Basic Information | |
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IMG/M Taxon OID | 3300025970 Open in IMG/M |
GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0101403 | Ga0210081 |
Sample Name | Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqA_D1 (SPAdes) |
Sequencing Status | Permanent Draft |
Sequencing Center | DOE Joint Genome Institute (JGI) |
Published? | N |
Use Policy | Open |
Dataset Contents | |
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Total Genome Size | 119736411 |
Sequencing Scaffolds | 27 |
Novel Protein Genes | 29 |
Associated Families | 29 |
Dataset Phylogeny | |
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Taxonomy Groups | Number of Scaffolds |
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 3 |
All Organisms → cellular organisms → Archaea | 1 |
Not Available | 6 |
All Organisms → cellular organisms → Bacteria → Proteobacteria | 2 |
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium | 2 |
All Organisms → cellular organisms → Bacteria | 4 |
All Organisms → cellular organisms → Bacteria → FCB group | 1 |
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales | 1 |
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 2 |
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium → Phenylobacterium soli | 1 |
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 1 |
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 2 |
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium IS3 | 1 |
Ecosystem Assignment (GOLD) | |
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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 | |
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Environment Ontology (ENVO) | Unclassified |
Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
Location Information | ||||||||
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Location | USA: San Francisco Bay, California | |||||||
Coordinates | Lat. (o) | 38.131752 | Long. (o) | -122.266335 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
Zoom: | Powered by OpenStreetMap © |
Family | Category | Number of Sequences | 3D Structure? |
---|---|---|---|
F002477 | Metagenome / Metatranscriptome | 555 | Y |
F008627 | Metagenome / Metatranscriptome | 330 | Y |
F015245 | Metagenome / Metatranscriptome | 256 | Y |
F020261 | Metagenome / Metatranscriptome | 225 | Y |
F020359 | Metagenome / Metatranscriptome | 224 | Y |
F025254 | Metagenome / Metatranscriptome | 202 | Y |
F047211 | Metagenome | 150 | Y |
F048676 | Metagenome / Metatranscriptome | 148 | Y |
F052687 | Metagenome | 142 | Y |
F055469 | Metagenome / Metatranscriptome | 138 | Y |
F058158 | Metagenome / Metatranscriptome | 135 | Y |
F060099 | Metagenome | 133 | Y |
F061999 | Metagenome / Metatranscriptome | 131 | Y |
F062887 | Metagenome / Metatranscriptome | 130 | Y |
F074891 | Metagenome / Metatranscriptome | 119 | Y |
F076224 | Metagenome | 118 | Y |
F077315 | Metagenome / Metatranscriptome | 117 | Y |
F077325 | Metagenome | 117 | Y |
F078289 | Metagenome / Metatranscriptome | 116 | N |
F080179 | Metagenome | 115 | Y |
F082716 | Metagenome | 113 | Y |
F084254 | Metagenome / Metatranscriptome | 112 | Y |
F090405 | Metagenome / Metatranscriptome | 108 | Y |
F093897 | Metagenome | 106 | Y |
F103291 | Metagenome | 101 | Y |
F103506 | Metagenome / Metatranscriptome | 101 | Y |
F105200 | Metagenome / Metatranscriptome | 100 | Y |
F105202 | Metagenome | 100 | Y |
F105217 | Metagenome | 100 | Y |
Scaffold | Taxonomy | Length | IMG/M Link |
---|---|---|---|
Ga0210081_1000036 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 31964 | Open in IMG/M |
Ga0210081_1000059 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 25049 | Open in IMG/M |
Ga0210081_1000066 | All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus | 24209 | Open in IMG/M |
Ga0210081_1000146 | All Organisms → cellular organisms → Archaea | 11644 | Open in IMG/M |
Ga0210081_1000801 | Not Available | 3683 | Open in IMG/M |
Ga0210081_1001181 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 3093 | Open in IMG/M |
Ga0210081_1006553 | Not Available | 1542 | Open in IMG/M |
Ga0210081_1010453 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium | 1263 | Open in IMG/M |
Ga0210081_1012533 | All Organisms → cellular organisms → Bacteria | 1166 | Open in IMG/M |
Ga0210081_1013932 | All Organisms → cellular organisms → Bacteria | 1108 | Open in IMG/M |
Ga0210081_1017038 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium | 1011 | Open in IMG/M |
Ga0210081_1018505 | All Organisms → cellular organisms → Bacteria → FCB group | 972 | Open in IMG/M |
Ga0210081_1020435 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → Ignavibacteriales | 927 | Open in IMG/M |
Ga0210081_1021821 | All Organisms → cellular organisms → Bacteria | 899 | Open in IMG/M |
Ga0210081_1023061 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 875 | Open in IMG/M |
Ga0210081_1024298 | Not Available | 855 | Open in IMG/M |
Ga0210081_1026060 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 827 | Open in IMG/M |
Ga0210081_1030101 | All Organisms → cellular organisms → Bacteria | 774 | Open in IMG/M |
Ga0210081_1036011 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium → Phenylobacterium soli | 709 | Open in IMG/M |
Ga0210081_1049750 | Not Available | 609 | Open in IMG/M |
Ga0210081_1056962 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 571 | Open in IMG/M |
Ga0210081_1057899 | Not Available | 567 | Open in IMG/M |
Ga0210081_1058001 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 566 | Open in IMG/M |
Ga0210081_1059766 | Not Available | 558 | Open in IMG/M |
Ga0210081_1068413 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 522 | Open in IMG/M |
Ga0210081_1071354 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium IS3 | 512 | Open in IMG/M |
Ga0210081_1074166 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium | 501 | Open in IMG/M |
Scaffold ID | Protein ID | Family | Sequence |
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Ga0210081_1000036 | Ga0210081_10000367 | F105217 | MKMASNVNSNNERNSLIDSIQYRLFYAEINLDKIPTFIPLDIFPKDKIASEVAIDGFLFYANSALDLVFVEINKKLELGLPPNQINPENIMLNFNSKKSNDSKMMLEEFQKYFQKPTHEEKIISDKEFNDGLNRYGFDVIGFHAEYEARGQEKYQHFWNRASSRLWEIRNQQDLESYDSLLKNAGKRGKDEPRNYLRVKLADDNRPSVYWDSAHYENPKRYFTNVLSLVKQFIDRILEILKPLYPSDSSLVV |
Ga0210081_1000059 | Ga0210081_100005923 | F093897 | MKPGFYISMGIAIAGLIVGFVLLNDIQQEKESKNIWIQKIPIQCNDVWEREHQEFYDLNPELLNSNKEKSKEILETIIKNHYEKAGISILDLNLELDVIDEIRCESCDCLGSDRVSIKIPKNQFELISQSEGWKPLE |
Ga0210081_1000066 | Ga0210081_100006613 | F077325 | MSDKGNWTEKDEVAIHAIIVNMLNQKQMFQDLGKTTILPNSFNIKNSNEYILGLFTGIVINLFANYWVGEHESGLSPEDLSYLYYKISLFREEIVSGLFD |
Ga0210081_1000146 | Ga0210081_100014612 | F082716 | MISKKDIRLMPFTFIIAPILLISLTFVVVTAYYDVIEEKEFIAGLSCPELMIYTDKQTIESKLYFGNENYLIYAEERLHNMC |
Ga0210081_1000801 | Ga0210081_10008013 | F103291 | MEMFGLSPVFATILIVSMGVILQNFLGWLKSKEDYDIKNALASTIIAFIVGITIIGPQIEAIQDQMLSELSELTIFASLIASIAGFDVLTKNVFKIANSKIHLQNKPI |
Ga0210081_1001181 | Ga0210081_10011812 | F055469 | MLKRTVVILAAAAFFWGTVPTQTAQARDDIWDLMNPSWWADKMFDNDDDWRHYRHYAYNPYWGGPYAQRPRVIVIQPPETEAQNPDTRPPE |
Ga0210081_1006553 | Ga0210081_10065533 | F062887 | MPVKQCSGGHKFGNKGKCYKGKGSKAKAARQGRAIKASQAKRGK |
Ga0210081_1010453 | Ga0210081_10104531 | F025254 | MEESVREMVFLIVEQLKAYVDGDEDALLELTQVLDSGRHDADVVNQAFELIFRALEPYAREDFSEDPTTPRRSVRVPTGSERALLDAPGYQYLYGLIEQGRISPEQFEEIMSRVREDTSFLDTEASARELATTV |
Ga0210081_1012436 | Ga0210081_10124363 | F105200 | MKPVQGRHRRRNVPDSFERKLGQLLEYSDAPHAEAFTMNVMRSVRREQRRRKIILWSFGLVGALFGLSGALMLTGPVSELLTFSLEMPVMKTMQVTLFVVGATA |
Ga0210081_1012533 | Ga0210081_10125331 | F060099 | MGLTDDQRDDAAKALRAAQEAIEYTVKGVKGLEEAATLRGRIDEIELYLKRAKMALKFI |
Ga0210081_1013932 | Ga0210081_10139321 | F020359 | MAARQSRRHKTPDEFWSKVLAAPKVKRILERRGVSPDDFQRDYEADNSRGARTPKRPTRGQIDAVEAFQKSGDFEAFKRALSTNSSAVANSALRRVVQFKAMGGSKTIRRRGGAENA |
Ga0210081_1017038 | Ga0210081_10170382 | F080179 | MAVAAKSVTSTRPVDIRVRFEPGLGMALYASVAPGEVGSVTVARNLGRGRAMLRYRGFTLMTQGAPDWRDGESFSVVVKEVGPPLLLASTNRTAKDDQRVTTVDSAVVPGGGESAEAGR |
Ga0210081_1018505 | Ga0210081_10185052 | F076224 | IFVTPDSIFEDSFVFDPVLMEKRIEWTEKKIKANEEKIKEVTFKVEFDSAFRYYSEEMKGHPFTVAFDSNICRVDVPNFKAYRTELPEIAAIDPLIELATNNIHFYAYKIPKIEKSNSEIKIEYYNDDSVYSYVVDYNVINIDSIVQANAGGRDLITLDKFKPVQPNDDTMLIKYQFDRDYYKRFYSDEEFKKQMEELQKELQELSKDVNNQKIRVHTEVTKTPKK |
Ga0210081_1020435 | Ga0210081_10204351 | F052687 | YGLKTQYDKGTIFAKMLETVIRKSIETMVKFLTIVLLLTALGGGTYYLLSMETVEDVKVMGKLQISEQYGSYVMASQSKDANYYAVVEGKVKNNMKKPIKNVFIKYVIAGKETSATIFDLAPGQELHFNTSGVATTGSSPEYDFVGIYYD |
Ga0210081_1021821 | Ga0210081_10218212 | F008627 | MMCRFLNADFELALRCPVDKCNHNVRFQAYPQLRDHALEVIACDAAGDADRLTCGKNCRALIESGHYWQSIYPESAIYSRNL |
Ga0210081_1023061 | Ga0210081_10230612 | F090405 | MKAALAFVFAIGLLVPGIAASDPSDCGRLMYQINHFEGMADRAEALGRDDWAEKTQRHVDVLETRLANRCPAFSARDEQQEAARQMALLLKMAATAAAKFFTMGMY |
Ga0210081_1024298 | Ga0210081_10242981 | F058158 | MGVTKKDRENRIDKRIINQKSYMSEFTKTEKDDIDIWELHVKEREYILAQIANDRRTSRIRNWIELIFMLGFIYYMLYDIYKDKDLDTIIKFLKA |
Ga0210081_1026060 | Ga0210081_10260602 | F077315 | MMICRASTLFLSRLAYYQLWTLLLLGLLVPAQAAEALNPDALPQAQATLERLEEQLATARTANAQELKTLRKEVAMVRSTAQDCLQQAEPKIEILDSELAILQPAKPKDTQKKTAQETQPAEQAEAPVSPAIAGQLQELLSSKASLEGRIAICKLLLLKSNYLDSNVDDYLRTVQTRQLLARGPTLVSV |
Ga0210081_1030101 | Ga0210081_10301012 | F020261 | MVVQEDLAVESFMVSSFGAFVMSLCQGLFSLRSEQTLAFLACGWALASGERQTITTYLWLSGATRVKHFSRFYVFLGGALYQARWQLWGRVIQQAAQWVPAEAVIVLEVDDSTKKK |
Ga0210081_1036011 | Ga0210081_10360112 | F061999 | HFNRGILRGLEPKKIDVQMLHRNPPRLGEMLGEDDWFDKLGPKGRDYTRAAYMARLHAFTEQCRQRILRGGPPRPTR |
Ga0210081_1040304 | Ga0210081_10403042 | F103506 | MGTYMINTESMLETDHFIILDESNTVRGNEFDRSYPKVQIVYPSSMNSYPDNKVTESRPENGSNYKEKEKHPFTITLNVDAD |
Ga0210081_1049750 | Ga0210081_10497501 | F084254 | EVIRQSKRHPRADQVASALAIRGLPIAEKDVMTVFDQYDIEKKIADSH |
Ga0210081_1056962 | Ga0210081_10569622 | F015245 | EVPESNRLIEIMFGYHPKASAAHGIADPMHWELISKMPWAGLGTPRKHPKFRHMDGSVFNGQLYIDDRLVVDKHGMLDRSLLHHPEVLEVAAEFGDPYQVLAPVSHEAHGSNTAW |
Ga0210081_1057899 | Ga0210081_10578991 | F078289 | SIFILIIVVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE |
Ga0210081_1058001 | Ga0210081_10580011 | F002477 | IMAEPATGFLFAALVPAGNPSDVSYVVPLLDKVQGAIQRVTTTPKRQVHSVAGDLGINDATLRHTLHARGILTVGIPQTVEPLDPTPSPEASRAILTAASLTGKRTVHQVQGACTAGYSRPVVESYIASLLARGAGQLRYKGLAGAGVQLGMTVLAQNGATLVRIREQRLTKRAQKFRRFLRLPRPKP |
Ga0210081_1059766 | Ga0210081_10597661 | F105202 | PSISALKPEEYSGEIDKYNKIIQSDLHLDIQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELDILKRQSAAFRGSRQDIQSANLKLQKRIGQLQKKVRNLETSNAKLNKTIEMLSTLDSRLKEKRINFIKTDSIEE |
Ga0210081_1068413 | Ga0210081_10684131 | F074891 | MSAVTHDVVLKRKPRKKRNKGEAALRSLRRALARRKLELMREDEILHEQIYDVFEEEAGKKA |
Ga0210081_1071354 | Ga0210081_10713541 | F048676 | RLCGTASDAVGAVKLEIPKGFRLLKFKMSECLKNIIKLTISKI |
Ga0210081_1074166 | Ga0210081_10741661 | F047211 | EKETIDYAYEQMRQRATVDLVAPEAAIENLIKMVSYVDKRATTIDRSKLTDYSLLKELAQTGQLPAKR |
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