| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021302 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225712 | Ga0210328 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.270 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 107783936 |
| Sequencing Scaffolds | 15 |
| Novel Protein Genes | 16 |
| Associated Families | 16 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Eukaryota | 1 |
| Not Available | 9 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 3 |
| 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) | 46.27 | Long. (o) | -123.946 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F011154 | Metagenome / Metatranscriptome | 294 | Y |
| F012917 | Metagenome / Metatranscriptome | 276 | Y |
| F014821 | Metagenome / Metatranscriptome | 259 | Y |
| F030135 | Metagenome / Metatranscriptome | 186 | Y |
| F038650 | Metagenome / Metatranscriptome | 165 | Y |
| F038934 | Metagenome / Metatranscriptome | 164 | Y |
| F043774 | Metagenome / Metatranscriptome | 155 | Y |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F046120 | Metagenome / Metatranscriptome | 151 | Y |
| F060086 | Metagenome / Metatranscriptome | 133 | Y |
| F062310 | Metagenome / Metatranscriptome | 130 | Y |
| F067276 | Metagenome / Metatranscriptome | 125 | Y |
| F074319 | Metagenome / Metatranscriptome | 119 | Y |
| F084255 | Metagenome / Metatranscriptome | 112 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210328_1002795 | All Organisms → cellular organisms → Eukaryota | 645 | Open in IMG/M |
| Ga0210328_1035272 | Not Available | 594 | Open in IMG/M |
| Ga0210328_1036797 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 554 | Open in IMG/M |
| Ga0210328_1046169 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 757 | Open in IMG/M |
| Ga0210328_1047594 | Not Available | 520 | Open in IMG/M |
| Ga0210328_1073976 | Not Available | 627 | Open in IMG/M |
| Ga0210328_1074553 | Not Available | 762 | Open in IMG/M |
| Ga0210328_1076280 | Not Available | 896 | Open in IMG/M |
| Ga0210328_1076465 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 571 | Open in IMG/M |
| Ga0210328_1099213 | Not Available | 606 | Open in IMG/M |
| Ga0210328_1101040 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 620 | Open in IMG/M |
| Ga0210328_1117087 | Not Available | 670 | Open in IMG/M |
| Ga0210328_1200464 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 798 | Open in IMG/M |
| Ga0210328_1216693 | Not Available | 633 | Open in IMG/M |
| Ga0210328_1226229 | Not Available | 552 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210328_1002795 | Ga0210328_10027951 | F062310 | MSGLRKKLNSLDTELGLMEMVLAGIKSALTRQPFSVSQDLRNLAAAQEAIGWTNLFKGRISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGCANKLKDVAFREMTHLYTFEEAVPGDIRWLFQTPLEECLHWPLFRQRAW |
| Ga0210328_1035272 | Ga0210328_10352722 | F012917 | DKILNGMILFKFLRFPLNDCGYYEKYESFSDINRNWDKKKHLKRKRWSQE |
| Ga0210328_1036797 | Ga0210328_10367972 | F084255 | MESSRRYLLQAEIEYWHEMLKLNKNRVSRNRQEEMRNCLKQAVRALNSNMAPDFRVAA |
| Ga0210328_1046169 | Ga0210328_10461691 | F044534 | SRVTGEWIATAGVAFPSERRKSPRGIYHQFLWPESCPVSSHTNQELSGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP |
| Ga0210328_1046169 | Ga0210328_10461692 | F000344 | MRPIHPHAAESGVGKHTARESESAKACAIGKERVANAH |
| Ga0210328_1047594 | Ga0210328_10475941 | F011154 | IESSRPGRFRAWANRSYPEGIRLLLCISTGGRLWRPPEGGLPNERRRKAGQSERPNREGHAASAGPVKTFQAVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS |
| Ga0210328_1073976 | Ga0210328_10739761 | F046120 | LKELRNKKVDTFTMILTREPRPSKSMTRRAYDELELPDFDLDENLGEDYFATKGDLEGNSSMTNSHETNAFGTDYVPKIGTKIYKDFGTKGFFAGTITSGPHTRTKDGDDVTTWKVQYADGDREDMTASEIAYWKAPTEEVHTSTTGAKSKKPKKTIATKPSGDRSEELEDAIPTPGRDASAPTHLRRSTCLQQHALETARMNFLDSN |
| Ga0210328_1074553 | Ga0210328_10745531 | F030135 | RVELATLSTNTGIWHSTFVGCQFPDAILPGEEAIDLVAGPLNQLPDQVIE |
| Ga0210328_1076280 | Ga0210328_10762801 | F067276 | AESSVSSRDLPDLEYGASSVDSDLDDDRTISTVATDTDASSLFDLLHDDPEFDSLRLNSVVVSRVPDEVITIDDLEEDEWTDEESIKDKAYKNVQELKISEVATGSILTANRYEAHLGGGSQASTTNDKAVLWGFKWYTNKNPCRIRLICADGKTPIVPEGYGTVRIPADNAEGYVPIKCYYTPDIPNFILSPNSFKALLGKHYNGYKLECDDDKKNFRFSLNHKMRKSGLVLLRGTTRGGLCYTRPAVPPMPTTEGTAEMSLDMADRTAISMVEDQPENSYRHEVKLHALSAKAERL |
| Ga0210328_1076465 | Ga0210328_10764651 | F038934 | SSRHRAKIMEAVRDMKEKAHKDPAYIKFRCLVNNSFEEVVAYNDLVDHIKKDTTWDGVWTFEKILSHEKVRAGDKDHRGSGTNCLVLWSTGEQTWEPLHDRSGKTGLWIDDPVMVAMYARDNGLLDEPGWKLPGLKKMAKTQKKLIRMANKAKLHSFRSKPIYMYGFQVPHNHAEALELDRVNGNTM |
| Ga0210328_1099213 | Ga0210328_10992131 | F038650 | TNRGNSYKLLHGITSTTYGIWDAIRLTAGTDTPDANQPTESDIWDLIQKVSGISGKDAMLRPQEFMLMTTPGVGKKLMESFVGQRRFDAKDTARVIKGGYKAVEVCGLPLVMDYYVPAGTIYLIHIPSLALVDAKDWGFVEYEGAGPVRWLDGRDAFEMTYGYYGNLAALQRNSHGSIVGYTDTVFYSHAAVQTA |
| Ga0210328_1101040 | Ga0210328_11010401 | F074319 | SAVRYPHLDFSEASISTEEMEMVVQAIQSQAITPAEQAIGRFTRRKLRSLSTWDQWRAGEHKQLDHFHDLKMYGEPVRKPPGAIVLRPHWQYSIKRDGTRRSRNCCDGSPRSAPLLHGIASTYSSCVEQPVQRLFFALAARENYRVYAGDAQDAYAHSPPPETPTFVSIDDAYADWYEHQFKKKLDRSLVLPVLHALQGHPESGKL |
| Ga0210328_1117087 | Ga0210328_11170871 | F060086 | GQEDPFELDSNLLLSSGRHGEDRKRQYLYDHETPLLDDLADLLY |
| Ga0210328_1200464 | Ga0210328_12004642 | F014821 | RIHLCDDDPYKELLHNVDEVETLLQDPVVLTAIHRLLDPDADLDELRVNALQSEAISPEERALPRFSRRALKRLPTWDLWHKNEAERLDQMKALGMFGAPIKLPEGGILMRFHWQYRIKVNGKRRSRLCCDGSPRAAPEVHSTTNTYASCLEHPIF |
| Ga0210328_1216693 | Ga0210328_12166932 | F006508 | VALANASSKAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPHSKFSAVRRWTA |
| Ga0210328_1226229 | Ga0210328_12262291 | F043774 | MFDSNCSITAELLAGAQALSLADRHHFELNLSDLLDKSMQYKRNWLLNVIAARQRFERQQANFEGNQSLSIANSKLIKWMTTGRAS |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |