| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021264 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0131209 | Gp0238792 | Ga0213895 |
| Sample Name | Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_1 |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 22028185 |
| Sequencing Scaffolds | 16 |
| Novel Protein Genes | 16 |
| Associated Families | 16 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Rhodocyclales → Rhodocyclaceae → Aromatoleum → Aromatoleum aromaticum → Aromatoleum aromaticum EbN1 | 1 |
| All Organisms → cellular organisms → Bacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. SCGC AG-212-E16 | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Myxococcaceae → unclassified Myxococcaceae → Myxococcaceae bacterium | 1 |
| Not Available | 7 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 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? |
|---|---|---|---|
| F012081 | Metagenome / Metatranscriptome | 284 | Y |
| F013740 | Metagenome / Metatranscriptome | 268 | Y |
| F021258 | Metagenome / Metatranscriptome | 219 | Y |
| F030799 | Metagenome | 184 | Y |
| F032460 | Metagenome / Metatranscriptome | 180 | Y |
| F038633 | Metagenome / Metatranscriptome | 165 | Y |
| F040166 | Metagenome / Metatranscriptome | 162 | Y |
| F042599 | Metagenome / Metatranscriptome | 158 | Y |
| F044764 | Metagenome / Metatranscriptome | 154 | Y |
| F062538 | Metagenome / Metatranscriptome | 130 | Y |
| F069810 | Metagenome / Metatranscriptome | 123 | Y |
| F077001 | Metagenome | 117 | Y |
| F081517 | Metagenome | 114 | N |
| F085328 | Metagenome | 111 | Y |
| F092317 | Metagenome | 107 | Y |
| F103522 | Metagenome | 101 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0213895_100040 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Rhodocyclales → Rhodocyclaceae → Aromatoleum → Aromatoleum aromaticum → Aromatoleum aromaticum EbN1 | 2114 | Open in IMG/M |
| Ga0213895_100454 | All Organisms → cellular organisms → Bacteria | 1234 | Open in IMG/M |
| Ga0213895_100609 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1135 | Open in IMG/M |
| Ga0213895_100804 | All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. SCGC AG-212-E16 | 1049 | Open in IMG/M |
| Ga0213895_100828 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales | 1039 | Open in IMG/M |
| Ga0213895_100836 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Myxococcaceae → unclassified Myxococcaceae → Myxococcaceae bacterium | 1037 | Open in IMG/M |
| Ga0213895_101360 | Not Available | 894 | Open in IMG/M |
| Ga0213895_101495 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 866 | Open in IMG/M |
| Ga0213895_101835 | Not Available | 812 | Open in IMG/M |
| Ga0213895_102926 | Not Available | 694 | Open in IMG/M |
| Ga0213895_103284 | Not Available | 668 | Open in IMG/M |
| Ga0213895_104014 | Not Available | 622 | Open in IMG/M |
| Ga0213895_104875 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 581 | Open in IMG/M |
| Ga0213895_105700 | Not Available | 547 | Open in IMG/M |
| Ga0213895_106069 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 535 | Open in IMG/M |
| Ga0213895_106150 | Not Available | 532 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0213895_100040 | Ga0213895_1000402 | F021258 | MKVKLSFPRLLDRVDLRPQVIGAQEIVGDPQPAGRIAF |
| Ga0213895_100454 | Ga0213895_1004542 | F081517 | MHPILIADVPSMDARYWAALAGWSLAFTRTMEEARATLAAQRCAAVVIGVYFDDSQMFDLVRAIRADDFQNEVPIVCVRGTPSYTAVSTSTLETALRVLAADAFVDLLHFAQEQSGDAALRATVQRYLKG |
| Ga0213895_100609 | Ga0213895_1006091 | F012081 | MSNMRGIRFWKNWGLVSRLMLAVGIAIITGGGVQTALLVAEGAAEHSARLKRELNETLTFMAPLIADQALVGEYAVIS |
| Ga0213895_100804 | Ga0213895_1008041 | F044764 | MFSAWDFNSWFFSVGTVLFMLGFLTGFSALASVLMSRMWGDACDDAATVRLCRRTKEVPIRHVP |
| Ga0213895_100828 | Ga0213895_1008281 | F013740 | VRFSLLALIAALPGCAAPSLAPESSVAVVWNRVEEPHAVCESLSGRKNFFNVLGCSHWSAPAAEGGARVCSIYAPAPRSERDLQRFATLGHELMHCFDGNWHDRWGRMNPSTQSAAAGGS |
| Ga0213895_100836 | Ga0213895_1008362 | F077001 | MKKFWLAALLSACSTPQWEKAGAAPDDVALDLKQCEAAAPLAPRAAPGPRSKPGSNVIDFDSASERSFERMRKDDEHIAACMRAKGYSR |
| Ga0213895_101360 | Ga0213895_1013601 | F092317 | PQVPYWAMPLWLSIPIVAALWVSSWISGLDLTTGDRAETYIMWGVTAIASALLLRRLVRA |
| Ga0213895_101495 | Ga0213895_1014952 | F062538 | MRYDFTYIQALQSRARRERSEAIYEMLIAPLVALFTRRPARKELQHAPRPHFAR |
| Ga0213895_101835 | Ga0213895_1018352 | F103522 | MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWLLPTGTDFGFRHVAAVSVLFGLAAAGLFHL |
| Ga0213895_102926 | Ga0213895_1029261 | F040166 | MSLHRLVCLAAALLSGCSMHSNWYLMDSGYSINPVDGDAQAYAVEVHVNQLKQLGGDVNSAEARLFIAERLKWHGVCPAGWQPLPCVQDGSCVQRTRRSVTVPGRCVTP |
| Ga0213895_103284 | Ga0213895_1032842 | F038633 | QLMADQVGKGLESMVTRKLLTATAVGLSVGLLAQHATGAETPTVQKAPVAEEFTVDAELFRNEIADYVRELNRQMRTTLNEELRRELAPKVVASNELRTRS |
| Ga0213895_104014 | Ga0213895_1040141 | F032460 | MAVHVVFGPPLEAPMRSEEAKPLQVAAQAAAKWCMQKLDMKEGGFGKNHEHSESERAALHVAHSIAACEVARLQSIVDGR |
| Ga0213895_104875 | Ga0213895_1048751 | F085328 | VTTYSIEPNLFSEPKTMNDPLPASPDPAVHKAQLARMLLAAARSHIHAVPERAADCTAIYTLADPRDVRCPRYVGQTRDPRRRFAQHLHTARLWLPDSTPWWVRSPKYRPLYDWIRALYRDGGRLPFMWVAEWAEPGTDALAAERAAIMRLLAQRAELLNVEARLLGAQLPLL |
| Ga0213895_105700 | Ga0213895_1057001 | F069810 | DWRRRPAPLSEVLERAGIGLALRILLLLSVLLALGACQVQDPTARGTVLSVQEAKQALPEDLLKFDDGNLRLPEVAWHVEVQLDDGSQVSTLHTGGRRYAPGERVRLLIDADGALLL |
| Ga0213895_106069 | Ga0213895_1060692 | F030799 | SGYPENDYICVHTDADPLDDTVVLATIERVTDRTKGKVKRVKTLLARVRMSIDAALGLATSYAEWKQVPVVYADSPPRHTL |
| Ga0213895_106150 | Ga0213895_1061501 | F042599 | MHPLSRPVRFIIGLCVVIIGLNVFMLWWLQKLTPTTVPQVEHTPIRVEPPPAVAPCEPIVAGNEGEIAERDTMIARLEAEVERMKRAHDDDRSAWRTKAEQIEKDLMMLEKAAERVLRMDAQHWHEG |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |