Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome

The protein coding sequences of S. oneidensis MR-1 were analyzed, and new annotations were given to 491 gene products, 306 of which were previously of unknown function. New information was mainly brought in from structural domain predictions for S. oneidensis proteins of the SUPERFAM database (http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/) and newly identified and experimentally verified functions of homologous proteins. Proteins encoded by fused genes were identified and separated into modules, protein units of at least 83 aa with independent functions and distinct evolutionary histories. A reannotation of the fused gene products was done to assign functions to the appropriate module within the protein. Groups of sequence-similar proteins of S. oneidensis were assembled. The fused gene products were represented by their modular entities for the grouping process. The protein groups were analyzed for their size and functions, and they were used to indicate activities that are of importance to the environmental adaptation of this organism. Making use of several approaches not commonly used in annotation, we have been able to enrich our understanding of the functions encoded by the S. oneidensis genome.