[7] Finding protein similarities with nucleotide sequence databases
- 1 January 1990
- book chapter
- research article
- Published by Elsevier BV in Methods in enzymology
- Vol. 183, 111-132
- https://doi.org/10.1016/0076-6879(90)83009-x
Abstract
In this chapter we describe strategies for the searching of translated nucleotide sequence databases. By applying standard searching techniques developed for protein databases,6 we have found that previously unrecognized homologies can be detected. In addition, we have shown that extremely high sensitivity can be obtained using the scoring matrix strategy11 for short regions of similarity. The latter approach is particularly effective for detecting homologs found at the ends of sequences and within data of poor quality. These individual methods are demonstrated for the LysR family of bacterial activator proteins. Successive applications of these methods allow for sensitive detection of complex relationships, as demonstrated for the AraC family and for the complex LuxR-OmpR-NtrC families of bacterial activator proteins. Although our examples are drawn from bacterial sequences, these methods are likewise effective for higher eukaryotic genomic sequences, where protein-coding sequences are usually interrupted by introns. This should be particularly important in the future, since much of the expected increase in nucleotide sequence databases is likely to come from eukaryotic genomic sequencing projects.Keywords
This publication has 21 references indexed in Scilit:
- Cascade regulation of nif gene expression in Rhizobium melilotiCell, 1988
- Nucleotide sequence of the luxR and luxI genes and structure of the primary regulatory region of the lux regulon of Vibrio fischeri ATCC 7744Biochemistry, 1988
- Positive regulation of the Escherichia coli l-rhamnose operon is mediated by the products of tandemly repeated regulatory genesJournal of Molecular Biology, 1987
- Primary structure of the bc1 complex of Rhodopseudomonas capsulata: Nucleotide sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteinsJournal of Molecular Biology, 1987
- Systematic method for the detection of potential λ Cro-like DNA-binding regions in proteinsJournal of Molecular Biology, 1987
- Organisation of the regulatory region of the Escherichia coli melibiose operonGene, 1987
- Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein productGene, 1986
- Rapid and Sensitive Protein Similarity SearchesScience, 1985
- Similar Amino Acid Sequences: Chance or Common Ancestry?Science, 1981
- A general method applicable to the search for similarities in the amino acid sequence of two proteinsJournal of Molecular Biology, 1970