A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins
| Autor: | Frank W. Larimer, Alexander S. Beliaev, Christal Yost, Loren Hauser, Jizhong Zhou, Dong Xu, Dorothea K. Thompson, Ying Xu |
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| Rok vydání: | 2003 |
| Předmět: |
Models
Molecular Protein Folding Shewanella Databases Factual Protein Conformation Amino Acid Motifs computer.software_genre Biochemistry Genome Protein Structure Secondary Protein structure Shewanella oneidensis Databases Protein Conserved Sequence Heat-Shock Proteins biology Chromosome Mapping Molecular Medicine Protein folding Databases Nucleic Acid Hydrophobic and Hydrophilic Interactions Algorithms Biotechnology Signal peptide Dynamins Iron Molecular Sequence Data Sequence alignment Protein Sorting Signals Machine learning Amidohydrolases Bacterial Proteins Genetics Amino Acid Sequence Molecular Biology Molybdenum Microarray analysis techniques business.industry Computational Biology biology.organism_classification Protein Structure Tertiary Repressor Proteins Structural Homology Protein ATP-Binding Cassette Transporters Artificial intelligence Threading (protein sequence) business Carrier Proteins computer Sequence Alignment Genome Bacterial |
| Zdroj: | Omics : a journal of integrative biology. 7(2) |
| ISSN: | 1536-2310 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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