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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 | 3300021292 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114516 | Gp0225739 | Ga0210355 |
| Sample Name | Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Oregon, United States ? S.493 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 52448269 |
| Sequencing Scaffolds | 30 |
| Novel Protein Genes | 30 |
| Associated Families | 13 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 3 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| Not Available | 13 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya | 3 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 4 |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar | 1 |
| All Organisms → cellular organisms → Eukaryota | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales 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: Oregon | |||||||
| 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 |
| F008361 | Metagenome / Metatranscriptome | 334 | Y |
| F014854 | Metagenome / Metatranscriptome | 259 | Y |
| F020183 | Metagenome / Metatranscriptome | 225 | Y |
| F024806 | Metagenome / Metatranscriptome | 204 | Y |
| F025295 | Metagenome / Metatranscriptome | 202 | Y |
| F046726 | Metagenome / Metatranscriptome | 151 | Y |
| F054425 | Metagenome / Metatranscriptome | 140 | Y |
| F083433 | Metagenome / Metatranscriptome | 113 | Y |
| F105419 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210355_1000278 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 4353 | Open in IMG/M |
| Ga0210355_1001928 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 806 | Open in IMG/M |
| Ga0210355_1003376 | Not Available | 622 | Open in IMG/M |
| Ga0210355_1006421 | Not Available | 819 | Open in IMG/M |
| Ga0210355_1006454 | Not Available | 810 | Open in IMG/M |
| Ga0210355_1012106 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 2181 | Open in IMG/M |
| Ga0210355_1012370 | Not Available | 508 | Open in IMG/M |
| Ga0210355_1014181 | Not Available | 727 | Open in IMG/M |
| Ga0210355_1016981 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya | 3745 | Open in IMG/M |
| Ga0210355_1021585 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 1996 | Open in IMG/M |
| Ga0210355_1028492 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 529 | Open in IMG/M |
| Ga0210355_1042320 | Not Available | 683 | Open in IMG/M |
| Ga0210355_1045562 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya | 4597 | Open in IMG/M |
| Ga0210355_1047444 | Not Available | 541 | Open in IMG/M |
| Ga0210355_1047993 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 1250 | Open in IMG/M |
| Ga0210355_1055740 | Not Available | 788 | Open in IMG/M |
| Ga0210355_1056169 | All Organisms → cellular organisms → Eukaryota → Sar | 699 | Open in IMG/M |
| Ga0210355_1057121 | Not Available | 914 | Open in IMG/M |
| Ga0210355_1059425 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 622 | Open in IMG/M |
| Ga0210355_1059865 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales | 641 | Open in IMG/M |
| Ga0210355_1061970 | Not Available | 855 | Open in IMG/M |
| Ga0210355_1072597 | All Organisms → cellular organisms → Eukaryota | 2531 | Open in IMG/M |
| Ga0210355_1073424 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 7837 | Open in IMG/M |
| Ga0210355_1073907 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 1239 | Open in IMG/M |
| Ga0210355_1088526 | Not Available | 1134 | Open in IMG/M |
| Ga0210355_1092118 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya | 3359 | Open in IMG/M |
| Ga0210355_1096786 | Not Available | 713 | Open in IMG/M |
| Ga0210355_1101012 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta | 651 | Open in IMG/M |
| Ga0210355_1101179 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → unclassified Syntrophobacterales → Syntrophobacterales bacterium | 536 | Open in IMG/M |
| Ga0210355_1105456 | Not Available | 717 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210355_1000278 | Ga0210355_10002784 | F020183 | MSLTINTKTFTADRYGQDAIGYVGPAHTLSLLDDVQLSRVAPKPTSVFSGVGRTSAKLTRTLTLTDALTPTGNAIVSISVSVPVGAASADVDDLLNDMGSFLSSATAKTHVKGLQISY |
| Ga0210355_1001928 | Ga0210355_10019281 | F000344 | MRPKHPHAAESGVGKHTARESERAQACATGKERVANAHS |
| Ga0210355_1003376 | Ga0210355_10033761 | F046726 | LGKIPEEEQIEIIKTGFQLQAEGKLSLKKYYESTDPNSLFQSKGYNIKYDTIRKNNLYQPLKE |
| Ga0210355_1006421 | Ga0210355_10064211 | F008361 | VNDVEELTNIELSEAIKELEQATAAVENAETGKARLDASVELKKATARLEAVNYLS |
| Ga0210355_1006454 | Ga0210355_10064542 | F000344 | MRPKSAHAALSGVGEHPARESESAKWSADGKERVANAHP |
| Ga0210355_1012106 | Ga0210355_10121062 | F020183 | MSLTINAKAFTADKYGQDLVGYIGPAHTLSLLDDVQLSRVAPKPTSVFSGVGRTSAKLTRTFTLTGALTTTGNAICQISCSVPVGAAGADVDALLNDFGSFLSSATFKTHVKGLQITF |
| Ga0210355_1012370 | Ga0210355_10123701 | F004323 | MPLDDLRRLEGMATPAVAIHSPVTRDYPSRALSDVFQAAALRLF |
| Ga0210355_1014181 | Ga0210355_10141811 | F025295 | IMVTGPGEDTELLRRREVLIPEKLKFLTRKSNLQKPI |
| Ga0210355_1016981 | Ga0210355_10169811 | F001506 | MNRILYENRCRCNEEFSLTKKRQSTTRSEGKPLQYPNYTESTSKTFQIKYDKKLSSLAKAILNSFQKKYIYYAIDDILYFLKGNSIEQENLLAILYSPILSLHNNFSINFFDIWIGEVYIEEISKVNKFLTKDSQTFTQFSYITIKLFYKT |
| Ga0210355_1021585 | Ga0210355_10215853 | F001506 | MNRILYEKRCKCNEEFSIIKKRKTKTRSEGKPLEYPQSSEMTSKTFQIKYQKNLSTTAKCILNSFHNKYIYYAIDDILYLLKSQPMERDNLLAVIYSPILSLQNNFSVNFFDIWIHEVYIDEISKNNKFLKNDLTTLKQFNYITIKFFYKTRVPVKKQESFW |
| Ga0210355_1028492 | Ga0210355_10284921 | F105419 | RAGTALMAKPTVVASREGESTNMRKTIAFCSLMLAAAITNGCISTTMYGCEITETLAPGASEGEVVMKHGAPDNILYLGNQYMNPQTGERGEVDKYLYEYRIGGGTTLLGKVFATDEFHNIGYLIEGGKVMGGGYVGEGKGTIILGNTPISLPVIGKFDMGGYFLHPKVRAGYGG |
| Ga0210355_1042320 | Ga0210355_10423201 | F002557 | VLMHSSNRYPLGNCDSSGSETNPDYLTQFGAASHRSWLPSSFFAFTGRARTPPEELVNSASAAK |
| Ga0210355_1045562 | Ga0210355_10455626 | F001506 | MNRILYKNRCRCNEEISITKKRNSSNRSEGKPLQYPKPNEITSKTFQITYEKKLSPIAKLVLNSFHNKYIYYAIDDILYSFQSNPHERDNLLAILYSPVLSLQNNFSINFFDIWIHEIYINEVSKINKFLNNDSLNFEQFSYITIKLLYKTRVPIKKQDSLW |
| Ga0210355_1047444 | Ga0210355_10474442 | F046726 | LGRISEQEKIEIIQRGFQLQAEGKISLKKYYESTDPNSLVQSKGYSIKYESIRRTKLYQQLKPSNN |
| Ga0210355_1047993 | Ga0210355_10479932 | F001506 | MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTRLSTTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIRDVYIDEISKTNRFLKNDSTTLKEFNYITIKFFYKTRVPVKKQESLW |
| Ga0210355_1055740 | Ga0210355_10557401 | F054425 | RSLSHAGIGRLVGCQLPDAILHGKRSFRPRSRAVQNLAASGLSSEAFQLVSADGCATGLRTRSRHVYDFSPRLDRLTPGRPPLLAVRWPGVTGLAS |
| Ga0210355_1056169 | Ga0210355_10561691 | F046726 | KDEQTEISQRLFQLQAQGIISLKKYYQSTDPDSLFQSKGYFIKYESIRRTKLYQQLKPSN |
| Ga0210355_1057121 | Ga0210355_10571212 | F024806 | MATNSNFNFTNNTAVTLELPFSEHIEELRQRIFLLFWIILVLTCGAFIEVKS |
| Ga0210355_1059425 | Ga0210355_10594251 | F001506 | MNRLLYENRCKCNEEFSVMKKRKIKTRSEGKPLQYPKSSEIKSKTFQMKYQKNLSPTAKSILNSFQNKYIYYAIDDILYSLKSKPVERDNLLAVLYSPILSLQNNLSVNFFDIWISDIFIDEISKTNKFLKKDSITLKQFNSITIKFFYKTRVPVKKQESLW |
| Ga0210355_1059865 | Ga0210355_10598651 | F020183 | MSLTINAKTFTADRFGVDAVGYIGPAHTLSILDDVQLSRVAPKPTVVFSGVGRTSTKLTRTLTLTGSLTTSGNAIVQINVSVPVGAASADIDALLNDMGSFLSSASYKTHVKGLQISY |
| Ga0210355_1061970 | Ga0210355_10619702 | F025295 | VTGPGEAAELLKRREVLIPKKLKHLTRKSNLQKLN |
| Ga0210355_1072597 | Ga0210355_10725974 | F046726 | KDEQTEISQRLFQLQAQGIISLKKYYQSTDPDSLFQSKGYSIKYESIRRRPLFKQLKPSN |
| Ga0210355_1073424 | Ga0210355_10734242 | F001506 | MNRILYESRCRCKEEISITPKRKLSARSEGKPLQYPNEMMSKTFQIRYDKKLSSLARFILNSFRNKYIYYAIDDILYLMKSNPIERENLLALLYSPVLSLHNNLCINFFDIWIHEIYINETFKVNKFLENESQNLEQFTDITIKFLYKTRIPVKKLDSLW |
| Ga0210355_1073907 | Ga0210355_10739072 | F001506 | MNRILYESRCRCKEEISITPKRKLTARSEGKPLQYPNEMMSKTFQIKYEKKLSSLARFILTSFRNKYIYYAIDDILYLLKSNPVERESLLALLYSPVLSLHNNLCINFFDIWIHEVYINETSKVNKFLTTESQNLEQFTYITIKFLYKTRVPVKKPDSLW |
| Ga0210355_1088526 | Ga0210355_10885262 | F046726 | LGKISEQEKREIIQTGFRINQEGKISLKKYYQSKQEFILFQSKGYFIKYESIRRTKLYQQ |
| Ga0210355_1092118 | Ga0210355_10921181 | F001506 | MNRILYENRCKCNEEFSITKKRKSPTKSEGKPLQYPKPNEIISKTFQIRYDKKLSTTSKFILNSFQNKYIYYAIDDILYLFELNKTERNNLLAILYSPVLSLQNNFFVNFFDIWIREIYIDEVSKVNKFLNHDSQTSEQFSYIIIKFFYKTRVPVKKQESLW |
| Ga0210355_1096786 | Ga0210355_10967861 | F014854 | LRWTAVDERKSLVVSRMIPGNWGKVESGWLARPLLDRIARSGGGGRIHQFLWSRSHAVSYAKRNLAARGDKKPLRVGSSSSGRFRAWANRSYPEGKWLLLCIGTGRVTLADSINRLKPPNESH |
| Ga0210355_1101012 | Ga0210355_11010121 | F001506 | GKPFVYPNPNELTSKTFQIKYEKNLSSVAKFLLNSFQNKYLYYAIDDILYLLKSNPSERDNLLALLYSPVLSLQNNFSINFFDIWIQEIYITEVSKTNKFLQMTDSSFESFHSITIKLLYRTKIPMKQQESLW |
| Ga0210355_1101179 | Ga0210355_11011791 | F083433 | MKHRALFIAFMIVALAAFYSVPKANAEPLTIMAIVGVVAVLSASSVDMVATSHEDTKDQRAQLDEAANMHAKVEASGVTSGSEEAVAASN |
| Ga0210355_1105456 | Ga0210355_11054561 | F002557 | VLMHSSNHYPLGNCDSPGSETNPDYLTQFGAVSHRPSLPSSFFAFTDGARTPPEELVNSASSIACVSTRLRRGRVN |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |