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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| Taxon OID | 3300024343 Open in IMG/M |
| Scaffold ID | Ga0244777_10002688 Open in IMG/M |
| Source Dataset Name | Combined assembly of estuarine microbial communities from Columbia River, Washington, USA >3um size fraction |
| Source Dataset Category | Metagenome |
| Source Dataset Use Policy | Open |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Sequencing Status | Permanent Draft |
| Scaffold Components | |
|---|---|
| Scaffold Length (bps) | 12106 |
| Total Scaffold Genes | 43 (view) |
| Total Scaffold Genes with Ribosome Binding Sites (RBS) | 40 (93.02%) |
| Novel Protein Genes | 14 (view) |
| Novel Protein Genes with Ribosome Binding Sites (RBS) | 14 (100.00%) |
| Associated Families | 14 |
| Taxonomy | |
|---|---|
| Not Available | (Source: ) |
| Source Dataset Ecosystem |
|---|
| Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series |
| Source Dataset Sampling Location | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location Name | Columbia River Estuary, USA | |||||||
| Coordinates | Lat. (o) | 46.234 | Long. (o) | -123.9135 | Alt. (m) | Depth (m) | Location on Map | |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000263 | Metagenome / Metatranscriptome | 1424 | Y |
| F000311 | Metagenome / Metatranscriptome | 1326 | Y |
| F000441 | Metagenome / Metatranscriptome | 1136 | Y |
| F000447 | Metagenome / Metatranscriptome | 1128 | Y |
| F000852 | Metagenome / Metatranscriptome | 860 | Y |
| F001043 | Metagenome / Metatranscriptome | 794 | Y |
| F001460 | Metagenome / Metatranscriptome | 690 | Y |
| F001562 | Metagenome / Metatranscriptome | 670 | Y |
| F004051 | Metagenome / Metatranscriptome | 455 | Y |
| F004840 | Metagenome / Metatranscriptome | 421 | Y |
| F009530 | Metagenome / Metatranscriptome | 316 | Y |
| F023344 | Metagenome / Metatranscriptome | 210 | Y |
| F036238 | Metagenome | 170 | Y |
| F047059 | Metagenome / Metatranscriptome | 150 | Y |
| Protein ID | Family | RBS | Sequence |
|---|---|---|---|
| Ga0244777_1000268811 | F023344 | AGGCGG | MEAFTDTVGEHILGAIQVDIEQALFEDWNQSNLDEGEAYAEYRFMQFAPDTLKQSYNEYYGYIEGDEFLL |
| Ga0244777_1000268813 | F036238 | GGCGG | MGDRANFGFKQSNGETIVLYGHWAGHGMLERLADAVEAARSRWGDESYATRIAVSHLVGEQWQDTTGWGLSVNNILDNEHKIPLIDWNTQTFSLHEEAPWSESTEYKVRGMQDEPMFTMTLDSFINKYSRVNA |
| Ga0244777_1000268815 | F001043 | AGGAG | MSDYKDGFQDGYKFAREEIIEKLAEIDITDIDTWILDRLSDMIEGGTI |
| Ga0244777_1000268816 | F000311 | GAG | MYFELTAPDRLSMERAYWDAEITGLDPEAMSALTFNIGTGSIEKVSRLRDKYNLIESYVSDSKVTGY |
| Ga0244777_1000268823 | F004051 | GAGG | MTIQDKLYQVGDLFTTLKSKKTGVIKEIHPQASGSVRVLLEMPTKETRWTTVSASTLAGA |
| Ga0244777_1000268829 | F004840 | GGA | MYKITCAYDGNAPHWSAEYENEYGAWENFFLFTDWGFADEYSTVNLYTPAGKCHTKVFYRAGRKVVIK |
| Ga0244777_1000268830 | F000447 | GAGG | MGYIEIFRMDQDGAGWVDLSEATPDELFTIEVGLLNEGALFYTPEAE |
| Ga0244777_1000268834 | F001562 | AGGAGG | MKSQLEKDIETKESFIDLLNDVYPSVKIGYSTFTPAEILECCDPIAFAIGLAEHEDYLAEMENE |
| Ga0244777_100026884 | F000852 | AGGAG | MATKREYLKAQGITVGVRGRFSGAAKVALAEAVAKGVTFTAETPAKKAK |
| Ga0244777_1000268840 | F009530 | GGAG | MTIKYSIWQGSKLISIDNIAHDVNAIDHLIQSLNNSELGKGKKFTANVMDIKVTA |
| Ga0244777_100026885 | F000441 | AGGAGG | MKMSDDYINDQLNKAQKLLWGGSETENIEAHNIISRLIKDKIEQVS |
| Ga0244777_100026887 | F000263 | AGG | MNKEDIGLPPHLQRMVNARVSGLDIIHGELKNLMLIAEQDLADALEQEERSEEAMDSMVRTECEGRLDTLVALYELTYQLSFAIGEQIEV |
| Ga0244777_100026888 | F047059 | GGA | MKIHKISLEQDLEDARNNIPLNEDEYFESDAYYTGAIDTMEHILSVADDIMNNSNERYIN |
| Ga0244777_100026889 | F001460 | GGAGG | MLGYEKKDLDTMINSVHDAKLFYLRSPSDLMDKTELRTNLEMTVSFLQGLWAEGYFD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |