GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.
PMID:12368813
| Citation |
Heidelberg, JF, Paulsen, IT, Nelson, KE, Gaidos, EJ, Nelson, WC, Read, TD, Eisen, JA, Seshadri, R, Ward, N, Methe, B, Clayton, RA, Meyer, T, Tsapin, A, Scott, J, Beanan, M, Brinkac, L, Daugherty, S, DeBoy, RT, Dodson, RJ, Durkin, AS, Haft, DH, Kolonay, JF, Madupu, R, Peterson, JD, Umayam, LA, White, O, Wolf, AM, Vamathevan, J, Weidman, J, Impraim, M, Lee, K, Berry, K, Lee, C, Mueller, J, Khouri, H, Gill, J, Utterback, TR, McDonald, LA, Feldblyum, TV, Smith, HO, Venter, JC, Nealson, KH and Fraser, CM (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-23 |
|---|---|
| Abstract |
Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion-reducing capabilities. |
| Links |
PubMed Online version:10.1038/nbt749 |
| Keywords |
Amino Acid Sequence; Biodegradation, Environmental; Cell Respiration; Electron Transport; Gene Expression; Gene Expression Regulation, Bacterial; Genome, Bacterial; Metals/metabolism; Molecular Sequence Data; Open Reading Frames/genetics; Organic Chemicals/metabolism; Oxidation-Reduction; Plasmids; Proteomics/methods; Sequence Alignment/methods; Sequence Analysis, DNA; Sequence Analysis, Protein; Shewanella/classification; Shewanella/genetics; Shewanella/metabolism; Shewanella/pathogenicity; Species Specificity; Water Pollutants, Chemical/metabolism; Water Purification/methods |
| edit table |
Significance
Annotations
| Gene product | Qualifier | GO Term | Evidence Code | with/from | Aspect | Extension | Notes | Status |
|---|---|---|---|---|---|---|---|---|
|
SHEON:Q8E8A6 |
enables |
GO:0015666: restriction endodeoxyribonuclease activity |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
F |
Seeded From UniProt |
complete | ||
|
SHEON:Q8E8A6 |
involved_in |
GO:0009307: DNA restriction-modification system |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
P |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EBG2 |
enables |
GO:0004721: phosphoprotein phosphatase activity |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
F |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EBG2 |
involved_in |
GO:0006470: protein dephosphorylation |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
P |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EF28 |
enables |
GO:0004721: phosphoprotein phosphatase activity |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
F |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EF28 |
involved_in |
GO:0006470: protein dephosphorylation |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
P |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EGX8 |
enables |
GO:0003677: DNA binding |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
F |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EGX8 |
part_of |
GO:0019812: type I site-specific deoxyribonuclease complex |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
C |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EGX8 |
involved_in |
GO:0009307: DNA restriction-modification system |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
P |
Seeded From UniProt |
complete | ||
|
SHEON:Q8EGX8 |
involved_in |
GO:0006304: DNA modification |
ECO:0000304: author statement supported by traceable reference used in manual assertion |
P |
Seeded From UniProt |
complete | ||
|
enables |
GO:0009055: electron transfer activity |
ECO:0000250: sequence similarity evidence used in manual assertion |
NCBI_gi:3628770 |
F |
Seeded From UniProt |
complete | ||
|
enables |
GO:0009055: electron transfer activity |
ECO:0000250: sequence similarity evidence used in manual assertion |
UniProtKB:P07598 |
F |
Seeded From UniProt |
complete | ||
|
enables |
GO:0016730: oxidoreductase activity, acting on iron-sulfur proteins as donors |
ECO:0000250: sequence similarity evidence used in manual assertion |
UniProtKB:P07598 |
F |
Seeded From UniProt |
complete | ||
See also
References
See Help:References for how to manage references in GONUTS.
