| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021283 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225741 | Ga0210357 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Oregon, United States ? S.587 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 49158149 |
| Sequencing Scaffolds | 30 |
| Novel Protein Genes | 31 |
| Associated Families | 26 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 14 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 2 |
| All Organisms → Viruses → Predicted Viral | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium | 1 |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 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) | 46.178 | Long. (o) | -123.853 | 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 |
| F001506 | Metagenome / Metatranscriptome | 681 | Y |
| F002557 | Metagenome / Metatranscriptome | 548 | Y |
| F004323 | Metagenome / Metatranscriptome | 443 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F007695 | Metagenome / Metatranscriptome | 346 | Y |
| F008361 | Metagenome / Metatranscriptome | 334 | Y |
| F012678 | Metagenome / Metatranscriptome | 278 | Y |
| F020183 | Metagenome / Metatranscriptome | 225 | Y |
| F020700 | Metagenome / Metatranscriptome | 222 | Y |
| F021307 | Metagenome / Metatranscriptome | 219 | Y |
| F024439 | Metagenome / Metatranscriptome | 206 | Y |
| F030647 | Metagenome / Metatranscriptome | 184 | N |
| F034767 | Metagenome / Metatranscriptome | 174 | Y |
| F038530 | Metagenome / Metatranscriptome | 165 | Y |
| F041780 | Metagenome / Metatranscriptome | 159 | Y |
| F043395 | Metagenome / Metatranscriptome | 156 | N |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F053640 | Metagenome / Metatranscriptome | 141 | Y |
| F054425 | Metagenome / Metatranscriptome | 140 | Y |
| F082263 | Metagenome / Metatranscriptome | 113 | Y |
| F082737 | Metagenome / Metatranscriptome | 113 | Y |
| F083351 | Metagenome / Metatranscriptome | 113 | Y |
| F083433 | Metagenome / Metatranscriptome | 113 | Y |
| F094695 | Metagenome / Metatranscriptome | 105 | Y |
| F105419 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210357_1007740 | Not Available | 2343 | Open in IMG/M |
| Ga0210357_1011443 | Not Available | 1087 | Open in IMG/M |
| Ga0210357_1017739 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 635 | Open in IMG/M |
| Ga0210357_1023549 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 512 | Open in IMG/M |
| Ga0210357_1024596 | Not Available | 632 | Open in IMG/M |
| Ga0210357_1025290 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 823 | Open in IMG/M |
| Ga0210357_1030961 | Not Available | 879 | Open in IMG/M |
| Ga0210357_1033738 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 919 | Open in IMG/M |
| Ga0210357_1038498 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 523 | Open in IMG/M |
| Ga0210357_1038651 | All Organisms → Viruses → Predicted Viral | 1085 | Open in IMG/M |
| Ga0210357_1039815 | Not Available | 667 | Open in IMG/M |
| Ga0210357_1039846 | Not Available | 578 | Open in IMG/M |
| Ga0210357_1043323 | Not Available | 717 | Open in IMG/M |
| Ga0210357_1046586 | All Organisms → cellular organisms → Eukaryota → Sar | 1534 | Open in IMG/M |
| Ga0210357_1046699 | Not Available | 827 | Open in IMG/M |
| Ga0210357_1047627 | Not Available | 1046 | Open in IMG/M |
| Ga0210357_1052858 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium | 512 | Open in IMG/M |
| Ga0210357_1058906 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 629 | Open in IMG/M |
| Ga0210357_1062765 | Not Available | 755 | Open in IMG/M |
| Ga0210357_1063149 | Not Available | 675 | Open in IMG/M |
| Ga0210357_1063716 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 705 | Open in IMG/M |
| Ga0210357_1066894 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 591 | Open in IMG/M |
| Ga0210357_1075703 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 4012 | Open in IMG/M |
| Ga0210357_1082644 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 552 | Open in IMG/M |
| Ga0210357_1082684 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 824 | Open in IMG/M |
| Ga0210357_1090095 | Not Available | 502 | Open in IMG/M |
| Ga0210357_1094532 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 773 | Open in IMG/M |
| Ga0210357_1094859 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 598 | Open in IMG/M |
| Ga0210357_1099398 | Not Available | 515 | Open in IMG/M |
| Ga0210357_1105314 | Not Available | 512 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210357_1007740 | Ga0210357_10077403 | F083351 | VGHPRCESGESEPGTHEVRVHAVRLGGRNRLDALRVFSTGRLQGLLVKREGASQEQIRSI |
| Ga0210357_1011443 | Ga0210357_10114432 | F008361 | EKATLAIEKAETSKDRLDASVELKKATARLEAINYLS |
| Ga0210357_1017739 | Ga0210357_10177391 | F001506 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQINLSTTAKCLLNNFQNKYIYYAIDDILYSMKAKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDLTTLKEFNYITIKFFYKIRVPVKKQESLW |
| Ga0210357_1023549 | Ga0210357_10235491 | F004323 | MPLDDLRRLEGRATPAVAIHSPVTRDYPSRALSDVFQ |
| Ga0210357_1024596 | Ga0210357_10245961 | F006508 | VVRANALPQAAADPNQTVKTQKNIRRSVLAWFASRWRNHQPKRAEKPHSKS |
| Ga0210357_1025290 | Ga0210357_10252901 | F000344 | MRPIHPHAAESGVGKHTARESERAQACATGKERVANAHSH |
| Ga0210357_1030961 | Ga0210357_10309611 | F094695 | LDGGITVCSVRDPYFRETWAAVQRFSDESIGPSWVQPIPVQRLPFPAASFGFSLSAVVRELSHPRHSSLRLTCLLEALPPINRPRMRTREHLSCDFVPYSAQQKQASVSPGDSNLRHCPSSGFLTLSTSYSACNPDQLVSSGLRSWGSTGSVYSPSPFGHGRVRRFRVSSSKLSPFPR |
| Ga0210357_1033738 | Ga0210357_10337382 | F000344 | MRPKHPHAAESGVGEHTARESESAKRCAVGKERVANAHP |
| Ga0210357_1038498 | Ga0210357_10384981 | F053640 | SKRSGLKDVAESTAGIIPGDRGMDGDSWCCPPLQAAQVVERHISPVPLAGVVSGQSTHESGTERQGAIRNRVEPSQAHGEFRPVSRRSYHRGFWLLLRRPERSHGARRANPARRPRSPHERGAQGSRDGGERADLAKSVKPPRRGGVKNHVTPLQKRKQP |
| Ga0210357_1038651 | Ga0210357_10386512 | F105419 | MRKTIAFCSLMLAAAITNGCISTTMYGCEITETLAPGASEGEVVMKHGAPDNILYLGNQYMNPQTGERGEVDKYLYEYRIGGGTTLLGKVFATDEFHNIGYLIEGGKVMGGGYVGEGKGTIILGNTPISLPIIGKFDMGGYFLHPKVRAGYGGDGNPEGGFHMND |
| Ga0210357_1038900 | Ga0210357_10389001 | F043395 | TLYPNSSVAPFDVQPSSFTKTHDGFNFQSYGDVADNLPMLSKEWMSGEWNVIATIPFSGNLANGDKFEFTECGFDATTDPYFSNMDAKGNYGQFAPNLIRNGSAGANLAVANAVIVYPNPTMGDLHVDVSSATVTRATFKVMDMTGKTVKTIESDLVEGLNNITVNVGELANGMYMLKVVDGK |
| Ga0210357_1039815 | Ga0210357_10398152 | F020700 | MTARHSLHLRFAGLDPKTSPSVFSDAAAGIAATSIRLNFFVLFPEVSPEKVRRIL |
| Ga0210357_1039846 | Ga0210357_10398461 | F082737 | MPGLSLSQPSRRTPFRLAPRLRSFSVGASLLSGTPASLPVRSQNLEADFHSPTTTSLLPDRRGGVRIPALLLQLCGTLPNCPVRSDLHPRPVSRTAWGLPRPEPVAARSCATPACRAKPLLPFRAIPLPDQSTRPRWPTGSLLPVTPDLPSLPTGGRIRNQHQRIIVPAPLRLCQLTVP |
| Ga0210357_1043323 | Ga0210357_10433231 | F007695 | VKRRDPWHWANAPSKAVAVPALSGQDAEDSHRRVLAWFAGEWRNHPLKRAEKPHSKFSDRKALDGPATRPITPLAVENSVGK |
| Ga0210357_1046586 | Ga0210357_10465863 | F021307 | MNRILYEKRCKCNEEFSIIKKRKTKTRSEGKPLEYPQSSEMTSKTFQIKYQKNLSTTAKCILNSFHNKYIYYAIDDILYLLKSQPMERDNLLAVIYSPILSLQNNFSVNFFDIWIHEVYI |
| Ga0210357_1046699 | Ga0210357_10466991 | F000344 | MRPKSAHAALSGVGEHPARESESAKWSADGKERVANAHPHFDPG |
| Ga0210357_1047627 | Ga0210357_10476272 | F024439 | PVVGTDKSVEAPPGVSASPQLVDRDVAVPGTTLSGLTGLSERSARRSGAIGSPPPPRRLYDHEEFRRSAIRAVRRPPGSSRRLRRPLRVRAEVPSPAMPGQVAPPGVSCPFSGISGGIRITRVCLTRHVPSSGFLAPSTVSSPSGLADSLGPLPLMGFPLVQLFRAAGP |
| Ga0210357_1052858 | Ga0210357_10528581 | F083433 | MKHRVLFIAFMIVALAAFYSVPKANAEPLTIMAIVGVVAVLSASSVDMVAASHEDTKDQRAQLDEAANMHAKVEASGVTSGSEEAVAASN |
| Ga0210357_1058906 | Ga0210357_10589061 | F012678 | MLNQHSLEEIADIYNLLGDIKEEYEKGIKPILIKNSPKLFQNPHTVAKLKKVQINRGLGLAAQNTNILKKNIEEFEKL |
| Ga0210357_1062765 | Ga0210357_10627651 | F054425 | GCRLPDAILHGKRSFRPRSRAVQNLAASGLSSEAFQLVSADGCATGLRTRSRHVYDFSPRLDRLTPGRPPLLAVRWPGVTGLAS |
| Ga0210357_1063149 | Ga0210357_10631492 | F002557 | VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSHRSSLPSSFFAFTDGARTPPEELVNSASSIACVSTRLRRGRVN |
| Ga0210357_1063716 | Ga0210357_10637161 | F038530 | MRPTASHAAVSSVGKHTARESEAPNVVRKGKSAWRAPTP |
| Ga0210357_1066894 | Ga0210357_10668941 | F000344 | MRPKHPHAAESGVGKHTARESESAKACAAGKERVANAH |
| Ga0210357_1075703 | Ga0210357_10757032 | F020183 | MTLSINAKTYTGNNYSANSVGYNGPSKTASVKDDAKLSQTAPKPTESFSGLGRTQAKLTRTLTLTGAATATGDAILTIDVAVPVGFAGADVDTLLNDAGAFVSSATFKTHVKTPQVAF |
| Ga0210357_1082644 | Ga0210357_10826441 | F034767 | MFGSKIGKCTLDILKGVNATIWGGVQEADKVGKIVKTGISGADVVIGTSHALEDFGCNDYVCGSLDVIGSVSSAVGLVLGNIPSTKSLTFITGSVTVGCRSIRYYCKNYGTFWGCTVAAGQGIKESVKFIINK |
| Ga0210357_1082684 | Ga0210357_10826841 | F000344 | MRPKHPHAAESGVGKHTARESERAQACATGKERVANAHSHH |
| Ga0210357_1090095 | Ga0210357_10900951 | F030647 | PVLNSDHVHLSDMTVYMTSSSVHLSFVIQHGGKIKPKIGPKVIHILLALEKLLSLLKFVVFIETCFPIKSSQPTTSYGMI |
| Ga0210357_1094532 | Ga0210357_10945321 | F082263 | GLGAFLTDKELSRCLSSWKPLLRSADANNVGLALRWEAGLAGMEALASTPDHDRTVAVEEWASAVTDMVNTRSALDAWCVERSIVSIRVAKEGGWLNMSELRDLYRWMSMDVSGVVPDATNEEKAALSKPAYIGQPVDVSDTHAIVRIALGVESLLSYLDGKEQTLNEDQATVRKLAAISKFFNTLKESGL |
| Ga0210357_1094859 | Ga0210357_10948591 | F001506 | MNRILYENRCKCNEKTEKFSLTKKHKTRKEGKLYPHPDNEEIRSKTFQIKYEKRLSTAEKFILNSFQNKYIYYAIDDILDSLKLNLLERDNILAILYSPILSLQNNFAINFFDIWISEIYIEEISKVNKFLNTESQTSEQFSYITLKLFLST |
| Ga0210357_1099398 | Ga0210357_10993981 | F041780 | AFRMTGLDSLCSPRPLFGGCASTLRAQPASHSNRNRNLETAFLLLCDDFPYPELRDRLKRSQPASSISLPRPIRGRSALNSLPDAFGFRRGHGHKPRFPLAARQLQPILEPPLPFGVSSPPDHNAQSDSGRKVYLGKTPDHLLLPERINE |
| Ga0210357_1105314 | Ga0210357_11053141 | F044534 | QLVPPSPPDRVSGKAGISHQFLWPESCPVSPPTKKELSREARSETAPNGVRPTGRFDPCADAVTPEGSGCYCADQNASAISGGTTPPKGPARHTSGARKEITTAGRERTWQSP |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |