 |
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021294 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225709 | Ga0210325 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.264 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 107907025 |
| Sequencing Scaffolds | 28 |
| Novel Protein Genes | 33 |
| Associated Families | 27 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 13 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium 13_1_40CM_2_68_5 | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Corethrophycidae → Corethrales → Corethraceae → Corethron → Corethron hystrix | 1 |
| All Organisms → cellular organisms → Archaea | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 2 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → unclassified Bacillariophycidae → Endosymbiont of Durinskia baltica | 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? |
|---|---|---|---|
| F000203 | Metagenome / Metatranscriptome | 1619 | Y |
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F000734 | Metagenome / Metatranscriptome | 915 | Y |
| F001024 | Metagenome / Metatranscriptome | 803 | Y |
| F001506 | Metagenome / Metatranscriptome | 681 | Y |
| F001758 | Metagenome / Metatranscriptome | 640 | Y |
| F002557 | Metagenome / Metatranscriptome | 548 | Y |
| F004323 | Metagenome / Metatranscriptome | 443 | Y |
| F005564 | Metagenome / Metatranscriptome | 396 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F008361 | Metagenome / Metatranscriptome | 334 | Y |
| F014821 | Metagenome / Metatranscriptome | 259 | Y |
| F016728 | Metagenome / Metatranscriptome | 245 | Y |
| F017072 | Metagenome / Metatranscriptome | 243 | Y |
| F021307 | Metagenome / Metatranscriptome | 219 | Y |
| F025295 | Metagenome / Metatranscriptome | 202 | Y |
| F030134 | Metagenome / Metatranscriptome | 186 | Y |
| F030135 | Metagenome / Metatranscriptome | 186 | Y |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F053640 | Metagenome / Metatranscriptome | 141 | Y |
| F064269 | Metagenome / Metatranscriptome | 128 | Y |
| F064356 | Metagenome / Metatranscriptome | 128 | Y |
| F089490 | Metagenome / Metatranscriptome | 109 | Y |
| F096552 | Metagenome / Metatranscriptome | 104 | Y |
| F098745 | Metagenome / Metatranscriptome | 103 | Y |
| F100493 | Metagenome / Metatranscriptome | 102 | Y |
| F104597 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210325_1012025 | Not Available | 570 | Open in IMG/M |
| Ga0210325_1012677 | Not Available | 611 | Open in IMG/M |
| Ga0210325_1036506 | Not Available | 632 | Open in IMG/M |
| Ga0210325_1046990 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae | 2761 | Open in IMG/M |
| Ga0210325_1047596 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 620 | Open in IMG/M |
| Ga0210325_1048890 | Not Available | 646 | Open in IMG/M |
| Ga0210325_1049988 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 685 | Open in IMG/M |
| Ga0210325_1062532 | Not Available | 613 | Open in IMG/M |
| Ga0210325_1063264 | Not Available | 547 | Open in IMG/M |
| Ga0210325_1068724 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1016 | Open in IMG/M |
| Ga0210325_1072448 | Not Available | 741 | Open in IMG/M |
| Ga0210325_1074202 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 506 | Open in IMG/M |
| Ga0210325_1089473 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 807 | Open in IMG/M |
| Ga0210325_1106380 | Not Available | 519 | Open in IMG/M |
| Ga0210325_1118761 | Not Available | 668 | Open in IMG/M |
| Ga0210325_1126635 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 661 | Open in IMG/M |
| Ga0210325_1135766 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 525 | Open in IMG/M |
| Ga0210325_1143381 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium 13_1_40CM_2_68_5 | 1087 | Open in IMG/M |
| Ga0210325_1148554 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Corethrophycidae → Corethrales → Corethraceae → Corethron → Corethron hystrix | 555 | Open in IMG/M |
| Ga0210325_1154561 | All Organisms → cellular organisms → Archaea | 1036 | Open in IMG/M |
| Ga0210325_1159701 | Not Available | 595 | Open in IMG/M |
| Ga0210325_1171109 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 586 | Open in IMG/M |
| Ga0210325_1184837 | Not Available | 601 | Open in IMG/M |
| Ga0210325_1185658 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 1010 | Open in IMG/M |
| Ga0210325_1190646 | Not Available | 744 | Open in IMG/M |
| Ga0210325_1197129 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 520 | Open in IMG/M |
| Ga0210325_1209698 | Not Available | 685 | Open in IMG/M |
| Ga0210325_1233659 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → unclassified Bacillariophycidae → Endosymbiont of Durinskia baltica | 660 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210325_1006501 | Ga0210325_10065011 | F000203 | LGASGAAGFPTLFSTASGVSGLVAGPSSASPLLDFE |
| Ga0210325_1012025 | Ga0210325_10120252 | F005564 | MNKIFIALMIIFFIGDPGMETLSWLGDMKNYIVAAAIALCSMPFIVS |
| Ga0210325_1012677 | Ga0210325_10126771 | F001024 | MRPAIPFATENSVGKLAASQGRPMPAREREFGALPP |
| Ga0210325_1021513 | Ga0210325_10215131 | F000203 | LFPMPTLGAIQAAGFPTLFSMASGMFGLIAGPSSALRSLNY |
| Ga0210325_1036506 | Ga0210325_10365062 | F002557 | VLIHSSNRYPLGNCDSPKSETNLGYLTQFGTVSHRSSPPSSFFAFTDSARTLPEELVNPA |
| Ga0210325_1046990 | Ga0210325_10469903 | F001506 | MNRILYESRCRCNEEFLITKKRSLSNRSEGKPLQYPKPNEITSKTFQIKYEKELSSIAKFVLNSFQNKYIYYAIDDILYLLKSNPIERDNLLAIIYSPVLSLQNNFSINFFDIWIHEIYINEVPKVNKFITNDFQNLEQFSYITIKLLYKTRVPIKKQDSLW |
| Ga0210325_1047596 | Ga0210325_10475961 | F104597 | ERVVQGDWTVGCEGQRYQLDRQHEALSLVRRKVIVRRLRDGRVQLVYQGKQLKWRTLPEGAARKHSPVRKERVAGKAKMVAKPPAQNHPWRRDGVGAGRPYWNGIKAQGRAVRVAVRDSGQPPLRSGLSASRTATRGIPATKTKQRRGHSLLSLTGDISKEF |
| Ga0210325_1048890 | Ga0210325_10488902 | F008361 | LEKATLAVETAESSKARLDASVELKKATARLEAVNYLS |
| Ga0210325_1049988 | Ga0210325_10499881 | F044534 | RGIYHQFLWPESCPVSSHTNQELSGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP |
| Ga0210325_1049988 | Ga0210325_10499882 | F000344 | MRPIHPHAAESGVGKHTARESESAKACAIGKERVANA |
| Ga0210325_1062532 | Ga0210325_10625322 | F001758 | QGYARVTGERLGQAGWRDPSKVGSKGSMAEAGFTSSSGGVRAPSVNANKELGGEAR |
| Ga0210325_1063264 | Ga0210325_10632641 | F089490 | MYHLMKSEKFTLDHLISGVMSSYRQTEIGHFQQFRTALGACEVANDRGRSRYYVVNESGQEYYDGTW |
| Ga0210325_1068724 | Ga0210325_10687241 | F021307 | MNRILYESRCRCNGEFSITKKRNSNTRSEGKPLQYPKPNEITSKVFQIKYEKKLSSIAKLVLNSFQNKYIYYAMDDILYHLKCSPFERENLLAILYSPI |
| Ga0210325_1072448 | Ga0210325_10724481 | F030134 | SVLKYLKIKAKDKIQPVSQRFKLRSCTVLIVEQTNPLNTYNQGGTIIQHRGSNHVFR |
| Ga0210325_1074202 | Ga0210325_10742021 | F053640 | SKRSGLKNVAESTAGIIPGDRGMEGDSWCCPPLQATQVVARHISPVPLAGVVSGQFTHESGTERQGVIRNRAEPSQAHGEFRPVRRRSYPRGFWLLLRRPERSRGTRRANPAKRSRSQHERGAQGNRDGGERADLAKSVKPPRRGGVKNHVTPLQKRKQP |
| Ga0210325_1089473 | Ga0210325_10894731 | F000344 | MRPRHPHAAESGVGKHTARESESAKACAIGKERVANAHS |
| Ga0210325_1106380 | Ga0210325_11063801 | F017072 | MRMRDLAVGSDEKPLRTESSSPETFRFRMNRSHPEGEQLLLCISTVRAALAGSNQIEAAQRKTPKGGQKERGHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKCNLREKRRDPWFR |
| Ga0210325_1118761 | Ga0210325_11187611 | F000734 | MHREGHGVSAGPVKTFRNVGDVKNGTADLWTKGDLRVKRRDPWFRANALSRAAADLELAGEDAEKKT |
| Ga0210325_1126635 | Ga0210325_11266351 | F004323 | MPLDDLRRLEGMATPAVAIHSPVTRDYPSRALSDVFQAAALRL |
| Ga0210325_1127744 | Ga0210325_11277443 | F016728 | LARKCLTVCVTCVWAGVDSVWEQEKPEARKMLENAAESHTSGARFVGRWMNARLVGF |
| Ga0210325_1135766 | Ga0210325_11357661 | F014821 | AISPEERALPRFSRRALKRLPTWDLWHKNEVEQLDQMKALGMFGAPIKLPEGGILMRFHWQYLIKVNGKRRSRLCCDGSPRAAPEVHSTTNTYASCLEHPVFRLFIALCTPDNLTIYGGDAKDAFAHSPGPSMPTFMKIDDAFRDWYQECTGVLLDKDLELPVLRALQGHLEAAK |
| Ga0210325_1143381 | Ga0210325_11433812 | F096552 | MKMKNVFVTASAGLILLLLAACAALKPTPTQPAPTAEVLPATVIQYHFVTNKLMLPTTQAQTQEFALNVDGDSQQNLDNKFGELLTLLTSAAPGLELQSTLDQAVNNGQLVTLHVVKADDPLNDPSVLWSLFLGQKTQSAPSFDGSDQFLIDSATPTDSSIVGSLTNG |
| Ga0210325_1148554 | Ga0210325_11485542 | F008361 | VELSEATKELEKATLAVENAESSKTRLDASVELKKATARLEAVNYLS |
| Ga0210325_1154561 | Ga0210325_11545613 | F064356 | MIHGVKDQPVHENFTVSDAQGNLITGIDTTTGFTPYVYDPSGAEVTGLVSGFFTELGDGNYRYTFTPNANGVWYVNVTNLEYFPWGKNDDVYVDTSDLSGIYEIVIRTLGLVHHNFYIDQATYDEFGNLISSRVRIYNSAANVGTNAGVIETYMLTADAEACGQFSFWKQVVSP |
| Ga0210325_1159701 | Ga0210325_11597011 | F006508 | VALANAPSKAVADQCQMVKTRKRNRRRVLTWFASRWRNHQPKRAEKPHSKS |
| Ga0210325_1171109 | Ga0210325_11711091 | F100493 | MAINDLHQVYPNRNIGLRSAAKQCYEFGQTIAREPSAAHSNGLDEHAIKRQRQYIQKARDVVERLHAKPIPDRPATHPTQMPIDFAVPYVYFTEDLNGNKVPLNEATQELAENWLTVAVELAKSQSAAIAGSLVEYDYVRAINNIAVLEELVN |
| Ga0210325_1184837 | Ga0210325_11848371 | F006508 | VALANAPSEAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPHSKFSAVRRWTALLRGRRLR |
| Ga0210325_1185658 | Ga0210325_11856581 | F001506 | TKLMNRILYEIRCKCKEEISITKKRKSSNRSEGKPFLYPNPNELRSKTFQIKYERKLSSVAKFLLNSFQNKYLYYAIDDILYLLKSNPIERDNLLAILYSPVLSLQNNLSINFFDIWIHEIYISEVSKVNKFLATNRQNFEPFSYITIKLLYRTKIPIKKQESLW |
| Ga0210325_1190646 | Ga0210325_11906461 | F030135 | TLSTNTGIWHSTFVGCQFPDAILPGEEAIDLVAGPLNQLPDQVIE |
| Ga0210325_1197129 | Ga0210325_11971291 | F001506 | MNQILYENRCKCNEEFSITKKRKSPTKSEGKPLQYPKPNEIISKTFQIRYDKKLSTTSKFILNSFQNKYIYYAIDDILYSFQANSSEREHLLAVLYSPILSLPNNFSINFFNIWIREVSIDEISKTNKFLNSKSLKQYNSITIEFFYKTKVP |
| Ga0210325_1209698 | Ga0210325_12096982 | F025295 | VTGPGEAAELLRRREVLIPEKLKFITRKSNLQKPI |
| Ga0210325_1214295 | Ga0210325_12142951 | F064269 | VLRLITLLPLSVLMFMIPVLLSVCMVFACVPEVLYWLFGINTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTNNVVNTLLLPTKEQRLQRPSKRKALDRMFFMFLLMNHGRVSAKSARRTSYRVRPELSKIPQAIPQDLSAEMLAPWDSIPQGWS |
| Ga0210325_1233659 | Ga0210325_12336592 | F098745 | MKKLFAKDQKNRKTIKQLELDHFVLKQISTNSNFLK |
| ⦗Top⦘ |
|
Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |