Phylogenetic continuum indicates “Galaxies” in the protein universe: Preliminary results on the natural group structures of proteins

István Ladunga

doi:10.1007/bf00160244

journal article Open Access Apr 01, 1992

Phylogenetic continuum indicates “Galaxies” in the protein universe: Preliminary results on the natural group structures of proteins

István Ladunga

Journal of Molecular Evolution Vol. 34 No. 4 pp. 358-375 · Springer Science and Business Media LLC

View at Publisher Save 10.1007/bf00160244

Topics

No keywords indexed for this article. Browse by subject →

References

69

[1]

Aitken A (1990) Identification of protein consensus sequences. Horwood, New York

[2]

Bánfalvi A, Kondorosi É, Kondorosi Á (1985) Rhizobium carries two megaplasmids. Plasmid 13:129–138 10.1016/0147-619x(85)90065-4

[3]

Barker WC, Hunt LT, George DG, Yeh LS, Chen HR, Blomquist MC, Seibel-Ross El, Elzanowski A, Hong MK, Ferrick DA, Bair JR, Chen SL, Ledley RS (1986, 1989, 1990) Protein Identification Resource (Releases 11, 23, 25). National Biomedical Research Foundation, Washington DC

[4]

Blaisdell BE (1986) A measure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci USA 83:5155–5159 10.1073/pnas.83.14.5155

[5]

Blaisdell BE (1989a) Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarity of natural sequences. J Mol Evol 29:526–537 10.1007/bf02602924

[6]

Blaisdell BE (1989b) Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a computer-generated model system. J Mol Evol 29:538–547 10.1007/bf02602925

[7]

Brenner S (1988) The molecular evolution of genes and proteins: a tale of two serines. Nature (London) 334:528–530 10.1038/334528a0

[8]

Broda P (1979) Plasmids. Freeman, San Francisco

[9]

Campbell A (1981) Evolutionary significance of accessory DNA elements in bacteria. Annu Rev Microbiol 35:55–83 10.1146/annurev.mi.35.100181.000415

[10]

Cavalier-Smith T (1985) Introduction: the evolutionary of genome size. In: Cavalier-Smith T (ed) The evolution of genome size. Wiley, New York, pp 1–36

[11]

Clewell DB (1981) Plasmids, drug resistance, and gene transfer in the genus Streptococcus. Microbiol Rev 45:409–436 10.1128/mr.45.3.409-436.1981

[12]

Structure of the catalytic and antigenic sites in influenza virus neuraminidase

P. M. Colman, J. N. Varghese, W. G. Laver

Nature 1983 10.1038/303041a0

[13]

Cornish-Bowden A (1979) How reliably do amino acid composition comparisons predict sequence similarities between proteins? J Theor Biol 76:369–386 10.1016/0022-5193(79)90007-9

[14]

Cramér H (1974) Mathematical methods of statistics. Princeton University Press, Princeton

[15]

Dayhoff MO (1972) Atlas of proteins: sequence and structure. National Biomedical Research Foundation, Washington DC

[16]

Dayhoff MO (1974) Computer analysis of protein sequences. Fed Proc 33:2314–2316

[17]

Dayhoff MO, Barker WC (1978) Supplement to the (1972) atlas of protein sequence and structure. National Biomedical Research Foundation, Washington DC

[18]

Sequence and structure homologies in bacterial and mammalian-type cytochromes

Richard E. Dickerson

Journal of Molecular Biology 1971 10.1016/0022-2836(71)90116-1

[19]

Similar Amino Acid Sequences: Chance or Common Ancestry?

Russell F. Doolittle

Science 1981 10.1126/science.7280687

[20]

Doolittle RF (1983) Angiotensinogen is related to the antitrypsin-antithrombin-ovalbumin family. Science 222:417–419 10.1126/science.6604942

[21]

Doolittle RF (1988) Redundancies in protein sequences. Trends Biochem Sci 13:599–623

[22]

Doolittle RF (1989) Similar amino acid sequences revisited. Trends Biochem Sci 14:244–245 10.1016/0968-0004(89)90055-8

[23]

Doolittle RF (1991) Counting and discounting the universe of exons. Science 253:677–679 10.1126/science.1871603

[24]

How Big Is the Universe of Exons?

Robert L. Dorit, Lloyd Schoenbach, Walter Gilbert

Science 1990 10.1126/science.2255907

[25]

Döring HP, Startlinger DL (1986) Molecular genetics of transposable elements in plants. Annu Rev Genet 20:175–200 10.1146/annurev.ge.20.120186.001135

[26]

Eberhard WG (1990) Evolution in bacterial plasmids and levels of selection. Quart Rev Biol 65:3–22 10.1086/416582

[27]

Everitt BS (1980) Cluster analysis, ed 2. Heinemann, London

[28]

Fischer G, Wittman-Liebold B, Lang K, Kiefhaber T, Schmid FX (1989) Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature 337:476–478 10.1038/337476a0

[29]

Homologous sequences in non-structural proteins from cowpea mosaic virus and picornaviruses

Henk Franssen, Jack Leunissen, Rob Goldbach et al.

The EMBO Journal 1984 10.1002/j.1460-2075.1984.tb01896.x

[30]

Gierasch LM (1989) Signal sequences. Biochemistry 28:923–930 10.1021/bi00429a001

[31]

Gibbs AJ, Dale MB, Kinns HR, Mackenzie HG (1971) The transition matrix method for comparing sequences; its use in describing and classifying proteins by their amino acid sequence. Syst Zool 20:417–1125 10.2307/2412117

[32]

Henikoff S, Haughn GW, Calvo JM, Wallace JC (1988) A large family of bacterial activator proteins. Proc Natl Acad Sci USA 85:6601–6606 10.1073/pnas.85.18.6602

[33]

Herdman M (1985) The evolution of bacterial genomes. In: Cavalier-Smith T (ed) The evolution of genome size. Wiley, New York, pp 37–68

[34]

Higgins DG, Sharp PM (1989) Fast and multiple sequence alignments on a microcomputer. Comput Appl Biosci 5:151–153

[35]

Holland J, Spindeler K, Horodyski F, Grabau E, Nichol S, Vandepol S (1982) Rapid evolution of RNA genomes. Science 215:1577–1585 10.1126/science.7041255

[36]

Hunt LT, Dayhoff MO (1980) A surprising new protein superfamily containing ovalbumin, antithrombin-III, and alpha1 proteinase inhibitor. Biochem Biophys Res Commun 95:864–971 10.1016/0006-291x(80)90867-0

[37]

Using known substructures in protein model building and crystallography.

T.Alwyn Jones, S. Thirup

The EMBO Journal 1986 10.1002/j.1460-2075.1986.tb04287.x

[38]

Karlin S, Morris M, Ghandour G, Leung MY (1988) Efficient algorithms for molecular sequence analysis. Proc Natl Acad Sci USA 85:841–845 10.1073/pnas.85.3.841

[39]

Karlin S, Blaisdell BE, Brendel V (1989) Identification of significant sequence patterns in proteins. Methods Enzymol 183: 388–402 10.1016/0076-6879(90)83026-6

[40]

Kaziro Y (1978) The role of guanosine 5′-triphosphate in polypeptide chain elongation. Biochim Biophys Acta 505:95–127 10.1016/0304-4173(78)90009-5

[41]

Klein P, Jacquez JA, Delisi C (1986) Prediction of protein function by discriminant analysis. Math Biosci 81:177–189 10.1016/0025-5564(86)90116-1

[42]

Koch AL (1981) Evolution of antibiotic resistance gene function. Microbiol Rev 45:355–378 10.1128/mr.45.2.355-378.1981

[43]

Kofoid EC, Parkinson JS (1988) Transmitter and receiver modules in bacterial signaling proteins. Proc Natl Acad Sci USA 85:4981–4985 10.1073/pnas.85.14.4981

[44]

A simple method for displaying the hydropathic character of a protein

Jack Kyte, Russell F. Doolittle

Journal of Molecular Biology 1982 10.1016/0022-2836(82)90515-0

[45]

Lewin B (1977) Gene expression, vol 3. Plasmids and phages. Wiley, New York.

[46]

Rapid and Sensitive Protein Similarity Searches

David J. Lipman, William R. Pearson

Science 1985 10.1126/science.2983426

[47]

Maizel JV Jr, Lenk RP (1981) Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci USA 78:7665–7669 10.1073/pnas.78.12.7665

[48]

Maynard Smith J (1982) Overview—unresolved evolutionary problems. In: Dover GA, Flavell RB (eds), Genome evolution. Academic Press, New York, pp 375–382

[49]

Mimura CS, Holbrook SR, Ames GFL (1991) Structural model of the nucleotide-binding conserved component of periplasmic permeases. Proc Natl Acad Sci USA 88:84–88 10.1073/pnas.88.1.84

[50]

Moller W, Amons R (1985) Phosphate-binding sequences in nucleotide-binding proteins. FEBS Lett 186:1–7 10.1016/0014-5793(85)81326-0

Showing 50 of 69 references

Cited By

13

Analysis of peptides from known proteins: Clusterization in sequence space

Victor B. Strelets, Ilya N. Shindyalov · 1994

Journal of Molecular Evolution

Metrics

13

Citations

69

References

Details

Published: Apr 01, 1992
Vol/Issue: 34(4)
Pages: 358-375
License: View

Authors

I

István Ladunga

Cite This Article

István Ladunga (1992). Phylogenetic continuum indicates “Galaxies” in the protein universe: Preliminary results on the natural group structures of proteins. Journal of Molecular Evolution, 34(4), 358-375. https://doi.org/10.1007/bf00160244

Phylogenetic continuum indicates “Galaxies” in the protein universe: Preliminary results on the natural group structures of proteins

You May Also Like