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PMID: 8019419 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Modular arrangement of proteins as inferred from analysis of homology.

Protein science : a publication of the Protein Society ·Vol. 3 ·No. 3 ·1994-03-00 ·Pages 482-92

Sonnhammer EL, Kahn D

Abstract

The structure of many proteins consists of a combination of discrete modules that have been shuffled during evolution. Such modules can frequently be recognized from the analysis of homology. Here we present a systematic analysis of the modular organization of all sequenced proteins. To achieve this we have developed an automatic method to identify protein domains from sequence comparisons. Homologous domains can then be clustered into consistent families. The method was applied to all 21,098 nonfragment protein sequences in SWISS-PROT 21.0, which was automatically reorganized into a comprehensive protein domain database, ProDom. We have constructed multiple sequence alignments for each domain family in ProDom, from which consensus sequences were generated. These nonreduntant domain consensuses are useful for fast homology searches. Domain organization in ProDom is exemplified for proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PEP:PTS) and for bacterial 2-component regulators. We provide 2 examples of previously unrecognized domain arrangements discovered with the help of ProDom.

MeSH Terms
Amino Acid Sequence Bacterial Proteins/chemistry,genetics Biological Evolution Databases, Factual Molecular Sequence Data Molecular Structure Phosphoenolpyruvate Sugar Phosphotransferase System/genetics Proteins/chemistry,classification,genetics Sequence Alignment Sequence Homology, Amino Acid Software Software Design
Chemicals
Bacterial Proteins Proteins Phosphoenolpyruvate Sugar Phosphotransferase System
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sonnhammer E L
Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam.
Kahn D
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34 references, click to expand
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Article Info
Journal
Protein science : a publication of the Protein Society
Abbr.
Protein Sci
ISSN
0961-8368
DOI
10.1002/pro.5560030314
Published
1994-03-00
Pages
482-92
Language
English
Region
United States
NLM ID
9211750
PMCID
PMC2142695
Subset
IM
External Links
PubMed source DOI: 10.1002/pro.5560030314 PMC Full Text View journal details
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