai and Horton, 1999) was carried out to identify signal peptides.”
Method
Addressing protein localization within the nucleus
Bickmore, W. A., & Sutherland, H. G. E. (2002) · The EMBO Journal · doi:10.1093/emboj/21.6.1248 · Cited by 64
“The results using PSORT to correctly predict nuclear localization, for proteins in subnuclear compartments, using the k-nearest neighbour method (Nakai and Horton, 1999) are similar (84% prediction for chromatinassociated proteins, 40% prediction for proteins at the nuclear periphery).”
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“…Author M anuscript N IH -PA Author M anuscript analysis using fluorescent reporters (Westermann and Neupert 2000), deletion phenotyping (Pan et al. 2004), and many computational methods designed to identify mitochondrial proteins by virtue of signature trafficking sequences (Nakai and Horton 1999).”
BackgroundMethod
The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome
Gray, M. W., Burger, G., Derelle, R., Klimeš, V., Leger, M. M., Sarrasin, M., Vlček, Č., Roger, A. J., Eliáš, M., & Lang, B. F. (2020) · BMC Biology · doi:10.1186/s12915-020-0741-6 · Cited by 64
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“The programmes PSORT (Nakai and Horton, 1999), iPSORT (Bannai et al.”
Background
Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs
Watanabe, J., Sasaki, M., Suzuki, Y., et al. (2002) · Gene · doi:10.1016/s0378-1119(02)00552-8 · Cited by 63
Cloning and characterization of FAM13A1—a gene near a milk protein QTL on BTA6: evidence for population-wide linkage disequilibrium in Israeli Holsteins☆
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“[5] and contain predictions using four different methods: TargetP [6], TMHMM [7], SOSUI [8], and PSORTII [ 9 ].”
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pTARGET: a web server for predicting protein subcellular localization
Guda, C. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl093 · Cited by 62
Screening for Glycosylphosphatidylinositol-Modified Cell Wall Proteins in Pichia pastoris and Their Recombinant Expression on the Cell Surface
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TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR4 Interacts with WRINKLED1 to Mediate Seed Oil Biosynthesis
Kong, Q., Singh, S. K., Mantyla, J. J., Pattanaik, S., Guo, L., Yuan, L., Christoph Benning, A., & Ma, W. (2020) · PLANT PHYSIOLOGY · doi:10.1104/pp.20.00547 · Cited by 62
Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis
Inácio, J. M., Correia, I. L., & Sá‐Nogueira, I. (2008) · Microbiology · doi:10.1099/mic.0.2008/018978-0 · Cited by 62
“However, using the PSORT program ( Nakai & Horton, 1999 ) AbfA was predicted to have a putative transmembrane motif (residues 342–358); thus we tested the possibility of a potential membrane association of AbfA.”
Method
FLAGdb++: a database for the functional analysis of the Arabidopsis genome
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“... a chromosome locus; GST: designed by SPADS (7) are all 100% identical to only one locus; SAGE tags are mapped by BLASTn to loci 100% identical to them (31% match to only one locus); Pfam domains have been searched for by HMMER (8), first using the predicted proteome and second using the six-frame translated chromo…”
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Comparative genomic analysis of the Hsp70s from five diverse photosynthetic eukaryotes
Renner, T., & Waters, E. (2007) · Cell stress & chaperones (Print) · doi:10.1379/csc-230r1.1 · Cited by 61
“The newly identified Hsp70 sequences were submitted to the prediction programs Psort, Predotar, and TargetP (Nakai and Horton 1999; Emanuelsson et al 2000; Small et al 2004) to determine their possible subcellular localization.”
Method
Characterisation and Expression of Calpain Family Members in Relation to Nutritional Status, Diet Composition and Flesh Texture in Gilthead Sea Bream (Sparus aurata)
Salmerón, C., de la serrana, D. G., Jiménez-Amilburu, V., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075349 · Cited by 61
“Finally, analysis of the calpain amino acid sequences using the PSORTII program predicted that all were cytoplasmic proteins.”
Method
Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with β-glucosidase, β-fucosidase and β-galactosidase activities
Wierzbicka-Woś, A., Bartasun, P., Cieśliński, H., & Kur, J. (2013) · BMC Biotechnology · doi:10.1186/1472-6750-13-22 · Cited by 60
Vacuole Membrane Protein 1 Is an Endoplasmic Reticulum Protein Required for Organelle Biogenesis, Protein Secretion, and Development
Calvo‐Garrido, J., Carilla-Latorre, S., Lázaro‐Diéguez, F., Egea, G., & Escalante, R. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e08-01-0075 · Cited by 62
“The amino acid sequence of Dictyostelium Vmp1 showed a conserved KKXX-like ER-membrane retention signal at the C terminus as detected by the PSORT program (Nakai and Horton, 1999), resulting in a K-NN prediction 66,7% for ER, which is confirmed by our results.”
Result
Recent developments and future directions in computational genomics
Tsoka, S., & Ouzounis, C. A. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01776-2 · Cited by 61
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“For the prediction of the subcellular localization and the corresponding target peptides the programs TargetP V1.0 (Emanuelsson et al. 2000) and iPSORT ( Nakai and Horton 1999 ) were used.”
Method
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“uk/), the COG database [21], and the protein localization prediction software, PSORT [22] described in [20].”
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“First, two putative nuclear localization sites of four amino residues (positions 212/213 and 302) in addition to the B box were identified (PSORT, http://psort.ims.u-tokyo.ac. jp/; Nakai and Horton, 1999), with a probability of 0.7 for SlZF2 to be a nuclear protein.”
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“Proteins predicted to contain signal peptides by at least one of the three data sets were then examined using Psort (Nakai and Horton 1999; http://www.psort.nibb.ac.jp), a computer program designed to predict subcellular localization.”
Method
An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria
Khazi, F. R., Edmondson, A. C., & Nielsen, B. L. (2003) · Molecular Genetics and Genomics · doi:10.1007/s00438-003-0859-6 · Cited by 60
“Potential targeting presequences were predicted using the PSORT (Nakai and Horton 1999; Nakai 2000), TargetP (Emanuelsson et al.”
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“jp/) [77] was used to identify putative nuclear localization signals in RXLR proteins.”
Method
A Membrane-Bound Vertebrate Globin
Blank, M., Wollberg, J., Gerlach, F., Reimann, K., Roesner, A., Hankeln, T., Fago, A., Weber, R. E., & Burmester, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025292 · Cited by 57
“localization [26].”
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Gottschling, M., Bravo, I. G., Ehrke‐Schulz, E., Bracho, M. A., Deaville, R., Jepson, P. D., Bressem, M. V., Stockfleth, E., & Nindl, I. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.12.013 · Cited by 59
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Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation
Varani, A. M., Souza, R. C., Nakaya, H. I., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0004059 · Cited by 59
“For putative functional attribution, BLAST searches [39] and COG [46], INTERPRO [47], PRINTS [48], PSORT [49] and SWISSPROT [50] databases were used.”
Method
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Biagini, M., Garibaldi, M., Aprea, S., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.045880 · Cited by 59
“In silico predictions with different algorithms (PSORT (26), LipoP (27) DOLOP (28), PredLipo (29)) or bibliographic reference (30), as reported in Table I, were used to include all the possible Lpps.”
Method
HIPKs: Jack of all trades in basic nuclear activities
Rinaldo, C., Siepi, F., Prodosmo, A., & Soddu, S. (2008) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2008.06.006 · Cited by 61
“indicate the sorting signals that predict nuclear localization by the PSORT program [52].”
Method
The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development
Zhang, X., Cui, J., Nilsson, D., Gunasekera, K., Chanfon, A., Song, X., Wang, H., Xu, Y., & Ochsenreiter, T. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq618 · Cited by 58
“These methods use different protein features, such as amino acid composition [AAC; e.g. MitPred (24), Predotar (25), PSORTII (26), PLOC (27), NNPSL (28)], physicochemical properties [e.g. Predotar (25), Proteome Analyst (29), LOCSVMPSI (30), ESLpred (31), LOCtree (32)], N-terminal signal peptides [e.g. TargetP (33), i…”
BackgroundInfluential
A newly identified protein of Leptospira interrogans mediates binding to laminin
Longhi, M. T., de Oliveira, T. R., Romero, E. C., et al. (2009) · Journal of Medical Microbiology · doi:10.1099/jmm.0.011916-0 · Cited by 58
“…Copenhageni genome sequences (Nascimento et al., 2004a, b) based on its cellular localization prediction by the PSORT (http://psort.nibb. ac.jp; Nakai & Horton, 1999; Nakai & Kanehisa, 1991) and P- Classifier (http://protein.bii.a-star.edu.sg/localization/gram-negative/ index.html; Wang et…”
Background
Spatial control of protein phosphatase 2A (de)methylation
Longin, S., Zwaenepoel, K., Martens, E., Louis, J. V., Rondelez, E., Goris, J., & Janssens, V. (2007) · Experimental Cell Research · doi:10.1016/j.yexcr.2007.07.030 · Cited by 59
Analysis of Structure and Function of Putative Surface-Exposed Proteins Encoded in theStreptococcus pneumoniaeGenome: A Bioinformatics-Based Approach to Vaccine and Drug Design
Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2003) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/713609215 · Cited by 58
“A useful tool for such manual examination of extracellular localization is the PSORT set of programs (Nakai and Horton, 1999; Nakai, 2001).”
Method
A Nuclear Localization Signal and a Membrane Association Domain Contribute to the Cellular Localization of the Tobacco Mosaic Virus 126-kDa Replicase Protein
Figueira, A. D. R., Golem, S., Goregaoker, S. P., et al. (2002) · Virology · doi:10.1006/viro.2002.1560 · Cited by 58
An iTRAQ-Based Quantitative Analysis To Elaborate the Proteomic Response of Nostoc sp. PCC 7120 under N2 Fixing Conditions
Stensjö, K., Ow, S. Y., Barrios-Llerena, M. E., et al. (2007) · Journal of Proteome Research · doi:10.1021/pr060517v · Cited by 58
Genes involved in the synthesis of the exopolysaccharide methanolan by the obligate methylotroph Methylobacillus sp. strain 12S
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“Signal sequences in the predicted amino acid sequences were found by PSORT (Nakai & Horton, 1999).”
Method
Cloning and Characterization of an Intracellular Esterase from the Wine-Associated Lactic Acid Bacterium Oenococcus oeni
Sumby, K. M., Matthews, A. H., Grbin, P. R., & Jiranek, V. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01563-09 · Cited by 57
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Stepwise engineering of a Pichia pastoris D-amino acid oxidase whole cell catalyst
Abad, S., Nahálka, J., Bergler, G., et al. (2010) · Microbial Cell Factories · doi:10.1186/1475-2859-9-24 · Cited by 57
“1 [23] and PSORTII [24] revealed the absence of a Pex7p-selective motif PTS2.”
BackgroundInfluential
Analysis of the Yeast Kinome Reveals a Network of Regulated Protein Localization during Filamentous Growth
Bharucha, N., Ma, J., Dobry, C. J., Lawson, S. K., Yang, Z., & Kumar, A. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-11-1199 · Cited by 57
“Little has been reported describing nuclear localization signals (NLSs) in these proteins, and sequence analysis by the program PSORTII (Nakai and Horton, 1999) suggests the presence of a putative NLS in only Ksp1p.”
Background
Interactome Mapping of the Phosphatidylinositol 3-Kinase-Mammalian Target of Rapamycin Pathway Identifies Deformed Epidermal Autoregulatory Factor-1 as a New Glycogen Synthase Kinase-3 Interactor
Pilot‐Storck, F., Chopin, E., Rual, J.-F. M., Baudot, A., Dobrokhotov, P., Robinson‐Rechavi, M., Brun, C., Cusick, M. E., HILL, D. E., Schaeffer, L., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900568-mcp200 · Cited by 63
“Y2H interactions were retrieved with RHEB and RHEBL1 only when their last amino acids that constitute a prenylation motif (25) were removed (supplemental Fig.”
Method
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Harding, S. V., Sarkar‐Tyson, M., Smither, S. J., et al. (2007) · Vaccine · doi:10.1016/j.vaccine.2006.12.006 · Cited by 57
Both Cleavage Products of the mCLCA3 Protein Are Secreted Soluble Proteins
Mundhenk, L., Alfalah, M., Elble, R. C., et al. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m606489200 · Cited by 57
Gene organisation, sequence variation and isochore structure at the centromeric boundary of the human MHC
Stephens, R., Horton, R., Humphray, S., Rowen, L., Trowsdale, J., & Beck, S. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3004 · Cited by 57
The globin gene family of the cephalochordate amphioxus: implications for chordate globin evolution
Ebner, B., Panopoulou, G., Vinogradov, S. N., Kiger, L., Marden, M. C., Burmester, T., & Hankeln, T. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-370 · Cited by 55
“However, computer predictions using the PSORT II program [39] indicate that none of the amphioxus globins appears to contain a leader signal peptide, and all variants are predicted to be located in the cytoplasm.”
Method
Localization and Evolution of Putative Triose Phosphate Translocators in the DiatomPhaeodactylum tricornutum
Moog, D., Rensing, S. A., Archibald, J. M., Maier, U. G., & Ullrich, K. K. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv190 · Cited by 56
“…last accessed October 19, 2015) (Horton et al. 2007), PSORTII (http://psort.hgc.jp/form2.html, last accessed October 19, 2015) (Nakai and Horton 1999), PTS1 predictor (http:// mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp, last accessed October 19, 2015) (Neuberger et…”
Background
Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution
Shi, J., Zhang, S.-W., Pan, Q., & Zhou, G. (2008) · Amino Acids · doi:10.1007/s00726-007-0623-z · Cited by 56
“These methods can be broadly classified into four types (Guda and Subramaniam, 2005): (1) Methods based on the sorting signals which rely on the presence of protein targeting or signal peptides (Nakai and Horton, 1999).”
Background
Functional annotation of putative hypothetical proteins from Candida dubliniensis
Kumar, K., Prakash, A., Tasleem, M., Islam, A., Ahmad, F., & Hassan, M. I. (2014) · Gene · doi:10.1016/j.gene.2014.03.060 · Cited by 56
“We used PSORT II tool (Nakai and Horton, 1999) for the prediction of sub-cellular localization protein.”
Method
Evidence for Base Excision Repair of Oxidative DNA Damage in Chloroplasts of Arabidopsis thaliana
Gutman, B. L., & Niyogi, K. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.008342 · Cited by 56
The human FK506-binding proteins: characterization of human FKBP19
Rulten, S. L., Kinloch, R. A., Tateossian, H., et al. (2006) · Mammalian Genome · doi:10.1007/s00335-005-0127-7 · Cited by 56
“The C-terminus of this protein differs from the other secretory-pathway FKBPs in that it lacks a calcium-binding EF hand that is typical of several other secretory pathway FKBPs and contains a putative transmembrane domain (as predicted by PSORT; Nakai and Horton, 1999), followed by a lysine-rich C-terminal tail, cont…”
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach
Lin, H.-N., Chen, C.-T., Sung, T.-Y., et al. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-s15-s8 · Cited by 56
“Since the dataset is from ngLOC and ngLOC has been shown to be better than PSORT [30], pTARGET [31] and PLOC [32] using the same dataset, we directly compare KnowPred site against ngLOC using ten-fold cross validation.”
Method
Evaluation of Unconventional Protein Secretion by Saccharomyces cerevisiae and other Fungi
Miura, N., & Ueda, M. (2018) · Cells · doi:10.3390/cells7090128 · Cited by 56
“Using SignalP [18,19], PSort [20,21], TargetP [22,23], or relevant software, the secretion signal sequence is predictable and it is easier to predict conventionally secreted proteins based on the fungal genome or using transcriptome data [24].”
Background
Delineation and Modelling of a Nucleolar Retention Signal in the Coronavirus Nucleocapsid Protein
Reed, M. L., Dove, B. K., Jackson, R. M., Collins, R., Brooks, G., & Hiscox, J. A. (2006) · Traffic · doi:10.1111/j.1600-0854.2006.00424.x · Cited by 59
“PredictNLS found no NLSs, whereas PSORTII indicated that IBV N protein contained two potential overlapping NLSs in region 3 between residues 358– 366, a pat4 motif (RPKK) and a pat7 motif (PKKEKKL) (Figure 1A).”
Method
Cytochromes P460 and c′‐beta; A new family of high‐spin cytochromes c
Elmore, B. O., Bergmann, D., Klotz, M. G., & Hooper, A. B. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.01.068 · Cited by 56
Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana
Edmondson, A. C., Song, D., Alvarez, L. A., et al. (2005) · Molecular Genetics and Genomics · doi:10.1007/s00438-004-1106-5 · Cited by 56
“Mitochondrially targeted SSB was predicted with high probability to be targeted to the mitochondrial matrix by the PSORT (0.810) and MitoP (0.8877) prediction programs.”
MethodInfluential
Myosin16b: The COOH‐tail region directs localization to the nucleus and overexpression delays S‐phase progression
Cameron, R. S., Liu, C., Mixon, A. S., et al. (2006) · Cell Motility and the Cytoskeleton · doi:10.1002/cm.20162 · Cited by 56
Sequence of Leptospira santarosai serovar Shermani genome and prediction of virulence-associated genes
Chou, L., Chen, Y.-T., Lu, C., Ko, Y.-C., Tang, C. Y., Pan, M.-J., Tian, Y., Chiu, C., Hung, C., & Yang, C. (2012) · Gene · doi:10.1016/j.gene.2012.09.074 · Cited by 57
High Temperature Requirement A3 (HtrA3) Promotes Etoposide- and Cisplatin-induced Cytotoxicity in Lung Cancer Cell Lines
Beleford, D. T., Rattan, R., CHIEN, J. R., & Shridhar, V. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.097790 · Cited by 55
Genome Analysis and Phylogenetic Relatedness of Gallibacterium anatis Strains from Poultry
Johnson, T. J., Danzeisen, J. L., Trampel, D. W., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054844 · Cited by 55
“All predicted proteins of UMN179 were analyzed for their predicted subcellular location using PSORT 3.0 [23].”
Influential
Use of solid‐phase subtractive hybridization for the identification of parasitism gene candidates from the root‐knot nematode Meloidogyne incognita
Huang, G., Dong, R., Maier, T. R., et al. (2004) · Molecular Plant Pathology · doi:10.1111/j.1364-3703.2004.00220.x · Cited by 55
Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
Chen, W., Li, Y., Wang, Q., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096436 · Cited by 55
“For putative secreted proteins, PSORT [27] was further applied to predict their localization within plant and animal cells.”
Method
Outer Membrane Vesicles (OMV)-based and Proteomics-driven Antigen Selection Identifies Novel Factors Contributing to Bordetella pertussis Adhesion to Epithelial Cells
Gasperini, G., Biagini, M., Arato, V., et al. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000045 · Cited by 55
Hybrid Transcription Factor Engineering Activates the Silent Secondary Metabolite Gene Cluster for (+)-Asperlin in Aspergillus nidulans
Grau, M. F., Entwistle, R., Chiang, Y., Ahuja, M., Oakley, C. E., Akashi, T., Wang, C. C. C., Todd, R. B., & Oakley, B. R. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00679 · Cited by 55
The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility
Corredor‐Moreno, P., Minter, F., Davey, P., Wegel, E., Kular, B., Brett, P., Lewis, C. M., Morgan, Y. M. L., Perez, L., Korolev, A. V., et al. (2021) · The Plant Cell · doi:10.1093/plcell/koab049 · Cited by 52
“This analysis indicated potential mitochondrial localization for TaBCAT1-A, TaBCAT1-B, and TaBCAT1-D, with iPSORT (Nakai and Horton, 1999) identifying a mitochondrial targeting peptide in the first 30 amino acids and MitoProt (Claros, 1995) and TargetP (Emanuelsson et al.”
Method
Getting tRNA synthetases into the nucleus
SCHIMMEL, P. R., & Wang, C. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(99)01369-9 · Cited by 55
Identification of two new members of the CSMD gene family☆
Lau, W. L., & Scholnick, S. B. (2003) · Genomics · doi:10.1016/s0888-7543(03)00149-6 · Cited by 55
A M eloidogyne incognita effector is imported into the nucleus and exhibits transcriptional activation activity in planta
Zhang, L., Davies, L. J., & Elling, A. A. (2014) · Molecular Plant Pathology · doi:10.1111/mpp.12160 · Cited by 61
“Nine of the 13 effectors were predicted by PSORTII to localize to the nucleus; only two effectors, 7H08 and 2G02, were predicted to contain putative monopartite NLSs, based on sequence similarity to the simian virus 40 (SV40) large T-antigen NLS (Kalderon et al., 1984a, 1984b).”
BackgroundMethodInfluential
Adhesins of Leptospira interrogans Mediate the Interaction to Fibrinogen and Inhibit Fibrin Clot Formation In Vitro
Oliveira, R., Domingos, R. F., Siqueira, G. H., Fernandes, L. G. V., Souza, N. M., Vieira, M. L., de Morais, Z. M., Vasconcellos, S. A., & Nascimento, A. L. T. O. (2013) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0002396 · Cited by 54
“jp [24,25].”
Annotation of microsporidian genomes using transcriptional signals
Peyretaillade, É., Parisot, N., Polonais, V., et al. (2012) · Nature Communications · doi:10.1038/ncomms2156 · Cited by 54
A stress-induced rice (Oryza sativa L.) β-glucosidase represents a new subfamily of glycosyl hydrolase family 5 containing a fascin-like domain
Opassiri, R., Pomthong, B., Akiyama, T., et al. (2007) · Biochemical Journal · doi:10.1042/bj20070734 · Cited by 54
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins
Garg, A., & Raghava, G. P. S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-503 · Cited by 54
“After PSORT [1,2] the first method developed to predict the subcellular localizations, ample of novice, improved, generalized and organism specific prediction methods have been developed for predicting subcellular locations of eukaryotic and prokaryotic proteins, namely, NNPSL, PSORTB, FKNN, TargetP, SubLoc, SignalP,…”
Method
Prediction of Golgi Type II membrane proteins based on their transmembrane domains
Yuan, Z., & Teasdale, R. D. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.8.1109 · Cited by 54
“These motifs can be predicted using PSORT II (Nakai and Horton, 1999; http://psort.nibb.ac.jp/) and if present will override any prediction based on our method.”
BackgroundMethodInfluential
Coexpression Analysis Identifies Two Oxidoreductases Involved in the Biosynthesis of the Monoterpene Acid Moiety of Natural Pyrethrin Insecticides in Tanacetum cinerariifolium
Xu, H., Moghe, G. D., Wiegert-Rininger, K. E., et al. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01330 · Cited by 54
The Peripheral Olfactory Repertoire of the Lightbrown Apple Moth, Epiphyas postvittana
Corcoran, J. A., Jordan, M. D., Thrimawithana, A. H., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128596 · Cited by 54
“Cellular localization of CXEs was predicted using PSORT [49].”
MethodInfluential
In through the out door: nuclear localization of the regulators of G protein signaling
Burchett, S. A. (2003) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2003.02047.x · Cited by 54
Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins
Egland, K. A., Vincent, J. J., Strausberg, R. L., Lee, B., & Pastan, I. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0337425100 · Cited by 54
Molecular analysis of the CRINKLY4 gene family in Arabidopsis thaliana
Cao, X., Li, K., Suh, S. G., et al. (2004) · Planta · doi:10.1007/s00425-004-1378-3 · Cited by 54
“1997), PSORT (Nakai and Horton 1999), iPSORT (Bannai et al.”
Method
Molecular identification of wheat endoxylanase inhibitor TAXI‐I1, member of a new class of plant proteins
Fierens, K., Brijs, K., Courtin, C. M., et al. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)00276-x · Cited by 54
An MMP liberates the Ninjurin A ectodomain to signal a lossof cell adhesionPreprint
Zhang, S., Dailey, G. M., Kwan, E., Glasheen, B. M., Sroga, G. E., & Page, A. W. (2006) · Genes & Development · doi:10.1101/gad.1426906 · Cited by 54
“Sequences were BLASTed to retrieve predicted full-length genes, and assigned cellular locations with SignalP (Nielsen and Krogh 1998), PSORT (Nakai and Horton 1999), and TMHMM (Krogh et al. 2001).”
Method
Prediction of protein submitochondria locations based on data fusion of various features of sequences
Zakeri, P., Moshiri, B., & Sadeghi, M. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.10.026 · Cited by 53
“Terminal signaling peptides (Emanuelsson et al., 2000; Hoglund et al., 2006; Nakai and Horton, 1999), amino acid composition (AAC) (Bhasin et al., 2005; Cedano et al., 1997; Cui et al., 2004; Hoglund et al., 2006; Hua and Sun, 2001; Zhou and Doctor, 2003) dipeptide composition (DC) (Bhasin et al.,…”
Background
Phytochelatin synthase is required for tolerating metal toxicity in a basidiomycete yeast and is a conserved factor involved in metal homeostasis in fungi
Shine, A. M., Shakya, V. P. S., & Idnurm, A. (2015) · Fungal Biology and Biotechnology · doi:10.1186/s40694-015-0013-3 · Cited by 53
“For predicting subcellular localization of Pcs1 homologs, the MitoProt and Psort II programs were used [54,55].”
Method
Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages
Redrejo‐Rodríguez, M., Muñoz‐Espín, D., Holguera, I., Mencı́a, M., & Salas, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216635109 · Cited by 51
“The PSORT server (35) found similar patterns, although it could not find any pNLS in the TPs of Φ29-like phages (Table S1).”
Background
Protein–protein interactions and nuclear trafficking of coat protein and βC1 protein associated with Bhendi yellow vein mosaic disease
P., P. K., Usha, R., Zrachya, A., et al. (2006) · Virus Research · doi:10.1016/j.virusres.2006.07.007 · Cited by 53
Novel Breast Cancer Biomarkers Identified by Integrative Proteomic and Gene Expression Mapping
Ou, K., Yu, K., Kesuma, D., Hooi, M. Y. S., Huang, N., Chen, W., Lee, S. Y., Goh, X. P., Tan, L. K., Liu, J., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr700820g · Cited by 53
Identification of protein associations in organelles, using mass spectrometry‐based proteomics
Warnock, D. E., Fahy, E., & Taylor, S. W. (2004) · Mass Spectrometry Reviews · doi:10.1002/mas.10077 · Cited by 53
SubLoc: a server/client suite for protein subcellular location based on SOAP
Chen, H., Huang, N., & Sun, Z. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti822 · Cited by 52
“The database contains >60 000 protein sequences from virus, bacteria, fungi, plant and animal.”
BackgroundMethodInfluential
Molecular cloning of a unique CMP-sialic acid synthetase that effectively utilizes both deaminoneuraminic acid (KDN) and N-acetylneuraminic acid (Neu5Ac) as substrates
Nakata, D., Münster, A.-K., Gerardy‐Schahn, R., et al. (2001) · Glycobiology · doi:10.1093/glycob/11.8.685 · Cited by 52
“program search (Nakai and Horton, 1999) revealed two predicted”
Background
Genome-wide identification and comparison of legume MLO gene family
Rispail, N., & Rubiales, D. (2016) · Scientific Reports · doi:10.1038/srep32673 · Cited by 52
Prediction subcellular localization of Gram-negative bacterial proteins by support vector machine using wavelet denoising and Chou's pseudo amino acid composition
Yu, B., Li, S., Chen, C., Xu, J., Qiu, W., Wu, X., & Chen, R. (2017) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2017.05.009 · Cited by 52
Accumulated Evidence Substantiates a Role for Three Classes of Wheat Xylanase Inhibitors in Plant Defense
Dornez, E., Croes, E., Gebruers, K., et al. (2010) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2010.487780 · Cited by 52
“, 2008), but the PSORT program for protein localization prediction (Nakai and Horton, 1999) gives the highest score to the possibility that TAXI-IA and TLXI are secreted outside the plant cell (Fierens et al.”
Background
Glycoengineering of the methylotrophic yeast Hansenula polymorpha for the production of glycoproteins with trimannosyl core N‐glycan by blocking core oligosaccharide assembly
Oh, D., Park, J., Kim, M. W., et al. (2008) · Biotechnology Journal · doi:10.1002/biot.200700252 · Cited by 52
A genome‐wide analysis of sumoylation‐related biological processes and functions in human nucleus
Zhou, F., Xue, Y., Lu, H., et al. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.04.076 · Cited by 52
“By PSORT II [31], we predicted the sub-cellular localization of the retained sequences.”
Background
Yeast mitochondrial biogenesis: a model system for humans?
Foury, F., & Kucej, M. (2002) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(01)00276-9 · Cited by 49

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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