Abstract
Amino acid sequence data is a rich source of knowledge about structure, function, and molecular evolution of proteins. However, it is still difficult to extract such information from a single amino acid sequence. Sequence comparison of homologous proteins is regarded as a practical approach to investigate sequence data, and is widely utilized in the research of molecular biology and molecular evolution. In this paper, we will review the general procedure of sequence analysis and use the firefly luciferase family to describe how protein function can be investigated by sequence analysis. The sequence data used in this paper were obtained from NBRF and PRF protein primary structure databases.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Doolittle, R. F., 1990 Searching through sequence databases, in: Methods in Enzymology, Vol. 183, Doolittle, R. F., ed., Academic Press, Inc., San Diego, New York, Boston, London, Sydney, Tokyo, Toronto.
Haeggström, J. Z., Wetterholm, A., Shapiro, R., Vallee, B. L. and Samuelsson, B., 1990a Leukotriene A4 hydrolase: A zinc metalloenzyme, Biochem. Biophys. Res. Commun. 172:965.
Haeggström, J., Wetterholm, A., Vallee, B. L. and Samuelsson, B., 1990b Leukotriene A4 hydrolase: An epoxide hydrolase with peptidase activity, Biochem. Biophys. Res. Commun. 173:431.
Iwasaki, H., Ishino, Y., Toh, H., Nakata, A. and Shinagawa, H., 1991 Esherichia coli DNA polymerase II is homologous to α-like DNA polymerases, Mol. Gen. Genet. 226:24.
Kleinkauf, H. and von Döhren, H., 1990 Nonribosomal biosynthesis of peptide antibiotics, Eur. J. Biochem. 192:1.
Miller, M., Jaskolski, M., Rao, J. K. M., Leis, J. and Wlodawer, A., 1989 Crystal structure of a retroviral protease proves relationship to aspartic protease family, Nature 337:576.
Minami, M., Ohishi, N., Mutoh, H., Izumi, T., Bito, H., Wada, H., Seyama, Y., Toh, H. and Shimizu, T., 1990 Leukotriene A4 hydrolase is a zinc-containing aminopeptidase, Biochem. Biophys. Res. Commun. 173:620.
Navia, M. A., Fitzgerald, P. M. D., McKeever, B. M., Leu, C.-T., Heibach, J. C., Herber, W. K., Sigal, I. S., Darke, P. L. and Springer, J. P., 1989 Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1, Nature 337:615.
Nishikawa, K., Nakashima, H., Kanehisa, M. and Ooi, T., 1987 Detection of weak sequence homology of proteins for tertiary structure prediction. Prot. Seq. Data Anal. 1:107.
Schwartz, R. M. and Dayhoff, M. O., 1978 Metrices for detecting distant relationships, in: Atlas of Protein Sequence and Structure, Vol. 5, Dayhoff, M. O., eds., National Biomedical Research Foundation, Washington DC.
Staden, R., 1990 Searching for patterns in proteins and nucleic acid sequences, in: Methods in Enzymology, Vol. 183, Doolittle, R. F., eds., Academic Press, Inc., San Diego, New York, Boston, London, Sydney, Tokyo, Toronto.
Storomo, G. D., 1990 Consensus Patterns in DNA, in: Methods in Enzymology, Vol. 183, Doolittle, R. F., eds., Academic Press, Inc., San Diego, New York, Boston, London, Sydney, Tokyo, Toronto.
Toh, H., 1990 N-terminal halves of gramicidin S synthetase 1 and tyrocidine synthetase 1 as novel members of firefly luciferase family, Prot. Seq. Data Anal. 3:517–521.
Toh, H., 1991 Sequence analysis of firefly luciferase family reveals a conservative sequence motif, Prot. Seq. Data Anal. 4:111.
Toh, H., Kikuno, R., Hayashida, H., Miyata, T., Kugimiya, W., Inouye, S., Yuki, S. and Saigo, K., 1985a Close structural resemblance between putative polymerase of a Dorosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus, EMBO J. 4:1267.
Toh, H., Minami, M. and Shimizu, T., 1990 Molecular evolution and zinc ion binding motif of leukotriene A4 hydrolase, Biochem. Biophys. Res. Commun. 171:216.
Toh, H., Ono, M., Saigo, K. and Miyata, T., 1985b Retroviral protease-like sequence in the yeast transposon, Ty1. Nature 315:691.
Vallee, B. L. and Auld, D. S., 1990 Zinc coordination, function, and structure of zinc enzymes and other proteins, Biochemistry 29:5647.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1993 Springer Science+Business Media New York
About this chapter
Cite this chapter
Toh, H. (1993). Homology Search and Prediction of Biological Function of Protein from Amino Acid Sequences. In: Imahori, K., Sakiyama, F. (eds) Methods in Protein Sequence Analysis. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1603-7_30
Download citation
DOI: https://doi.org/10.1007/978-1-4899-1603-7_30
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-1605-1
Online ISBN: 978-1-4899-1603-7
eBook Packages: Springer Book Archive