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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\u2010PROT 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\u2010component regulators. We provide 2 examples of previously unrecognized domain arrangements discovered with the help of, ProDom.<\/jats:p>","DOI":"10.1002\/pro.5560030314","type":"journal-article","created":{"date-parts":[[2010,7,12]],"date-time":"2010-07-12T05:35:44Z","timestamp":1278912944000},"page":"482-492","source":"Crossref","is-referenced-by-count":167,"title":["Modular arrangement of proteins as inferred from analysis of homology"],"prefix":"10.1002","volume":"3","author":[{"given":"Erik 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