title: A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins.
abstract: The genomes of many organisms have been sequenced in the last 5 years. Typically about 30% of predicted genes from a newly sequenced genome cannot be given functional assignments using sequence comparison methods. In these situations three-dimensional structural predictions combined with a suite of computational tools can suggest possible functions for these hypothetical proteins. Suggesting functions may allow better interpretation of experimental data (e.g., microarray data and mass spectroscopy data) and help experimentalists design new experiments. In this paper, we focus on three hypothetical proteins of Shewanella oneidensis MR-1 that are potentially related to iron transport/metabolism based on microarray experiments. The threading program PROSPECT was used for protein structural predictions and functional annotation, in conjunction with literature search and other computational tools. Computational tools were used to perform transmembrane domain predictions, coiled coil predictions, signal peptide predictions, sub-cellular localization predictions, motif prediction, and operon structure evaluations. Combined computational results from all tools were used to predict roles for the hypothetical proteins. This method, which uses a suite of computational tools that are freely available to academic users, can be used to annotate hypothetical proteins in general.
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D000465:Algorithms; D000581:Amidohydrolases / Q000235:genetics; D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D016208:Databases, Factual; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D034281:Dynamins / Q000235:genetics; D016680:Genome, Bacterial; D006360:Heat-Shock Proteins / Q000235:genetics; D057927:Hydrophobic and Hydrophilic Interactions; D007501:Iron / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008982:Molybdenum / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D021382:Protein Sorting Signals / Q000235:genetics; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D020592:Shewanella / Q000235:genetics* / Q000502:physiology; D040681:Structural Homology, Protein
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D002352:Carrier Proteins; D006360:Heat-Shock Proteins; D021382:Protein Sorting Signals; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; C044659:molybdate; D008982:Molybdenum; D007501:Iron; D000581:Amidohydrolases; C438834:N-terminal nucleophile hydrolase; D034281:Dynamins