| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300000860 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0084963 | Gp0057246 | Ga0011713 |
| Sample Name | Marine microbial communities from the coastal margin of the Columbia River, USA - metatranscriptome 33 PSU, 16m |
| Sequencing Status | Permanent Draft |
| Sequencing Center | University of Maryland |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 9628445 |
| Sequencing Scaffolds | 7 |
| Novel Protein Genes | 8 |
| Associated Families | 8 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodobacterales → Rhodobacteraceae → unclassified Rhodobacteraceae → Rhodobacteraceae bacterium TMED160 | 1 |
| All Organisms → Viruses → Predicted Viral | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Freshwater And Marine Microbial Communities From The Columbia River, Usa, Of Estuaries And Plumes Across Salinity Gradients |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Marine → Neritic Zone → Unclassified → Freshwater And Marine → Freshwater And Marine Microbial Communities From The Columbia River, Usa, Of Estuaries And Plumes Across Salinity Gradients |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | marine biome → marine neritic zone → sea water |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Columbia River plume, coastal ocean | |||||||
| Coordinates | Lat. (o) | 46.233 | Long. (o) | -124.16 | Alt. (m) | N/A | Depth (m) | 16 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F003977 | Metagenome / Metatranscriptome | 459 | Y |
| F019651 | Metagenome / Metatranscriptome | 228 | Y |
| F029925 | Metagenome / Metatranscriptome | 187 | Y |
| F033962 | Metagenome / Metatranscriptome | 176 | N |
| F050663 | Metagenome | 145 | Y |
| F059360 | Metagenome / Metatranscriptome | 134 | Y |
| F065210 | Metagenome / Metatranscriptome | 128 | Y |
| F077260 | Metagenome / Metatranscriptome | 117 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| BpTDRAFT_101003 | Not Available | 1426 | Open in IMG/M |
| BpTDRAFT_102227 | Not Available | 1925 | Open in IMG/M |
| BpTDRAFT_104808 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodobacterales → Rhodobacteraceae → unclassified Rhodobacteraceae → Rhodobacteraceae bacterium TMED160 | 1741 | Open in IMG/M |
| BpTDRAFT_105945 | Not Available | 1500 | Open in IMG/M |
| BpTDRAFT_109060 | All Organisms → Viruses → Predicted Viral | 1350 | Open in IMG/M |
| BpTDRAFT_109887 | Not Available | 676 | Open in IMG/M |
| BpTDRAFT_110259 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium | 917 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| BpTDRAFT_101003 | BpTDRAFT_1010032 | F059360 | MTLFKEVLVPANLVPAAAVIREGQALSNITGRKESVDCNISYMLKPKASL* |
| BpTDRAFT_102227 | BpTDRAFT_1022276 | F050663 | MSDMTKEEAIEQARRNYMELFHDQETKLSNLYDECDELEEGDLEEWRIE* |
| BpTDRAFT_104808 | BpTDRAFT_1048081 | F077260 | MRVLLLLVFVISFSAKIMELDAKDPNLSEIDTKLTESSISSDQLDAVFQDFFGLEAKSKIENETIISVVFENVQEEDALLVLQRSQEVKVLKLHKASIISGESEKSYNLEIIYVAG* |
| BpTDRAFT_105945 | BpTDRAFT_1059452 | F003977 | MPRTKLSKQQLDYKEGLAHFKTWLKMNKQFEDRGLHGTDYYVRIVEELEAKVKQLEAKLKRKAKK* |
| BpTDRAFT_109060 | BpTDRAFT_1090602 | F033962 | MTELKQYMAEQKRIKVIQWNKDREGNHCQGFTQKEFEQSMEVDRIKSRTRRTHSKGNLWVFNDTKDRELFTK* |
| BpTDRAFT_109060 | BpTDRAFT_1090603 | F019651 | MTTLEKFQEEANINFVQTPSHADVELGELQTADGYELYYVTQDIQNLNYENELFYYKPDFDTIMAAIDDYRHREDTANVVCYDIEDWFDEYDMLNWLESEMDEESFEAFTNET* |
| BpTDRAFT_109887 | BpTDRAFT_1098872 | F065210 | VIFMEITKSQFKSYDGIHELVITHSPHIRSIDIAQHIIDTQNEVVMLKNIIEDLRQREKKKEAIIDNTR* |
| BpTDRAFT_110259 | BpTDRAFT_1102594 | F029925 | MFILKSILTQAGSVWQVESIAMRERDAKRILKRRQAQNDGSRRYG |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |