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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300026107 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114514 | Gp0125946 | Ga0209950 |
| Sample Name | Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_B_D1_MG (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 121235774 |
| Sequencing Scaffolds | 5 |
| Novel Protein Genes | 5 |
| Associated Families | 5 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → unclassified Chromatiales → Chromatiales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Woeseiaceae → environmental samples → uncultured Woeseiaceae bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration. |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Wetlands → Unclassified → Soil → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration. |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → wetland area → soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | South San Francisco, USA | |||||||
| Coordinates | Lat. (o) | 37.496 | Long. (o) | -122.1329 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F003627 | Metagenome / Metatranscriptome | 476 | Y |
| F005789 | Metagenome / Metatranscriptome | 390 | Y |
| F029446 | Metagenome / Metatranscriptome | 188 | Y |
| F088283 | Metagenome / Metatranscriptome | 109 | Y |
| F093897 | Metagenome | 106 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0209950_1005058 | Not Available | 1410 | Open in IMG/M |
| Ga0209950_1007577 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → unclassified Solirubrobacterales → Solirubrobacterales bacterium | 1212 | Open in IMG/M |
| Ga0209950_1027457 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 720 | Open in IMG/M |
| Ga0209950_1039037 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → unclassified Chromatiales → Chromatiales bacterium | 620 | Open in IMG/M |
| Ga0209950_1056902 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Woeseiaceae → environmental samples → uncultured Woeseiaceae bacterium | 527 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0209950_1005058 | Ga0209950_10050583 | F003627 | VDRETSKREMAAGLQAGAFAAAVFALCFVAAMLYIAS |
| Ga0209950_1007577 | Ga0209950_10075772 | F005789 | MKAGKTRTRDGALSALRTPTNPPVPTMLVPLDASPLNVVRSMRGAIVDARIAYPEVLHVEIKDSDGELWRLATQDAEWSPSDPAELVGRSVADADIDAETGELRCKLSDGAVLDVKPAEREADDDPSNWELIAPGGVALEFGPGVRWQIGSADSPAS |
| Ga0209950_1027457 | Ga0209950_10274571 | F093897 | SVGFILLNDVQQEKETQAIWLQRTPTQCNDVWQVEFDEFFETNPEIKEIPKEKMKEILESIIKNHYEKQGIKILDLNLELDVYEGVRCEACNCLGWDRLSIKIPKSQFELVNKSEGWISL |
| Ga0209950_1039037 | Ga0209950_10390371 | F088283 | CVAGCATNDHVTGTYAPSCVAFEGNTIELADSRFTWDKFTDEVRVDDAGNTIDPFPGFPVRGTYTVVDDVVRLVTDVGDLAAELHLVRRPGQVYLLTDSEFDAWQSNGTVPNCALLLGAG |
| Ga0209950_1056902 | Ga0209950_10569021 | F029446 | AEVSCIQVAGATMLIISVLVTGIVVGILPGLLKLDKMFSRTNIVVGVIGALVGAFLGFGDLPLFLEYSFFSEMTLMVSVSFLFVIIKLLIARKRMAP |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |