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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| Taxon OID | 3300007258 Open in IMG/M |
| Scaffold ID | Ga0099793_10000633 Open in IMG/M |
| Source Dataset Name | Vadose zone soil and rhizosphere microbial communities from the Eel River Critical Zone Observatory, Northern California to study diel carbon cycling - Rivendell_Oct2014_Saprolite_2_DNA_Bulk_3 |
| 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) | 9933 |
| Total Scaffold Genes | 12 (view) |
| Total Scaffold Genes with Ribosome Binding Sites (RBS) | 8 (66.67%) |
| Novel Protein Genes | 4 (view) |
| Novel Protein Genes with Ribosome Binding Sites (RBS) | 1 (25.00%) |
| Associated Families | 4 |
| 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 | Eel River Critical Zone Observatory, California, USA | |||||||
| 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? |
|---|---|---|---|
| F014368 | Metagenome / Metatranscriptome | 263 | N |
| F016387 | Metagenome / Metatranscriptome | 247 | N |
| F022177 | Metagenome / Metatranscriptome | 215 | Y |
| F029395 | Metagenome | 188 | Y |
| Protein ID | Family | RBS | Sequence |
|---|---|---|---|
| Ga0099793_100006331 | F022177 | AGGAGG | MESHEWTAFLKLKGQTSLRNEEEILDEFDGFVQALQRVGVDYNIIVMVKGRASRQLHSEYSTRETEPKIAREGSGA* |
| Ga0099793_100006332 | F029395 | N/A | MDAVLSGNGKREGLAYSEVREAKADGRLKDLLVDLIDSSKALDVRVWLDGIYTDIGDEQVRGDWMNDRDVYFKVEGRVDKRNGS* |
| Ga0099793_100006334 | F016387 | N/A | MLELKSIPVSSSRSVTRTLRLDEDVEAGIVEMAEREQFSFNLLANRALRKLVEWEDKAGKFGFIQVPTSLVEKVFSILSDEEARELGREAGTNTLPEMVLFWFKKFNMENALKAMEMIGSYGNAFRLQYTLDGETDTVVLKHDRGPRVSAFYGEMFQSLFKPMGAKVETRETDGQVVATIIRPLTGLAREHKDALLIPSFAGAKNGRGYKR* |
| Ga0099793_100006335 | F014368 | N/A | MTQLENAPKPEVRRSPDTVTRTFRIDRDVDRKMEGLSSEGRVSMNQMANKALRRYVEWEVNAEKFGTVTTSASTIRKFFDYLTIEQAKEMGSWWGENQAPGIITFWFKKFDFDSVLKALEFLGAQYGRAFTSDYAFDGRSHTLIVKHDMGLKASVFYAEAVKAAFSHLGLGTDIFVTDDQVIAISPPDPAHPLNRSYEGAADLKYPTSATSRPIPKLRKGQRTDSDNRDG* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |