DOI: 10.1104/pp.011577. ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins

ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins

10.1104/pp.011577

Crossref journal-article

Oxford University Press (OUP)

Plant Physiology (286)

Abstract

Abstract A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.

Bibliography

Schwacke, R., Schneider, A., van der Graaff, E., Fischer, K., Catoni, E., Desimone, M., Frommer, W. B., FluÌgge, U.-I., & Kunze, R. (2003). ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins. Plant Physiology, 131(1), 16â26.

Authors 9

Rainer Schwacke (first)
Anja Schneider (additional)
Eric van der Graaff (additional)
Karsten Fischer (additional)
Elisabetta Catoni (additional)
Marcelo Desimone (additional)
Wolf B. Frommer (additional)
Ulf-Ingo Flügge (additional)
Reinhard Kunze (additional)

References 50 Referenced 535

10.1002/yea.320111605 / Yeast / An overview of membrane transport proteins in Saccharomyces cerevisiae. by Andre (1995)
10.1038/35048692 / Nature / Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. by Arabidopsis Genome Initiative (2000)
10.1093/bioinformatics/18.2.298 / Bioinformatics / Extensive feature detection of N-terminal protein sorting signals. by Bannai (2002)
10.1107/S0907444902003451 / Acta Crystallogr D Biol Crystallogr / The protein data bank. by Berman (2002)
10.1111/j.1432-1033.1996.00779.x / Eur J Biochem / Computational method to predict mitochondrially imported proteins and their targeting sequences. by Claros (1996)
{'key': '2021042809140951000_R6', 'first-page': '685', 'article-title': 'TopPred II: an improved software for membrane protein structure predictions.', 'volume': '10', 'author': 'Claros', 'year': '1994', 'journal-title': 'Comput Appl Biosci'} / Comput Appl Biosci / TopPred II: an improved software for membrane protein structure predictions. by Claros (1994)
10.1104/pp.010576 / Plant Physiol / The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose phosphate pathways in plants. by Eicks (2002)
10.1016/0022-2836(84)90309-7 / J Mol Biol / Analysis of membrane and surface protein sequences with the hydrophobic moment plot. by Eisenberg (1984)
10.1006/jmbi.2000.3903 / J Mol Biol / Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. by Emanuelsson (2000)
10.1110/ps.8.5.978 / Protein Sci / ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. by Emanuelsson (1999)
10.1016/S0167-4889(01)00145-8 / Biochim Biophys Acta / Prediction of organellar targeting signals. by Emanuelsson (2001)
10.1146/annurev.pp.46.060195.002223 / Annu Rev Plant Physiol Plant Mol Biol / Heterologous expression of genes in bacterial, fungal, animal, and plant cells. by Frommer (1995)
10.1126/science.1068275 / Science / A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). by Goff (2002)
10.1093/bioinformatics/14.4.378 / Bioinformatics / SOSUI: classification and secondary structure prediction system for membrane proteins. by Hirokawa (1998)
{'key': '2021042809140951000_R15', 'first-page': '166', 'article-title': 'TMbase: a database of membrane spanning proteins segments.', 'volume': '374', 'author': 'Hofmann', 'year': '1993', 'journal-title': 'Biol Chem Hoppe-Seyler'} / Biol Chem Hoppe-Seyler / TMbase: a database of membrane spanning proteins segments. by Hofmann (1993)
{'key': '2021042809140951000_R16', 'first-page': '843', 'article-title': 'The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.', 'volume': '12', 'author': 'Huelsenbeck', 'year': '1995', 'journal-title': 'Mol Biol Evol'} / Mol Biol Evol / The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. by Huelsenbeck (1995)
{'key': '2021042809140951000_R17', 'first-page': '19', 'article-title': 'Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies.', 'volume': '2', 'author': 'Ikeda', 'year': '2002', 'journal-title': 'In Silico Biol'} / In Silico Biol / Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies. by Ikeda (2002)
10.1093/dnares/3.3.109 / DNA Res / Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803: II. Sequence determination of the entire genome and assignment of potential protein-coding regions. by Kaneko (1996)
{'key': '2021042809140951000_R19'}
10.1105/tpc.010352 / Plant Cell / A novel family of magnesium transport genes in Arabidopsis. by Li (2001)
10.1104/pp.126.4.1646 / Plant Physiol / Phylogenetic relationships within cation transporter families of Arabidopsis. by Mäser (2001)
10.1016/S0301-4622(99)00116-7 / Biophys Chem / Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. by Mitaku (1999)
10.1093/bioinformatics/17.7.646 / Bioinformatics / Evaluation of methods for the prediction of membrane spanning regions. by Möller (2001)
10.1093/bioinformatics/18.1.218 / Bioinformatics / Evaluation of methods for the prediction of membrane spanning regions (erratum). by Möller (2002)
10.1016/S0888-7543(05)80111-9 / Genomics / A knowledge base for predicting protein localization sites in eukaryotic cells. by Nakai (1992)
10.1093/protein/10.1.1 / Protein Eng / Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. by Nielsen (1997)
10.1142/S0129065797000537 / Int J Neural Syst / A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. by Nielsen (1997)
{'key': '2021042809140951000_R28', 'first-page': '122', 'article-title': 'Prediction of signal peptides and signal anchors by a hidden Markov model.', 'volume': '6', 'author': 'Nielsen', 'year': '1998', 'journal-title': 'Proc Int Conf Intell Syst Mol Biol'} / Proc Int Conf Intell Syst Mol Biol / Prediction of signal peptides and signal anchors by a hidden Markov model. by Nielsen (1998)
10.1016/S0014-5793(00)02321-8 / FEBS Lett / Consensus predictions of membrane protein topology. by Nilsson (2000)
10.1016/S0076-6879(96)66017-0 / Methods Enzymol / Effective protein sequence comparison. by Pearson (1996)
10.1073/pnas.85.8.2444 / Proc Natl Acad Sci USA / Improved tools for biological sequence comparison. by Pearson (1988)
10.1016/S0167-4889(01)00146-X / Biochim Biophys Acta / Dual targeting to mitochondria and chloroplasts. by Peeters (2001)
10.1006/jmbi.1994.1220 / J Mol Biol / Prediction of transmembrane segments in proteins utilising multiple sequence alignments. by Persson (1994)
10.1002/pro.5560050221 / Protein Sci / Topology prediction of membrane proteins. by Persson (1996)
10.1002/pro.5560050824 / Protein Sci / Topology prediction for helical transmembrane proteins at 86% accuracy. by Rost (1996)
10.1002/(SICI)1097-4644(1999)75:32+<84::AID-JCB11>3.0.CO;2-M / J Cell Biochem / A functional-phylogenetic system for the classification of transport proteins. by Saier (1999)
10.1093/nar/29.16.e82 / Nucleic Acids Res / Chloroplast transit peptide prediction: a peek inside the black box. by Schein (2001)
{'key': '2021042809140951000_R38', 'first-page': '1409', 'article-title': 'A statistical method for evaluating systematic relationships.', 'volume': '28', 'author': 'Sokal', 'year': '1958', 'journal-title': 'Univ Kans Sci Bull'} / Univ Kans Sci Bull / A statistical method for evaluating systematic relationships. by Sokal (1958)
{'key': '2021042809140951000_R39', 'first-page': '175', 'article-title': 'A hidden Markov model for predicting transmembrane helices in protein sequences.', 'volume': '6', 'author': 'Sonnhammer', 'year': '1998', 'journal-title': 'Proc Int Conf Intell Syst Mol Biol'} / Proc Int Conf Intell Syst Mol Biol / A hidden Markov model for predicting transmembrane helices in protein sequences. by Sonnhammer (1998)
10.1002/(SICI)1097-0134(20000601)39:4<417::AID-PROT140>3.0.CO;2-Y / Proteins / Do more complex organisms have a greater proportion of membrane proteins in their genomes? by Stevens (2000)
10.1093/nar/25.24.4876 / Nucleic Acids Res / The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. by Thompson (1997)
10.1006/jmbi.1998.2107 / J Mol Biol / Principles governing amino acid composition of integral membrane proteins: application to topology prediction. by Tusnady (1998)
10.1093/bioinformatics/17.9.849 / Bioinformatics / The HMMTOP transmembrane topology prediction server. by Tusnady (2001)
10.1016/S0955-0674(00)00226-X / Curr Opin Cell Biol / A genomic view of yeast membrane transporters. by Van Belle (2001)
10.1016/0022-2836(92)90934-C / J Mol Biol / Membrane protein structure prediction: hydrophobicity analysis and the “positive inside” rule. by von Heijne (1992)
10.1002/pro.5560070420 / Protein Sci / Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. by Wallin (1998)
10.1093/nar/30.1.249 / Nucleic Acids Res / MMDB: Entrez's 3D-structure database. by Wang (2002)
10.1093/bioinformatics/17.6.560 / Bioinformatics / Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. by Ward (2001)
10.1016/S0968-0004(01)02054-0 / Trends Biochem Sci / Conservation of amino acid transporters in fungi, plants and animals. by Wipf (2002)
10.1126/science.1068037 / Science / A draft sequence of the rice genome (Oryza sativa L. ssp. indica). by Yu (2002)

Dates

Type	When
Created	22 years, 7 months ago (Jan. 15, 2003, 4:06 p.m.)
Deposited	4 years, 4 months ago (April 28, 2021, 5 p.m.)
Indexed	4 weeks, 2 days ago (Aug. 7, 2025, 4:52 a.m.)
Issued	22 years, 8 months ago (Jan. 1, 2003)
Published	22 years, 8 months ago (Jan. 1, 2003)
Published Online	22 years, 8 months ago (Jan. 1, 2003)
Published Print	22 years, 8 months ago (Jan. 1, 2003)

Funders 0

None

BibTeX

@article{Schwacke_2003, title={ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins}, volume={131}, ISSN={0032-0889}, url={http://dx.doi.org/10.1104/pp.011577}, DOI={10.1104/pp.011577}, number={1}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Schwacke, Rainer and Schneider, Anja and van der Graaff, Eric and Fischer, Karsten and Catoni, Elisabetta and Desimone, Marcelo and Frommer, Wolf B. and Flügge, Ulf-Ingo and Kunze, Reinhard}, year={2003}, month=jan, pages={16–26} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        7
      ]
    ],
    "date-time": "2025-08-07T08:52:36Z",
    "timestamp": 1754556756169
  },
  "reference-count": 50,
  "publisher": "Oxford University Press (OUP)",
  "issue": "1",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2003,
            1,
            1
          ]
        ],
        "date-time": "2003-01-01T00:00:00Z",
        "timestamp": 1041379200000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2003,
        1,
        1
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.</jats:p>",
  "DOI": "10.1104/pp.011577",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2003,
        1,
        15
      ]
    ],
    "date-time": "2003-01-15T21:06:00Z",
    "timestamp": 1042664760000
  },
  "page": "16-26",
  "source": "Crossref",
  "is-referenced-by-count": 535,
  "title": "ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins",
  "prefix": "10.1093",
  "volume": "131",
  "author": [
    {
      "given": "Rainer",
      "family": "Schwacke",
      "sequence": "first",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    },
    {
      "given": "Anja",
      "family": "Schneider",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    },
    {
      "given": "Eric",
      "family": "van der Graaff",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    },
    {
      "given": "Karsten",
      "family": "Fischer",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    },
    {
      "given": "Elisabetta",
      "family": "Catoni",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t Tu\u0308bingen, Zentrum fu\u0308r Molekularbiologie der Pflanzen, Auf der Morgenstelle 1, 72076 Tu\u0308bingen, Germany (E.C., M.D., W.B.F.)"
        }
      ]
    },
    {
      "given": "Marcelo",
      "family": "Desimone",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t Tu\u0308bingen, Zentrum fu\u0308r Molekularbiologie der Pflanzen, Auf der Morgenstelle 1, 72076 Tu\u0308bingen, Germany (E.C., M.D., W.B.F.)"
        }
      ]
    },
    {
      "given": "Wolf B.",
      "family": "Frommer",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t Tu\u0308bingen, Zentrum fu\u0308r Molekularbiologie der Pflanzen, Auf der Morgenstelle 1, 72076 Tu\u0308bingen, Germany (E.C., M.D., W.B.F.)"
        }
      ]
    },
    {
      "given": "Ulf-Ingo",
      "family": "Flu\u0308gge",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    },
    {
      "given": "Reinhard",
      "family": "Kunze",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Universita\u0308t zu Ko\u0308ln, Botanisches Institut, Gyrhofstrasse 15, 50931 Ko\u0308ln, Germany (R.S., A.S., E.v.d.G., K.F., U.-I.F., R.K.); and"
        }
      ]
    }
  ],
  "member": "286",
  "published-online": {
    "date-parts": [
      [
        2003,
        1,
        1
      ]
    ]
  },
  "reference": [
    {
      "key": "2021042809140951000_R1",
      "doi-asserted-by": "crossref",
      "first-page": "1575",
      "DOI": "10.1002/yea.320111605",
      "article-title": "An overview of membrane transport proteins in Saccharomyces cerevisiae.",
      "volume": "11",
      "author": "Andre",
      "year": "1995",
      "journal-title": "Yeast"
    },
    {
      "key": "2021042809140951000_R2",
      "doi-asserted-by": "crossref",
      "first-page": "796",
      "DOI": "10.1038/35048692",
      "article-title": "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.",
      "volume": "408",
      "author": "Arabidopsis Genome Initiative",
      "year": "2000",
      "journal-title": "Nature"
    },
    {
      "key": "2021042809140951000_R3",
      "doi-asserted-by": "crossref",
      "first-page": "298",
      "DOI": "10.1093/bioinformatics/18.2.298",
      "article-title": "Extensive feature detection of N-terminal protein sorting signals.",
      "volume": "18",
      "author": "Bannai",
      "year": "2002",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R4",
      "doi-asserted-by": "crossref",
      "first-page": "899",
      "DOI": "10.1107/S0907444902003451",
      "article-title": "The protein data bank.",
      "volume": "58",
      "author": "Berman",
      "year": "2002",
      "journal-title": "Acta Crystallogr D Biol Crystallogr"
    },
    {
      "key": "2021042809140951000_R5",
      "doi-asserted-by": "crossref",
      "first-page": "779",
      "DOI": "10.1111/j.1432-1033.1996.00779.x",
      "article-title": "Computational method to predict mitochondrially imported proteins and their targeting sequences.",
      "volume": "241",
      "author": "Claros",
      "year": "1996",
      "journal-title": "Eur J Biochem"
    },
    {
      "key": "2021042809140951000_R6",
      "first-page": "685",
      "article-title": "TopPred II: an improved software for membrane protein structure predictions.",
      "volume": "10",
      "author": "Claros",
      "year": "1994",
      "journal-title": "Comput Appl Biosci"
    },
    {
      "key": "2021042809140951000_R7",
      "doi-asserted-by": "crossref",
      "first-page": "512",
      "DOI": "10.1104/pp.010576",
      "article-title": "The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose phosphate pathways in plants.",
      "volume": "128",
      "author": "Eicks",
      "year": "2002",
      "journal-title": "Plant Physiol"
    },
    {
      "key": "2021042809140951000_R8",
      "doi-asserted-by": "crossref",
      "first-page": "125",
      "DOI": "10.1016/0022-2836(84)90309-7",
      "article-title": "Analysis of membrane and surface protein sequences with the hydrophobic moment plot.",
      "volume": "179",
      "author": "Eisenberg",
      "year": "1984",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "2021042809140951000_R9",
      "doi-asserted-by": "crossref",
      "first-page": "1005",
      "DOI": "10.1006/jmbi.2000.3903",
      "article-title": "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.",
      "volume": "300",
      "author": "Emanuelsson",
      "year": "2000",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "2021042809140951000_R10",
      "doi-asserted-by": "crossref",
      "first-page": "978",
      "DOI": "10.1110/ps.8.5.978",
      "article-title": "ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.",
      "volume": "8",
      "author": "Emanuelsson",
      "year": "1999",
      "journal-title": "Protein Sci"
    },
    {
      "key": "2021042809140951000_R11",
      "doi-asserted-by": "crossref",
      "first-page": "114",
      "DOI": "10.1016/S0167-4889(01)00145-8",
      "article-title": "Prediction of organellar targeting signals.",
      "volume": "1541",
      "author": "Emanuelsson",
      "year": "2001",
      "journal-title": "Biochim Biophys Acta"
    },
    {
      "key": "2021042809140951000_R12",
      "doi-asserted-by": "crossref",
      "first-page": "419",
      "DOI": "10.1146/annurev.pp.46.060195.002223",
      "article-title": "Heterologous expression of genes in bacterial, fungal, animal, and plant cells.",
      "volume": "46",
      "author": "Frommer",
      "year": "1995",
      "journal-title": "Annu Rev Plant Physiol Plant Mol Biol"
    },
    {
      "key": "2021042809140951000_R13",
      "doi-asserted-by": "crossref",
      "first-page": "92",
      "DOI": "10.1126/science.1068275",
      "article-title": "A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).",
      "volume": "296",
      "author": "Goff",
      "year": "2002",
      "journal-title": "Science"
    },
    {
      "key": "2021042809140951000_R14",
      "doi-asserted-by": "crossref",
      "first-page": "378",
      "DOI": "10.1093/bioinformatics/14.4.378",
      "article-title": "SOSUI: classification and secondary structure prediction system for membrane proteins.",
      "volume": "14",
      "author": "Hirokawa",
      "year": "1998",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R15",
      "first-page": "166",
      "article-title": "TMbase: a database of membrane spanning proteins segments.",
      "volume": "374",
      "author": "Hofmann",
      "year": "1993",
      "journal-title": "Biol Chem Hoppe-Seyler"
    },
    {
      "key": "2021042809140951000_R16",
      "first-page": "843",
      "article-title": "The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.",
      "volume": "12",
      "author": "Huelsenbeck",
      "year": "1995",
      "journal-title": "Mol Biol Evol"
    },
    {
      "key": "2021042809140951000_R17",
      "first-page": "19",
      "article-title": "Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies.",
      "volume": "2",
      "author": "Ikeda",
      "year": "2002",
      "journal-title": "In Silico Biol"
    },
    {
      "key": "2021042809140951000_R18",
      "doi-asserted-by": "crossref",
      "first-page": "109",
      "DOI": "10.1093/dnares/3.3.109",
      "article-title": "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803: II. Sequence determination of the entire genome and assignment of potential protein-coding regions.",
      "volume": "3",
      "author": "Kaneko",
      "year": "1996",
      "journal-title": "DNA Res"
    },
    {
      "key": "2021042809140951000_R19"
    },
    {
      "key": "2021042809140951000_R20",
      "doi-asserted-by": "crossref",
      "first-page": "2761",
      "DOI": "10.1105/tpc.010352",
      "article-title": "A novel family of magnesium transport genes in Arabidopsis.",
      "volume": "13",
      "author": "Li",
      "year": "2001",
      "journal-title": "Plant Cell"
    },
    {
      "key": "2021042809140951000_R21",
      "doi-asserted-by": "crossref",
      "first-page": "1646",
      "DOI": "10.1104/pp.126.4.1646",
      "article-title": "Phylogenetic relationships within cation transporter families of Arabidopsis.",
      "volume": "126",
      "author": "Ma\u0308ser",
      "year": "2001",
      "journal-title": "Plant Physiol"
    },
    {
      "key": "2021042809140951000_R22",
      "doi-asserted-by": "crossref",
      "first-page": "165",
      "DOI": "10.1016/S0301-4622(99)00116-7",
      "article-title": "Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system.",
      "volume": "82",
      "author": "Mitaku",
      "year": "1999",
      "journal-title": "Biophys Chem"
    },
    {
      "key": "2021042809140951000_R23",
      "doi-asserted-by": "crossref",
      "first-page": "646",
      "DOI": "10.1093/bioinformatics/17.7.646",
      "article-title": "Evaluation of methods for the prediction of membrane spanning regions.",
      "volume": "17",
      "author": "Mo\u0308ller",
      "year": "2001",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R24",
      "doi-asserted-by": "crossref",
      "first-page": "218",
      "DOI": "10.1093/bioinformatics/18.1.218",
      "article-title": "Evaluation of methods for the prediction of membrane spanning regions (erratum).",
      "volume": "18",
      "author": "Mo\u0308ller",
      "year": "2002",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R25",
      "doi-asserted-by": "crossref",
      "first-page": "897",
      "DOI": "10.1016/S0888-7543(05)80111-9",
      "article-title": "A knowledge base for predicting protein localization sites in eukaryotic cells.",
      "volume": "14",
      "author": "Nakai",
      "year": "1992",
      "journal-title": "Genomics"
    },
    {
      "key": "2021042809140951000_R26",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1093/protein/10.1.1",
      "article-title": "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.",
      "volume": "10",
      "author": "Nielsen",
      "year": "1997",
      "journal-title": "Protein Eng"
    },
    {
      "key": "2021042809140951000_R27",
      "doi-asserted-by": "crossref",
      "first-page": "581",
      "DOI": "10.1142/S0129065797000537",
      "article-title": "A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.",
      "volume": "8",
      "author": "Nielsen",
      "year": "1997",
      "journal-title": "Int J Neural Syst"
    },
    {
      "key": "2021042809140951000_R28",
      "first-page": "122",
      "article-title": "Prediction of signal peptides and signal anchors by a hidden Markov model.",
      "volume": "6",
      "author": "Nielsen",
      "year": "1998",
      "journal-title": "Proc Int Conf Intell Syst Mol Biol"
    },
    {
      "key": "2021042809140951000_R29",
      "doi-asserted-by": "crossref",
      "first-page": "267",
      "DOI": "10.1016/S0014-5793(00)02321-8",
      "article-title": "Consensus predictions of membrane protein topology.",
      "volume": "486",
      "author": "Nilsson",
      "year": "2000",
      "journal-title": "FEBS Lett"
    },
    {
      "key": "2021042809140951000_R30",
      "doi-asserted-by": "crossref",
      "first-page": "227",
      "DOI": "10.1016/S0076-6879(96)66017-0",
      "article-title": "Effective protein sequence comparison.",
      "volume": "266",
      "author": "Pearson",
      "year": "1996",
      "journal-title": "Methods Enzymol"
    },
    {
      "key": "2021042809140951000_R31",
      "doi-asserted-by": "crossref",
      "first-page": "2444",
      "DOI": "10.1073/pnas.85.8.2444",
      "article-title": "Improved tools for biological sequence comparison.",
      "volume": "85",
      "author": "Pearson",
      "year": "1988",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "2021042809140951000_R32",
      "doi-asserted-by": "crossref",
      "first-page": "54",
      "DOI": "10.1016/S0167-4889(01)00146-X",
      "article-title": "Dual targeting to mitochondria and chloroplasts.",
      "volume": "1541",
      "author": "Peeters",
      "year": "2001",
      "journal-title": "Biochim Biophys Acta"
    },
    {
      "key": "2021042809140951000_R33",
      "doi-asserted-by": "crossref",
      "first-page": "182",
      "DOI": "10.1006/jmbi.1994.1220",
      "article-title": "Prediction of transmembrane segments in proteins utilising multiple sequence alignments.",
      "volume": "237",
      "author": "Persson",
      "year": "1994",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "2021042809140951000_R34",
      "doi-asserted-by": "crossref",
      "first-page": "363",
      "DOI": "10.1002/pro.5560050221",
      "article-title": "Topology prediction of membrane proteins.",
      "volume": "5",
      "author": "Persson",
      "year": "1996",
      "journal-title": "Protein Sci"
    },
    {
      "key": "2021042809140951000_R35",
      "doi-asserted-by": "crossref",
      "first-page": "1704",
      "DOI": "10.1002/pro.5560050824",
      "article-title": "Topology prediction for helical transmembrane proteins at 86% accuracy.",
      "volume": "5",
      "author": "Rost",
      "year": "1996",
      "journal-title": "Protein Sci"
    },
    {
      "key": "2021042809140951000_R36",
      "doi-asserted-by": "crossref",
      "first-page": "84",
      "DOI": "10.1002/(SICI)1097-4644(1999)75:32+<84::AID-JCB11>3.0.CO;2-M",
      "article-title": "A functional-phylogenetic system for the classification of transport proteins.",
      "volume": "Suppl",
      "author": "Saier",
      "year": "1999",
      "journal-title": "J Cell Biochem"
    },
    {
      "key": "2021042809140951000_R37",
      "doi-asserted-by": "crossref",
      "first-page": "E82",
      "DOI": "10.1093/nar/29.16.e82",
      "article-title": "Chloroplast transit peptide prediction: a peek inside the black box.",
      "volume": "29",
      "author": "Schein",
      "year": "2001",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "2021042809140951000_R38",
      "first-page": "1409",
      "article-title": "A statistical method for evaluating systematic relationships.",
      "volume": "28",
      "author": "Sokal",
      "year": "1958",
      "journal-title": "Univ Kans Sci Bull"
    },
    {
      "key": "2021042809140951000_R39",
      "first-page": "175",
      "article-title": "A hidden Markov model for predicting transmembrane helices in protein sequences.",
      "volume": "6",
      "author": "Sonnhammer",
      "year": "1998",
      "journal-title": "Proc Int Conf Intell Syst Mol Biol"
    },
    {
      "key": "2021042809140951000_R40",
      "doi-asserted-by": "crossref",
      "first-page": "417",
      "DOI": "10.1002/(SICI)1097-0134(20000601)39:4<417::AID-PROT140>3.0.CO;2-Y",
      "article-title": "Do more complex organisms have a greater proportion of membrane proteins in their genomes?",
      "volume": "39",
      "author": "Stevens",
      "year": "2000",
      "journal-title": "Proteins"
    },
    {
      "key": "2021042809140951000_R41",
      "doi-asserted-by": "crossref",
      "first-page": "4876",
      "DOI": "10.1093/nar/25.24.4876",
      "article-title": "The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.",
      "volume": "25",
      "author": "Thompson",
      "year": "1997",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "2021042809140951000_R42",
      "doi-asserted-by": "crossref",
      "first-page": "489",
      "DOI": "10.1006/jmbi.1998.2107",
      "article-title": "Principles governing amino acid composition of integral membrane proteins: application to topology prediction.",
      "volume": "283",
      "author": "Tusnady",
      "year": "1998",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "2021042809140951000_R43",
      "doi-asserted-by": "crossref",
      "first-page": "849",
      "DOI": "10.1093/bioinformatics/17.9.849",
      "article-title": "The HMMTOP transmembrane topology prediction server.",
      "volume": "17",
      "author": "Tusnady",
      "year": "2001",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R44",
      "doi-asserted-by": "crossref",
      "first-page": "389",
      "DOI": "10.1016/S0955-0674(00)00226-X",
      "article-title": "A genomic view of yeast membrane transporters.",
      "volume": "13",
      "author": "Van Belle",
      "year": "2001",
      "journal-title": "Curr Opin Cell Biol"
    },
    {
      "key": "2021042809140951000_R45",
      "doi-asserted-by": "crossref",
      "first-page": "487",
      "DOI": "10.1016/0022-2836(92)90934-C",
      "article-title": "Membrane protein structure prediction: hydrophobicity analysis and the \u201cpositive inside\u201d rule.",
      "volume": "225",
      "author": "von Heijne",
      "year": "1992",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "2021042809140951000_R46",
      "doi-asserted-by": "crossref",
      "first-page": "1029",
      "DOI": "10.1002/pro.5560070420",
      "article-title": "Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms.",
      "volume": "7",
      "author": "Wallin",
      "year": "1998",
      "journal-title": "Protein Sci"
    },
    {
      "key": "2021042809140951000_R47",
      "doi-asserted-by": "crossref",
      "first-page": "249",
      "DOI": "10.1093/nar/30.1.249",
      "article-title": "MMDB: Entrez's 3D-structure database.",
      "volume": "30",
      "author": "Wang",
      "year": "2002",
      "journal-title": "Nucleic Acids Res"
    },
    {
      "key": "2021042809140951000_R48",
      "doi-asserted-by": "crossref",
      "first-page": "560",
      "DOI": "10.1093/bioinformatics/17.6.560",
      "article-title": "Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana.",
      "volume": "17",
      "author": "Ward",
      "year": "2001",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "2021042809140951000_R49",
      "doi-asserted-by": "crossref",
      "first-page": "139",
      "DOI": "10.1016/S0968-0004(01)02054-0",
      "article-title": "Conservation of amino acid transporters in fungi, plants and animals.",
      "volume": "27",
      "author": "Wipf",
      "year": "2002",
      "journal-title": "Trends Biochem Sci"
    },
    {
      "key": "2021042809140951000_R50",
      "doi-asserted-by": "crossref",
      "first-page": "79",
      "DOI": "10.1126/science.1068037",
      "article-title": "A draft sequence of the rice genome (Oryza sativa L. ssp. indica).",
      "volume": "296",
      "author": "Yu",
      "year": "2002",
      "journal-title": "Science"
    }
  ],
  "container-title": "Plant Physiology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://academic.oup.com/plphys/article-pdf/131/1/16/37471431/plphys_v131_1_16.pdf",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "syndication"
    },
    {
      "URL": "http://academic.oup.com/plphys/article-pdf/131/1/16/37471431/plphys_v131_1_16.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2021,
        4,
        28
      ]
    ],
    "date-time": "2021-04-28T21:00:16Z",
    "timestamp": 1619643616000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://academic.oup.com/plphys/article/131/1/16/6114365"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2003,
        1,
        1
      ]
    ]
  },
  "references-count": 50,
  "journal-issue": {
    "issue": "1",
    "published-online": {
      "date-parts": [
        [
          2003,
          1,
          1
        ]
      ]
    },
    "published-print": {
      "date-parts": [
        [
          2003,
          1,
          1
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1104/pp.011577",
  "relation": {},
  "ISSN": [
    "1532-2548",
    "0032-0889"
  ],
  "subject": [],
  "published-other": {
    "date-parts": [
      [
        2003,
        1,
        1
      ]
    ]
  },
  "published": {
    "date-parts": [
      [
        2003,
        1,
        1
      ]
    ]
  }
}