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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 | 3300004586 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114290 | Gp0111155 | Ga0066491 |
| Sample Name | Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metatranscriptome 3_LOW4 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 39926473 |
| Sequencing Scaffolds | 11 |
| Novel Protein Genes | 12 |
| Associated Families | 10 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 6 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 2 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces → unclassified Streptomyces → Streptomyces sp. CNQ329 | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Freshwater → Sediment → Unclassified → Freshwater Sediment → Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | freshwater lake biome → freshwater lake → lake sediment |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Sediment (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Lake Washington, Seattle, Washington | |||||||
| Coordinates | Lat. (o) | 48.3807 | Long. (o) | -122.1599 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001233 | Metagenome / Metatranscriptome | 741 | Y |
| F001633 | Metagenome / Metatranscriptome | 660 | Y |
| F003427 | Metagenome / Metatranscriptome | 487 | Y |
| F004925 | Metagenome / Metatranscriptome | 418 | Y |
| F014145 | Metagenome / Metatranscriptome | 265 | Y |
| F014854 | Metagenome / Metatranscriptome | 259 | Y |
| F019442 | Metagenome / Metatranscriptome | 229 | Y |
| F042356 | Metagenome / Metatranscriptome | 158 | Y |
| F053640 | Metagenome / Metatranscriptome | 141 | Y |
| F082737 | Metagenome / Metatranscriptome | 113 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0066491_1002284 | Not Available | 765 | Open in IMG/M |
| Ga0066491_1009675 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 746 | Open in IMG/M |
| Ga0066491_1009944 | Not Available | 734 | Open in IMG/M |
| Ga0066491_1015270 | Not Available | 598 | Open in IMG/M |
| Ga0066491_1015474 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 788 | Open in IMG/M |
| Ga0066491_1022330 | Not Available | 517 | Open in IMG/M |
| Ga0066491_1025054 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 795 | Open in IMG/M |
| Ga0066491_1096128 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 717 | Open in IMG/M |
| Ga0066491_1097016 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces → unclassified Streptomyces → Streptomyces sp. CNQ329 | 556 | Open in IMG/M |
| Ga0066491_1098827 | Not Available | 506 | Open in IMG/M |
| Ga0066491_1102539 | Not Available | 751 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0066491_1002284 | Ga0066491_10022841 | F003427 | MVETRISNHKRVSTWFAGRRPQTPAEASLEASLEILRPQGAGRPCYEAEGTPLAVENSVGKPAACEAPNVGTGKRAWR |
| Ga0066491_1009675 | Ga0066491_10096751 | F053640 | LKNVAESTAGIIPGDRGMEGDSWCCPPLQAAQAVERHISPVPLAGVVSGQFTHESGTERQGAIRNRVEPSQAHGRFRPVCRRSYPRGFWLLLRRPERSHGSRRANPAKRPHSQHEGGAQGSRDGGERADLAKSVKPPQGGGVKNHVTPLQKRKQP* |
| Ga0066491_1009944 | Ga0066491_10099441 | F042356 | VYQHGAGDSGGFNKPFETAKRKTPKGGQKERTAREGHGDEAGPVKTFQEPAMLKTTPLACERKAT*E*RGETRGAG* |
| Ga0066491_1015270 | Ga0066491_10152701 | F014854 | RWTAVIERMSQVVSRIIPGNWGKVGPGWLARPLLNRIARFGSGGRIHQFLWSRSHAVSHAKRNLAARGDKKPLRVGSSSSGKFRAWANRSYPEGKWLLLCIGTGRVTLAGSINRLKPPNESHRKVDKGSTRTGKITQTGQVA* |
| Ga0066491_1015474 | Ga0066491_10154741 | F001633 | VRHALFPGGTRLGALAFAGGVLPDATLRGMRMSRSHGGTVLTVAGRDLSSEASAPGSVAPCRERHAGRGADTPATFIISRLHRYHGDSTSFWLAVCPALRV* |
| Ga0066491_1022330 | Ga0066491_10223301 | F014145 | GSLPACTASSTANKSAGRFASPLPVGRFLQPPDQCFLARRWPPLARNRSLVTAFRSPATATASRRPPFRGQSSQPATSLPSKFASVPVRPFGSTTASRFAPVAAVSLPLARCTSTTRFSLPRLRSPLPSGTFTSLGIKAFNRVCRLPVHLTNPPDFLSLPAARPDESWGCGS |
| Ga0066491_1025054 | Ga0066491_10250542 | F001633 | LFPGGTRLGALAFAGGVLPDATLRGMRMFRSHGGTVLTVTGRDLLSEASSPGSDAPCRERRAGRGADTPAIFIVSRLHPYHGDGTSFWPAVGPALRV* |
| Ga0066491_1031849 | Ga0066491_10318492 | F001633 | RHALFPGGTRLGALAFAGCVLPDATLRGRRMFRSHGGTVLTVAGRDLLSEASSPSSVAPAGSGTPDVVRTRLQSYFASARYHGDGASLWLAVGPALRV* |
| Ga0066491_1096128 | Ga0066491_10961282 | F001233 | LNVSRIIPGDWGKVGPGWLAQPLSSRSARSGSGGRIHQFLWRRSRAVSKREKGTER* |
| Ga0066491_1097016 | Ga0066491_10970161 | F019442 | SPPACTVLSIANRSAERFASWLPDNRFWAITGSKPPGASQTFSCSGSDARDDLSLARNDFRFHGRHSGVKAPGLPLRFPASRFLCPFDLSAQLPKPVRPVSGRFLASGPLQFQRPARPTAPPAPTPRRESYLPLDQSVQLDLRSINPPSESARFPLAPRSRFLSLVFQLRIIVPGPLRFRRLAV |
| Ga0066491_1098827 | Ga0066491_10988271 | F082737 | APQPACQV*ARHIQHAGRCPRLAPRPRSFTRSASLLGDTPASLLVRSQNFEAAFHSPTTTSLLPDLRGGVKVPALPLQLCGTLPVCPVRSDLHPRPVSRTAWDFHDQNPLPSGPAPLLPASLNRCSPSGFFALPDQSTRSNRPTGNLLPDTPDLPSLPTGGRIRYQHQ |
| Ga0066491_1102539 | Ga0066491_11025391 | F004925 | EIIPGDWGKAVPGWWARLLGNRAERRGGGGRIHQFLWRRSRAVSNAKKELGGEGR* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |