| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021848 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225752 | Ga0210368 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.667 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 31700259 |
| Sequencing Scaffolds | 11 |
| Novel Protein Genes | 15 |
| Associated Families | 14 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Amphiprora → Amphiprora paludosa | 1 |
| All Organisms → cellular organisms → Eukaryota | 1 |
| Not Available | 5 |
| 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 → Viruses → Predicted Viral | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Fragilariophyceae → Fragilariophycidae → Rhabdonematales → Grammatophoraceae → Grammatophora → Grammatophora oceanica | 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) | 46.302 | Long. (o) | -123.036 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F007629 | Metagenome / Metatranscriptome | 347 | Y |
| F022655 | Metagenome / Metatranscriptome | 213 | N |
| F024006 | Metagenome / Metatranscriptome | 207 | Y |
| F033314 | Metagenome / Metatranscriptome | 177 | Y |
| F038082 | Metagenome / Metatranscriptome | 166 | Y |
| F042669 | Metagenome / Metatranscriptome | 157 | Y |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F046120 | Metagenome / Metatranscriptome | 151 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F054544 | Metagenome / Metatranscriptome | 139 | Y |
| F056298 | Metagenome / Metatranscriptome | 137 | Y |
| F094641 | Metagenome / Metatranscriptome | 105 | Y |
| F106082 | Metagenome / Metatranscriptome | 100 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210368_109781 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Amphiprora → Amphiprora paludosa | 652 | Open in IMG/M |
| Ga0210368_119052 | All Organisms → cellular organisms → Eukaryota | 740 | Open in IMG/M |
| Ga0210368_132169 | Not Available | 882 | Open in IMG/M |
| Ga0210368_133377 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 826 | Open in IMG/M |
| Ga0210368_136425 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 550 | Open in IMG/M |
| Ga0210368_154768 | Not Available | 679 | Open in IMG/M |
| Ga0210368_161254 | Not Available | 812 | Open in IMG/M |
| Ga0210368_165630 | Not Available | 532 | Open in IMG/M |
| Ga0210368_166083 | All Organisms → Viruses → Predicted Viral | 1575 | Open in IMG/M |
| Ga0210368_167051 | Not Available | 554 | Open in IMG/M |
| Ga0210368_168363 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Fragilariophyceae → Fragilariophycidae → Rhabdonematales → Grammatophoraceae → Grammatophora → Grammatophora oceanica | 504 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210368_109781 | Ga0210368_1097812 | F033314 | MSAGTVDFVVGVDKKLWIGSGLFKNCKSFFGAKGAVFGSECFDHTDWIALPEDAAGYSAALISWGWVGVIELGCEMFGVGVRFLALID |
| Ga0210368_112943 | Ga0210368_1129431 | F024006 | ISSGQVIIVIRRYWWHSSLGTGCITSCGYVLQPNIQEREFGRYAPTLEDLDPAKIRNWYMDMVRVAHDFGIFLPAYEDYRPEETFSTIECGDTRTARLPSFCRSQIPRWQAIIHHHLKRDKVIPSSHPQFNEIRHNPNGYEALMLLLAPYHPAFTDNGILIQAHPRQGR |
| Ga0210368_119052 | Ga0210368_1190521 | F054544 | LDPMRITHVYDNGTVRLVKVANNGGAVSQTWNIRNIEPRKA |
| Ga0210368_125779 | Ga0210368_1257791 | F038082 | KAFAYIMHDYCTDGLKTRLVALPDFTTSIQDDPLALLKAIKTCVHENAVTQYPPVTIQQHWSRLLQLKQSSDEDPPTYAKRFEQQLETVKGYVGNTFTDGFAEHMPDYKANAYKHDSGKITALLATHVTDDAARQALATDLHDLFSHYKPKETQAQLDLKAQVRSEFEAYLFLRSASKAK |
| Ga0210368_132169 | Ga0210368_1321692 | F046726 | LGKISEEEKIEIIQRGFQLQAEGKISLKKYYESTDSNSLFQSKGYSIKYESIRRTKLYQKLKEIFT |
| Ga0210368_133377 | Ga0210368_1333771 | F042669 | VGFKNTTHEKNIYTGTFCGEKVLLVRQVDDFALGCRQESTAKSVYATIGAKLTLHNEAEAPFEYLGLVDSFDGYDVLQTRDYIKLSAESYIRRLLKAHGWENPSPRESSNKPKPPLHESDVANLFNLAAGPVENTPEHKALEAEHGFGYRSVLGEILFAYVLCRPDIGFAVTTLAKFSTAANAL |
| Ga0210368_136425 | Ga0210368_1364251 | F044534 | VAFPSERRKSPRGIYHQFLWPESCPVSSHTNQELSGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP |
| Ga0210368_142072 | Ga0210368_1420721 | F007629 | VGAKWLGQKAHPHRRRFTKPNQGSNVKQKDVAELVSKLDAKYNVKVTAQGKGQKNDHVLIEGSDNGSISPVIQAGNQGSRPENTVRPKGKDTNPRTEQSKGIKK |
| Ga0210368_143943 | Ga0210368_1439431 | F056298 | VCLAANMKSRNRGDGETRTATKPGQGLSLDFSFAGQHSKNATDPKKMRINDYMGIHGETCYLLLYDHATERLDGVCRQLKAPPLAWLKRWLKKNVKDEVKDRYVYMDQGEELYRSKAIRDLFEKEFGYKIRVTGAGAHHQNGLVERGNQTMDKAIRAMLIGAGLP |
| Ga0210368_154768 | Ga0210368_1547681 | F045132 | VLMHSSNHYPLGNCDSPESETNPGYLTQFRAASNRPWLPSSFFAFTGRARTPPEELVNTASAAKCVSTSPLRGLINQPDLTFP |
| Ga0210368_161254 | Ga0210368_1612543 | F046726 | LSKISEEDKIEIIQTGFRLNQEGKITLKKCSESTAEYSLFQLKGYSIKYKSIRR |
| Ga0210368_165630 | Ga0210368_1656301 | F022655 | MTMKTMMTNEEAAKQLFGHLVDTCESCKQKLGVWTENPFDADVRNEHNMMFLCKECFHELQMDV |
| Ga0210368_166083 | Ga0210368_1660832 | F106082 | MGSIRNNDGEVVVGRGAELTNLQEQFIERIREEGINAQGKVAKELNYTSYYRDKNNPGTAFYLALRDVVRLSEERIEVAKGSNLDMLVKMRDEAFINGDTKVALETIKIINDMQGYKAPVKVQQTKIDVKATIDLTKSPDENEQLYIDVDYED |
| Ga0210368_167051 | Ga0210368_1670511 | F046120 | ELRNKNVDTFTMILAREPRPSKSMTRRAYDELELPEFDLDENLGEDYFASDGNLEGDSSMTASGETNAFGTDYAPPIGTKISKDFGTKGFFTGIVTSGPHIRDKDGDDVTVWKVQYEDGDREDMTASEIAHWKMPTEEVHTSQTKAKSKKPKQTMATKPSGDRSEELEDAIPKPGRDASAPTHV |
| Ga0210368_168363 | Ga0210368_1683631 | F094641 | LMQALHIAKVIMEMRNGASEHGVSFSQNCICQKGVKKFGERGRKAAGKELDQLHQRNCYTPIDVSAMTPEEKAQAMEALMFPQEKKDGTVKGRMVYNGKPTREWLSREDSASPTAALESIFLTSIIDAKEERDVMSADVPNAFIQTPMPDDNKKVIMKITGVLVHLM |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |