| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021271 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0131209 | Gp0238794 | Ga0213897 |
| Sample Name | Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_3 |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 18074534 |
| Sequencing Scaffolds | 7 |
| Novel Protein Genes | 8 |
| Associated Families | 8 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 2 |
| All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Unclassified → Soil → Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → land → soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: West Virginia | |||||||
| Coordinates | Lat. (o) | 39.458 | Long. (o) | -79.073 | Alt. (m) | N/A | Depth (m) | .1 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F002951 | Metagenome / Metatranscriptome | 518 | Y |
| F015483 | Metagenome / Metatranscriptome | 254 | Y |
| F021961 | Metagenome | 216 | Y |
| F032268 | Metagenome / Metatranscriptome | 180 | Y |
| F053878 | Metagenome / Metatranscriptome | 140 | Y |
| F062864 | Metagenome | 130 | N |
| F094088 | Metagenome | 106 | N |
| F097548 | Metagenome / Metatranscriptome | 104 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0213897_100880 | Not Available | 747 | Open in IMG/M |
| Ga0213897_100908 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 739 | Open in IMG/M |
| Ga0213897_101068 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 712 | Open in IMG/M |
| Ga0213897_101660 | Not Available | 639 | Open in IMG/M |
| Ga0213897_102408 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 584 | Open in IMG/M |
| Ga0213897_103118 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium | 548 | Open in IMG/M |
| Ga0213897_103751 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 523 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0213897_100880 | Ga0213897_1008801 | F021961 | LSSLAVLLALPSLASANCYSIYDAKNQLAFQSPIAPVDLSTRISDAMRTRFPGGHLVMVPDDGACREYRTGPTLSPRFDAGNAARTEARPDRTLEASPLLGGTGAGPDLTTREAARSGNVLNVKRP |
| Ga0213897_100908 | Ga0213897_1009081 | F032268 | MVGLFTTTIGFAALWIRARERATRAESLLEGMRMGGRGDAMSPALDAIAEEVERIGEGQRFITRIMSESAGRVEATRSRGPGSITPH |
| Ga0213897_101068 | Ga0213897_1010682 | F053878 | RVELLQNAELQRLATLEWATGERREAVAEVRRDLAVSIDALRGERAAVVADLRSIVDVIFLRVAVFLVVAVLLAPLVAHAYARVWPRRWREIGGQRSD |
| Ga0213897_101660 | Ga0213897_1016602 | F062864 | VRYTYTNPQLERERDAVLRTILDKRGMCTFLARELGISKAAVAQWYSIPEHHVAAISKLLDIPQYQLRGEPSPRAKVDA |
| Ga0213897_102408 | Ga0213897_1024082 | F015483 | MTDAEIERVIRRAGYDVRWDDVPNHGAAEVYALRDGKRHTRSHPNLLALAEYLGCLERPVKFIEDREALDTVIEKHAKERNAFTVQPGACRVVVFGRNKYVQLVSVGGHESAMYELRTDGLRRTSNGNLPPEVVAA |
| Ga0213897_103118 | Ga0213897_1031181 | F094088 | AHSQTNSVIGLIGLIAVIVLIIVSWAVLKRRRIKSKTLEKKGMLNSIDWILEQLTLLEKKQIPDKDAVKEYYHQLYQLCRQYFSIEFDINVLYCTTEEWVGILEGVELDKKNKAAFYELVKKADSVRFADRDIAEKQNEEISTARNFVKALHRLKTGSPDKN |
| Ga0213897_103751 | Ga0213897_1037511 | F002951 | MTPADIDRVFGRGRLRMVTGDHVEVFREHSLPGERRRYTKRFLATAAGDFSEWTEREWRILARLVGHGIKPVPDVVRFDRGAADRAALVQTFDAGVTVDHWATLLPLERDGTTLRNVFEDCAHWWALARHSLI |
| Ga0213897_104074 | Ga0213897_1040741 | F097548 | MPGYRSLSSNLSGTAAEHAREAELSQRHGDPQSAARLLEEALAASLRSRPEMPGWVCGRLASIYRTLKRYDDEVELLERYRESQTSEEARTRFDARLSKARAIADRKRRPVTGALETVRQVRYRSSQRRRTPPRSQAVSAT |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |