• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Jul 1987; 84(13): 4355–4358.
PMCID: PMC305087

Profile analysis: detection of distantly related proteins.

Abstract

Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other sequence (target) to the group of aligned sequences (probe) can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme. Tests with globin and immunoglobulin sequences show that profile analysis can distinguish all members of these families from all other sequences in a database containing 3800 protein sequences.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (803K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Fitch WM. An improved method of testing for evolutionary homology. J Mol Biol. 1966 Mar;16(1):9–16. [PubMed]
  • Doolittle RF. Similar amino acid sequences: chance or common ancestry? Science. 1981 Oct 9;214(4517):149–159. [PubMed]
  • Blundell T, Sibanda BL, Pearl L. Three-dimensional structure, specificity and catalytic mechanism of renin. Nature. 1983 Jul 21;304(5923):273–275. [PubMed]
  • Sweet RM. Evolutionary similarity among peptide segments is a basis for prediction of protein folding. Biopolymers. 1986 Aug;25(8):1565–1577. [PubMed]
  • Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci U S A. 1984 Feb;81(4):1075–1078. [PMC free article] [PubMed]
  • Sweet RM, Eisenberg D. Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol. 1983 Dec 25;171(4):479–488. [PubMed]
  • McLachlan AD. Analysis of gene duplication repeats in the myosin rod. J Mol Biol. 1983 Sep 5;169(1):15–30. [PubMed]
  • Maizel JV, Jr, Lenk RP. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. [PMC free article] [PubMed]
  • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. [PubMed]
  • Boswell DR, McLachlan AD. Sequence comparison by exponentially-damped alignment. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):457–464. [PMC free article] [PubMed]
  • Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. [PMC free article] [PubMed]
  • Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. [PubMed]
  • Gribskov M, Burgess RR. Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 1986 Aug 26;14(16):6745–6763. [PMC free article] [PubMed]
  • Staden R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505–519. [PMC free article] [PubMed]
  • Taylor WR. Identification of protein sequence homology by consensus template alignment. J Mol Biol. 1986 Mar 20;188(2):233–258. [PubMed]
  • Lesk AM, Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol. 1980 Jan 25;136(3):225–270. [PubMed]
  • Wakabayashi S, Matsubara H, Webster DA. Primary sequence of a dimeric bacterial haemoglobin from Vitreoscilla. Nature. 322(6078):481–483. [PubMed]
  • Yanagi Y, Yoshikai Y, Leggett K, Clark SP, Aleksander I, Mak TW. A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains. Nature. 1984 Mar 8;308(5955):145–149. [PubMed]
  • Murata M, Richardson JS, Sussman JL. Simultaneous comparison of three protein sequences. Proc Natl Acad Sci U S A. 1985 May;82(10):3073–3077. [PMC free article] [PubMed]
  • Taylor WR, Thornton JM. Recognition of super-secondary structure in proteins. J Mol Biol. 1984 Mar 15;173(4):487–512. [PubMed]
  • Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. [PMC free article] [PubMed]
  • Wierenga RK, Terpstra P, Hol WG. Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J Mol Biol. 1986 Jan 5;187(1):101–107. [PubMed]
  • Chou PY, Fasman GD. Empirical predictions of protein conformation. Annu Rev Biochem. 1978;47:251–276. [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...