Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1990 Jan;87(2):826–830. doi: 10.1073/pnas.87.2.826

Finding sequence motifs in groups of functionally related proteins.

H O Smith 1, T M Annau 1, S Chandrasegaran 1
PMCID: PMC53359  PMID: 1689055

Abstract

We have developed a method for rapidly finding patterns of conserved amino acid residues (motifs) in groups of functionally related proteins. All 3-amino acid patterns in a group of proteins of the type aa1 d1 aa2 d2 aa3, where d1 and d2 are distances that can be varied in a range up to 24 residues, are accumulated into an array. Segments of the proteins containing those patterns that occur most frequently are aligned on each other by a scoring method that obtains an average relatedness value for all the amino acids in each column of the aligned sequence block based on the Dayhoff relatedness odds matrix. The automated method successfully finds and displays nearly all of the sequence motifs that have been previously reported to occur in 33 reverse transcriptases, 18 DNA integrases, and 30 DNA methyltransferases.

Full text

PDF
826

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Argos P. Evidence for a repeating domain in type I restriction enzymes. EMBO J. 1985 May;4(5):1351–1355. doi: 10.1002/j.1460-2075.1985.tb03784.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Argos P., Landy A., Abremski K., Egan J. B., Haggard-Ljungquist E., Hoess R. H., Kahn M. L., Kalionis B., Narayana S. V., Pierson L. S., 3rd The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 1986 Feb;5(2):433–440. doi: 10.1002/j.1460-2075.1986.tb04229.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berget S. M., Moore C., Sharp P. A. Spliced segments at the 5' terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci U S A. 1977 Aug;74(8):3171–3175. doi: 10.1073/pnas.74.8.3171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Caserta M., Zacharias W., Nwankwo D., Wilson G. G., Wells R. D. Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4770–4777. [PubMed] [Google Scholar]
  5. Doolittle R. F., Feng D. F., Johnson M. S., McClure M. A. Origins and evolutionary relationships of retroviruses. Q Rev Biol. 1989 Mar;64(1):1–30. doi: 10.1086/416128. [DOI] [PubMed] [Google Scholar]
  6. Fry D. C., Kuby S. A., Mildvan A. S. ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc Natl Acad Sci U S A. 1986 Feb;83(4):907–911. doi: 10.1073/pnas.83.4.907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gilbert W. Why genes in pieces? Nature. 1978 Feb 9;271(5645):501–501. doi: 10.1038/271501a0. [DOI] [PubMed] [Google Scholar]
  8. Hunter T. A thousand and one protein kinases. Cell. 1987 Sep 11;50(6):823–829. doi: 10.1016/0092-8674(87)90509-5. [DOI] [PubMed] [Google Scholar]
  9. Lauster R. Evolution of type II DNA methyltransferases. A gene duplication model. J Mol Biol. 1989 Mar 20;206(2):313–321. doi: 10.1016/0022-2836(89)90481-6. [DOI] [PubMed] [Google Scholar]
  10. Lipman D. J., Altschul S. F., Kececioglu J. D. A tool for multiple sequence alignment. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4412–4415. doi: 10.1073/pnas.86.12.4412. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  12. Murata M., Richardson J. S., Sussman J. L. Simultaneous comparison of three protein sequences. Proc Natl Acad Sci U S A. 1985 May;82(10):3073–3077. doi: 10.1073/pnas.82.10.3073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Pósfai J., Bhagwat A. S., Pósfai G., Roberts R. J. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res. 1989 Apr 11;17(7):2421–2435. doi: 10.1093/nar/17.7.2421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Römisch K., Webb J., Herz J., Prehn S., Frank R., Vingron M., Dobberstein B. Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTP-binding domains. Nature. 1989 Aug 10;340(6233):478–482. doi: 10.1038/340478a0. [DOI] [PubMed] [Google Scholar]
  15. Som S., Bhagwat A. S., Friedman S. Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme. Nucleic Acids Res. 1987 Jan 12;15(1):313–332. doi: 10.1093/nar/15.1.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sznyter L. A., Slatko B., Moran L., O'Donnell K. H., Brooks J. E. Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein. Nucleic Acids Res. 1987 Oct 26;15(20):8249–8266. doi: 10.1093/nar/15.20.8249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Tao T., Walter J., Brennan K. J., Cotterman M. M., Blumenthal R. M. Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. Nucleic Acids Res. 1989 Jun 12;17(11):4161–4175. doi: 10.1093/nar/17.11.4161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Zalkin H., Argos P., Narayana S. V., Tiedeman A. A., Smith J. M. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. J Biol Chem. 1985 Mar 25;260(6):3350–3354. [PubMed] [Google Scholar]

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

RESOURCES