| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300007757 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114514 | Gp0125946 | Ga0102949 |
| Sample Name | Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_B_D1_MG |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 360035414 |
| Sequencing Scaffolds | 20 |
| Novel Protein Genes | 20 |
| Associated Families | 18 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Thermoleophilales → Thermoleophilaceae → Thermoleophilum → Thermoleophilum album | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Archaea | 2 |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → Lacipirellulaceae → Pirellulimonas → Pirellulimonas nuda | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 1 |
| Not Available | 3 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → unclassified Rhizobium → Rhizobium sp. | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales | 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) | 37.496 | 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? |
|---|---|---|---|
| F000532 | Metagenome / Metatranscriptome | 1046 | Y |
| F002483 | Metagenome / Metatranscriptome | 555 | Y |
| F003627 | Metagenome / Metatranscriptome | 476 | Y |
| F005789 | Metagenome / Metatranscriptome | 390 | Y |
| F009170 | Metagenome / Metatranscriptome | 322 | Y |
| F019205 | Metagenome / Metatranscriptome | 231 | Y |
| F028464 | Metagenome / Metatranscriptome | 191 | Y |
| F039119 | Metagenome / Metatranscriptome | 164 | Y |
| F049640 | Metagenome / Metatranscriptome | 146 | Y |
| F049899 | Metagenome | 146 | N |
| F054877 | Metagenome / Metatranscriptome | 139 | Y |
| F065013 | Metagenome / Metatranscriptome | 128 | Y |
| F070130 | Metagenome / Metatranscriptome | 123 | Y |
| F074892 | Metagenome / Metatranscriptome | 119 | Y |
| F077325 | Metagenome | 117 | Y |
| F082716 | Metagenome | 113 | Y |
| F088283 | Metagenome / Metatranscriptome | 109 | Y |
| F094435 | Metagenome / Metatranscriptome | 106 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0102949_1002687 | All Organisms → cellular organisms → Bacteria | 3303 | Open in IMG/M |
| Ga0102949_1005407 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Thermoleophilales → Thermoleophilaceae → Thermoleophilum → Thermoleophilum album | 2476 | Open in IMG/M |
| Ga0102949_1005764 | All Organisms → cellular organisms → Bacteria | 2418 | Open in IMG/M |
| Ga0102949_1009974 | All Organisms → cellular organisms → Bacteria | 1947 | Open in IMG/M |
| Ga0102949_1023509 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae | 1371 | Open in IMG/M |
| Ga0102949_1028044 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales | 1275 | Open in IMG/M |
| Ga0102949_1052570 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 982 | Open in IMG/M |
| Ga0102949_1086141 | All Organisms → cellular organisms → Archaea | 802 | Open in IMG/M |
| Ga0102949_1097491 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → Lacipirellulaceae → Pirellulimonas → Pirellulimonas nuda | 762 | Open in IMG/M |
| Ga0102949_1097884 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 760 | Open in IMG/M |
| Ga0102949_1102709 | Not Available | 745 | Open in IMG/M |
| Ga0102949_1109414 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 726 | Open in IMG/M |
| Ga0102949_1121116 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 697 | Open in IMG/M |
| Ga0102949_1127695 | All Organisms → cellular organisms → Archaea | 682 | Open in IMG/M |
| Ga0102949_1141233 | Not Available | 655 | Open in IMG/M |
| Ga0102949_1145378 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon | 647 | Open in IMG/M |
| Ga0102949_1168282 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → unclassified Rhizobium → Rhizobium sp. | 610 | Open in IMG/M |
| Ga0102949_1212799 | Not Available | 557 | Open in IMG/M |
| Ga0102949_1233941 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium | 537 | Open in IMG/M |
| Ga0102949_1242242 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales | 530 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0102949_1002687 | Ga0102949_10026873 | F005789 | MKAGKTRTRDGALSALRTPTNPPVPTMLVPLDASPLNVVRSMRGAIVDARIAYPEVLHVEIKDSDGELWRLATQDAEWSPSDPAELVGRSVADADIDAETGELRCKLSDGAVLDVKPAEREADDDPSNWELIAPGGVALEFGPGVRWQIGSADSPAS* |
| Ga0102949_1005407 | Ga0102949_10054074 | F003627 | VDRETSKREMAAGLQAGAFAAAVFALCFVAAMLYIAS* |
| Ga0102949_1005764 | Ga0102949_10057643 | F019205 | MASEGSRKFELMFDSRKTYRDKALDAADLVIDFATLGEYGLESVDTAPRACEGRRRLANQRSTGTWNAAIDRFAAQS* |
| Ga0102949_1009974 | Ga0102949_10099743 | F000532 | VALIKERLGIEAETKAGGTGEFEVIADGETIAERGGNWLTRGFGAGYPDLDGVVDELEARTR* |
| Ga0102949_1023509 | Ga0102949_10235093 | F082716 | IIAPVVLISLVYIVFITSNDMIEEKEFIVSLSCPELREYTQSQIIDSKLYFGHEVFLSYAEERYDTSC* |
| Ga0102949_1028044 | Ga0102949_10280443 | F002483 | LDRELERLRGLPVFAGSALATRRPQLKVRRASKRPNKLGFAVPAEFRLQVTAYPGIGVGDILETLLHELTHLHVGRAAEAHAWHGRTFKAALAQAMREAYGVEVPPPAHTRHGVYAAAITATL* |
| Ga0102949_1052570 | Ga0102949_10525702 | F094435 | MNFNWALLPAACLLLFPITQIAAQEQAVLGQGNVSCDAWLIDRRENNAQASGRIAWILGYVTAFNQYGSKPAGDVSAGMDTDEIMVWID |
| Ga0102949_1086141 | Ga0102949_10861412 | F077325 | LSKKGNWTEKDEATIKAIIVNMINQKQMFRNLGEKGELPSSFNVQNSREFVLGIFTGIVINLFANYWVGEHEAGLLPEDLDFLYHKIALSNELIFVGLFE* |
| Ga0102949_1097491 | Ga0102949_10974911 | F049640 | GGAATCGGVAPRPSTEKLRMARHPAIKLELLPHERAALLKWNYTPEVRAQLEACASSDNIETITITSVDANWLASDLTHAIVKRGCRDQDVIDLSERLEYVDQSGDGSLDGWYY* |
| Ga0102949_1097884 | Ga0102949_10978841 | F009170 | MVRIADACYCRRTTAQTQAQELKQNLSKVMRSFGRSCRGQGKVFVKLVRQTEQQLLDVGETISTLARQAQASLEQTTTLSETQRAWFNEHLTTAMRHHEQIRQQSKQLTQGKKLAHFKVVNAYDPTIAPIIKGKSNCPAQFGRKAGIMSEPASGYIFANLTPKGNPSDESYVLPLIDKVEQAIGRAQQGPKRSIHSLAGDLGVNDPVLRQALHERGILSVGIPKTVEPINAHPSAQ |
| Ga0102949_1102709 | Ga0102949_11027092 | F039119 | MFHLPEPASAEWQSRQLVVTPEQLGLHSVGDCQQRAEKLGLTPMPPLPYRQEFWRLDVLLKWSKRNGFEQLPMLGRGLGHRR* |
| Ga0102949_1109414 | Ga0102949_11094141 | F028464 | MPWVGLGTDRKNPTFRHVDGSVMNGRLYIDDRIIVHEQGMLDRSFLHDPEVLEAAAEYGDPYQVLAPVSHEAHGSGTLL* |
| Ga0102949_1121116 | Ga0102949_11211162 | F065013 | MEMGSTVSSQLVGWTRTALLPGDVVTLYVWPAKTGEPVGRFNKVEFDDGTVLRDSQRGADDGGRSDTGLRQ* |
| Ga0102949_1127695 | Ga0102949_11276952 | F077325 | MSGKGNWTEKDEATIMAIIVNMINQKEMLKDLGGKSEMQNSFKIENPKEYVLGLFSGIVINLFANYWVGEHEAGLRPEGLSYLYHKISESSDLITKGLFE* |
| Ga0102949_1141233 | Ga0102949_11412331 | F074892 | MRQRYAVIALLGLLLSACAERGENVYRTWVGPDRSNMAIVTLRLGEDVKDVTVRERVLPRSEYGTVLLAPGAYTLYEEDGASIGINIRPAIVSLERARANGELILGHTYVLRAGKSKQTGERALWIEDARSGDVFVDRR* |
| Ga0102949_1145378 | Ga0102949_11453782 | F082716 | MISKDDIKLMPFTFIVAPILLISLTFVVVITYEDMIDEKELIVSLSCPELREYTENQIIESKLYYGSEVYLSY |
| Ga0102949_1168282 | Ga0102949_11682822 | F049899 | MGLPPTTTAATVAAVVVGGNPIGGGLRGSVTATIVGALFLTYLGQLVLAVGFETSAQNIVQAIIIIASVGIVEAGRRIRFEWIRFKFWITSPDVEFRIRTTFTRTMSRLGLSKLLDVAPQVRWRWRTAYLRLKKRLEITE* |
| Ga0102949_1212799 | Ga0102949_12127991 | F054877 | VKKYRNLRVLARFRPMNTDDLDSELINLVGEEAEFRYHKFVDEDDTPYSNQWVLTAEDQRFGDYWFPEYDLEIRREKLSH* |
| Ga0102949_1233941 | Ga0102949_12339411 | F070130 | QMPATPASQPDSFVGWWEIVFHIKDGEQTDVTDIIEHVDAAGNFTVLRDGERIGAGHHVDFTVDPDGFTNVPVAADPDLQIARELAIYRFSRDVLEVCKASEHQGRPTSFASPRGSGWTHVAIRRISDDDPRVRTQR* |
| Ga0102949_1242242 | Ga0102949_12422421 | F088283 | GSLACVAGCATNDHVTGTYAPSCVAFEGNTIELADSRFTWDKFTDEVRVDDAGNTIDPFPGFPVRGTYTVVDDVVRLVTDVGDLAAELHLVRRPGQVYLLTDSEFDAWQSNGTVPNCALLLGAGE* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |