Modular arrangement of proteins as inferred from analysis of homology

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...

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Bibliographic Details
Published in:Protein science 1994-03, Vol.3 (3), p.482-492
Main Authors: Sonnhammer, Erik L.L., Kahn, Daniel
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Biological Evolution
Databases, Factual
domain database
domain families
Life Sciences
Molecular Sequence Data
Molecular Structure
Other
Phosphoenolpyruvate Sugar Phosphotransferase System - genetics
protein domains
protein evolution
protein homology
Proteins - chemistry
Proteins - classification
Proteins - genetics
Sequence Alignment
Sequence Homology, Amino Acid
Software
Software Design
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Summary: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 nonredundant 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.
ISSN:0961-8368
1469-896X
DOI:10.1002/pro.5560030314