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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 | 3300026106 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0114514 | Gp0125953 | Ga0209927 |
| Sample Name | Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_A_D1_MG (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 116748770 |
| Sequencing Scaffolds | 30 |
| Novel Protein Genes | 31 |
| Associated Families | 28 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Alkalispirochaeta → Alkalispirochaeta odontotermitis | 1 |
| Not Available | 11 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1 | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → unclassified Halieaceae → gamma proteobacterium HIMB55 | 1 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → unclassified Halobacteria → Halobacteria archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 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) | 37.4971 | Long. (o) | -122.129 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001488 | Metagenome / Metatranscriptome | 686 | Y |
| F004052 | Metagenome / Metatranscriptome | 455 | Y |
| F005815 | Metagenome / Metatranscriptome | 389 | Y |
| F010065 | Metagenome | 309 | Y |
| F012678 | Metagenome / Metatranscriptome | 278 | Y |
| F012874 | Metagenome / Metatranscriptome | 276 | Y |
| F037736 | Metagenome / Metatranscriptome | 167 | Y |
| F041201 | Metagenome / Metatranscriptome | 160 | Y |
| F042016 | Metagenome / Metatranscriptome | 159 | Y |
| F044506 | Metagenome / Metatranscriptome | 154 | Y |
| F050381 | Metagenome / Metatranscriptome | 145 | Y |
| F054047 | Metagenome / Metatranscriptome | 140 | Y |
| F057781 | Metagenome / Metatranscriptome | 136 | Y |
| F058158 | Metagenome / Metatranscriptome | 135 | Y |
| F059980 | Metagenome / Metatranscriptome | 133 | Y |
| F061862 | Metagenome | 131 | Y |
| F070125 | Metagenome / Metatranscriptome | 123 | N |
| F070127 | Metagenome / Metatranscriptome | 123 | Y |
| F070131 | Metagenome / Metatranscriptome | 123 | Y |
| F072360 | Metagenome / Metatranscriptome | 121 | Y |
| F081352 | Metagenome / Metatranscriptome | 114 | Y |
| F084253 | Metagenome | 112 | Y |
| F087210 | Metagenome / Metatranscriptome | 110 | Y |
| F088916 | Metagenome / Metatranscriptome | 109 | Y |
| F092076 | Metagenome / Metatranscriptome | 107 | Y |
| F099322 | Metagenome / Metatranscriptome | 103 | Y |
| F103280 | Metagenome | 101 | Y |
| F105202 | Metagenome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0209927_1002205 | All Organisms → cellular organisms → Bacteria | 2832 | Open in IMG/M |
| Ga0209927_1004146 | All Organisms → cellular organisms → Bacteria | 2131 | Open in IMG/M |
| Ga0209927_1006197 | All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Alkalispirochaeta → Alkalispirochaeta odontotermitis | 1750 | Open in IMG/M |
| Ga0209927_1009503 | Not Available | 1401 | Open in IMG/M |
| Ga0209927_1010604 | Not Available | 1326 | Open in IMG/M |
| Ga0209927_1011141 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1 | 1292 | Open in IMG/M |
| Ga0209927_1011341 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1280 | Open in IMG/M |
| Ga0209927_1012415 | All Organisms → cellular organisms → Bacteria | 1221 | Open in IMG/M |
| Ga0209927_1015427 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium | 1087 | Open in IMG/M |
| Ga0209927_1016347 | Not Available | 1053 | Open in IMG/M |
| Ga0209927_1020134 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales | 939 | Open in IMG/M |
| Ga0209927_1022786 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium | 877 | Open in IMG/M |
| Ga0209927_1026707 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 803 | Open in IMG/M |
| Ga0209927_1030024 | Not Available | 751 | Open in IMG/M |
| Ga0209927_1030134 | Not Available | 749 | Open in IMG/M |
| Ga0209927_1032625 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria | 716 | Open in IMG/M |
| Ga0209927_1034777 | Not Available | 691 | Open in IMG/M |
| Ga0209927_1035604 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → unclassified Halieaceae → gamma proteobacterium HIMB55 | 681 | Open in IMG/M |
| Ga0209927_1036790 | Not Available | 669 | Open in IMG/M |
| Ga0209927_1038061 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 656 | Open in IMG/M |
| Ga0209927_1042786 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium | 614 | Open in IMG/M |
| Ga0209927_1043086 | Not Available | 612 | Open in IMG/M |
| Ga0209927_1043259 | All Organisms → cellular organisms → Bacteria | 610 | Open in IMG/M |
| Ga0209927_1047553 | Not Available | 579 | Open in IMG/M |
| Ga0209927_1051600 | All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → unclassified Halobacteria → Halobacteria archaeon | 552 | Open in IMG/M |
| Ga0209927_1054634 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont | 535 | Open in IMG/M |
| Ga0209927_1055684 | Not Available | 529 | Open in IMG/M |
| Ga0209927_1058458 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria | 515 | Open in IMG/M |
| Ga0209927_1059441 | Not Available | 510 | Open in IMG/M |
| Ga0209927_1060378 | All Organisms → cellular organisms → Bacteria | 506 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0209927_1002205 | Ga0209927_10022053 | F084253 | IKAAQEFAVRRTSVRRSRKPAENAEQDKKGHLWMETN |
| Ga0209927_1004146 | Ga0209927_10041463 | F088916 | MPSTTLDNVKGSELPKTWADKINIIPDKTYTVIIQPQDERQTLQKIMSRISHTAKTRGMTPDILENILGEKIKHVL |
| Ga0209927_1006197 | Ga0209927_10061973 | F044506 | GMMKQWNSGIVGSGMMQCWINGPATGGIEDKIKMVNILLKTNNPSFHPSIIPFPGKIRRPQKTSIFSVGCRNSETLNHMVIPIRAKLLVLMHWRIF |
| Ga0209927_1009503 | Ga0209927_10095031 | F037736 | VPYRVQLDGLQILWLLANPLRTHGIGESGSKTITGWLLMSAADANHIWWLNTNPFTGLLLHLNSYRILHLPCGFLNMLCFLLLCHRQRNDNY |
| Ga0209927_1010604 | Ga0209927_10106041 | F058158 | MDQVMKEKQKSHKTHFTKTEKDDTDIWNLPVKEREHILTQIAKARRTNRARTWIELIFMLSFIYYMLYDIYKDGDLDTIIKFLKI |
| Ga0209927_1011141 | Ga0209927_10111411 | F044506 | MMEQWNSGIMGSGMVQCWINGPATSGIDDKIKMVNILLKTNIPSFHPSIIPFPGQIRKSQKTSIFSVGCRNSETYNYT |
| Ga0209927_1011341 | Ga0209927_10113413 | F054047 | IFCWVSFLYPTYTPAIFVLSAKPDKMAEDRIIPKIIKM |
| Ga0209927_1012415 | Ga0209927_10124151 | F012874 | KVRNSVMPAKAGIQNYLKTLDSRLRGNDVKGRFKTFYETINFEILN |
| Ga0209927_1015427 | Ga0209927_10154271 | F070127 | MQKLNFSITINLSLTLKEDKASINIKNVDLIPAVVSLPVRLNSGDSIPQPKPQKKKTVHDIILQTAKNCVVDAGQNKFTGAKLFHLALLNHPGLKRNTFAAQVIAAAPNHSSHRHYPNQKDYFTYLGNGYYKLNQRYLKIREDQMLRPSDWVRDHVKRKYIDPAKKDGK |
| Ga0209927_1016347 | Ga0209927_10163472 | F092076 | MFSHKIDKLQGIILIRASGTPTTITMIDHIQSVLNDPDYDPKYNSIIVLEENTHIAGVPTEKIELIRRVLDGYAQQRKGRHWAVVAPNERQEAFLKLNLELISPVKLNIRIFKSEEDALNWIKGR |
| Ga0209927_1020134 | Ga0209927_10201343 | F001488 | MARLELTLNFPKSFQIKTFNVKSEKTLSPLAKLILQSVQFKHFYYVRDDISYLLKSNPVERDFLLQALYSTVISLQNNLSINFFDMWVYEIYINKVSTHNKFMNQKSQNLE |
| Ga0209927_1022786 | Ga0209927_10227862 | F081352 | KISTITLACLLVLNLTAGAAVVVEHCPPLLGSSSPMDIDHCDGMLNFAFPMQGCCGECNDIFCDLIKNPLQDANAVNASPFQGSCYPFFLGTVDPIAESGTWVASSAPRYLFFAALAWSQIPLYIENLALII |
| Ga0209927_1026707 | Ga0209927_10267071 | F059980 | CKMGFSGGFEQGKPETALPELRRFIPVNMKWVNPQNKFCYG |
| Ga0209927_1030024 | Ga0209927_10300241 | F099322 | SVRMVLDGVSLIRYSDGAWCRVAPPSAHDLKDNWYRSSPSLLIRWLDAVGKVRPVKSNE |
| Ga0209927_1030134 | Ga0209927_10301341 | F070131 | MIGKMLTKIIIVGVLAFCFLLQVDLAGGDNGINNQKKTKINVPMEIEIFFSSTPMLNEYTVLNIEIRALIDTPNTLIEIEIPRDGFEIISGSTQFNEDLSSGSTATYQLEVLPTAQGQYTIAASAKSEETDYIFGKREELYVNIGEEFSELSKSSFIPEIADTRSGAVKIEDFSEPPIQVLPDQKPQEDQEVLYFAAPGTGQIQVRGYW |
| Ga0209927_1032625 | Ga0209927_10326251 | F005815 | MTMNTTRLTMYCTTGEAATVIDFIDTLRDALWETYGEQITRMHHEEHDDRIRDSNQCEFEFNDEIPF |
| Ga0209927_1034777 | Ga0209927_10347771 | F072360 | LRSGMNLKPNILKSFSRRTLWIFFILFVSVSFSTSGVIANSCQGGADCLNCAAAAHPHLPGMDVEMVNQGCQSTEQNRSCGFEAGHSADDFDRIATTVTSGTHSYSGIFSIASDESDQAHLHLEFLTQFQYPDRGELTPIFLLNQSLLC |
| Ga0209927_1035133 | Ga0209927_10351332 | F087210 | MRFLIAALAFAGAETALAHTPDTGFLSNFGHQLTSLHHSPAAMLLGVLVLVLMLVAVRKLTTR |
| Ga0209927_1035604 | Ga0209927_10356041 | F070125 | VTTAEQRRQWIEALHAYRDDSERLFGLVASLANLLDRKLIIETMESVLGIAAVHDGDCIIFDDLAIRFGSDDRVKSVFRTIDGL |
| Ga0209927_1036790 | Ga0209927_10367902 | F054047 | IGQGLFVGWVEHPGIFCWVSFLNPTYVPTIFLLSAKPNKMAEDRTVPDNFKRWEWN |
| Ga0209927_1038061 | Ga0209927_10380611 | F042016 | MAPERKLYQKIKKHFNEFSLIRLENLSLSGTPDLLVY |
| Ga0209927_1042786 | Ga0209927_10427861 | F044506 | MQCWINGSATGGSDDNIKMVNILLKTNIPSFHPSIIPFPGEISKSQKTSIFSVGCRNSETFNYLLFSVV |
| Ga0209927_1043086 | Ga0209927_10430861 | F050381 | MKKILVIIAIILIPTIAFANFSIQLDNNTGKKMFYLLYWVDHTYDWPHPFNLAGGELKSSESIDLRSDYRNGKYYVVWSDNGDWQNKVMLDVYDDVKSVIVTPIKSSMTK |
| Ga0209927_1043259 | Ga0209927_10432592 | F004052 | IRLEHLSMRTPTTIAYVTLAVLLASCDQRHPASDIDPELGLACFESHRASLPPGTQYEGIEKLDGTRLTIRIMNGVEVVTMDCTLNPDGTLK |
| Ga0209927_1047553 | Ga0209927_10475531 | F103280 | MLTTMKKLVAFLTISSIWLLPVILPEIQAQQTAAPPSTTASSPAITIEELKSRRMAIESMTDIDATVKTDSLKYIDQAISHAELALSTNHKANEFLQLIQTAPERLKILQAELKKSFMAPEKVEARAQQMSTLKLEQRLRQKKAE |
| Ga0209927_1051600 | Ga0209927_10516001 | F010065 | MRGESGISFTGLYICGAISLIMLVLKLSVIDTWSWWRVLLPLGLFVGFNVTNIVVAFIYLSFAHIPERPDGDEADILEPHTINVHYVAAMLFFVVFGDNMVRWIEGSETSHWFWLFSGKDEALAVFGSLSVLALFSYWSRLGRVLKAAG |
| Ga0209927_1054634 | Ga0209927_10546342 | F057781 | MKLPDLQMLAHWLDPALVATLETRRRKKKEWHRRRKLATLQTLWLMLA |
| Ga0209927_1055684 | Ga0209927_10556841 | F105202 | QLIQSDLHLDIQQRAHLYLASLYFSPMNPNRDYKLALKHLETYAIFDPDFVNGVDPRLLLAAIIELERLSAIADAQSKAIQALNQEVEILKIQASASRGSKYDTQEANRMLKKRIGRLQNKIRNLEASNAQLNKTIEMLSKLDSSLEEKRSNFIKMDSGKVE |
| Ga0209927_1058458 | Ga0209927_10584583 | F012678 | MLNQHSIEEIADIHNLLRDIKEEYNEGIKPILIKNSPKLFKNPHTVPK |
| Ga0209927_1059441 | Ga0209927_10594411 | F061862 | KGKLNMQDDETMWYENDAPVREYLDRELPRKTAGAEKDPKTVRFSWFKIMKKSFHIK |
| Ga0209927_1060378 | Ga0209927_10603782 | F041201 | RILVQDRGGSEFQTGGILLYVEDLKRGTNKDIGPKDIFEMGSSYLF |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |