메뉴 건너뛰기




Volumn 5, Issue 1, 2003, Pages 1-6

Web-based programs for the display and analysis of transmembrane α-helices in aligned protein sequences

Author keywords

BASS; Domains; Homologues; IC; Proteins; Repeat sequences; Sequence alignment; TMS_ALIGN; TMS_CUT; TMS_SPLIT

Indexed keywords

MEMBRANE PROTEIN;

EID: 0037636367     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000068718     Document Type: Review
Times cited : (19)

References (40)
  • 1
    • 0034607552 scopus 로고    scopus 로고
    • Homology-based method for identification of protein repeats using statistical significance estimates
    • Andrade, M.A., Ponting, C., Gibson, T. and Bork, P. 2000. Homology-based method for identification of protein repeats using statistical significance estimates. J. Mol. Biol. 298:521-537.
    • (2000) J. Mol. Biol. , vol.298 , pp. 521-537
    • Andrade, M.A.1    Ponting, C.2    Gibson, T.3    Bork, P.4
  • 2
    • 0021760092 scopus 로고
    • A comprehensive set of sequence analysis programs for the VAX
    • Devereaux, J., Haeberli, P. and Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 387-395
    • Devereaux, J.1    Haeberli, P.2    Smithies, O.3
  • 4
    • 0034003596 scopus 로고    scopus 로고
    • A novel ubiquitous family of putative efflux transporters
    • Harley, K.T. and Saier, M.H. Jr. 2000. A novel ubiquitous family of putative efflux transporters. J. Mol. Microbiol. Biotechnol. 2:195-198.
    • (2000) J. Mol. Microbiol. Biotechnol. , vol.2 , pp. 195-198
    • Harley, K.T.1    Saier Jr., M.H.2
  • 5
    • 0025716308 scopus 로고
    • Homologous sugar transport proteins in Escherichia coli and their relatives in both prokaryotes and eukaryotes
    • Henderson, P.J.F. and Maiden, M.C.J. 1990. Homologous sugar transport proteins in Escherichia coli and their relatives in both prokaryotes and eukaryotes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 326:391-410.
    • (1990) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.326 , pp. 391-410
    • Henderson, P.J.F.1    Maiden, M.C.J.2
  • 6
    • 0024234855 scopus 로고
    • Clustal: A package for performing multiple sequence alignment on a microcomputer
    • Higgins, D. G. and Sharp, P.M. 1988. Clustal: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244.
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 7
    • 0034824349 scopus 로고    scopus 로고
    • The drug/metabolite transporter superfamily
    • Jack, D.L., Yang, N.M. and Saier, M.H. Jr. 2001. The drug/metabolite transporter superfamily. Eur. J. Biochem. 268:3620-3639.
    • (2001) Eur. J. Biochem. , vol.268 , pp. 3620-3639
    • Jack, D.L.1    Yang, N.M.2    Saier Jr., M.H.3
  • 8
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin, S. and Altschul, S.F. 1990. Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 10
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh, A., Larsson, B., Heijne, G.V. and Sonnhammer, E.L.L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Heijne, G.V.3    Sonnhammer, E.L.L.4
  • 11
    • 0027160122 scopus 로고
    • The mitochondrial carrier family of transportproteins: Structural, functional and evolutionary relationships
    • Kuan, J. and Saier, M.H. Jr. 1993. The mitochondrial carrier family of transportproteins: structural, functional and evolutionary relationships. Crit. Rev. Biochem. Mol. Biol. 28:209-233.
    • (1993) Crit. Rev. Biochem. Mol. Biol. , vol.28 , pp. 209-233
    • Kuan, J.1    Saier Jr., M.H.2
  • 12
    • 0034647416 scopus 로고    scopus 로고
    • Accurate formula for P-values of gapped local sequence and profile alignments
    • Moot, R. 2000. Accurate formula for P-values of gapped local sequence and profile alignments. J. Mol. Biol. 300:649-659.
    • (2000) J. Mol. Biol. , vol.300 , pp. 649-659
    • Moot, R.1
  • 15
    • 0029910115 scopus 로고    scopus 로고
    • Phylogenetic characterization of the MIP family of transmembrane channel proteins
    • Park, J.H. and Saier, M.H. Jr. 1996. Phylogenetic characterization of the MIP family of transmembrane channel proteins. J. Membr. Biol. 153:171-180.
    • (1996) J. Membr. Biol. , vol.153 , pp. 171-180
    • Park, J.H.1    Saier Jr., M.H.2
  • 16
    • 0029872148 scopus 로고    scopus 로고
    • Multidrug resistance proteins QacA and QacB from Staphylococcus aureus: Membrane topology and identification of residues involved in substrate specificity
    • Paulsen, I.T., Brown, M.H., Littlejohn, T.G., Mitchell, B.A. and Skurray, R.A.1996a. Multidrug resistance proteins QacA and QacB from Staphylococcus aureus: membrane topology and identification of residues involved in substrate specificity. Proc. Natl. Acad. Sci. USA 93:3630-3635.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 3630-3635
    • Paulsen, I.T.1    Brown, M.H.2    Littlejohn, T.G.3    Mitchell, B.A.4    Skurray, R.A.5
  • 18
    • 0027408932 scopus 로고
    • Topology, structure and evolution of two families of proteins involved in antibiotic and antiseptic resistance in eukaryotes and prokaryotes - An analysis
    • Paulsen, I.T. and Skurray, R.A. 1993. Topology, structure and evolution of two families of proteins involved in antibiotic and antiseptic resistance in eukaryotes and prokaryotes - An analysis. Gene 124:1-11.
    • (1993) Gene , vol.124 , pp. 1-11
    • Paulsen, I.T.1    Skurray, R.A.2
  • 19
    • 0028345374 scopus 로고
    • Computer-aided analyses of transport protein sequence: Gleaning evidence concerning function, structure, biogenesis and evolution
    • Saier, M.H. Jr. 1994. Computer-aided analyses of transport protein sequence: gleaning evidence concerning function, structure, biogenesis and evolution. Microbiol. Rev. 58:71-93.
    • (1994) Microbiol. Rev. , vol.58 , pp. 71-93
    • Saier Jr., M.H.1
  • 20
    • 0030309453 scopus 로고    scopus 로고
    • Phylogenetic approaches to the identification and characterization of protein families and superfamilies
    • Saier, M.H. Jr. 1996. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. Microbial Comp. Genomics 1:129-150.
    • (1996) Microbial Comp. Genomics , vol.1 , pp. 129-150
    • Saier Jr., M.H.1
  • 21
    • 0031733149 scopus 로고    scopus 로고
    • Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya
    • Poole, R.K. (ed.) San Diego, Academic Press
    • Saier, M.H. Jr. 1998. Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya; in Advances in Microbial Physiology. Poole, R.K. (ed.) San Diego, Academic Press, vol. 40, pp. 81-136.
    • (1998) Advances in Microbial Physiology , vol.40 , pp. 81-136
    • Saier Jr., M.H.1
  • 22
    • 0344172785 scopus 로고    scopus 로고
    • Genome archeology leading to the characterization and classification of transport proteins
    • Saier, M.H. Jr. 1999. Genome archeology leading to the characterization and classification of transport proteins. Curr. Opin. Microbiol. 2:555-561.
    • (1999) Curr. Opin. Microbiol. , vol.2 , pp. 555-561
    • Saier Jr., M.H.1
  • 23
    • 0343603660 scopus 로고    scopus 로고
    • A functional phylogenetic classification system for transmembrane solute transporters
    • Saier, M.H. Jr. 2000a. A functional phylogenetic classification system for transmembrane solute transporters. Microbial Mol. Biol. Rev. 64:354-411.
    • (2000) Microbial Mol. Biol. Rev. , vol.64 , pp. 354-411
    • Saier Jr., M.H.1
  • 24
    • 0033821267 scopus 로고    scopus 로고
    • Vectorial metabolism and the evolution of transport systems
    • Saier, M.H. Jr. 2000b. Vectorial metabolism and the evolution of transport systems. J. Bacteriol. 182:5029-5035.
    • (2000) J. Bacteriol. , vol.182 , pp. 5029-5035
    • Saier Jr., M.H.1
  • 26
    • 0001865946 scopus 로고    scopus 로고
    • Evolutionary origins of transmembrane transport systems
    • Symposium 58. Society for General Microbiology. Broome-Smith, J.K., Baumberg S., Stirling C.J. and Ward F.B. (eds.). Cambridge, Cambridge University Press
    • Saier, M.H. Jr. and Tseng, T.T. 1999. Evolutionary origins of transmembrane transport systems; in Transport of Molecules Across Microbial Membranes. Symposium 58. Society for General Microbiology. Broome-Smith, J.K., Baumberg S., Stirling C.J. and Ward F.B. (eds.). Cambridge, Cambridge University Press, pp. 252-274.
    • (1999) Transport of Molecules Across Microbial Membranes , pp. 252-274
    • Saier Jr., M.H.1    Tseng, T.T.2
  • 27
    • 0035449197 scopus 로고    scopus 로고
    • Facilitative urea transporters
    • Smith, C.P. and Rousselet, G. 2001. Facilitative urea transporters. J. Membr. Biol. 183:1-14.
    • (2001) J. Membr. Biol. , vol.183 , pp. 1-14
    • Smith, C.P.1    Rousselet, G.2
  • 28
    • 0023101580 scopus 로고
    • Lysosomal cystine transport. Effect of intralysosomal pH and membrane potential
    • Smith, M.L., Greene, A.A., Potashnik, R., Mendoza, S.A. and Schneider, J.A. 1987. Lysosomal cystine transport. Effect of intralysosomal pH and membrane potential. J. Biol. Chem. 262:1244-1253.
    • (1987) J. Biol. Chem. , vol.262 , pp. 1244-1253
    • Smith, M.L.1    Greene, A.A.2    Potashnik, R.3    Mendoza, S.A.4    Schneider, J.A.5
  • 30
    • 0031614678 scopus 로고    scopus 로고
    • A hidden Markov model for predicting transmembrane helices in protein sequences
    • Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. and Sensen, C. (eds) Menlo Park, AAAI Press
    • Sonnhammer, E.L.L., Heijne, G.V. and Krogh. A. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences; in Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. and Sensen, C. (eds) Menlo Park, AAAI Press, pp. 175-182.
    • (1998) Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology , pp. 175-182
    • Sonnhammer, E.L.L.1    Heijne, G.V.2    Krogh, A.3
  • 31
    • 0031574072 scopus 로고    scopus 로고
    • The Clustal X window interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J.D., Gibson, T. J., Plewniak, F., Jeanmougin, F. and Higgins, D. G. 1997. The Clustal X window interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
    • (1997) Nucleic Acids Res. , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 33
    • 0033170990 scopus 로고    scopus 로고
    • The RND permease superfamily: An ancient, ubiquitous and diverse family that includes human disease and development proteins
    • Tseng, T.T., Gratwick, K.S., Kollman, J., Park, D., Nies, D.H., Goffeau, A. and Saier, H. M. 1999. The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J. Mol. Microbiol. Biotechnol. 1:107-125.
    • (1999) J. Mol. Microbiol. Biotechnol. , vol.1 , pp. 107-125
    • Tseng, T.T.1    Gratwick, K.S.2    Kollman, J.3    Park, D.4    Nies, D.H.5    Goffeau, A.6    Saier, H.M.7
  • 34
    • 0032561132 scopus 로고    scopus 로고
    • Principles governing amino acid composition of integral membrane proteins: Applications to topology prediction
    • Tusnády, G.E. and Simon, I 1998. Principles governing amino acid composition of integral membrane proteins: applications to topology prediction. J. Mol. Biol. 283:489-506.
    • (1998) J. Mol. Biol. , vol.283 , pp. 489-506
    • Tusnády, G.E.1    Simon, I.2
  • 35
    • 0033038516 scopus 로고    scopus 로고
    • Cells of Escherichia coli contain a protein-tyrosine kinase, Wzc, and a phosphotyrosine-protein phosphatase, Wzb
    • Vincent, C., Doublet, P., Grangeasse, C., Vaganay, E., Cozzone, A.J. and Duclos, B. 1999. Cells of Escherichia coli contain a protein-tyrosine kinase, Wzc, and a phosphotyrosine-protein phosphatase, Wzb. J. Bacteriol. 181:3472-3477.
    • (1999) J. Bacteriol. , vol.181 , pp. 3472-3477
    • Vincent, C.1    Doublet, P.2    Grangeasse, C.3    Vaganay, E.4    Cozzone, A.J.5    Duclos, B.6
  • 36
    • 0033022996 scopus 로고    scopus 로고
    • Structure, assembly and regulation of expression of capsules in Escherichia coli
    • Whitfield, C. and Roberts, I.S. 1999. Structure, assembly and regulation of expression of capsules in Escherichia coli. Mol. Microbiol. 31:1307-1319.
    • (1999) Mol. Microbiol. , vol.31 , pp. 1307-1319
    • Whitfield, C.1    Roberts, I.S.2
  • 37
    • 0032540009 scopus 로고    scopus 로고
    • Urea transporter UT3 functions as an efficient water channel
    • Yang, B. and Verkman, A.S. 1998. Urea transporter UT3 functions as an efficient water channel. J. Bacteriol. 272:9369-9372.
    • (1998) J. Bacteriol. , vol.272 , pp. 9369-9372
    • Yang, B.1    Verkman, A.S.2
  • 38
    • 0036151174 scopus 로고    scopus 로고
    • The ubiquitous ThrE family of putative transmembrane amino acid efflux transporters
    • Yen, M.-R., Tseng, Y.-H., Simic, P., Sahm, H., Eggeling, L. and Saier, H. M. 2000. The ubiquitous ThrE family of putative transmembrane amino acid efflux transporters. Res. Microbiol. 153:19-25.
    • (2000) Res. Microbiol. , vol.153 , pp. 19-25
    • Yen, M.-R.1    Tseng, Y.-H.2    Simic, P.3    Sahm, H.4    Eggeling, L.5    Saier, H.M.6
  • 39
    • 0035795114 scopus 로고    scopus 로고
    • Homologues of archaeal rhodopsins in plants, animals and fungi: Structural and functional predictions for a putative fungal chaperone proteins
    • Zhai, Y.F., Heijne, W.H.M., Smith, D.W. and Saier, H. M. 2001. Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predictions for a putative fungal chaperone proteins. Biochim. Biophys. Acta 1511:206-223.
    • (2001) Biochim. Biophys. Acta , vol.1511 , pp. 206-223
    • Zhai, Y.F.1    Heijne, W.H.M.2    Smith, D.W.3    Saier, H.M.4
  • 40
    • 0035988281 scopus 로고    scopus 로고
    • A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins
    • Zhai, Y.F and Saier, H. M. 2002. A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins. J. Mol. Microbiol. Biotechnol. 4(4):29-31.
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , Issue.4 , pp. 29-31
    • Zhai, Y.F.1    Saier, H.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.