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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 | 2046860007 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0060820 | Gp0051555 | Ga0026416 |
| Sample Name | Freshwater sediment microbial communities from Lake Washington, Seattle, for methane and nitrogen Cycles - Microc enrich af exp to meth lab w 13Ccarbon-no added nitrate |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 76631179 |
| Sequencing Scaffolds | 14 |
| Novel Protein Genes | 16 |
| Associated Families | 15 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 10 |
| All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica | 1 |
| All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Freshwater Sediment Microbial Communities From Lake Washington, Seattle, Usa, For Methane And Nitrogen Cycles |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Freshwater → Lentic → Sediment → Freshwater Sediment → Freshwater Sediment Microbial Communities From Lake Washington, Seattle, Usa, For Methane And Nitrogen Cycles |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | freshwater lake biome → freshwater lake → lake sediment |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Sediment (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Lake Washington, Seattle, Washington, USA | |||||||
| Coordinates | Lat. (o) | 47.07 | Long. (o) | -122.27889 | Alt. (m) | N/A | Depth (m) | 62 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F008881 | Metagenome / Metatranscriptome | 326 | Y |
| F009004 | Metagenome / Metatranscriptome | 324 | Y |
| F022903 | Metagenome | 212 | Y |
| F027186 | Metagenome / Metatranscriptome | 195 | Y |
| F027195 | Metagenome | 195 | Y |
| F031100 | Metagenome / Metatranscriptome | 183 | Y |
| F031499 | Metagenome / Metatranscriptome | 182 | Y |
| F031548 | Metagenome / Metatranscriptome | 182 | Y |
| F034983 | Metagenome | 173 | Y |
| F046728 | Metagenome | 151 | Y |
| F055309 | Metagenome | 139 | Y |
| F074886 | Metagenome / Metatranscriptome | 119 | N |
| F082695 | Metagenome / Metatranscriptome | 113 | N |
| F098877 | Metagenome | 103 | Y |
| F104669 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| LWAeNNiSIP_contig00183 | Not Available | 1023 | Open in IMG/M |
| LWAeNNiSIP_contig00524 | All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica | 2745 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02G6Z6Y | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium | 530 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02GALZ5 | Not Available | 507 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02GECEU | Not Available | 509 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02HFTHT | Not Available | 529 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02HL67P | Not Available | 544 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02HMKT7 | Not Available | 558 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02HQ712 | Not Available | 520 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02HWUNM | Not Available | 530 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02IBEKN | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 534 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02IE003 | Not Available | 537 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02J33FC | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 521 | Open in IMG/M |
| LWAeNNiSIP_GDP3C2T02JYRK1 | Not Available | 508 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| LWAeNNiSIP_contig00183 | LWAeNNiSIP_1848190 | F074886 | MPKIPRNFIQEFPYGVSIEDSLNKGMKYLNADPNYITNWKDIIFTPIENFIHHQVFIFSEGKDMLIGFLVSQQATFLPDFISATIQLFGGVYTIDDTTNSIFIQEFIYYSILFLIGLGSARLAISMWLIINPYTMPWFLLLTATEWFMDSFAGIFPAVFGIEMTGSIVLGLLGSLAVYVKNLVLTMPYLPSEAIKQTIGIHEVYTFGGIPILWKIFSVPDKLREEWYKSTPYLIENLIKYYGDEGVEFVPSRILKEFYNNTPVADYTYYFAFVFSEFK |
| LWAeNNiSIP_contig00524 | LWAeNNiSIP_4647590 | F082695 | LFVQFTFFSYESETGDETDVAKWAHKLMNRSVANRTITKQEAMCELGGLPMVICSESIETISITGSTKCATDTNTSTILSQYRNRPDAQQHLSLHQFYHIKKNKKLASTPSYREFIPHYVGGKGQPVYPITRSYARSELLKHLPWGRKNPMPNDCDLITMFKQFLENPKCPVGVRLGFERAKLRKELKEKGIQEAFQPDIEHSSNTDDVDDDEVGEVIALTESLGYTEDELEKLENNGFFLGKDYDWGKRIYTVSNPTIHHTRFGIILNY |
| LWAeNNiSIP_GDP3C2T02G6Z6Y | LWAeNNiSIP_3623920 | F031100 | MSDAPSSLDTAKYRHLVLDSLAAIQGFQVPEYDDLVVTYYGATNNIATVTYKKASVVVATLTLLYSVQP |
| LWAeNNiSIP_GDP3C2T02GALZ5 | LWAeNNiSIP_33470 | F027186 | MISNFDFNFKNTPTLTLELPFSEHIEELRQRIIHIFWIILLLSLLVIY |
| LWAeNNiSIP_GDP3C2T02GECEU | LWAeNNiSIP_3996030 | F027195 | VSYTAVSYTFYDYLELPQDATPARVEAAYVGLLERFGYGTTDAGQDMSNRVAMIHAAYNVLANP |
| LWAeNNiSIP_GDP3C2T02HFTHT | LWAeNNiSIP_540370 | F046728 | MLRYMVYGVLPLLLLFALLQRFGAGDIGALVVVLAALLPFIAIGWLGYQHFRHRRK |
| LWAeNNiSIP_GDP3C2T02HL67P | LWAeNNiSIP_2095760 | F008881 | MKKVVCINDKNLPQGAEVVNGKEYYVVNEFVNTFDQRVFIISGITNKGTTKFRLNWLGYCSTRFADLDDI |
| LWAeNNiSIP_GDP3C2T02HLG94 | LWAeNNiSIP_1880170 | F034983 | TLPAVIAGLDEDAGRLMSEIAVEGVPAEGISAEDCVRELRRQPLKARMAEIQKRLAGTSGDAQEALLAEKTRLVRQMAGL |
| LWAeNNiSIP_GDP3C2T02HMKT7 | LWAeNNiSIP_4626600 | F009004 | MKTEFNKVIDFLELQQQEDKLNTNQLHLIIQTLCTFLDDEQLQEVENLFNQFKK |
| LWAeNNiSIP_GDP3C2T02HQ712 | LWAeNNiSIP_4669390 | F098877 | LNLIVSVVIGVLAAQKFFQLFDKTVPAGSMTDLVRAGTHTAYLVTGVVFGLVIFAWTAAAAWLARFFPAAGSEAHAPGQAAK |
| LWAeNNiSIP_GDP3C2T02HWUNM | LWAeNNiSIP_3243830 | F031499 | MANIPVNFGGVILTAGNSVTGSFAGITSLGTGSSVAITGSIILAFKYGVGLQADQAIIQATGPSFTIPAGVTVPLMITSCSLAALSAPVLLYT |
| LWAeNNiSIP_GDP3C2T02IBEKN | LWAeNNiSIP_653910 | F031548 | VKTNILKIFAIATLMIFIGAGVSMADGWKENGGNRGHAYGHYKQREYQHYQYYAPRPVYVERQYYPVVVERHVYHSPVVYQAPSPSGYFVGISVFEPGMAFSFGMSGH |
| LWAeNNiSIP_GDP3C2T02IE003 | LWAeNNiSIP_3901670 | F031100 | MSDAPSSLDTAKYRHLVLDSLAAIQGFQVPEYDDLVVTYYGATNNIATVTYKKASVVVATLTLLYSVQPPTANDANLVRVTIS |
| LWAeNNiSIP_GDP3C2T02IVOZZ | LWAeNNiSIP_4835080 | F104669 | MNTLARNGGFWIVVGTAAGTATGMALGVASVGLALGLALGILGGCLTRR |
| LWAeNNiSIP_GDP3C2T02J33FC | LWAeNNiSIP_74140 | F055309 | RNREEVLRIFKKWCLLTRDMISLNRADPVAKARHRQIDAPVGPLSDIHSLQYANNVRHILTVNSLQTLKPPRNQRINPQSRSAPEAV |
| LWAeNNiSIP_GDP3C2T02JYRK1 | LWAeNNiSIP_230070 | F022903 | VSWALFWLVSFAVAFVGFSAISLVIAVRGVAEIRDLFSALEEERRRKASRKD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |