| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021278 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225716 | Ga0210332 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.302 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 34715935 |
| Sequencing Scaffolds | 15 |
| Novel Protein Genes | 17 |
| Associated Families | 16 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 10 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Crustacea → Multicrustacea → Hexanauplia → Copepoda → Neocopepoda | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | estuarine biome → estuary → sediment |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Washington | |||||||
| Coordinates | Lat. (o) | 46.313 | Long. (o) | -123.997 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000237 | Metagenome / Metatranscriptome | 1498 | Y |
| F002557 | Metagenome / Metatranscriptome | 548 | Y |
| F004323 | Metagenome / Metatranscriptome | 443 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F014031 | Metagenome / Metatranscriptome | 266 | Y |
| F017072 | Metagenome / Metatranscriptome | 243 | Y |
| F023281 | Metagenome / Metatranscriptome | 210 | Y |
| F034200 | Metagenome / Metatranscriptome | 175 | Y |
| F037756 | Metagenome / Metatranscriptome | 167 | Y |
| F042355 | Metagenome / Metatranscriptome | 158 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F053305 | Metagenome / Metatranscriptome | 141 | Y |
| F060086 | Metagenome / Metatranscriptome | 133 | Y |
| F075465 | Metagenome / Metatranscriptome | 119 | Y |
| F089490 | Metagenome / Metatranscriptome | 109 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210332_117227 | Not Available | 609 | Open in IMG/M |
| Ga0210332_118651 | Not Available | 690 | Open in IMG/M |
| Ga0210332_120905 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 716 | Open in IMG/M |
| Ga0210332_123224 | Not Available | 766 | Open in IMG/M |
| Ga0210332_125491 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 761 | Open in IMG/M |
| Ga0210332_131321 | Not Available | 559 | Open in IMG/M |
| Ga0210332_131606 | All Organisms → cellular organisms → Bacteria | 840 | Open in IMG/M |
| Ga0210332_136718 | Not Available | 647 | Open in IMG/M |
| Ga0210332_140134 | Not Available | 519 | Open in IMG/M |
| Ga0210332_145697 | Not Available | 619 | Open in IMG/M |
| Ga0210332_150774 | Not Available | 694 | Open in IMG/M |
| Ga0210332_159113 | Not Available | 786 | Open in IMG/M |
| Ga0210332_164666 | Not Available | 657 | Open in IMG/M |
| Ga0210332_168319 | All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Crustacea → Multicrustacea → Hexanauplia → Copepoda → Neocopepoda | 648 | Open in IMG/M |
| Ga0210332_174174 | All Organisms → cellular organisms → Bacteria | 550 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210332_117227 | Ga0210332_1172271 | F060086 | NLLLSSGRHGEDRKRQYLYDHETPLLDDLADLLYLALPLLLLFK |
| Ga0210332_118651 | Ga0210332_1186511 | F017072 | MRMRDLAVGSDEKPLRTESSSPEKFRFRMNRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKRRDPWFRANAPSKAVADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS |
| Ga0210332_120048 | Ga0210332_1200481 | F046726 | LPPSEQPNFITLGNISEEEKIEIIQRGFQLQKEGRISLKNYYETRDQDSLFQWKGYSIKYESIRRTKLYRHLKP |
| Ga0210332_120905 | Ga0210332_1209051 | F075465 | AANLESHQGKAYSLILRQCTRLLQDRMKQDADWLTVSTRYNPLSLYRLIEKTVLAQTEDQYPFATVYDQEHAFYLFRQETMTNPQMYEKFNTRVDVGEAIGVTCQHKVLLEFVAQENHTKAFVALGAAEQEAVRVDAQEGYQSYAFLRQSRAQHGHLKQSLQNDFTTGDNHYPKTHQQTLHLLDKFSKTVVPKAVVSEGTAFAQDDGGSDETPFDKEYWKDKKCFNCHKKGHPASHCK |
| Ga0210332_123224 | Ga0210332_1232241 | F053305 | MLKKSLSIVLTALFVLSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKSLMADPKAVDLKMLKEGDMVSVES |
| Ga0210332_125491 | Ga0210332_1254911 | F004323 | MPLGDLRRSEGKATPAVAIHSPVTRDYPSRALSNVFQAAALRL |
| Ga0210332_128393 | Ga0210332_1283931 | F000237 | ISLSATHLSDITLTIVANIFWSLFNNVYKTYYIIFTNKHLNTDQLTRFMILHYFTPXYYLYLVKLHVMFCHESWDTDSGENTYEDKSGSYVSXFYDAFLKEIQDAXYWTIFIFSYFFMHHFDGGTVNYFFFERXNISELDEIRFYGVAPHXYFRPFMGILTISPTHYEGLMXFALXLVLLAFLPVINTFYNPYNRYQSVIPTQNSXLQSAFFMVFMMSLYCASSMLPCGRYYYEPEGGYVGNPXVKFSYQYGYIYLMXTIHHLDALDHXIFNFTQNLKRRYTQNLRVKRTRFWY |
| Ga0210332_131321 | Ga0210332_1313211 | F002557 | VLMHSSNHYPLGNCDSPGSETNLDYLTQFGTVSNRSSLPRSFFAFTDGARTPPAELVNSASFAKC |
| Ga0210332_131606 | Ga0210332_1316061 | F042355 | MTSDLKKINKKPNFRRKQNIQEPKLVERLIKISRV |
| Ga0210332_136718 | Ga0210332_1367181 | F006508 | VAVVNAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSKSSV |
| Ga0210332_140134 | Ga0210332_1401342 | F089490 | MYRLMKSEKFTLDDAVSGLVSSYRQTEIGHFEKFRAAHHACEVANNDGWSRCYVINESGQEYYGHTWID |
| Ga0210332_145697 | Ga0210332_1456971 | F034200 | VALGQRTATRGGRPSANGKEAEMKSQTCLYLVRKPA |
| Ga0210332_150774 | Ga0210332_1507741 | F045132 | VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSNRSSLPSSFFAFTDGARTPPEELVNSASSAKCLSPSLKRGLVNQPDLTFP |
| Ga0210332_159113 | Ga0210332_1591131 | F037756 | PVPTLGAHLAVAAGFPTLFSTASGVFGLVAGPSSVSRR |
| Ga0210332_164666 | Ga0210332_1646662 | F046726 | LGKISEQERLEIIQTGFQRQAEGKISLKKYYESTDPDSLFQWKGYSIKYETIRRTKLYQSLKD |
| Ga0210332_168319 | Ga0210332_1683191 | F023281 | DEYLDANSRSESTKNCEEFFQCPYSIKESFKRNLSGNSL |
| Ga0210332_174174 | Ga0210332_1741741 | F014031 | MRRHRGRVGLMAVAIMGVLVSGASADIVTERSASVLVFPKVIANGTRDTLIQITNTSNSMVHAHCFYVNAAPTFRDLPPDPVLNPPLWQEIDFDIWLTKQQPTYWRVSTGRQDNYIEGIDDACSFDPRNLD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |