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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 | 3300026047 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116117 | Ga0208658 |
| Sample Name | Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Sandmound_ThreeSqA_D1_rd (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 63153588 |
| Sequencing Scaffolds | 36 |
| Novel Protein Genes | 39 |
| Associated Families | 38 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria | 3 |
| Not Available | 19 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → Rhodoplanes piscinae | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 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: Antioch, San Francisco Bay, California | |||||||
| Coordinates | Lat. (o) | 38.000637 | Long. (o) | -121.624207 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001574 | Metagenome / Metatranscriptome | 669 | Y |
| F001984 | Metagenome / Metatranscriptome | 608 | Y |
| F002389 | Metagenome / Metatranscriptome | 565 | Y |
| F003307 | Metagenome / Metatranscriptome | 494 | Y |
| F006263 | Metagenome / Metatranscriptome | 377 | Y |
| F006520 | Metagenome / Metatranscriptome | 371 | Y |
| F007886 | Metagenome / Metatranscriptome | 343 | Y |
| F008969 | Metagenome / Metatranscriptome | 325 | Y |
| F016461 | Metagenome / Metatranscriptome | 247 | Y |
| F017505 | Metagenome / Metatranscriptome | 240 | N |
| F021258 | Metagenome / Metatranscriptome | 219 | Y |
| F021571 | Metagenome / Metatranscriptome | 218 | Y |
| F023288 | Metagenome | 210 | Y |
| F023433 | Metagenome / Metatranscriptome | 210 | Y |
| F025363 | Metagenome / Metatranscriptome | 202 | Y |
| F027190 | Metagenome / Metatranscriptome | 195 | Y |
| F028610 | Metagenome / Metatranscriptome | 191 | Y |
| F029270 | Metagenome | 189 | N |
| F031088 | Metagenome / Metatranscriptome | 183 | Y |
| F034962 | Metagenome / Metatranscriptome | 173 | Y |
| F035133 | Metagenome | 173 | Y |
| F036745 | Metagenome | 169 | Y |
| F037023 | Metagenome / Metatranscriptome | 168 | Y |
| F041796 | Metagenome / Metatranscriptome | 159 | Y |
| F044348 | Metagenome / Metatranscriptome | 154 | Y |
| F049465 | Metagenome | 146 | Y |
| F061029 | Metagenome | 132 | Y |
| F062737 | Metagenome / Metatranscriptome | 130 | Y |
| F063749 | Metagenome / Metatranscriptome | 129 | Y |
| F068886 | Metagenome / Metatranscriptome | 124 | Y |
| F070242 | Metagenome | 123 | Y |
| F070780 | Metagenome / Metatranscriptome | 122 | Y |
| F089000 | Metagenome | 109 | N |
| F091213 | Metagenome / Metatranscriptome | 107 | Y |
| F093175 | Metagenome / Metatranscriptome | 106 | Y |
| F098734 | Metagenome / Metatranscriptome | 103 | Y |
| F100042 | Metagenome | 103 | Y |
| F103796 | Metagenome | 101 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208658_1002231 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1493 | Open in IMG/M |
| Ga0208658_1004899 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1022 | Open in IMG/M |
| Ga0208658_1005111 | All Organisms → cellular organisms → Bacteria | 1001 | Open in IMG/M |
| Ga0208658_1005350 | Not Available | 980 | Open in IMG/M |
| Ga0208658_1005497 | Not Available | 968 | Open in IMG/M |
| Ga0208658_1006269 | All Organisms → cellular organisms → Bacteria | 909 | Open in IMG/M |
| Ga0208658_1007211 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 855 | Open in IMG/M |
| Ga0208658_1007462 | Not Available | 841 | Open in IMG/M |
| Ga0208658_1009598 | Not Available | 752 | Open in IMG/M |
| Ga0208658_1009953 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 739 | Open in IMG/M |
| Ga0208658_1011801 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 686 | Open in IMG/M |
| Ga0208658_1011917 | Not Available | 683 | Open in IMG/M |
| Ga0208658_1012281 | Not Available | 675 | Open in IMG/M |
| Ga0208658_1012667 | Not Available | 666 | Open in IMG/M |
| Ga0208658_1013435 | All Organisms → cellular organisms → Bacteria | 649 | Open in IMG/M |
| Ga0208658_1013566 | Not Available | 646 | Open in IMG/M |
| Ga0208658_1013695 | All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae | 644 | Open in IMG/M |
| Ga0208658_1015237 | Not Available | 616 | Open in IMG/M |
| Ga0208658_1015537 | Not Available | 612 | Open in IMG/M |
| Ga0208658_1016259 | Not Available | 601 | Open in IMG/M |
| Ga0208658_1017101 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 588 | Open in IMG/M |
| Ga0208658_1017937 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 577 | Open in IMG/M |
| Ga0208658_1018761 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 566 | Open in IMG/M |
| Ga0208658_1019088 | Not Available | 562 | Open in IMG/M |
| Ga0208658_1020539 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 545 | Open in IMG/M |
| Ga0208658_1021118 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 539 | Open in IMG/M |
| Ga0208658_1021635 | Not Available | 534 | Open in IMG/M |
| Ga0208658_1021670 | Not Available | 534 | Open in IMG/M |
| Ga0208658_1022004 | Not Available | 530 | Open in IMG/M |
| Ga0208658_1022728 | Not Available | 524 | Open in IMG/M |
| Ga0208658_1022912 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium | 522 | Open in IMG/M |
| Ga0208658_1023050 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → Rhodoplanes piscinae | 521 | Open in IMG/M |
| Ga0208658_1023232 | Not Available | 519 | Open in IMG/M |
| Ga0208658_1023719 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 515 | Open in IMG/M |
| Ga0208658_1023781 | Not Available | 514 | Open in IMG/M |
| Ga0208658_1024082 | Not Available | 512 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208658_1002231 | Ga0208658_10022312 | F008969 | MTDASEVTGRDSYVIAQALYEFIRLEQSKPIAERRGSDERDAKAILHARFDDELELLVQSDEAAGRKPPDCKRRVTIGG |
| Ga0208658_1004899 | Ga0208658_10048992 | F003307 | MADSLLDNVDVHDAGDKIILSSPDEMTLNAVLQQMKKEGAQGIQQPMKVGRKWIASFEHPGLGQCKVEKIGFQIVITGMSEGAVVARSGEFREKGALVTRGPEQEDGAWKLYLDDAGARTGNMVTG |
| Ga0208658_1005111 | Ga0208658_10051112 | F016461 | MYHPTIFFDPQFTVGVMAGWLLQAAGVGALLLAGLWFSIAGEWRRGTPAPTAFRALAGLGLAMFLGGILWQFVGYFRTGTLSW |
| Ga0208658_1005350 | Ga0208658_10053502 | F006263 | MGTGWQLLEGVGTLLVSIALTYWLFVAPSRIKREQRQKARDLRDPRNR |
| Ga0208658_1005497 | Ga0208658_10054971 | F091213 | MGRAVQMLICNEDAPRRETRGIGRETLGIQSVGLSTPREKLRSGVGQKELAVDQVLANFVAELLVVLHPATLPMLERMFEDVKQDAETDGEWELKRRAEIGIAAARVAAREQEAIEN |
| Ga0208658_1006269 | Ga0208658_10062691 | F037023 | MTFYVEGVSKHDEPEPEVRRIGEYESLTEAIAVAQKAIEKFLRDAHRRGMTAKRLFTVYEEEGEHMFIFQDEAGTFNVPSFDHTDYARTMAATICGRLK |
| Ga0208658_1007211 | Ga0208658_10072111 | F001984 | MNRFRRTATDIAAVIFVLVLPACGIFQETYGIQEVDNWVRSNEPLAESGQMKWSVYYAGYFEKVAATPVISEGPVMEGAGIMLTAALFFEQGRLDRAGFDSVRGVMRKYQTVDDAAANLLAREALVRALEQKDKVAPRSSP |
| Ga0208658_1007462 | Ga0208658_10074621 | F091213 | VRTSGQMLICNDVGAYREGFGIEGVCLSTPREKLRSGAGQNELAVDQVLANFVAELFVILHPATLPMLERMFEDVKQDAETDGEWGLKRRAEIGIAAARIAAREQEAIET |
| Ga0208658_1009598 | Ga0208658_10095982 | F041796 | MARRSFLRACGGSAALLVPLLRDIEARADGAGAPLRFLIIHKPLGVQWPLWRPAVFP |
| Ga0208658_1009953 | Ga0208658_10099531 | F031088 | MKLNVLAVAVAATAIGAFSTNAQVVIEERRDPAVVIEHDRPDTSVTIEKRDGFLGTEKKTITKETTGSGDCTSKTVHKEDITGSEIQKTNCN |
| Ga0208658_1011801 | Ga0208658_10118012 | F021258 | VQVEFGRAGFFDRMDLRAQVIRAQEVVGYPEPAGRVAF |
| Ga0208658_1011917 | Ga0208658_10119172 | F089000 | MGEPTPETPASKYFVATVAMIAGAFFFAVGAGLLPIPGGPSNLHGPLWLVLCVGLAFFLTGGAIILQLLGHANDSGDRPAGAPLWLRAVQYLIDLCIFVCFGAISSWVAFGP |
| Ga0208658_1012281 | Ga0208658_10122811 | F070780 | MSAFFESLARRRAALVQRSTRQRGDIAAAVASVRRASAEPLLLGAGIAATVLTSSPKLRG |
| Ga0208658_1012667 | Ga0208658_10126672 | F017505 | VKARFAVAPNFHCSGSWKDRLLVAEGSGWCAPHDDELASLTLTKPGSDPACCCLFSVPAHMRNRFWAMLNEEAAEGTGDFDEFSEDLANFLTFKELPPPKDSVSELLIQSPDGKVETGDVWALINFGEEPVLLTWPQFQLRLGPAQGCRMAVGLPPNVVPPPKDELNVLLAIRLGPA |
| Ga0208658_1013435 | Ga0208658_10134352 | F044348 | ADYASGRDLFSEGQWDWLIAASYSDFALIEPERVTIVYPASYEIRDRDYRLVAHPTPPRDSLRAAQKEMSRFFR |
| Ga0208658_1013566 | Ga0208658_10135662 | F070242 | KIARMLPRRQRRAFEQAALSFRDGGMFEADRWRAGLLHTAHRAALVASGDVLGAFDQIVREDRHLAGDVARGGEALLKAARENREIVEMINFAVSDDLSTMNRRLGID |
| Ga0208658_1013695 | Ga0208658_10136951 | F007886 | YLVVEGGDAVVAVFEVLEVVLAGVLAGGDTAVEAGVEGAVDVVCSDVLGADSFLSPVRGAGASLPGDGFSLSE |
| Ga0208658_1015237 | Ga0208658_10152371 | F027190 | RAHLNGRVQVPDLADTVGPVTESNCAGAISPGGEQLEVNYQSVTKSGIPDEVNSIRSAVLTSLLGKERSPNKIVPPALREWIAAGGEPQMVGDGMVGSSSDVNQGTTAGGQRAGRGQSPRSSEEAGNDRGAKEGRNVVLGVVGVSSQKDPGSAVRLCARMLRKTGLELLLRPGNGPPETQVSGAQACAAGATLPKALSRVPEPVH |
| Ga0208658_1015537 | Ga0208658_10155372 | F062737 | TLWKNTRQVVHTAAEPPNHGRICLAMMGWTRNSRNDERKIVAAYGRVAARGARITWA |
| Ga0208658_1016259 | Ga0208658_10162592 | F006520 | MWILIVYVFIAAVGEAVVIAIGLTLDRIYPLASLPISLSLFFAVLAFGWPLAVRSTKPNHAKSEKLAN |
| Ga0208658_1017101 | Ga0208658_10171012 | F034962 | MRALVVTSNPATASSEPETPAAALSDLGCEVVAVGYDVDQLPEDIELQRPSVVVVDAGA |
| Ga0208658_1017937 | Ga0208658_10179372 | F093175 | GDGWHLVGLDAEGRVWFGSPRRTAKGRMLAWALMDESVESEDAPQAPITAPERIEALVPERHWPTKPRA |
| Ga0208658_1018761 | Ga0208658_10187611 | F049465 | MSLQRELPRMDLRFAKLCIELDCSTVFDSAIFRHCPTCGSVECYPVESWLNRERSETAPVVIGNGNMDRAARVADMPRPVWLERLRAKRVEGDA |
| Ga0208658_1019088 | Ga0208658_10190882 | F068886 | LGRSSSSRWRWIVLCDRAALGGLALGLALYVMPLWREGRLRVAFWITLLSTLA |
| Ga0208658_1020539 | Ga0208658_10205392 | F035133 | TRHMNSEQLEAPMANAFIDWTSRAAIATRIAEEQRHPVESWKELIVPEDYDLSLEKIEYQIKPAKWPWLVHII |
| Ga0208658_1021118 | Ga0208658_10211181 | F002389 | MAAGDAAGGPLARLAADPRDPEAALQAVRFELYRENIYGALEMLEAAHAAHPHPGYAEQAARIRSWLVHLASREAYISAQDEQYRRLRWRGGLKLIEKRIRMMLGRKTRKMIER |
| Ga0208658_1021635 | Ga0208658_10216351 | F098734 | MKKKPPGVFSLIVTAFTGFGSHIMTLCVTGRDRLLAL |
| Ga0208658_1021670 | Ga0208658_10216701 | F023288 | MGGLALLAVGAATSWWAMSLGWAALVIAFFARVAEADGFAVPRPGRVAIRRGGFDIPLAFKVRRGERWLLFVCEEDPERGGWSDVYTVLDQPKGTDGSDGFEPLYSLPPASPPSGWSLRGRVPVDDLRFEYHERSTYVTRGSLERSLSAAGM |
| Ga0208658_1022004 | Ga0208658_10220041 | F036745 | GFPLTVPAPNGQGTVVATGNAFAGLRIFEAPGAAGMSTINGFVAWQNAQNGLRLYGGEKVKVRNSVFLANVLNGVYVTGYDASAAGNDLSQVDLGSVSDAGRNVLQASVGSMPDLAGLCVGMSPSRGLLTLSARGNVFAGPTDCTTSTAGIVRSAVCGGFVDLGVVSAAGTTVNVD |
| Ga0208658_1022186 | Ga0208658_10221861 | F100042 | VSLMSRLMTLARPTGVGHAISTYTIPIDGRDEWIAAARRQA |
| Ga0208658_1022728 | Ga0208658_10227281 | F029270 | MAQELIIDVHGHEISVHVRGTSLRTTYRKGDAPWLVCTELRADDPDAIFTRDEFKAMAWNTANATARKLGWLV |
| Ga0208658_1022834 | Ga0208658_10228342 | F103796 | ESDHAGAEPWQYMVCYEFDSEASLQAFVRSDTLRAMTRDYNARFGGAGDRARLAYRQIYP |
| Ga0208658_1022912 | Ga0208658_10229121 | F021571 | QGKKLPHCKIVNAYDPTIAPIMKGKSNCPAQFGRKPGLLSEPTAGFIFATAVPVGNPSDASYVLPLLDKVQHAIARVRGPKTPAIHSVAGDLGVNDTALRQALHDRGILSVGIPKTVAPINPEPRPEAILDLLNEAGLNRKRTPHQVQLACACGYSRPVVESHIASLLARGAGQ |
| Ga0208658_1023050 | Ga0208658_10230502 | F028610 | PRPAFVYDDAIQHHAVDPTLPLPAEKILWIQDQMVKAGKLKAPLDLKTVTAPEYRERALKVIGH |
| Ga0208658_1023232 | Ga0208658_10232322 | F061029 | MADTNTNCPVCKLPVGDSKFRCHLCRAAGKDVRFDSGPCEAEHLTKAHTKAEIERFDVEQTIRKP |
| Ga0208658_1023719 | Ga0208658_10237191 | F001574 | VNRYVAIPKRGVNVMTSLRLGTSVLDFMNPNGLVRPAIEKFAGAWLACFVVMAHGDFANALSLDHAQLASICGTIGALVAVALLAQMDRTTNSLPRQMTISAFATFIGDVFAHPSHFPPQWGEPLVTAVVSAVIAVAVWHAKRLVFSR |
| Ga0208658_1023781 | Ga0208658_10237812 | F063749 | MKNLFAVILALTAATAAVAKPSPIEPVRSANPIALARVSAEFNIGPAGATLERNYFRAPESDSHSGLYLCRFEPSMFAKVRLTQSCK |
| Ga0208658_1024082 | Ga0208658_10240821 | F023433 | MNLLRSICCLFGSRCEGEEPKPTKETIRDEPSADLGQKEAKLEKTGKEQMGHMEGGDASKTAQQPT |
| Ga0208658_1024616 | Ga0208658_10246161 | F025363 | GVQTWGDRTEPSITVIPRSGSAVTVSVSGTGLRSNDHLVVEVDQLLRSPDEDGQPSWTRGQPLYGASLGPNGAGEIEHTVTLTLPAGDFDDLGARAWVGAEPEPCYGHGNTTGCVRVHIPRPQERPQLSVTWETFVKVPRLLVRLKARNLAQRPSRWMTLRAYGLLAA |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |