| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021322 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225714 | Ga0210330 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.298 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 142286757 |
| Sequencing Scaffolds | 25 |
| Novel Protein Genes | 27 |
| Associated Families | 27 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 7 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 3 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Desulfobia → Candidatus Desulfobia pelagia | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 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) | 46.286 | Long. (o) | -124.052 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001314 | Metagenome / Metatranscriptome | 725 | Y |
| F006082 | Metagenome / Metatranscriptome | 382 | Y |
| F016165 | Metagenome / Metatranscriptome | 249 | Y |
| F016664 | Metagenome / Metatranscriptome | 245 | Y |
| F020930 | Metagenome / Metatranscriptome | 221 | Y |
| F033058 | Metagenome / Metatranscriptome | 178 | Y |
| F049002 | Metagenome / Metatranscriptome | 147 | Y |
| F052020 | Metagenome / Metatranscriptome | 143 | Y |
| F053923 | Metagenome / Metatranscriptome | 140 | Y |
| F054044 | Metagenome / Metatranscriptome | 140 | Y |
| F055829 | Metagenome / Metatranscriptome | 138 | Y |
| F058634 | Metagenome / Metatranscriptome | 134 | Y |
| F059103 | Metagenome / Metatranscriptome | 134 | Y |
| F059980 | Metagenome / Metatranscriptome | 133 | Y |
| F065171 | Metagenome / Metatranscriptome | 128 | Y |
| F069124 | Metagenome / Metatranscriptome | 124 | Y |
| F070130 | Metagenome / Metatranscriptome | 123 | Y |
| F072362 | Metagenome / Metatranscriptome | 121 | Y |
| F074834 | Metagenome / Metatranscriptome | 119 | Y |
| F074892 | Metagenome / Metatranscriptome | 119 | Y |
| F077315 | Metagenome / Metatranscriptome | 117 | Y |
| F077370 | Metatranscriptome | 117 | Y |
| F079376 | Metagenome / Metatranscriptome | 116 | Y |
| F088148 | Metagenome / Metatranscriptome | 109 | Y |
| F090573 | Metagenome / Metatranscriptome | 108 | Y |
| F095879 | Metagenome / Metatranscriptome | 105 | Y |
| F102756 | Metagenome / Metatranscriptome | 101 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210330_1008403 | Not Available | 629 | Open in IMG/M |
| Ga0210330_1010167 | Not Available | 521 | Open in IMG/M |
| Ga0210330_1023925 | Not Available | 915 | Open in IMG/M |
| Ga0210330_1041037 | Not Available | 583 | Open in IMG/M |
| Ga0210330_1083134 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 678 | Open in IMG/M |
| Ga0210330_1094721 | All Organisms → cellular organisms → Bacteria | 2339 | Open in IMG/M |
| Ga0210330_1107435 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 811 | Open in IMG/M |
| Ga0210330_1118722 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1272 | Open in IMG/M |
| Ga0210330_1131167 | All Organisms → cellular organisms → Bacteria | 505 | Open in IMG/M |
| Ga0210330_1155126 | All Organisms → cellular organisms → Bacteria | 603 | Open in IMG/M |
| Ga0210330_1159566 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 964 | Open in IMG/M |
| Ga0210330_1167914 | Not Available | 720 | Open in IMG/M |
| Ga0210330_1182491 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Desulfobia → Candidatus Desulfobia pelagia | 890 | Open in IMG/M |
| Ga0210330_1186486 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 574 | Open in IMG/M |
| Ga0210330_1187516 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 790 | Open in IMG/M |
| Ga0210330_1197039 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 663 | Open in IMG/M |
| Ga0210330_1240444 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 600 | Open in IMG/M |
| Ga0210330_1251368 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 786 | Open in IMG/M |
| Ga0210330_1256478 | Not Available | 522 | Open in IMG/M |
| Ga0210330_1257083 | Not Available | 510 | Open in IMG/M |
| Ga0210330_1264003 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 660 | Open in IMG/M |
| Ga0210330_1274247 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 698 | Open in IMG/M |
| Ga0210330_1284191 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 572 | Open in IMG/M |
| Ga0210330_1288895 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 754 | Open in IMG/M |
| Ga0210330_1327546 | All Organisms → cellular organisms → Bacteria | 567 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210330_1008403 | Ga0210330_10084031 | F053923 | GDPPHASSVVNVLARAGQATLTGRSIKRTLQLRYAAHTIWNRGTCGCRAGADSAKAEPARKTLLCALAGATGVRATAWGEGTGRVNWGPSAVGGLDPQPDGIIHKPFGGRQRRRCGHSKRRSGRTTQPAGEPRATGLAVLVRSSRCRLVARPTTDKTPGMEIRTVAAYKRAGGRPRRWPRGQAGLKPYWGKPTVRNFRGGGGNEVQGLM |
| Ga0210330_1010167 | Ga0210330_10101672 | F072362 | EYEMHRLFAIGFLVYLVGDPSLSMLASFSETRELIIASALALIAVPWVVSQIDN |
| Ga0210330_1023925 | Ga0210330_10239252 | F095879 | PHYHPGTTVLGVVSGSFGWTLKAGKAHVVRGAGAGATGPVEDVTEPGTDVVLNAGDAIYYESDVVHTARGAGDTEAVILGSLVLKTGAPLLIRVDM |
| Ga0210330_1041037 | Ga0210330_10410371 | F077370 | GKTNDRAIDILVNIFAVNSLGTPFYSFSTSAGSPQLSSNLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNFIGGGTTILQNTPSIFLQASTIPYSTGSVVLQRAIAQSDNSIELDLQTYDPKSYEIFLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNLPDLFLNLGSLATPTFDPSTTSGNSVLI |
| Ga0210330_1083134 | Ga0210330_10831341 | F058634 | MRHLSAVTATLILALGLSGCSSDQTQGVEGVGNVGMEVTLATPPAGPNEQIDTVDVSFYCDGIDPVLGVPRPPQSSPEEFTINTSTSQGPEPKNTIGLFEKQGLPAGNCYFSFTAASNTGNTQCTGELTVAVVTNETTEGTVVLACIHTPRYGGVRGDGTFNQCAEYRQIL |
| Ga0210330_1094721 | Ga0210330_10947212 | F069124 | MGGWRFMEKWFCGSGFVAARDARRCSGFARTAIADSAIAVRLAAEKPGGGNTVLPTGGIRGVRKAGSIIGTGNVLTVSATRQPA |
| Ga0210330_1107435 | Ga0210330_11074351 | F059980 | DFDIKSLHLMEEACSIGFSGGCEQGKPETALPELRRVIPVNEKRVNPQNKFCCS |
| Ga0210330_1118722 | Ga0210330_11187221 | F102756 | LTPPASPAPPLHRLHDEEVERLLASGEHRRELIALFGEAGYRELSGLARRAAAVRRRGVAVYVLPGLMGSRIGARGRLVDDVI |
| Ga0210330_1131167 | Ga0210330_11311672 | F074834 | VDDNRRALDDAALNAIRDQVRSTAAALREVHIEPGSPRAQALFGG |
| Ga0210330_1155126 | Ga0210330_11551262 | F088148 | DAAHTTKANARQLTQGNGADYLLILKANQPTAWAKAQQLLPGAIPPSGPDDRQGPRAG |
| Ga0210330_1159566 | Ga0210330_11595662 | F049002 | MAKTDLDEAQTELTRAIQKDAPCTFDEPIPVLVTLDNGVKYEGVAFEVQPKSTNFPRGLVMVRTGNTDIGVPVNYIRGR |
| Ga0210330_1167914 | Ga0210330_11679141 | F033058 | MNRRRVLIWFAGRWRNHQSKRAEKPHSKSSSGDALDGPATRPETPLAVENSVGKPAAPEAPNAGTGKREW |
| Ga0210330_1178541 | Ga0210330_11785411 | F006082 | NACRHGGGRVYAADGTEITWAIEAEYDRKVRRVQFRSK |
| Ga0210330_1182491 | Ga0210330_11824911 | F079376 | MFDIVSTRQPGRPCVSFEVSRVCWTTEEGGRQMRYRESDSLVVPEKAGNAAGGKEATHGSVV |
| Ga0210330_1186486 | Ga0210330_11864861 | F016165 | MLLKILSGVLGVAGLCWLALLFSSRAILVGERVEAAALHQQLVCTYFTGSGTMRKEYWYSKSDRFGRAACPRWESVREPE |
| Ga0210330_1187516 | Ga0210330_11875162 | F016664 | MDQVVYEMPTLNEAKNAVEIVVHISESLEDRQRNNLVVALEKEDGIVSAEFCPLRYHLMLVRYDRDQYSSQDVLSAVGAQKLQARLIGPI |
| Ga0210330_1197039 | Ga0210330_11970391 | F054044 | MISKYYSNSDIFSVPADRLGISHTVGILVLVIALTALILLFVDSSFRSAADQEECLQLVRALGLNSLSLAPSGRPLRNPGAIDPSIDLRFGPKFGRLPIDGADLF |
| Ga0210330_1240444 | Ga0210330_12404441 | F065171 | PRSTEGFYVDLASKRGLVRRTGGEAGPTMHFLDTTPLADQLERAIHALRQADIGEPGAAAALSQQRIGVLEKVRPVVAPNLYGDLRRAPRTPVTMAAKVRIGLARICAELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVPDEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAID |
| Ga0210330_1251368 | Ga0210330_12513682 | F059103 | MSAPDPRDFVLRFAPLDARTAAWMLDFCGHLQQEIWRAYGDQIEAHWAATDPEQPIY |
| Ga0210330_1256478 | Ga0210330_12564781 | F077315 | VICKASILFQSRFACCQVWVLLLLGLLVPAQAAEALKPDALPQAQATLERLEQQLATARTATAQQLKTLKKAIATVRSSAQDCIQQAQPKIEILDSELAIFQPAKSKDTQKKTAGETQPAEQPEAPFSPAIARQLQDLQSRKASLEGRIAICKLMLLRSNDLASDVDDYLSSLQ |
| Ga0210330_1257083 | Ga0210330_12570832 | F090573 | MRVIRHSDPDTFLAAAAPMAERGQASASFFIGWAHAMKRTPPVAG |
| Ga0210330_1264003 | Ga0210330_12640032 | F020930 | ELDTGSARYLIRFTQTLERQPGWAWTLFSAVRKLTP |
| Ga0210330_1274247 | Ga0210330_12742471 | F001314 | MWILFTAPCPTPDGQTAEDLYRKRLPWITPEMQTSAREHGCRFHRAWYAEDGSAFYALANWDSREGASEFFRLWDIEDEPGEIAITLLGDVGLVPDP |
| Ga0210330_1284191 | Ga0210330_12841912 | F070130 | LSRREHVYVRQMPDTPASQPDFFVGWWEIVFRSRDDEQTDVTGILEHVDAAGNFTVFRDGERIGAGHHVEFTVDPDGFTNLQEVAGAHKQIGRELAVYRFSGDVLEVCKASEHTGRPTSFASPRGSGWTHVAIRRISDDDPRIRAQR |
| Ga0210330_1288895 | Ga0210330_12888951 | F074892 | MIPKYASIVLLGLLLSGCAEKGENVYKSWVGPDRSNMAIVTLRLGDDVRDITVRERVLPRSEYGTLLLVPGQYTLYEDDGASIGITIRPVLMNTEKARANGELILGHTYTLRAGKSQDGGERALWIEDARSGEIFIDTR |
| Ga0210330_1293276 | Ga0210330_12932761 | F055829 | GTRLPLSILYTTEGDLMGAKPAFAEAALRITQHELNSCGIPATAKAGIILGEHGFPPGNEEDDVIDLNMERVRQNMRLVYERNLPKLRDGVTEFCFGMNEFNNHPDSWHLSSMECMVDYLHRGFDVIIFQPYYFINESIDLFEHLRHWAYEVEGIDEHEFHGGHEIAHNYRSDFN |
| Ga0210330_1327546 | Ga0210330_13275462 | F052020 | EIRDRESGRLQILTYAALLWQLFRALIEGALDGLVRELNRKVVKKVLAAIDQTVEGFLNEALQISPQQVSVQLKAEELGYL |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |