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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 | 3300025983 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0101393 | Ga0210106 |
| Sample Name | Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Tolay_CordC_D2 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 145181152 |
| Sequencing Scaffolds | 38 |
| Novel Protein Genes | 41 |
| Associated Families | 37 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → unclassified Phycisphaerae → Phycisphaerae bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 6 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis | 2 |
| Not Available | 19 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → unclassified Proteobacteria → Proteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Paenibacillaceae → Aneurinibacillus group → Aneurinibacillus → Aneurinibacillus tyrosinisolvens | 1 |
| All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium | 1 |
| All Organisms → cellular organisms → Archaea | 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 → Aquatic → Marine → 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) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: San Francisco Bay, California | |||||||
| Coordinates | Lat. (o) | 38.15012 | Long. (o) | -122.438774 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F005055 | Metagenome / Metatranscriptome | 413 | N |
| F005727 | Metagenome / Metatranscriptome | 392 | Y |
| F014614 | Metagenome / Metatranscriptome | 261 | Y |
| F021303 | Metagenome / Metatranscriptome | 219 | Y |
| F025653 | Metagenome / Metatranscriptome | 200 | Y |
| F027171 | Metagenome / Metatranscriptome | 195 | N |
| F029111 | Metagenome / Metatranscriptome | 189 | Y |
| F036767 | Metagenome / Metatranscriptome | 169 | Y |
| F039643 | Metagenome | 163 | Y |
| F041201 | Metagenome / Metatranscriptome | 160 | Y |
| F042907 | Metagenome / Metatranscriptome | 157 | Y |
| F042909 | Metagenome | 157 | Y |
| F048676 | Metagenome / Metatranscriptome | 148 | Y |
| F050381 | Metagenome / Metatranscriptome | 145 | Y |
| F051215 | Metagenome / Metatranscriptome | 144 | Y |
| F052508 | Metagenome / Metatranscriptome | 142 | N |
| F053305 | Metagenome / Metatranscriptome | 141 | Y |
| F054044 | Metagenome / Metatranscriptome | 140 | Y |
| F054047 | Metagenome / Metatranscriptome | 140 | Y |
| F057384 | Metagenome / Metatranscriptome | 136 | Y |
| F058175 | Metagenome / Metatranscriptome | 135 | Y |
| F058721 | Metagenome / Metatranscriptome | 134 | Y |
| F066735 | Metagenome / Metatranscriptome | 126 | N |
| F070131 | Metagenome / Metatranscriptome | 123 | Y |
| F076109 | Metagenome | 118 | Y |
| F077317 | Metagenome / Metatranscriptome | 117 | Y |
| F077987 | Metagenome / Metatranscriptome | 117 | Y |
| F081352 | Metagenome / Metatranscriptome | 114 | Y |
| F084254 | Metagenome / Metatranscriptome | 112 | Y |
| F087210 | Metagenome / Metatranscriptome | 110 | Y |
| F087950 | Metagenome / Metatranscriptome | 110 | Y |
| F090406 | Metagenome | 108 | N |
| F097951 | Metagenome / Metatranscriptome | 104 | Y |
| F098573 | Metagenome / Metatranscriptome | 103 | Y |
| F099322 | Metagenome / Metatranscriptome | 103 | Y |
| F099325 | Metagenome / Metatranscriptome | 103 | Y |
| F102142 | Metagenome / Metatranscriptome | 102 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0210106_1001210 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → unclassified Phycisphaerae → Phycisphaerae bacterium | 3384 | Open in IMG/M |
| Ga0210106_1004793 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1956 | Open in IMG/M |
| Ga0210106_1009816 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1442 | Open in IMG/M |
| Ga0210106_1009994 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1431 | Open in IMG/M |
| Ga0210106_1010418 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis | 1408 | Open in IMG/M |
| Ga0210106_1012239 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1314 | Open in IMG/M |
| Ga0210106_1015323 | Not Available | 1186 | Open in IMG/M |
| Ga0210106_1017190 | Not Available | 1124 | Open in IMG/M |
| Ga0210106_1018369 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1090 | Open in IMG/M |
| Ga0210106_1019888 | All Organisms → cellular organisms → Bacteria | 1050 | Open in IMG/M |
| Ga0210106_1022643 | Not Available | 990 | Open in IMG/M |
| Ga0210106_1024240 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales | 960 | Open in IMG/M |
| Ga0210106_1025202 | All Organisms → cellular organisms → Bacteria | 942 | Open in IMG/M |
| Ga0210106_1030301 | Not Available | 864 | Open in IMG/M |
| Ga0210106_1033638 | Not Available | 823 | Open in IMG/M |
| Ga0210106_1038066 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 776 | Open in IMG/M |
| Ga0210106_1038634 | Not Available | 770 | Open in IMG/M |
| Ga0210106_1039670 | All Organisms → cellular organisms → Bacteria → Proteobacteria → unclassified Proteobacteria → Proteobacteria bacterium | 760 | Open in IMG/M |
| Ga0210106_1044168 | Not Available | 722 | Open in IMG/M |
| Ga0210106_1046836 | Not Available | 701 | Open in IMG/M |
| Ga0210106_1047249 | Not Available | 698 | Open in IMG/M |
| Ga0210106_1052418 | Not Available | 664 | Open in IMG/M |
| Ga0210106_1053059 | All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon | 660 | Open in IMG/M |
| Ga0210106_1053242 | Not Available | 659 | Open in IMG/M |
| Ga0210106_1059343 | Not Available | 625 | Open in IMG/M |
| Ga0210106_1061586 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → Pseudohalioglobus → Pseudohalioglobus sediminis | 613 | Open in IMG/M |
| Ga0210106_1066134 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Paenibacillaceae → Aneurinibacillus group → Aneurinibacillus → Aneurinibacillus tyrosinisolvens | 592 | Open in IMG/M |
| Ga0210106_1070267 | All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon | 575 | Open in IMG/M |
| Ga0210106_1073261 | Not Available | 564 | Open in IMG/M |
| Ga0210106_1076639 | Not Available | 551 | Open in IMG/M |
| Ga0210106_1076879 | Not Available | 550 | Open in IMG/M |
| Ga0210106_1077641 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 548 | Open in IMG/M |
| Ga0210106_1080727 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium | 537 | Open in IMG/M |
| Ga0210106_1080759 | Not Available | 537 | Open in IMG/M |
| Ga0210106_1081224 | Not Available | 536 | Open in IMG/M |
| Ga0210106_1082981 | Not Available | 530 | Open in IMG/M |
| Ga0210106_1084435 | All Organisms → cellular organisms → Archaea | 525 | Open in IMG/M |
| Ga0210106_1086016 | Not Available | 519 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0210106_1001210 | Ga0210106_10012106 | F052508 | MSYLYQKKSYKKIILNTNDAIASVGKANAGTGNSEFVFYNFNTITIKEPSYLKVIGASADISTNSVWTIKLDNVSYNETSYYNSDADGSPTILTRCFNGKSSLMLDNIALELPPQDMSDIKLIILDEAGNGLNGAKMMFE |
| Ga0210106_1004793 | Ga0210106_10047931 | F099322 | MVRRASISDDDSMRIVLDGVSLIRNSDGAWCCVAPPSAHDLKDNWYRASPSLLIRWLDAVGQVTPVN |
| Ga0210106_1009816 | Ga0210106_10098161 | F077317 | MEESLINPVDETVWYENDQPIKEFLESFRKPAVLEADPQSEEPSWLKIIEKSIQI |
| Ga0210106_1009994 | Ga0210106_10099942 | F054044 | MNYRNSDRLNHLPADRLGMSNTVGILVLVFALTALILLFLDFSFRSAADQEECLQLVRALGLNSLSLAPSGRPLRNPGAIDPSIDLRFDPKLWRTQK |
| Ga0210106_1010418 | Ga0210106_10104182 | F090406 | QMKCERNVLWLIVVLAGLAACSTTLTSVDKEGGNVYALPPTVVDQMLKDAMSTEISTGTLRRGSKPYPSYLGEVTWGSLDKDTITASARPAKGRKLDGTIIDGYVFEVTRKGTAPATGEPTVKRIFAKLQNDAELTGTGVAFVEFTD |
| Ga0210106_1012239 | Ga0210106_10122392 | F087950 | MQCWINGPATGGIDDKIKMVNILLKTNIPSFHPSIIPFPGKIRKPQKTSIL |
| Ga0210106_1015323 | Ga0210106_10153233 | F039643 | MRKFWKKQVEDLGGDPSVLIKGRTQLAKEMVMALIAAHKEAITMRNAGYVIGRAACIVKNPCVEF |
| Ga0210106_1017190 | Ga0210106_10171901 | F084254 | SMQARRIPVFISESIVIEILAEVIRQSKRHPRADQVASALAKRGLPIAEKDVMSVFDHYDIEKKTADSHYFDT |
| Ga0210106_1018369 | Ga0210106_10183691 | F053305 | LMALFVFSFIAVATVSADETQKITGTVMSVNVETGEVIVKDDAGEMKSLMADPKAGVDLKMLKEGDPVNVESDSNGVIKSLKAAE |
| Ga0210106_1019888 | Ga0210106_10198882 | F021303 | VQADVLHHAAEFVELVYRQAPAEYHRLLAADRFHSDLERGGAFNHGKLYAYAEFSVFRREFLDRFPEASPAACINAFSGLFLKNDISIHNLVEFVEGADDRTQLRLNSPNP |
| Ga0210106_1022643 | Ga0210106_10226432 | F048676 | SRLCGKASDTVDAVKLEIPKGFKLLKFKMSEYLKLILKLTISKI |
| Ga0210106_1024240 | Ga0210106_10242401 | F048676 | ASDAVDAVKLEIPKGFKLLKFKMSEYLKNIVKLTISKI |
| Ga0210106_1025202 | Ga0210106_10252021 | F054047 | GSDIGHGLFVGWVEHLDIFRWVSFLNPTLPAIFVVSAKPNKMASIF |
| Ga0210106_1030301 | Ga0210106_10303012 | F014614 | MTDWYADYYRQSRGYNWNDLRELSYQKPKVELTVPDVFKHRFATRAEYDAWVEERRKLYF |
| Ga0210106_1030301 | Ga0210106_10303014 | F027171 | IDSLEFDPDGLIRVTAVVDQVVLTHHATQWDPEEYGSALCRGSFYLSDEDLIPATDAELCKLIAERVDDWAPVDPDE |
| Ga0210106_1033638 | Ga0210106_10336381 | F099325 | MRDALLRFWRWSQKSPAERRAAKARARFWLELREGQREAEVHSRP |
| Ga0210106_1038066 | Ga0210106_10380662 | F048676 | ASDAVDAVKLEIPKGFKLLKFKMSEYLKNIVKLPISKI |
| Ga0210106_1038634 | Ga0210106_10386342 | F042909 | MVELLTFIGSLNLWTFIVIWTSTIFLVIFISLLLISVSQMNKETIKISEKVKILIEDLSKKKLKLGNHDNKFF |
| Ga0210106_1038770 | Ga0210106_10387701 | F087210 | MRFLMGVLALAGAETALAHTPDTGFLSNFGHQLTSLHHSPAAMLLGVLVLALLLVA |
| Ga0210106_1039670 | Ga0210106_10396701 | F036767 | MRKNSCGKVDILKTDYDAKISKVPELIGKHPGVIAPVTICKPKPLEFIKPASASRVSGSMEVEVKIREGNEELERNLKKIVLTIDGNRFEFDKPPYKVYFDTSHARYRVITLTAEALGKDEEQEDAVLSSFYTNVIAENGECDKTKPLLLFAGVFEPKIENRRETWTPEMYSKAYTFSEKMMSHLMHYGF |
| Ga0210106_1044168 | Ga0210106_10441681 | F070131 | FSSTPMLNEYTVLNIEIRALIDTPNTLIEIEIPRDGFEIISGSTQFNEDLSSGSTATYQLEVLPTAQGQYTIAASARSEETDYIFGKREELYVNIGEGFSELSKTSFTPEIANNRSGAIKIGNLSGPPTQVLPDHKPIEDQAVSYFAAPGSGQIVVRGYWFYQDKNEVNQPLREAMVEIWDSGSGSSGDTLLDTTYTNDSGYYASGNISNSDDEGVGQDIYVKVFSTDNRSVRVTDFSTP |
| Ga0210106_1046836 | Ga0210106_10468361 | F102142 | QFIAQLVGISYDEFHGGMPTQYLFPLFLIYTAIALVLAKMKKNLNVSKRGAFFIIFAFHYFIVSFLPELEGKIYLPDFPFLSTLISTFILALAVVSLIFYLWKQEDHPEAKTGQQIRSYFSSRSILSWAWRFFLVWILFYVVTMIIGIVALPFNGEYLDDATNTLGMVVPSMGALFAITQFRSLFYILVTLPFIIFWSSSKRSLLLYLALILIIQYPLLGDGLAYFWPGMYRL |
| Ga0210106_1047249 | Ga0210106_10472492 | F081352 | MIRLIRKISTITLACLLVLNLTAGAAVVVEHCPPLLGSSSPMDIDHCDGMLNFAFPMQGCCGECNDIFCDLIKNPLQDANAVNASPFQGSYYFFILGTVDSIAESGAWIAASAPRYLFCAAPAWSQIPLYIENLALII |
| Ga0210106_1052418 | Ga0210106_10524181 | F041201 | KNRILVQDRDGAEFKTAGILLYVEDLKRGTNKDIGPKDIFAIGL |
| Ga0210106_1053059 | Ga0210106_10530592 | F058721 | MTMLRATLPCADPKCKEKMRLVFQNERFIGYRCLLKPNTHNFRYDRASKKWEKIIIKTKPIIGYKECPHHIAYKDELVVESI |
| Ga0210106_1053242 | Ga0210106_10532421 | F005727 | TRSRSADFHRATMLKLIVAAGLLYLLWEPIKPVRLVTADLLHTTGDLVAR |
| Ga0210106_1059343 | Ga0210106_10593431 | F042907 | MTDEMRVEAEEKLFNDLRDEPCIVCGDPYLHVLGSYTPEEPKRSKNREDRAPVLYYTLCRTCFNNGRIPTARIESAYKSKFGKMAA |
| Ga0210106_1061586 | Ga0210106_10615861 | F090406 | MKFRLNVWWWIIVFAGLTSCSTTLTSVDGKGGNVYALPPTVVDQMLQDAMSTEISSGTLRRGSTPYPSYLGEVTWGSLDKDTITASARPAKGRKLDGTVVDGYVFEVSRKGTAPATGEPTVKRIFAKLQKDAELTGTGAAFVEFPD |
| Ga0210106_1066134 | Ga0210106_10661341 | F077987 | MRIEYKCSGGFGGLRLAYRGETDDLPSEQAKELSDLVEAAGIFELTPKQLSKKSPTIPDDFSCLLTVLKAGKRKTLSFNELGAPANLRRLSVHLRKLAIQQKGR |
| Ga0210106_1070267 | Ga0210106_10702671 | F066735 | MNDVDKFVAAIVEQDSLAGSNPILSEDDIQQMQLMNSIDDVQMYAIEKGIDAGKVNNALISTGLDTASDPMADLTGLFGFGEAEKSIIGGLPSDYSPRNAGATDFYREGDEYNIFANLPTEDLYSLQARLIQGGLLARGAFT |
| Ga0210106_1073261 | Ga0210106_10732612 | F050381 | MKKILVIIAIILIPTIAFANFSIQLDNNTGKKMFYLLYWVDHTYDWPHPFNLAGGELKSSESIDLRSDYRNGKYFVVWSDNGDWQNKVMMN |
| Ga0210106_1075701 | Ga0210106_10757011 | F098573 | ALIIRYKRYETDAVEKLMTLLFITEDSYRMAGVSQALGLDTQQAGTWLALEGENSRAIQPMALWGLVQWLGQLSPAQLNLALGVEPPHHIIEDEKHTKECGQKAYIPMVYAPKEALIWWIDYIHSVSEVELTASLERFKTISDRLKDITGATVDGWEAAQNALQAAFEGIILAECHFHAMLKLGQ |
| Ga0210106_1076639 | Ga0210106_10766391 | F058175 | QTGADGTALTAAAGDVVLGYAREAGVDGQIIEIEMIQGGNVVPA |
| Ga0210106_1076879 | Ga0210106_10768791 | F029111 | GGNRTAGSSPDSDDSRTVSRTGVDGNTSKEHEQNALPDILMTMSQIPDVNRELVEVGAMFAVFRAVNNDPPRS |
| Ga0210106_1077641 | Ga0210106_10776411 | F057384 | MTRTRMDEATINASLDACLHGAKEGDTDQARRLHEMLDLMLTERETENGKLWLTEHGKLLLAEMHRALSHCEGSGHRLEETVLDAVQLKPRQGHWRDTCEYLHDLRVAIAVANELCEQRAAGDKPSVSQAAKAVAGRGEFDMGAPRIREVYDEIASTLGGF |
| Ga0210106_1080727 | Ga0210106_10807271 | F051215 | VAVDRTQGSGSYGTSRTVLVGSLVGLVLAAIGVTVLIDKEGGQKLLASIYDMLGNAAGAEALRNGQGDQFFAKLLLAAIAMLVGVGGIWLLFTGVS |
| Ga0210106_1080759 | Ga0210106_10807591 | F042909 | MVELMTFIGNLNLGTFIVLWTSTILFVICVSLLLFYIRQMNKEAITISKKVK |
| Ga0210106_1081224 | Ga0210106_10812241 | F097951 | AARAALHTLNVPGRQRHSERAQKARPKFRHATATKTTVTGKPEVRVFAPGFY |
| Ga0210106_1082981 | Ga0210106_10829811 | F005055 | QTILMTASTRGFTFKPATINDVHELTSQMLDRGLLDFERVGQHPVLSLAMYIHEDDSYLIYGPDGSLYGAYGVSEDNAVWIQMTKQVKKNPRTTVRFGKALMEHINRPYLWTTIDIKNTDLINLARYLGFKVLRVFPDGPDNVYSIEIVRL |
| Ga0210106_1084435 | Ga0210106_10844352 | F025653 | MEAIKYFETKLKTMSLAELQDYKKRLDESITEKISKTVPNEQIAPLILYRGILEHEIKKRTNLR |
| Ga0210106_1086016 | Ga0210106_10860161 | F076109 | MEVLFKMLFVIALIATIFCLCVFIGGLFNAFQKEE |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |