| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300026033 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116070 | Ga0208652 |
| Sample Name | Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLA_D1 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 87604917 |
| Sequencing Scaffolds | 14 |
| Novel Protein Genes | 14 |
| Associated Families | 13 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1 | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 3 |
| Not Available | 4 |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 1 |
| All Organisms → cellular organisms → Bacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Wetlands → Unclassified → Natural And Restored Wetlands → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → wetland area → soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Fairfield, San Francisco Bay, California | |||||||
| Coordinates | Lat. (o) | 38.197102 | Long. (o) | -122.010033 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001823 | Metagenome / Metatranscriptome | 630 | Y |
| F007858 | Metagenome / Metatranscriptome | 343 | Y |
| F013110 | Metagenome / Metatranscriptome | 274 | Y |
| F018387 | Metagenome / Metatranscriptome | 235 | Y |
| F024001 | Metagenome / Metatranscriptome | 208 | Y |
| F027172 | Metagenome / Metatranscriptome | 195 | Y |
| F052268 | Metagenome | 143 | Y |
| F065699 | Metagenome / Metatranscriptome | 127 | Y |
| F068909 | Metagenome / Metatranscriptome | 124 | Y |
| F085674 | Metagenome / Metatranscriptome | 111 | Y |
| F095691 | Metagenome | 105 | Y |
| F105202 | Metagenome | 100 | Y |
| F105468 | Metagenome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208652_1000641 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1 | 4600 | Open in IMG/M |
| Ga0208652_1001837 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 2644 | Open in IMG/M |
| Ga0208652_1005702 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 1533 | Open in IMG/M |
| Ga0208652_1012264 | Not Available | 1031 | Open in IMG/M |
| Ga0208652_1016160 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 887 | Open in IMG/M |
| Ga0208652_1016890 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 865 | Open in IMG/M |
| Ga0208652_1017212 | Not Available | 856 | Open in IMG/M |
| Ga0208652_1017525 | Not Available | 847 | Open in IMG/M |
| Ga0208652_1021587 | All Organisms → cellular organisms → Bacteria | 753 | Open in IMG/M |
| Ga0208652_1036796 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 558 | Open in IMG/M |
| Ga0208652_1037255 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 554 | Open in IMG/M |
| Ga0208652_1041015 | Not Available | 525 | Open in IMG/M |
| Ga0208652_1041861 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 519 | Open in IMG/M |
| Ga0208652_1042513 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 515 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208652_1000641 | Ga0208652_10006414 | F105202 | QSDLHLDVQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELNILKRQSLAFRGSRQDIQSANLKLQKRIGQLQKKVRNLERSNAKLNKTIEMLSTLDSRLEEKRINFIKTDSIEEK |
| Ga0208652_1001837 | Ga0208652_10018373 | F018387 | MIGVEVPLLDQGSVQFILLGVMILAVLALLWITIAK |
| Ga0208652_1005702 | Ga0208652_10057022 | F007858 | VCRALVVLCVADDREALVALKASTVSAEWELAPGAIDLRSTLDQIDADRPHVMVAFGDHVELVGIVRERFPSMRIVTDRDTPGATVVATSLDEVRGLVLGLPRPGGPVGA |
| Ga0208652_1012264 | Ga0208652_10122641 | F105468 | ETTPSVREKTLERENRELKEKLAELYLENAQLKKLGDWLRRRRNASTSVITAQSLTRSPKDSKS |
| Ga0208652_1016160 | Ga0208652_10161603 | F013110 | MSGSRKDTLLRALEAEVGIAPADPGSLFTDDVVGWSPYASVSGLTAVSELAALRDMAFSGVSIS |
| Ga0208652_1016890 | Ga0208652_10168902 | F007858 | MCRALIVLCVATDVASLSALKQATVSAEWELTPGATNETDALGQVDAERPHVLVAFGPYERLVALCAERFPGMRIVADRDVPGATVVAT |
| Ga0208652_1017212 | Ga0208652_10172121 | F052268 | PGLPGEWRGTRYDFVKGGAGLTIPGLPDAVRGCLDGT |
| Ga0208652_1017525 | Ga0208652_10175252 | F001823 | MRAYDRDLIRGGHYGQRPCVPHLKAEHMAAPTNAANVKKALANSEPSTH |
| Ga0208652_1021587 | Ga0208652_10215871 | F095691 | MLQHDGSIRIAWQADGFEAILVRARFRPASQRDEFARGVADVALLERNLPDLQAALRACYPGAFDLITDRSLSGPGRVIVSFHPPP |
| Ga0208652_1036796 | Ga0208652_10367962 | F068909 | STKPAPPCPKCGSDEVTRLLSRINTEWLPSDVAWDRVGRSWD |
| Ga0208652_1037255 | Ga0208652_10372552 | F027172 | MAEKTILVCDACGKPAAETVTMKTSRGNFVKDLCSTHVNELVAGARKPRPGRRKGTTVTAAAKPAAKAATAAPKKRGRPRKKPAS |
| Ga0208652_1041015 | Ga0208652_10410151 | F085674 | MPGEVMLVGIATIAIAIAGFTAITSALEPPGGSWSPAMRLRQRSIVSTSFNVGLESFAPLIAFAWLEELHSALVVASLVVAIYTTSVVLFRGRQFVRAGGMHTGVAGLTLFALGPTATLLFWANAIVFASLAIFALALLVQLLVAMISF |
| Ga0208652_1041861 | Ga0208652_10418612 | F065699 | VTEQYIGWALALGLVVGGALVWFAVGRLPRSGEEIPDEERAAEAAWISASIDERGGKAPADLVEEVLELHAEYLDRQSQELA |
| Ga0208652_1042513 | Ga0208652_10425131 | F024001 | KNKLMILGVEAPGRQGVKPQEYLDIPRFCNAAGRDASATKMAGYF |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |