| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300026068 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116116 | Ga0208657 |
| Sample Name | Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_TuleC_D1 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 72966976 |
| Sequencing Scaffolds | 36 |
| Novel Protein Genes | 37 |
| Associated Families | 35 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium 21-66-5 | 1 |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Nitrospirae | 1 |
| Not Available | 11 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 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) | 38.224476 | Long. (o) | -122.019341 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000676 | Metagenome / Metatranscriptome | 941 | Y |
| F002140 | Metagenome / Metatranscriptome | 590 | Y |
| F005060 | Metagenome / Metatranscriptome | 413 | Y |
| F007886 | Metagenome / Metatranscriptome | 343 | Y |
| F009970 | Metagenome / Metatranscriptome | 310 | Y |
| F012266 | Metagenome / Metatranscriptome | 282 | Y |
| F015847 | Metagenome | 251 | Y |
| F016087 | Metagenome / Metatranscriptome | 250 | Y |
| F016687 | Metagenome / Metatranscriptome | 245 | Y |
| F017154 | Metagenome / Metatranscriptome | 242 | Y |
| F019578 | Metagenome | 229 | Y |
| F020200 | Metagenome | 225 | Y |
| F023288 | Metagenome | 210 | Y |
| F023894 | Metagenome / Metatranscriptome | 208 | Y |
| F024435 | Metagenome / Metatranscriptome | 206 | Y |
| F024580 | Metagenome / Metatranscriptome | 205 | Y |
| F026912 | Metagenome | 196 | Y |
| F029799 | Metagenome | 187 | Y |
| F031021 | Metagenome / Metatranscriptome | 183 | Y |
| F031537 | Metagenome | 182 | Y |
| F035813 | Metagenome / Metatranscriptome | 171 | Y |
| F040161 | Metagenome | 162 | Y |
| F040163 | Metagenome | 162 | Y |
| F042500 | Metagenome / Metatranscriptome | 158 | Y |
| F045132 | Metagenome / Metatranscriptome | 153 | Y |
| F045445 | Metagenome / Metatranscriptome | 153 | Y |
| F046145 | Metagenome | 151 | Y |
| F056185 | Metagenome | 138 | Y |
| F058256 | Metagenome / Metatranscriptome | 135 | Y |
| F058543 | Metagenome | 135 | N |
| F060098 | Metagenome / Metatranscriptome | 133 | Y |
| F085853 | Metagenome / Metatranscriptome | 111 | Y |
| F093171 | Metagenome | 106 | Y |
| F095691 | Metagenome | 105 | Y |
| F105956 | Metagenome / Metatranscriptome | 100 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208657_1003293 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium 21-66-5 | 1343 | Open in IMG/M |
| Ga0208657_1005716 | All Organisms → cellular organisms → Bacteria | 1086 | Open in IMG/M |
| Ga0208657_1006502 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1034 | Open in IMG/M |
| Ga0208657_1008225 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 940 | Open in IMG/M |
| Ga0208657_1009177 | All Organisms → cellular organisms → Bacteria → Nitrospirae | 900 | Open in IMG/M |
| Ga0208657_1009397 | Not Available | 891 | Open in IMG/M |
| Ga0208657_1010181 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 863 | Open in IMG/M |
| Ga0208657_1011291 | Not Available | 826 | Open in IMG/M |
| Ga0208657_1011334 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 825 | Open in IMG/M |
| Ga0208657_1011939 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 806 | Open in IMG/M |
| Ga0208657_1012741 | All Organisms → cellular organisms → Bacteria | 784 | Open in IMG/M |
| Ga0208657_1014477 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 742 | Open in IMG/M |
| Ga0208657_1014941 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 732 | Open in IMG/M |
| Ga0208657_1015297 | All Organisms → cellular organisms → Bacteria | 724 | Open in IMG/M |
| Ga0208657_1016127 | Not Available | 708 | Open in IMG/M |
| Ga0208657_1016270 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 705 | Open in IMG/M |
| Ga0208657_1016625 | Not Available | 699 | Open in IMG/M |
| Ga0208657_1017473 | Not Available | 684 | Open in IMG/M |
| Ga0208657_1018134 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 674 | Open in IMG/M |
| Ga0208657_1018679 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium | 665 | Open in IMG/M |
| Ga0208657_1019425 | All Organisms → cellular organisms → Bacteria | 654 | Open in IMG/M |
| Ga0208657_1020288 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 642 | Open in IMG/M |
| Ga0208657_1021494 | Not Available | 626 | Open in IMG/M |
| Ga0208657_1022477 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 614 | Open in IMG/M |
| Ga0208657_1022972 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 608 | Open in IMG/M |
| Ga0208657_1023599 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 601 | Open in IMG/M |
| Ga0208657_1024509 | Not Available | 592 | Open in IMG/M |
| Ga0208657_1024538 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 592 | Open in IMG/M |
| Ga0208657_1026480 | All Organisms → cellular organisms → Bacteria | 572 | Open in IMG/M |
| Ga0208657_1027353 | Not Available | 564 | Open in IMG/M |
| Ga0208657_1030316 | Not Available | 540 | Open in IMG/M |
| Ga0208657_1031197 | Not Available | 534 | Open in IMG/M |
| Ga0208657_1031834 | Not Available | 529 | Open in IMG/M |
| Ga0208657_1032199 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 526 | Open in IMG/M |
| Ga0208657_1032582 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 523 | Open in IMG/M |
| Ga0208657_1033631 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 516 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208657_1002315 | Ga0208657_10023151 | F085853 | ILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFASLNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDAFPGLTGMDYVKYILYYLLSAGLFFFGFQRIRDAVKNYGV |
| Ga0208657_1003293 | Ga0208657_10032931 | F016087 | RRAMKKLWNPLGRLLDFVDIMVVVLLFTALAFSVGYQIGFTAGLDTKVTLVGEKYTMLLKGNSKR |
| Ga0208657_1005716 | Ga0208657_10057161 | F046145 | MLQVCLNFYWKLFEWITDRYEKTIPDLLECDHMALKPKPFSEAKTGFFIMSCYLR |
| Ga0208657_1006502 | Ga0208657_10065022 | F019578 | VGVIAANSSVVAVLPRKKAGEDTRLKEAYLLAAAPLLFDACSKINSILESSLIVTPEGIKINCTDIKKSLSDALLRAMGYRKSPEEP |
| Ga0208657_1008225 | Ga0208657_10082252 | F040163 | MNPADPALLAEVLHHALDGVAIVEAGGDSSTRLVYGNATLAGLLRRPEEWLPGRALEEIEIEAPADPNATSTGAGQRVRLRRADGSTVECERWAHMLPDARLAMFYRPLPRSAPGALAAAVDRASGLSTPEHLMEVLRRDWTVAQRDGRSITLMRFSVDGYGDYLEVF |
| Ga0208657_1009177 | Ga0208657_10091771 | F105956 | MKPEEPTLVEKLPIYMVAWSLPPCFVILAVIVLALDSFNDAGVAILKGKYMFLLLVGGTLLNLWFYAVRQFKLKRKFSPLHIIASLLFPAAYMSFYYGADTTLVVAICLVGIPVSILSARQSMNMV |
| Ga0208657_1009397 | Ga0208657_10093972 | F058256 | TGLDPPPGLVEAGCLQRAWNRLLTRVPILKHAFGQLLPSKLHTAQQLWKALRRGMGSAEEMLRFLARSCKRSLLGDYTCLRPAP |
| Ga0208657_1010181 | Ga0208657_10101811 | F045445 | LYLLEQARKGDIAKMIEVIDDLGGIGAGKPVPGAGNKRPQEFADYCKVGPTRVPFVTFPEAELDKAHKRAAHWMELNKKYRPLVETLRSRSAA |
| Ga0208657_1011291 | Ga0208657_10112912 | F035813 | LAESRYPDTETAAEAKRLMRDVLDHYLDSRRIESRRILADLQALNGDH |
| Ga0208657_1011334 | Ga0208657_10113342 | F020200 | MCWVCERLENLITSWNEEQEFQEQTSSDDYHRGLSKGFSECVKDLSEAVASMRLKGICEKFPEYERVLNDKQRLDILEDLLKLRDEDSNQE |
| Ga0208657_1011939 | Ga0208657_10119392 | F031537 | MSGTNSKKALHVATFSGWYRFEQNGKEFIQTKRDLSYWTITCMTVDPEDPKTLYAGTEHSGLFYTKDAG |
| Ga0208657_1012741 | Ga0208657_10127412 | F046145 | VSLNFYWKLFEWITARYENTFPDWLECDHTALKPKPFSEAKISFFITSRYLRVLSEKI |
| Ga0208657_1014477 | Ga0208657_10144772 | F031021 | MNARKDRWESYTDKAGRRHWRWPATNAAAERGGRDAEADSRPRAGLPSPQQTSFALLPLRGK |
| Ga0208657_1014941 | Ga0208657_10149412 | F026912 | MDRNEHKPHFSIIDPMIDDSEPLRSEYLRGFHRGIEVQVFGVSDEWIEEHRMLIDYSNGGSGDSYIDTYARGYRHGFDGRTPESPSLSSESLPIASIV |
| Ga0208657_1015297 | Ga0208657_10152971 | F095691 | MLQQDGSIRIAWQTDGYEAIFVRARFRPAPERDDFARGVADVALLERTLPDLRRALRARYPGAFDLLTDEPLDQPGRVIVNFHPPRGEPNPDPW |
| Ga0208657_1016127 | Ga0208657_10161272 | F005060 | MPTALDWLAIAEECFADEYGSLRQGLLTSVFSLVIGMERIFHLDEMEDAGFARLCGGRRCPSRHTVGGWRRNLS |
| Ga0208657_1016270 | Ga0208657_10162702 | F060098 | MDASSLRGATAAAAMSVGGLLWLSAILFMARTAQHSEPFSRLHPW |
| Ga0208657_1016625 | Ga0208657_10166251 | F023894 | LVIAGALMLLACDQPSGQSDLSKKAPPSLGAIANVDGSDDEKKDGKKAQAGSEQAPAQSPAGGQPAQAAPKQ |
| Ga0208657_1017473 | Ga0208657_10174731 | F029799 | GRPGPPASGLMLALTLSTVGCVLLCYTLGRYNRTVTLQRWQFVLNAPGRQAVDTLRAQMQLDSVLAQQALDAASRARAAGRAPDAVTVLRVALSVLEEAGTDRLTRLKAMGIYSRMVRALQPLPAPTAEPFRGAQLRTVVASAGLVHHFLVGAEERFRLWLLMLGLGVRIVLRGGRRSAEAATRHPHAPRPWDQFAEGLTDFRTLDDAHLAAFEALAASLAAVDRGG |
| Ga0208657_1018134 | Ga0208657_10181341 | F024435 | MFGFLTPHTKDDADPLVSARTISAWLRHLPTQDVIARQHNVMRVFDGMRQSSRQVDLARVTAIQFLDTALGADRRQLVKQYVENIDRMARVADRAWQAAQEMSQGFVYAYQTSLEQALSEGGNPRWKPVIPQLFARLLHYH |
| Ga0208657_1018679 | Ga0208657_10186791 | F058543 | METVTILASINEKKKAEFFQTMESLTGLVESQCNDLDIRVKDDNSLIIKITFDGKEQMERNFYNNEFTIIKGTVKSLCKDVIIKVNDSIVSHN |
| Ga0208657_1019425 | Ga0208657_10194252 | F042500 | MDPVGELVAAAVVDERVWEAYGAQANDGVYLVGQPGPALPFVIFRAWKVPVGVVSEEIRLIGPSGRTIFRWGPQPRRMAGAMDLTT |
| Ga0208657_1020288 | Ga0208657_10202881 | F015847 | EGQQLIMQGGLWSPRDDIGTVDQRFKKSYLDERYSLEELEIKYDQWEQLIRRLFGQRK |
| Ga0208657_1021494 | Ga0208657_10214942 | F009970 | MAANDGVKLHGKNGAIYVNGPKGTGTKVATKSQWDLNLARDYVEVTTFGDTNKEYVAGLKDITGTFNGVLDVSGDLMVNNTSIDDVPLYLYADDGASPVLVASGPALIDSSITLSN |
| Ga0208657_1022477 | Ga0208657_10224772 | F002140 | MDDVKGQMEGVTRVYTELDNKISDKGGVQNLFGMNRKIRQALETITLGELDSMLAEIHRAKEGLTRLQEDIVEIRVLKEVLSAPMSGKVNGAT |
| Ga0208657_1022972 | Ga0208657_10229721 | F046145 | VCLNFYWKLFEWITNRYEKTIQNLLECDHMALKPKPFSEAKTGFFIMSRYLRVLSEKN |
| Ga0208657_1023599 | Ga0208657_10235991 | F000676 | AELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVADEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAIDWVLGAVRRLNKVSNDEVEAGVSIIADRIVPITVHAKRPTQDDLGMVVNGVDVSVMGTRFDALYLPPPSRPERPLAVKTLIVPTSEYADGRNVILTTGHSVYTIALRH |
| Ga0208657_1024509 | Ga0208657_10245091 | F045132 | GRQSRPSVLMHSSNRYPLGNCDSSGSETNPDYLTQFGAASHRSWLPSSFFAFTGRARTPPEELVNSASAAKYVSTPLLRGRVNQPDPTFPRSPGRILETVSGKLSSTDPPFQFFQ |
| Ga0208657_1024538 | Ga0208657_10245381 | F016687 | RPRAYHLIEIEEKSRLISEEVPMKTLKFFAGLMTISMIALGAGSASAWDTRWQFKQDAPSNNYGSGTRDIEMQKKFDYNSMNKFKGTIETSSGYTIMRNLNGDTMRGYIDKDGSGLLRDQNGNFHNVNTRW |
| Ga0208657_1026480 | Ga0208657_10264801 | F056185 | RMQSSPTHWTLGGLQIMRPRMLLLFRLLMVLVSLFIVVGCSGPQAKIRKVDLPKEKELRANWKNYNTYCLGSRGGNVDFADAMLFQLRSDKTIQRDDDWREVTSDQMASGCASLLSDSSPVMELLGENDEIFGYVIYNFNDQIWASIIDPKTIRLFYHVHPKGP |
| Ga0208657_1027353 | Ga0208657_10273531 | F007886 | VEGGGAVVAVFEGLEVVLAGVLAGGDTAAEAGVEGAVDVVCSDALGADSFFSPVAGAGASLPGD |
| Ga0208657_1030316 | Ga0208657_10303161 | F024580 | MTTFNRNYRTAAAFAAVVIVGLTGLTLDRGHAGALPQGVIEIGELETVMVGDMNIASLPAVEVIGSREVQLADVVANDADTQG |
| Ga0208657_1031197 | Ga0208657_10311972 | F023288 | LALLVVGAATSWWAMTLGWAALAIAFFAWVAEADGLLALPRLGRVAIRRGGFDIPLAFKVRRGERVLFFVREEDPERGGWSDVYTVLDRPNGTDGFEPCYYLQTAIPSGWSLRGHVPVDDLRFEHHERVVYVTRGSLERSLSAAGM |
| Ga0208657_1031834 | Ga0208657_10318342 | F017154 | RIRRGSLALLVAGAGLTLVLGHSLFELLGDEEHRRSFTSSSMIFGLVLLALCGICWQAGYRLAFQRPDRTGTLFSRPAWLAIGTGLVVITASMVVAISQVRQMTLLDLQVLLFLGGIGVWCLVLSFRGGGGTR |
| Ga0208657_1032199 | Ga0208657_10321991 | F040161 | PSTAWTAAEGLGRGSGLVVRVTPPRRLSALVVGVDLRDSPLAVPWVAQVGGAVVAQGPARSGLAWVNGAPRAGKQALLVAPLGGRSTGEVRLVFQGPGPQLRVSEVFAYGPEEAEQPRAGEENARAAFEASRAGRWDEAERLYAEALRREPGRASLHAAWARVRWRAAGRRWLDV |
| Ga0208657_1032582 | Ga0208657_10325821 | F012266 | SLLALQLPFCFEVRALSGRLVSSSPARPCDDMRGLNSLLSESDGDAADFLD |
| Ga0208657_1033631 | Ga0208657_10336311 | F093171 | MIVVAVGVVAALGALWLDPARAAVGPMSAQGLVLPADARYLMGFDVKRFAASPFYARYGSQKGMRPEALAQLEEKTGLNPERDIDQILVAGTGTVRGGVPGIALVTGRFDLYKLGRAIETQGKARGYGHDGVTVYAYGEEGPRATAVAFLDESTLLFGQKDRVEAAVASRTR |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |