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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300021267 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225737 | Ga0210353 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.489 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 32143958 |
| Sequencing Scaffolds | 34 |
| Novel Protein Genes | 34 |
| Associated Families | 31 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 18 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Eukaryota → Sar | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Nitzschia → Nitzschia inconspicua | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Chaetocerotophycidae → Leptocylindrales → Leptocylindraceae → Leptocylindrus → Leptocylindrus aporus | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 4 |
| All Organisms → cellular organisms → Eukaryota | 2 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 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 → Phaeodactylaceae → Phaeodactylum → Phaeodactylum tricornutum | 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) | 46.313 | Long. (o) | -123.997 | 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 |
| F001346 | Metagenome / Metatranscriptome | 718 | Y |
| F001506 | Metagenome / Metatranscriptome | 681 | Y |
| F006508 | Metagenome / Metatranscriptome | 371 | Y |
| F007629 | Metagenome / Metatranscriptome | 347 | Y |
| F012917 | Metagenome / Metatranscriptome | 276 | Y |
| F014219 | Metagenome / Metatranscriptome | 264 | Y |
| F014821 | Metagenome / Metatranscriptome | 259 | Y |
| F017072 | Metagenome / Metatranscriptome | 243 | Y |
| F022124 | Metagenome / Metatranscriptome | 215 | Y |
| F023254 | Metagenome / Metatranscriptome | 210 | Y |
| F024483 | Metagenome / Metatranscriptome | 205 | Y |
| F024806 | Metagenome / Metatranscriptome | 204 | Y |
| F030135 | Metagenome / Metatranscriptome | 186 | Y |
| F031322 | Metagenome / Metatranscriptome | 182 | Y |
| F037573 | Metagenome / Metatranscriptome | 167 | Y |
| F038934 | Metagenome / Metatranscriptome | 164 | Y |
| F041277 | Metagenome / Metatranscriptome | 160 | Y |
| F042355 | Metagenome / Metatranscriptome | 158 | Y |
| F043774 | Metagenome / Metatranscriptome | 155 | Y |
| F044534 | Metagenome / Metatranscriptome | 154 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F054544 | Metagenome / Metatranscriptome | 139 | Y |
| F061006 | Metagenome / Metatranscriptome | 132 | Y |
| F062310 | Metagenome / Metatranscriptome | 130 | Y |
| F062410 | Metagenome / Metatranscriptome | 130 | Y |
| F065810 | Metagenome / Metatranscriptome | 127 | Y |
| F074319 | Metagenome / Metatranscriptome | 119 | Y |
| F079410 | Metagenome / Metatranscriptome | 115 | Y |
| F100201 | Metagenome / Metatranscriptome | 102 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210353_100528 | Not Available | 953 | Open in IMG/M |
| Ga0210353_100927 | Not Available | 794 | Open in IMG/M |
| Ga0210353_103869 | All Organisms → cellular organisms → Bacteria | 1657 | Open in IMG/M |
| Ga0210353_107425 | All Organisms → cellular organisms → Eukaryota → Sar | 2031 | Open in IMG/M |
| Ga0210353_108348 | Not Available | 808 | Open in IMG/M |
| Ga0210353_110462 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Nitzschia → Nitzschia inconspicua | 779 | Open in IMG/M |
| Ga0210353_112047 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Chaetocerotophycidae → Leptocylindrales → Leptocylindraceae → Leptocylindrus → Leptocylindrus aporus | 617 | Open in IMG/M |
| Ga0210353_112590 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 512 | Open in IMG/M |
| Ga0210353_112932 | Not Available | 579 | Open in IMG/M |
| Ga0210353_117967 | Not Available | 641 | Open in IMG/M |
| Ga0210353_120136 | Not Available | 516 | Open in IMG/M |
| Ga0210353_120222 | Not Available | 588 | Open in IMG/M |
| Ga0210353_123146 | All Organisms → cellular organisms → Eukaryota | 568 | Open in IMG/M |
| Ga0210353_125427 | All Organisms → cellular organisms → Bacteria | 2848 | Open in IMG/M |
| Ga0210353_125939 | Not Available | 610 | Open in IMG/M |
| Ga0210353_130040 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 504 | Open in IMG/M |
| Ga0210353_130100 | Not Available | 525 | Open in IMG/M |
| Ga0210353_130635 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 612 | Open in IMG/M |
| Ga0210353_138069 | Not Available | 612 | Open in IMG/M |
| Ga0210353_138119 | Not Available | 504 | Open in IMG/M |
| Ga0210353_138637 | Not Available | 656 | Open in IMG/M |
| Ga0210353_142945 | Not Available | 516 | Open in IMG/M |
| Ga0210353_143114 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1689 | Open in IMG/M |
| Ga0210353_143141 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 707 | Open in IMG/M |
| Ga0210353_145188 | Not Available | 500 | Open in IMG/M |
| Ga0210353_145941 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 681 | Open in IMG/M |
| Ga0210353_146676 | Not Available | 711 | Open in IMG/M |
| Ga0210353_150018 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris | 535 | Open in IMG/M |
| Ga0210353_156151 | Not Available | 507 | Open in IMG/M |
| Ga0210353_158985 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Phaeodactylaceae → Phaeodactylum → Phaeodactylum tricornutum | 733 | Open in IMG/M |
| Ga0210353_159015 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 531 | Open in IMG/M |
| Ga0210353_159183 | All Organisms → cellular organisms → Eukaryota | 1028 | Open in IMG/M |
| Ga0210353_160807 | Not Available | 532 | Open in IMG/M |
| Ga0210353_164858 | Not Available | 688 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210353_100528 | Ga0210353_1005281 | F014219 | MILSINKQSLLLEFAGTKSCSKWVNSNENDWLLGATTGKCEEKDGELVCALRAR |
| Ga0210353_100927 | Ga0210353_1009271 | F001346 | VVWAGPVKTFRKVGDVKNDTADLWTKGNLRVKRRDPWHRANALPRAAADPALIGEDADKKTQTCLDLVRKPVAQPPVQAS |
| Ga0210353_103869 | Ga0210353_1038694 | F012917 | LRFPLNDCGYYDKYESFTEINRAWDKKRHLKRKRWSQE |
| Ga0210353_107425 | Ga0210353_1074252 | F001506 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIRDVYIDEISKTNRFLKNDSTTFKEFNYITIKFFYKTRVPVKKQESLW |
| Ga0210353_108348 | Ga0210353_1083482 | F000344 | MRPKSAHAALSGVGEHPARESESAKWCAEGKERVANAH |
| Ga0210353_110462 | Ga0210353_1104621 | F024806 | MATNSNFNFTNNTAVTLELPFSEHIEELRQRIFLLFWIILVLTCGAFIEVKSLVKI |
| Ga0210353_112047 | Ga0210353_1120471 | F062410 | PQSNSMIERCHKTLHNMIRSAQIKDKRDLDSFFGFKGVLAACRKAMNSTVHTTARATPTQLVFGRDAMLNASFQADWQFIKERKQRLIIQNNKRESAKRKPHTYNVGDVVVVKAGVKRKHGSNPYLDPMRITQVNDNGTVKLAKVADNNGGAVSQTWNIRNIEPRMA |
| Ga0210353_112590 | Ga0210353_1125901 | F079410 | DATESAHQKLHGEKDNLGLLRTFSCCLWVKILAWQNRAKYIQDTKKGIFLGYRTNTLKNVVWYDPLTDRVKYGYHVRFDEGFNDLPLSKLPPNVVLMDRREERIPAETLTITIPPFTTSEHPFFHEDDVTVKVVCDSDLYGFEVREDDCMKRVYISDFKKDGKGTKGRRS |
| Ga0210353_112932 | Ga0210353_1129321 | F041277 | MRPETPLAVENGVGKPAAPEAPNVGTGKRAWRTPIP |
| Ga0210353_117967 | Ga0210353_1179671 | F006508 | VAVANAPLKAVADQSQVVKTRRRNRRRVLTWFASRWRNHQPKRAEKP |
| Ga0210353_120136 | Ga0210353_1201361 | F061006 | LPMPDSRTPEQKATDLDNVLNWVRNPKENDTPQTEPFKKIDQLLPKKPGQSPEDRAKDIDNALTWVRNRGVDQPEFEPTSPFDKLNSIPIDRRTPEQKARDVEDILNWKRNPTDNDSPKTEPFKRIDQLLPKKPGQSPEDRANDIDNTLTWLRNRGVDEPQFGPEEPFKKA |
| Ga0210353_120222 | Ga0210353_1202221 | F045132 | VLMHSSNHYPLGNCDSPESETNPGYLTQFRAASNRPWLPSSFFAFTGRARTPPEELVNTASAAKCVSTSPLRGLINQPDLTFPRSPGRILETSAVNFHSPASVS |
| Ga0210353_123146 | Ga0210353_1231461 | F054544 | MRITQVCDNGTVKLVKVADNNGGAVSQTWNIRNIEPRMA |
| Ga0210353_125427 | Ga0210353_1254272 | F042355 | MSSDLKQLNKGKKNSRRSTNLQEPKFVERLIKISRVSKVTKGGKN |
| Ga0210353_125939 | Ga0210353_1259391 | F006508 | VALANAPSKAVADQCQMVKTRKRNRRRVLTWFASRWRNHQPKRA |
| Ga0210353_130040 | Ga0210353_1300401 | F001506 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQKSLSTTAKCILNSFQNKYIYYAIDDILYLLKSKPSDRDNLLAVLYSPILSLQNNFSVNFFDIWVREVYIDEISKTNKFLKNDSTTLKQFN |
| Ga0210353_130100 | Ga0210353_1301001 | F007629 | KPLLFWNWKLMAPSAEEVKEGSNVKQKDVAELVSKLDAKCNVKATAQGKGLKNNHVLIEGSDNGAISPVIQTTNGSRVPSSRPRTDVRPNGKDTKSNAEHKVERKR |
| Ga0210353_130635 | Ga0210353_1306351 | F022124 | IEVGDVPVNSLSAEHEDDMDALRAQVDTGAHVSCTDQLHMLHDYRDFTRSLPSPVKLLPATVGSDAVPKGMGYLHVPAKNSKGFLAVQTFYSPYLRTTVIDERDLVKASNVREKDIESDSITKYKDSGTFTYRAKHRKNSNKDVIIHGILIDDKCYTGALIPPNLDPSDPKATPATSSVLAVESDPEFAEQCRKATILAIHEYQ |
| Ga0210353_138069 | Ga0210353_1380691 | F046726 | LGKISEQEKIEIIQRGFQLQAQGKISLKKYYESTDPNSLFQSKGYSIKYESIRRTKLYQQLKP |
| Ga0210353_138119 | Ga0210353_1381191 | F024483 | LTDRVKYGYHVPFDEGFNDLPLSKLPPNVVLMDRREERVPAETLTITIPPFTTSEHPFFHEDDVTVKVVCGSDLYGFELREDDCMKRVYISDFKKDGKGTKGRRSCNTICSTERATRRKYRGAYITAIDDEEIVTLNQAKEKLKELRDKNVDTFTMILAREPRPSKS |
| Ga0210353_138637 | Ga0210353_1386371 | F017072 | MRDSAARSDEKPLRVESSSSGWFRAWANRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKRRDPWFRANAPSKAVADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS |
| Ga0210353_142945 | Ga0210353_1429451 | F043774 | RHLRMLQQLDNSITAELLAGARALSLADRRHFELNLSDLLDKSMQYKRNWLLNVIAARRRFERQQANYDGTQTLSIANSKLIKWMTTGRAS |
| Ga0210353_143114 | Ga0210353_1431141 | F065810 | LILNSFQNKYIYYAMDDILYSFRSNPMERDNLLAILYSPVLSLQNNLSTNFFDIWIHEIHIHEVSKVNRFLKHDFKNVKQLNYITIKLFYKTRVPSKKRDSLW |
| Ga0210353_143141 | Ga0210353_1431411 | F044534 | VTGEWIATAGVAFPSERRKSPRGIYHQFLWPESCPVSSHTNQELSGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP |
| Ga0210353_145188 | Ga0210353_1451881 | F100201 | TPSQRTTRAQSIYLQMEKSRDDKVRNIKPKIKERQNHLKRALPAMTDESIKLRSLGWAKHEIEYRNRFQPQEMRAQVTQSVWELLFGAQGYKLDTTELRNVDVYYQRYKDHVKGYDISPKLDGR |
| Ga0210353_145941 | Ga0210353_1459411 | F031322 | KNILWYDTETHAVKIAKHVRFDEGMNDLPPDLVPPNVVHLQRTQNGEPLPAETEETSVDQFTFHLNPFSYTMVKGVPVTDDDPSFGLTLASDELSHRAYVADVKENSTADKLYASHKSTLKNVKGAYLVGINGKKVFSKEDAISMLRQLHDERAKNLQLELAIERKLSSAEAWRAVAEHNIMDPSAVPDVDHHHQLTLADIRSISAARYPHLDFSEAYISTEEMEM |
| Ga0210353_146676 | Ga0210353_1466761 | F014821 | MVATKPSGDRSEELEDALPKPGKDASAPTHLIRSTHLQQQALETARMNFLDSNPYLPMDSIGMYEAATCRIHLCDDDPYEELLHNVDEVETLLQDPVVLAAIHRLLDPDADLDELRVSALQSEAISPEERALPRFSRRALKRLPTWDLWHKNELEQLDQMKALGMFGSPIKLPEGGILMRFHWQYRIKVNGKRRSRLCCDGSPRAAPEVHSTTNTYAS |
| Ga0210353_150018 | Ga0210353_1500181 | F074319 | LADIRSISAARYPHLDLSEASISTEEMEMVVQAIQSQAITPAEQAIGRFTRRKLRSLSTWDQWRAGEHKQLDHFHDLKMYGEPVRKPPGAIVLRSHWQYSIKRDGTRRSRNCCDGSPRSAPLLHGIASTYSSCVEQPVQRLFFALAARENYRVYGGDAQDAYAHSPPPETPTFVSIDD |
| Ga0210353_156151 | Ga0210353_1561511 | F023254 | GFELREDDCMKRVYISDFKKDGKGTKGRRSCNTICSTERATGRKYCGSYITAIDDEEIVTLNQAKEKLKELRNKNVDTFTMILAREPRPSKSTTRRAYDELELPEFDLDENLGEDYFASDGNLEGDSSMTASGEANAFGTDYVPPIGTKISKDFGTKGFFTGTVTSGP |
| Ga0210353_158985 | Ga0210353_1589851 | F038934 | HRAKIMSEVRKMKDKAHESPEYIKFKCLVNNDYEDIVAYNDVVDFIEKDATWDGIWTFEKILTHQKVKSGDKNHRGSGTNCLVLWSTGEQTWEPLYNRTGKSGLWIDDPVTVAIYARDNGLLDEPGWKLPGLKKMAKTQKKLLRLANKAKLHSFRNKPVYMYGFQVPRNHIEAMELDRMNGNSMWRDAEVTELN |
| Ga0210353_159015 | Ga0210353_1590151 | F001506 | RKVTKRSEGKPLRYPNLDEIRAKTFQIKSEQKLSLIAKLVLNSFENKYLYYAIDDILYLLKSNPIERDHLLAILYYPVLSLQNNFSINFFDIWIDDIYISKTSKKNKFLSKNCQNLEPFSYITIKLLYKTTIPIKKKELYW |
| Ga0210353_159183 | Ga0210353_1591831 | F062310 | MSGLRKKLNSLDTELGLMEMVLAGIKSALTRQPFSVSQDLRNLAAAQEAIGWTNLFKGRISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGRANKLKDVAFREMTHLYTFEEAVPDDIRWLFQTPLEECLHWPLFRQRAWITNWEHIIKKEYATQMETG |
| Ga0210353_160807 | Ga0210353_1608071 | F037573 | MKITASKDFGSVRKPVLPLVPEPTTVLKKEDLTQVDLFSNPLDVNSTKVKFAFKILEGGTESPREVIHWLQNVERAFTG |
| Ga0210353_164858 | Ga0210353_1648581 | F030135 | EEFAKLSSTSDIWHSTFIGCQLPDAIPPGTEDFDLVAGPLD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |