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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| Taxon OID | 3300027671 Open in IMG/M |
| Scaffold ID | Ga0209588_1000037 Open in IMG/M |
| Source Dataset Name | Vadose zone soil microbial communities from the Eel River Critical Zone Observatory, Northern California, USA - Rivendell_Oct2014_Saprolite_2_DNA_Rhizosphere_1 (SPAdes) |
| Source Dataset Category | Metagenome |
| Source Dataset Use Policy | Open |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Sequencing Status | Permanent Draft |
| Scaffold Components | |
|---|---|
| Scaffold Length (bps) | 63830 |
| Total Scaffold Genes | 74 (view) |
| Total Scaffold Genes with Ribosome Binding Sites (RBS) | 55 (74.32%) |
| Novel Protein Genes | 5 (view) |
| Novel Protein Genes with Ribosome Binding Sites (RBS) | 5 (100.00%) |
| Associated Families | 5 |
| Taxonomy | |
|---|---|
| All Organisms → cellular organisms → Archaea | (Source: UniRef50) |
| Source Dataset Ecosystem |
|---|
| Environmental → Terrestrial → Soil → Unclassified → Unclassified → Vadose Zone Soil → Vadose Zone Soil And Rhizosphere Microbial Communities From The Eel River Critical Zone Observatory, Northern California To Study Diel Carbon Cycling |
| Source Dataset Sampling Location | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location Name | USA: California, Eel River Critical Zone Observatory | |||||||
| Coordinates | Lat. (o) | 39.7291 | Long. (o) | -123.6419 | Alt. (m) | Depth (m) | Location on Map | |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F005875 | Metagenome / Metatranscriptome | 387 | Y |
| F012855 | Metagenome / Metatranscriptome | 276 | Y |
| F014244 | Metagenome / Metatranscriptome | 264 | N |
| F016951 | Metagenome | 243 | Y |
| F104941 | Metagenome | 100 | Y |
| Protein ID | Family | RBS | Sequence |
|---|---|---|---|
| Ga0209588_100003714 | F014244 | AGG | VAFGEQTYTLLMGEARARGITIQELLRAVVIPDWFKAKYEPVPRQNPVIERRTREEEPVLPTSFSNKLRY |
| Ga0209588_100003727 | F016951 | GGA | LAIKLESSEIQYQTQIEVPITTADFFFARATTYARFRRWRPHLTDSQMIKDEELRSLLRKRGYKVVELAYNSYSDKKRDDLYQQLLNNLGRE |
| Ga0209588_100003734 | F005875 | GGAGG | LTRSVMIIGLTGGSLFLLAGFLSLLPWAVSGSIAGVLLGGWFGGEIKKRLDKGGNEGGKETRVIRFRKKALLEDNVSEMRTAGWEPRWESYRETQTGLLVRRIVYSVVMERKQRKHEFKGLRQLSKLLFPHKQHS |
| Ga0209588_100003738 | F104941 | AGGTGG | LFPDKAKMVRSANALFVTLAVATGVYLVIAILLTFGKPGFARDPNIIPWLFLGLALVSLANIGVTVFVQTSKKLMSERLRYDPISRTYLIMSTGAILSEAHAIYGLVLTLLSGSVFYGVGFTIVALASLWWVWKRFKQSLASLPNE |
| Ga0209588_10000374 | F012855 | GAGG | MSLGYSPETKEKAALSGSPWEKTGYVTIKKTGQRSIVLKGIASEIVKTRQKEAQAAEPKK |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |