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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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“PSORT and SIGNALP software [31,32] predict a 28amino acid signal peptide and the targeting of the cleaved product to the extracellular matrix.”
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“jp) (41) predicted that UL54 contained a classical NLS at aa 61 to 65 (RQRRR) and a short arginine- and glycine-rich sequence at aa 45 to 57, which resembles a functional NoLS as described for UL54’s homologue ICP27 (35, 36).”
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“The PSORT server was used to detect the presence of a classical signal sequence.(14) The screening predicted 36 ORFs having hydropathy profiles similar to those of the Inc proteins.”
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“Cleavage and glycosylation 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/.”
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“Co-localization analysis was done based on organelle prediction by PSORT 80,81 and DeepLoc 82 .”
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“Mitochondrial localization of EgKAT1-4 was deduced by in silico prediction using TargetP [26] and PSORT [27].”
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Method
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Method
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Method
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Background
TheSalmonellaTranslocated Effector SopA Is Targeted to the Mitochondria of Infected Cells
Layton, A. N., Brown, P. J., & Galyov, E. E. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.10.3565-3571.2005 · Cited by 39
“Interestingly, this region of SopA is not predicted to contain a classic mitochondrial targeting sequence (19) when analyzed using the PSORT II program (http://psort.nibb.ac.jp) ( 18 ).”
Method
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Klee, E. W., & Sosa, C. P. (2007) · Drug Discovery Today · doi:10.1016/j.drudis.2007.01.008 · Cited by 39
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Metastatic Lymph Node 51, a novel nucleo-cytoplasmic protein overexpressed in breast cancer
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Method
Localization of the Secretory Granule Marker Protein Chromogranin B in the Nucleus
Yoo, S. H., You, S. H., Kang, M. K., et al. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m105594200 · Cited by 39
The GeneMine system for genome/proteome annotation and collaborative data mining
Lee, C., & Irizarry, K. J. L. (2001) · IBM Systems Journal · doi:10.1147/sj.402.0592 · Cited by 39
How many signal peptides are there in bacteria?
Ivankov, D. N., Payne, S., Galperin, M. Y., Bonissone, S. R., Pevzner, P. A., & Frishman, D. (2013) · Environmental Microbiology · doi:10.1111/1462-2920.12105 · Cited by 38
“, 2008) and protein localization (Nakai and Horton, 1999; Yu et al., 2010) have been developed.”
Background
Bioinformatic and image analyses of the cellular localization of the apoptotic proteins endonuclease G, AIF, and AMID during apoptosis in human cells
Vařecha, M., Amrichová, J., Zimmermann, M., et al. (2007) · APOPTOSIS · doi:10.1007/s10495-007-0061-0 · Cited by 38
“These tools were PSORT II [34, 35 ], WoLF PSORT [36] at http://www.psort.org/, and MultiLoc [37] at http://www-bs.informatik.unituebingen.de/Services/MultiLoc/index html.”
Method
Alkyladenine DNA glycosylase (AAG) localizes to mitochondria and interacts with mitochondrial single-stranded binding protein (mtSSB)
van Loon, B., & Samson, L. D. (2013) · DNA repair · doi:10.1016/j.dnarep.2012.11.009 · Cited by 38
“Three software programs; MitoProt II [69], PSORT II [70] and iPSORT [71] predict that isoforms A and B most likely localize to the mitochondria (Table 1).”
Method
Meta-prediction of protein subcellular localization with reduced voting
Liu, J., Kang, S., Tang, C., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm562 · Cited by 38
“Peroxisome Plasma membrane PSORT (5) http://psort.”
MethodInfluential
The rice TRIANGULAR HULL1 protein acts as a transcriptional repressor in regulating lateral development of spikelet
Peng, P., Liu, L., Fang, J., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-14146-w · Cited by 38
e-Fungi: a data resource for comparative analysis of fungal genomes
Hedeler, C., Wong, H., Cornell, M. J., Alam, I. S., Soanes, D. M., Rattray, M., Hubbard, S. J., Talbot, N. J., Oliver, S. G., & Paton, N. W. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-426 · Cited by 38
“• Protein localisation predictions: Protein sub-cellular localisations were predicted using SignalP [33], PSort [34] and Wolf-PSort [35] with the default parameters.”
Method
Nuclear Import of HSV-1 DNA Polymerase Processivity Factor UL42 Is Mediated by a C-Terminally Located Bipartite Nuclear Localization Signal
Alvisi, G., Avanzi, S., Musiani, D., et al. (2008) · Biochemistry · doi:10.1021/bi800869y · Cited by 38
Cytoplasmic Nuclear Transfer of the Actin-capping Protein Tropomodulin
Kong, K. Y., & Kedes, L. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m302845200 · Cited by 38
Arabidopsis cyclin-dependent kinase inhibitors are nuclear-localized and show different localization patterns within the nucleoplasm
Bird, D. A., Buruiana, M. M., Zhou, Y., Fowke, L. C., & Wang, H. (2007) · Plant Cell Reports · doi:10.1007/s00299-006-0294-3 · Cited by 38
“PSort (http://www.psort.ims.u-tokyo.ac.jp/; Nakai and Horton 1999) uses an algorithm based on both the four amino acid NLS typified by the SV40 large T-antigen and the bipartite NLS proposed by (Robbins et al.”
Method
Characterization and Comparative Analysis of the Genes EncodingHaemophilus parasuisOuter Membrane Proteins P2 and P5
Mullins, M. A., Register, K. B., Bayles, D. O., et al. (2009) · Journal of Bacteriology · doi:10.1128/jb.00469-09 · Cited by 38
Evolution of DNA-methylation machinery: DNA methyltransferases and methyl-DNA binding proteins in the amphioxus Branchiostoma floridae
Albalat, R. (2008) · Development Genes and Evolution · doi:10.1007/s00427-008-0247-7 · Cited by 38
“ebi.ac.uk/InterProScan/ and http://www.ncbi.nlm.nih.gov/ Structure/cdd/wrpsb.cgi, respectively) were used to identify protein domains; and the PSORT-II program ( Nakai and Horton 1999 ), to predict the subcellular location of the deduced enzymes.”
Method
‘Harvester’: a fast meta search engine of human protein resources
Liebel, U., Kindler, B., & Pepperkok, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth146 · Cited by 38
“Harvester collects text-based information from the following selected public databases and prediction servers: Uniprot, SOURCE, Genome Browser, BLAST, SMART, SOSUI, PSORT II, CDART, MapView, NCBI-BLAST, SOSUI, STRING, Genome Browser and EMBL.”
Influential
Purification and cDNA Cloning of UDP-d-Glucuronate Carboxy-lyase (UDP-d-xylose Synthase) from Pea Seedlings
Kobayashi, M., Nakagawa, H., Suda, I., et al. (2002) · Plant and Cell Physiology · doi:10.1093/pcp/pcf157 · Cited by 38
Subcellular localization of ceramide kinase and ceramide kinase-like protein requires interplay of their Pleckstrin Homology domain-containing N-terminal regions together with C-terminal domains
Rovina, P., Schanzer, A., Graf, C., Mechtcheriakova, D., Jaritz, M., & Bornancin, F. (2009) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2009.05.009 · Cited by 39
Expression of a Novel Murine Type I IFN in the Pancreatic Islets Induces Diabetes in Mice
Vassileva, G., Chen, S.-C., Zeng, M., Abbondanzo, S. J., Jensen, K. K., Gorman, D. M., Baroudy, B. M., Jiang, Y., Murgolo, N., & Lira, S. A. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.170.11.5748 · Cited by 38
“site predicted by PSORT program (24) shown with an arrow.”
BackgroundMethod
Novel Role of Sphingolipid Synthesis Genes in Regulating Giardial Encystation
Hernandez, Y., Shpak, M., Duarte, T. T., Mendez, T. L., Maldonado, R. A., Roychowdhury, S., Rodrigues, M. L., & Das, S. (2008) · Infection and Immunity · doi:10.1128/iai.00116-08 · Cited by 38
“lyzed by using the ExPaSY/PSORT software as described previously (13, 31, 32).”
Method
Computational prediction of membrane-tethered transcription factors
Zupicich, J., Brenner, S. E., & Skarnes, W. C. (2001) · Genome biology · doi:10.1186/gb-2001-2-12-research0050 · Cited by 38
Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
Kucukkal, T. G., Yang, Y., Chapman, S. C., Cao, W., & Alexov, E. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms15069670 · Cited by 40
“Horton, P.; Park, K.-J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.J.; Nakai, K. WoLF PSORT: Protein localization predictor.”
BackgroundInfluential
Functional isolation of the Candida albicansFCR3 gene encoding a bZip transcription factor homologous to Saccharomyces cerevisiae Yap3p
Yang, X., Talibi, D., Weber, S., Poisson, G., & Raymond, M. (2001) · Yeast · doi:10.1002/yea.770 · Cited by 37
“Sequence analysis of Fcr3p using the PSORT II programpredicts a bipartite nuclear localization signal overlapping the basic domain ((215)KRKAQNRAAQRAFRERKE) and a nuclear localization for the protein (Nakai and Horton, 1999).”
MethodInfluential
Identification of the Nuclear Export and Adjacent Nuclear Localization Signals for ORF45 of Kaposi's Sarcoma-Associated Herpesvirus
Li, X., & Zhu, F. (2008) · Journal of Virology · doi:10.1128/jvi.02209-08 · Cited by 37
“3A) (13, 23), and the region of aa 297 to 300 contains a typical basic-residue-rich NLS signal, (297)KRKR(300) (16).”
Background
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Singer, E., Heidelberg, J. F., Dhillon, A., et al. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00052 · Cited by 37
SENP2 regulates MMP13 expression in a bladder cancer cell line through SUMOylation of TBL1/TBLR1
Tan, M., Gong, H. C., Wang, J., Tao, L., Xu, D., Bao, E., Liu, Z., & Qiu, J. (2015) · Scientific Reports · doi:10.1038/srep13996 · Cited by 37
Evolution, expression analysis, and functional verification of Catharanthus roseus RLK1-like kinase (CrRLK1L) family proteins in pear (Pyrus bretchneideri)
Kou, X., Qi, K., Qiao, X., Yin, H., Liu, X., Zhang, S., & Wu, J. (2017) · Genomics · doi:10.1016/j.ygeno.2017.05.003 · Cited by 37
Blast resistance gene Pi54 over-expressed in rice to understand its cellular and sub-cellular localization and response to different pathogens
Singh, J., Gupta, S. K., Devanna, B. N., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59027-x · Cited by 37
African swine fever virus ORF P1192R codes for a functional type II DNA topoisomerase
Coelho, J., Martins, C. L. V., Ferreira, F., et al. (2014) · Virology · doi:10.1016/j.virol.2014.10.034 · Cited by 37
Molecular Characterization of Tomato Leaf Curl China Virus, Infecting Tomato Plants in China, and Functional Analyses of Its Associated Betasatellite
Yang, X., Guo, W., Ma, X., et al. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00017-11 · Cited by 37
“jp/) (24) and PredictProtein (http://www”
The fruiting-specific Le.flp1 gene, encoding a novel fungal fasciclin-like protein, of the basidiomycetous mushroom Lentinula edodes
Miyazaki, Y., Kaneko, S., Sunagawa, M., Shishido, K., Yamazaki, T., Nakamura, M., & Babasaki, K. (2007) · Current Genetics · doi:10.1007/s00294-007-0133-2 · Cited by 35
“the N-terminus (von Heijne 1986) and a potential signal sequence for a GPI anchor in the C-terminus (Nakai and Horton 1999).”
BackgroundInfluential
Histamine Release Factor from Dermanyssus gallinae (De Geer): Characterization and in vitro assessment as a protective antigen
Bartley, K., Nisbet, A. J., Offer, J. E., et al. (2008) · International Journal for Parasitology · doi:10.1016/j.ijpara.2008.09.006 · Cited by 37
MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis
Reja, R., Venkatakrishnan, A., Lee, J.-W., Kim, B.-C., Ryu, J., Gong, S., Bhak, J., & Park, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-s3-s20 · Cited by 37
Analysis of the Genome of the Sexually Transmitted Insect Virus Helicoverpa zea Nudivirus 2
Burand, J. P., Kim, W., Afonso, C. L., Tulman, E. R., Kutish, G. F., Lu, Z., & Rock, D. L. (2012) · Viruses · doi:10.3390/v4010028 · Cited by 39
“CGC [105], EMBOSS [106], Psort [107], TMHMM [108,109], SignalP 3.”
MethodInfluential
Ecf, an Alternative Sigma Factor from Neisseria gonorrhoeae , Controls Expression of msrAB , Which Encodes Methionine Sulfoxide Reductase
Gunesekere, I. C., Kahler, C. M., Ryan, C. S., et al. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.10.3463-3469.2006 · Cited by 37
“The presence of possible transmembrane domains, as predicted by PSORT (15), suggests that NGO1948 might encode an integral membrane protein.”
Background
TheDrosophilahomolog of the putative phosphatidylserine receptor functions to inhibit apoptosis
Krieser, R. J., Moore, F. E., Dresnek, D., Pellock, B. J., Patel, R. G., Huang, A., Brachmann, C. B., & White, K. (2007) · Development · doi:10.1242/dev.02860 · Cited by 36
“However, analysis of the sequence of dPSR using PSORT II predicts that dPSR is a nuclear protein (Nakai and Horton, 1999).”
Method
Human ortholog to mouse gene imap38 encoding an ER-localizable G-protein belongs to a gene family clustered on chromosome 7q32–36
Stamm, O., Krücken, J., Schmitt-Wrede, H.-P., et al. (2002) · Gene · doi:10.1016/s0378-1119(01)00837-x · Cited by 37
Genome-wide screening reveals a role for subcellular localization of CRBN in the anti-myeloma activity of pomalidomide
Tateno, S., Iida, M., Fujii, S., Suwa, T., Katayama, M., Tokuyama, H., Yamamoto, J., Ito, T., Sakamoto, S., Handa, H., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-61027-w · Cited by 36

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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