| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300026144 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114514 | Gp0125945 | Ga0209954 |
| Sample Name | Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_A_D2_MG (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 218009731 |
| Sequencing Scaffolds | 12 |
| Novel Protein Genes | 15 |
| Associated Families | 13 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 3 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 1 |
| Not Available | 4 |
| All Organisms → cellular organisms → Bacteria | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Nitrosopumilus adriaticus | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration. |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Wetlands → Unclassified → Soil → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration. |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → wetland area → soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | South San Francisco, USA | |||||||
| Coordinates | Lat. (o) | 37.4962 | Long. (o) | -122.1329 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001127 | Metagenome / Metatranscriptome | 769 | Y |
| F003470 | Metagenome / Metatranscriptome | 485 | Y |
| F031688 | Metagenome / Metatranscriptome | 182 | Y |
| F035704 | Metagenome | 171 | N |
| F037805 | Metagenome / Metatranscriptome | 167 | Y |
| F043464 | Metagenome / Metatranscriptome | 156 | Y |
| F055778 | Metagenome / Metatranscriptome | 138 | Y |
| F071971 | Metagenome | 121 | N |
| F077325 | Metagenome | 117 | Y |
| F082716 | Metagenome | 113 | Y |
| F093463 | Metagenome | 106 | Y |
| F093897 | Metagenome | 106 | Y |
| F105217 | Metagenome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0209954_1001358 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 4713 | Open in IMG/M |
| Ga0209954_1001725 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis | 4223 | Open in IMG/M |
| Ga0209954_1002552 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 3438 | Open in IMG/M |
| Ga0209954_1002816 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 3281 | Open in IMG/M |
| Ga0209954_1009062 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium | 1749 | Open in IMG/M |
| Ga0209954_1012461 | Not Available | 1486 | Open in IMG/M |
| Ga0209954_1013028 | All Organisms → cellular organisms → Bacteria | 1453 | Open in IMG/M |
| Ga0209954_1014272 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 1384 | Open in IMG/M |
| Ga0209954_1035082 | Not Available | 883 | Open in IMG/M |
| Ga0209954_1035247 | Not Available | 881 | Open in IMG/M |
| Ga0209954_1046286 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Nitrosopumilus adriaticus | 773 | Open in IMG/M |
| Ga0209954_1100521 | Not Available | 535 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0209954_1001358 | Ga0209954_10013584 | F105217 | VDTIKEKNELVDSIQFRLFYAEINLDKIPVAIPLDIFPKDKISSEIAMDGFLFYANGALDLIFTEINKKLDLGLALNQINPSDIVQALEKKNSDETKKIIEVFQKNFQKPVHEEKIITDKEFNDGLNRYGYDVIGFHAEYENRDQVKYQHFWNRASSRLWEIRNQENLESYDSLLKNAGQKGTDKPRNHLRVKLASDDRPAVYWDSAHYENPKRYFTNILFLVKKFIDKILEILKPLYLPDSKTP |
| Ga0209954_1001725 | Ga0209954_10017253 | F082716 | LISKKDIKHMPVTFIIAPVVLISLVYIVFITSNDMIEEKEFIVSLSCPELREYTQSQIIDSKLYFGHEVFLSYAEERYDTSC |
| Ga0209954_1002552 | Ga0209954_10025524 | F077325 | LSKKGNWTEKDEATIKAIIVNMINQKQMFRNLGEKGELPSSFNVQNSREFVLGIFTGIVINLFANYWVGEHEAGLLPEDLDFLYHKIALSNELILVGLFE |
| Ga0209954_1002816 | Ga0209954_10028164 | F055778 | MLSNVDFPEPELPTIRTISPFSIENDTSSRALTLLSPSP |
| Ga0209954_1009062 | Ga0209954_10090622 | F003470 | MVRIADACYCRRTTAQTQAQELKQNLSKVMRSFGRSCRGQGKVFVKLVRQTEQQLLDVGETISTLARQAQASLEQTTTLSETQRAWFNEHLTTAMRHHEQIRQQSKQLTQGKKLAHFKVVNAYDPTIAPIIKGKSNCPAQFGRKPGIMSEPASGYIFANLTPKGNPSDESYVLPLIDKVEQAIGRAQQGPKRSIHSLAGDLGVNDPVLRQALHERGILSVGIPKTVEPINAHPSAQEVLDILNEADLNRKRTPHQVHLACASGFSRPVVESHIAALLSRGAGSVRYKGMEGAVVQQGMTVMSYNGAVLVRIRQQKLTKRAQKFRRLLGLKPPKVNEINQEKN |
| Ga0209954_1012461 | Ga0209954_10124614 | F031688 | MKTYIIYVKGYEKGVIKAASHNAAEKKAWKKFSDYPREQISVAYTEV |
| Ga0209954_1013028 | Ga0209954_10130281 | F043464 | IAATRTATDAELPLYGLTNGALVHTEARIPGTDVRVVFSEFTLAAGSQQSANPFQWRIQDVGAPQFQLQVAGLDALLDRTRQAGYRFLSVDGRPIPRPFGRFVFAIDPDGVLVEYVEPQTSR |
| Ga0209954_1014272 | Ga0209954_10142723 | F093897 | MKLGFYISIGVAIGALVVGFVLLNDIQQEKDAKTVWIQKIPTQCNDVWNAEYSEYYEINPEMKEISGEESKAILETIIKNHYENQGISILDLNLEVDYYDGVRCEACSCLGWDRLSIQISQNDLDGIPVSEGWEVLN |
| Ga0209954_1035082 | Ga0209954_10350822 | F001127 | MGHDHIEQYAAEEGGVTLHTWTDVQGAKKENFYITGMPGAPVPTWFRTVLRKKDLADIANFPNHPS |
| Ga0209954_1035247 | Ga0209954_10352472 | F001127 | MDHPHIEQYQARDGGVTLHTWTDMQGDKKENFYITGMPGAPVPAWFRTVLRKKHLADIANFPNHLS |
| Ga0209954_1046286 | Ga0209954_10462861 | F071971 | MRITVFYNAESTIKAINNTAKYGLENLNKVHDAFSMGLTITQIDNAIINAPDAIAVHRYTLPTISSPFSVVMKNGAIENNTITTVDPAMAR |
| Ga0209954_1049969 | Ga0209954_10499691 | F037805 | MRHLLLPAQAWWDAQRFDQPTWQVASWRDQKARHIHLHVAKALGKVVQMLDEAAPLTSNTALQGRVRDEALPDIAIYRSQLINLLPDGCALPASLSATTPGGNLQAEANWRHAALSLSRASAELAGYLEPQEHGAASPASHLMQAIEHLQASAAAL |
| Ga0209954_1100521 | Ga0209954_11005211 | F001127 | MDSYLEQYETKAESVTLHTWTEEQGAKKDHFYITGMPGTPIPGWFRKVLSQKRLADIANFPHTPSCFYD |
| Ga0209954_1105802 | Ga0209954_11058022 | F035704 | MALRINDSEYYAIDSHSHLGKRKTPLGHGVASFLG |
| Ga0209954_1114416 | Ga0209954_11144161 | F093463 | VGTEEPRGAVHWIDHFVVGTNDMVAWSNWGVNAIGLDRQPIVGLTTAQRK |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |