annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms注释的蛋白质域显示显著的保护功能蛋白质组在超界.pdfVIP

Genes 2011, 2, 869-911; doi:10.3390/genes2040869 OPEN ACCESS genes ISSN 2073-4425 /journal/genes Article Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms 1 2 2 3 Arshan Nasir , Aisha Naeem , Muhammad Jawad Khan , Horacio D. Lopez-Nicora and Gustavo Caetano-Anollés 1,* 1 Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; E-Mail: anasir@ 2 Mammalian NutriPhysioGenomics Laboratory, Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA; E-Mails: naeem1@ (A.Na.); khan41@ (M.J.K.) 3 Plant Pathology Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; E-Mail: hlopezn2@ * Author to whom correspondence should be addressed; E-Mail: gca@; Tel.: +1-217-333-8172; Fax: +1-217-333-8046. Received: 16 September 2011; in revised form: 28 October 2011 / Accepted: 28 October 2011 / Published: 8 November 2011 Abstract: The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the