| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300022384 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225705 | Ga0210321 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.184 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 175458629 |
| Sequencing Scaffolds | 32 |
| Novel Protein Genes | 36 |
| Associated Families | 35 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Alteromonadaceae → Glaciecola → unclassified Glaciecola → Glaciecola sp. | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 1 |
| Not Available | 15 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → unclassified Bacillariophycidae → Endosymbiont of Durinskia baltica | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiaceae | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria 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? |
|---|---|---|---|
| F001089 | Metagenome / Metatranscriptome | 781 | Y |
| F001314 | Metagenome / Metatranscriptome | 725 | Y |
| F001506 | Metagenome / Metatranscriptome | 681 | Y |
| F001633 | Metagenome / Metatranscriptome | 660 | Y |
| F008223 | Metagenome / Metatranscriptome | 337 | Y |
| F014031 | Metagenome / Metatranscriptome | 266 | Y |
| F016165 | Metagenome / Metatranscriptome | 249 | Y |
| F016975 | Metagenome / Metatranscriptome | 243 | Y |
| F017955 | Metagenome / Metatranscriptome | 237 | Y |
| F021217 | Metagenome / Metatranscriptome | 219 | Y |
| F023254 | Metagenome / Metatranscriptome | 210 | Y |
| F030371 | Metagenome / Metatranscriptome | 185 | Y |
| F031322 | Metagenome / Metatranscriptome | 182 | Y |
| F031901 | Metagenome / Metatranscriptome | 181 | Y |
| F033314 | Metagenome / Metatranscriptome | 177 | Y |
| F051237 | Metagenome / Metatranscriptome | 144 | Y |
| F053305 | Metagenome / Metatranscriptome | 141 | Y |
| F056993 | Metagenome / Metatranscriptome | 137 | Y |
| F068996 | Metagenome / Metatranscriptome | 124 | Y |
| F072362 | Metagenome / Metatranscriptome | 121 | Y |
| F072487 | Metagenome / Metatranscriptome | 121 | Y |
| F074891 | Metagenome / Metatranscriptome | 119 | Y |
| F074893 | Metagenome / Metatranscriptome | 119 | Y |
| F080000 | Metagenome / Metatranscriptome | 115 | N |
| F080062 | Metagenome / Metatranscriptome | 115 | Y |
| F080113 | Metagenome / Metatranscriptome | 115 | Y |
| F084254 | Metagenome / Metatranscriptome | 112 | Y |
| F084255 | Metagenome / Metatranscriptome | 112 | Y |
| F087143 | Metagenome / Metatranscriptome | 110 | N |
| F095737 | Metagenome / Metatranscriptome | 105 | Y |
| F096333 | Metagenome / Metatranscriptome | 104 | Y |
| F098745 | Metagenome / Metatranscriptome | 103 | Y |
| F100493 | Metagenome / Metatranscriptome | 102 | Y |
| F101435 | Metagenome / Metatranscriptome | 102 | Y |
| F105200 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210321_1001471 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1833 | Open in IMG/M |
| Ga0210321_1009590 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1016 | Open in IMG/M |
| Ga0210321_1015114 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Alteromonadaceae → Glaciecola → unclassified Glaciecola → Glaciecola sp. | 876 | Open in IMG/M |
| Ga0210321_1020553 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales | 792 | Open in IMG/M |
| Ga0210321_1021794 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 777 | Open in IMG/M |
| Ga0210321_1025022 | Not Available | 742 | Open in IMG/M |
| Ga0210321_1025085 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 741 | Open in IMG/M |
| Ga0210321_1025855 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 734 | Open in IMG/M |
| Ga0210321_1029339 | Not Available | 703 | Open in IMG/M |
| Ga0210321_1031189 | Not Available | 689 | Open in IMG/M |
| Ga0210321_1031432 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium | 687 | Open in IMG/M |
| Ga0210321_1034710 | Not Available | 665 | Open in IMG/M |
| Ga0210321_1040792 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 630 | Open in IMG/M |
| Ga0210321_1041336 | Not Available | 627 | Open in IMG/M |
| Ga0210321_1041995 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 624 | Open in IMG/M |
| Ga0210321_1042104 | Not Available | 624 | Open in IMG/M |
| Ga0210321_1042972 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 619 | Open in IMG/M |
| Ga0210321_1047507 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → unclassified Bacillariophycidae → Endosymbiont of Durinskia baltica | 600 | Open in IMG/M |
| Ga0210321_1053050 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 579 | Open in IMG/M |
| Ga0210321_1056912 | Not Available | 566 | Open in IMG/M |
| Ga0210321_1060741 | Not Available | 554 | Open in IMG/M |
| Ga0210321_1062707 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 548 | Open in IMG/M |
| Ga0210321_1062951 | Not Available | 548 | Open in IMG/M |
| Ga0210321_1063182 | All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon | 547 | Open in IMG/M |
| Ga0210321_1063307 | Not Available | 547 | Open in IMG/M |
| Ga0210321_1064623 | Not Available | 543 | Open in IMG/M |
| Ga0210321_1065950 | Not Available | 540 | Open in IMG/M |
| Ga0210321_1068425 | Not Available | 533 | Open in IMG/M |
| Ga0210321_1070360 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiaceae | 529 | Open in IMG/M |
| Ga0210321_1076390 | Not Available | 515 | Open in IMG/M |
| Ga0210321_1078717 | Not Available | 511 | Open in IMG/M |
| Ga0210321_1083034 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 502 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210321_1001471 | Ga0210321_10014711 | F001506 | MNQVFYKQRCKCNEEFSITKRRKLSNRSDGKPFLYPMQTEVTIKTFQIKYEKKLSTVAKFALNSFQNKYLYYAIDDLLYLLKSNLVEQENLLNILYSSVLALHNNFSINFFDIWIYEIYISEVKTTNKFLVQNISDPKSISYITIKLLYRTKVPIKKQESLW |
| Ga0210321_1005919 | Ga0210321_10059193 | F105200 | VPDSFDRKLEQLLEYAEAPQPEAFTMDVMRGVRREQRTRKIILWCFGLVGALFGITGALMLAGPLSELFTFSLAMPAMQTMQATLFIVGAAAFYLWFMNDDFSLGG |
| Ga0210321_1009590 | Ga0210321_10095901 | F068996 | MQSPRKEVGTMGYLVIGIAYIVLAVVAVVKPRADHA |
| Ga0210321_1011195 | Ga0210321_10111951 | F031322 | MLLGANLPIKFWPYAFHFWLRIDNSMASRDQLASPNYITTGKKDDLSALQTFGCRVWVRPPGRRAAKLIPNSRKGIFLGFIPNTDKNILWYDTETHAVKIAKHVRFDEGMNDLPPDLVPPNVVHLQRTQNGEPLPAETEETSVDQFTFHLNPFSYTMVKGVPVTDNDPSFGLTLASDELSHRAYVADVKENSTADKMYASHKSTLKNVKGAYLVGINGKKAFSKEDAISMLRQLHDERAENLQLELAIERKLSSAEAWRAVAEHNIMDPSDVPD |
| Ga0210321_1015114 | Ga0210321_10151142 | F084255 | MESSRRYLLQAEIEYWHEMLKLNKNRVSRNRQEEMRNCLKKAVRALNSNMAPDFRVAA |
| Ga0210321_1017842 | Ga0210321_10178421 | F014031 | MRRYRVGILAAALVGMMAGASSAEVTTERSASIMVFPKVIADGTRDTIIQMTNTSNSMVHAHCFYVNAAPVRRDLPPDPVLNPPLWQ |
| Ga0210321_1020553 | Ga0210321_10205531 | F008223 | MGIFGNLFTKPPRTPTAVKEVSRIIDRFATATSMGVDREDLGRYPAKQYQVMAFHYGAIEYLASQYGLDETQTLGVFVMFINTYFTMPITETGSISERLQGFRDKPAEHRFLEAGAAVFR |
| Ga0210321_1021794 | Ga0210321_10217942 | F100493 | MAINDLHKVYPNRNLGLRAAAKQCFEFGLTIAREPSAALSNGLDEHAIRRQLMYIDKARDIVERLNARPIPDRPATHPTDMPIDFSVPYVYFTEDLNGNQVPLNEATQELAESWLVLAVELAKSQSAAIAGSLVEYDYQRAINNIDVLAQL |
| Ga0210321_1025022 | Ga0210321_10250221 | F017955 | MKARLIIQNNKRENAKRKPHTYNVGDVVVVKAGVKRKHGSNPYLDPMRITQVNDNGTVTLVKVADNNGGAVSQTWNIRNIEPRMA |
| Ga0210321_1025085 | Ga0210321_10250851 | F001633 | VLPDATLRGLRMSRSHGGTVLTVAGRDLSSEASAPGSVASCRKRHAGRGADTPATFIFSRRHRYHGDGTSFWLAVGPVLRV |
| Ga0210321_1025855 | Ga0210321_10258551 | F080062 | VQLTLPRILWFVAALAIAWGLNAWRREAASDGLEAAQQGDRSAAEGWVDRALREGKCELHEARAYVQSPATRQYVRRPDYVESFVEKLYAGGAPKLEICDSDLVGFRFAHY |
| Ga0210321_1029339 | Ga0210321_10293392 | F023254 | MKRVYISDFKKDGKGTKGRRSCNTICSTERATRRKYRGAYITAIDDEEIVTLNQAKEKLKELRNKNVDTFTMILAREPRPSKSMTRRAYDELELPEFDLDENLGEDYFASDGNLEGDSSMTASGETNAFGTDYAPPIGTKISKDFGSKGFFTGTVTSGPHIREKDGDDVTIWKVQYEDGDREDMTASEIAYWKMP |
| Ga0210321_1031189 | Ga0210321_10311891 | F033314 | MSAGTVDFVVGVDKKLWIGSGLFENCKSFFGAQGAVFGSERFDYTDWIALPKDAAGYSDALVSWGWVGVIELGCKMFGVGVRFLALFD |
| Ga0210321_1031432 | Ga0210321_10314321 | F030371 | TISDIASKDEQRLVGSIAKALAANSPYLNLIRGGTFPAGVSDEIRSSVQMQAAPGDSYAVPTFVCDTDICGQIGHQDLTDTIEYVTRLESFRGRGPNVCVKKGYAAFKGSYTMAGDSLQKNVVQYINADVRAQLTIRSASKFVANANYDFDSLFTGGNATDLGVNFLGELPTGPMTFKALHYIARHLREVLFADWYSNSKDMPHFRFVGGTDQIEYFREEVGVNNVMV |
| Ga0210321_1034710 | Ga0210321_10347101 | F016975 | VSWSGPRAGGATTGSAGLRGLTQQFSDRKALDGPATRPKTPLAVENSVG |
| Ga0210321_1038556 | Ga0210321_10385562 | F031901 | MRVAFLLIVLGFPLVDLYATVRFARWTGVPTYAWLGLAAIAGLYLLRNERST |
| Ga0210321_1040792 | Ga0210321_10407922 | F072487 | MFPKEYKYIIGIGLILFGFFAVKFREYQHPIYGYINLGKHHIYLGVAIIIIGAIYIAHVRNENRK |
| Ga0210321_1041336 | Ga0210321_10413361 | F101435 | MISQMQEFVVEQTSNLTDQVQKIRKGSVETVREAAVGSAEGLKALKSPIRQLARSSVKLTSVSQAAVAGLIDLQSDMVTSAITDAALRLERASRASSIIDLVRDQYE |
| Ga0210321_1041995 | Ga0210321_10419951 | F056993 | MWVLFHVPCPTPDGQTAADLYRKREVGITTDMQQSAERHGCRFHRAWYARD |
| Ga0210321_1042104 | Ga0210321_10421041 | F096333 | NAALLQGVILAMQYMTQVHAESDKRNASMSQQQAKLQAATFHSQSQMLESLTRNLGNLGHDVGRAIASQPSQHNHTLRATLSPPNAVAGQSNDPTVLGSLTRVTPVGMSVAGYDYGPYVSAYQPQPNDKNTRRIDESTHNIIQRGLPPKVKDRYDAAHTSGTVLPVDDYLRGFIYLVEVELDKLSQVIRKFFWHPALGTGCITSSGFV |
| Ga0210321_1042972 | Ga0210321_10429721 | F016165 | RPMPGACRRSTGGPYTHRGIDAPGTRMLLKILSGVLGVAGLCWLALLFSSRAILVGERVEAAALHQQLVCTYFTGSGTMRKEYWYSKSDRFGRAACPRWESVREPE |
| Ga0210321_1047507 | Ga0210321_10475072 | F098745 | MKKLFAKDQKNRKTIKQLELDHFVLKQISTNSNFLKTIRWNALYKLSSLSKQSSKTVLSN |
| Ga0210321_1053050 | Ga0210321_10530501 | F001314 | MWILFQVPCPTTDGQSAKDLYDKRVTGITEAMQASAEQHGCQFHRAWHASDGSAFYAIAKWESREGASAFFEEWQIEDEPGEIAFILEGDVGLVPQP |
| Ga0210321_1056912 | Ga0210321_10569121 | F072362 | MHKLLAIGFAIYLAGDPGLSMLSMFNESKEVVVAFALALIAVPWVASQIDN |
| Ga0210321_1060741 | Ga0210321_10607411 | F087143 | MNSEGRTEVIGAFSITGFVQYLSDVQVWEPRIVIARIDGAAQDFVVPCGPECYRKNSQEALTAGWAAARQWLDGGKIPWHAPAATGAVPK |
| Ga0210321_1062707 | Ga0210321_10627071 | F080113 | EKSISVNVFMRDASKNELLVGTHIWPDYPDYNEFALQQFFAVMKALEPAYKQDDEVAYTWSGKGNVTKCSIYLESAEVPVKNGTGAIVGCEANGVSNVAVTSVADPKRAYSTSRDPKHIDDVMDLFKKQSERARASIHK |
| Ga0210321_1062951 | Ga0210321_10629511 | F051237 | ATRAAMSASPTPETRETIRLRASNRRTAFTLVSIAAVFFFGIIATKFMGGPATGIGVVGSAVLLYLVVAIGRNLRDRR |
| Ga0210321_1063182 | Ga0210321_10631822 | F095737 | MSVTISTTNKPLNPRAQDLSPKGYNRASLYSGKALDFDGVNDYVDCGTLDV |
| Ga0210321_1063307 | Ga0210321_10633071 | F053305 | MLKKSVSMALMALFVFSFIAVATLSADETQKITGTVMSVNAETGEVILKDDAGEMKTLMADPKAEGAVDIKMLKEGDSVDVESDSNGVIKSLKAGE |
| Ga0210321_1064623 | Ga0210321_10646232 | F080000 | HILEVQFDNNDGGTALAKSPTPAYKVGDEVQYEKNERGGVKIQRDQSNFSSNSNYSNNSPRMKQDNSEQIARSVVFKGAIDLVSSGKMQITDIPSFVDKYLSVVTGASAQGESYQAHFQESSMPF |
| Ga0210321_1065950 | Ga0210321_10659501 | F021217 | KEDEWTDEESIEGIAYKNVQELKISEVATGSILTANRYEAHLDGGSQASTTNDKAVLWGFKWYTNKNPCRIRLICADGKTPIVPEGYGTVRIPADNAEGYVPIKCYHTPDMPNFILSPNSFKASLGKHYNGYKLECDDDKKSFRFSLNHKMRKSGSVLLRGTTRGGLCYTRPAVPPMPTT |
| Ga0210321_1068425 | Ga0210321_10684251 | F053305 | MLKKSVSMALMALFVFSFIAVATVSADETQKITGTVMSVNVETGEVIVKDDAGEMKSLMADPKAEGAVDLKMLKEGDPV |
| Ga0210321_1070360 | Ga0210321_10703601 | F001089 | EIVTAAESDYLFRLATLSLSFVGFSAVVVTLRGALGGELSDRHLRLVRLYIEGGFLVTALALIPTLLNLLHIPDTVTWPLSSAVAASILTFVLVIQFRRRRTVEPGRFPLWVISIYGVSVVAVAGLWLNVAGLPFPPSVGPYAVALTWALGVSGFIFVRTIALFLHRTPRT |
| Ga0210321_1076390 | Ga0210321_10763901 | F084254 | IEQRDKLPMQARHIPVFISEPLVIEIMAEVIRQSKRHPRADQVASALTIRGLPIAEKDVMAVFDQYDIEKKIADSP |
| Ga0210321_1078717 | Ga0210321_10787171 | F074893 | MVPSQLHAVAGNESLTIRINGPMDLLLTMPLREHCQDTGAAYRRYIVDFQDVGIVRDSGLALLLMLKRWANRAGATLCVINGNRDLMRRCFLLGIGPA |
| Ga0210321_1083034 | Ga0210321_10830342 | F074891 | GKAMSVVTHDVVLKRKPRKKRGKGEAALRTLRRALARRTLEQMREDEILHEQIYDVFEDDTTSKA |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |