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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 | 3300026072 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116105 | Ga0208292 |
| Sample Name | Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_CattailNLC_D1 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 104468933 |
| Sequencing Scaffolds | 31 |
| Novel Protein Genes | 32 |
| Associated Families | 31 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 4 |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 5 |
| All Organisms → cellular organisms → Eukaryota | 1 |
| Not Available | 8 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → FCB group | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales 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: Fairfield, San Francisco Bay, California | |||||||
| Coordinates | Lat. (o) | 38.209923 | Long. (o) | -122.033409 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000690 | Metagenome / Metatranscriptome | 935 | Y |
| F000982 | Metagenome / Metatranscriptome | 814 | Y |
| F007038 | Metagenome / Metatranscriptome | 359 | Y |
| F009010 | Metagenome / Metatranscriptome | 324 | Y |
| F016687 | Metagenome / Metatranscriptome | 245 | Y |
| F024001 | Metagenome / Metatranscriptome | 208 | Y |
| F026705 | Metagenome / Metatranscriptome | 197 | Y |
| F031716 | Metagenome | 182 | Y |
| F033859 | Metagenome / Metatranscriptome | 176 | Y |
| F037791 | Metagenome / Metatranscriptome | 167 | Y |
| F041286 | Metagenome / Metatranscriptome | 160 | Y |
| F043793 | Metagenome / Metatranscriptome | 155 | Y |
| F044151 | Metagenome / Metatranscriptome | 155 | Y |
| F047153 | Metagenome | 150 | Y |
| F047753 | Metagenome / Metatranscriptome | 149 | N |
| F049078 | Metagenome / Metatranscriptome | 147 | Y |
| F049598 | Metagenome | 146 | Y |
| F053088 | Metagenome / Metatranscriptome | 141 | N |
| F063813 | Metagenome / Metatranscriptome | 129 | N |
| F069000 | Metagenome | 124 | Y |
| F073723 | Metagenome | 120 | Y |
| F073725 | Metagenome / Metatranscriptome | 120 | N |
| F076224 | Metagenome | 118 | Y |
| F076231 | Metagenome | 118 | Y |
| F077451 | Metagenome / Metatranscriptome | 117 | Y |
| F081923 | Metagenome / Metatranscriptome | 114 | N |
| F087402 | Metagenome / Metatranscriptome | 110 | Y |
| F087857 | Metagenome / Metatranscriptome | 110 | N |
| F089119 | Metagenome | 109 | N |
| F093898 | Metagenome / Metatranscriptome | 106 | Y |
| F103189 | Metagenome / Metatranscriptome | 101 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208292_1000185 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 4310 | Open in IMG/M |
| Ga0208292_1000267 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 3905 | Open in IMG/M |
| Ga0208292_1000531 | All Organisms → cellular organisms → Bacteria | 3207 | Open in IMG/M |
| Ga0208292_1001139 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 2515 | Open in IMG/M |
| Ga0208292_1001241 | All Organisms → cellular organisms → Eukaryota | 2441 | Open in IMG/M |
| Ga0208292_1001859 | All Organisms → cellular organisms → Bacteria | 2127 | Open in IMG/M |
| Ga0208292_1002557 | Not Available | 1893 | Open in IMG/M |
| Ga0208292_1005538 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 1445 | Open in IMG/M |
| Ga0208292_1005984 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1405 | Open in IMG/M |
| Ga0208292_1006128 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 1392 | Open in IMG/M |
| Ga0208292_1006147 | Not Available | 1390 | Open in IMG/M |
| Ga0208292_1007656 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes | 1277 | Open in IMG/M |
| Ga0208292_1010642 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1119 | Open in IMG/M |
| Ga0208292_1012166 | Not Available | 1057 | Open in IMG/M |
| Ga0208292_1012812 | All Organisms → cellular organisms → Bacteria | 1036 | Open in IMG/M |
| Ga0208292_1015803 | Not Available | 946 | Open in IMG/M |
| Ga0208292_1017213 | All Organisms → cellular organisms → Bacteria | 911 | Open in IMG/M |
| Ga0208292_1017690 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 902 | Open in IMG/M |
| Ga0208292_1018196 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Geobacteraceae → unclassified Geobacteraceae → Geobacteraceae bacterium | 890 | Open in IMG/M |
| Ga0208292_1019159 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → unclassified Acidimicrobiia → Acidimicrobiia bacterium | 868 | Open in IMG/M |
| Ga0208292_1020360 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 845 | Open in IMG/M |
| Ga0208292_1026647 | All Organisms → cellular organisms → Bacteria | 747 | Open in IMG/M |
| Ga0208292_1027705 | All Organisms → cellular organisms → Bacteria → FCB group | 733 | Open in IMG/M |
| Ga0208292_1028972 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium | 718 | Open in IMG/M |
| Ga0208292_1031206 | Not Available | 692 | Open in IMG/M |
| Ga0208292_1032067 | Not Available | 684 | Open in IMG/M |
| Ga0208292_1052478 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria | 536 | Open in IMG/M |
| Ga0208292_1053862 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 529 | Open in IMG/M |
| Ga0208292_1056121 | Not Available | 517 | Open in IMG/M |
| Ga0208292_1057134 | Not Available | 513 | Open in IMG/M |
| Ga0208292_1058736 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 505 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208292_1000185 | Ga0208292_10001851 | F081923 | MKRMIVNISAAIRPVMYRKHFFVMAILGAALAVACTMANTGSIQTSAEVTRQFEGLQVNPNYRYWYLNQENNPFGVIGLDREYGFAGGPVWRAVEPDSPIFRKVVGLVESFPVASSLTTGYTIFEQQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF |
| Ga0208292_1000267 | Ga0208292_10002678 | F073725 | MEKRATRRYRISTSIVCSYLNSVDFGKPVNGRMRNCCVNGLCAELGAHYKAGTVLVVRTTGSSCGYSDEEGFRSPAVAEVKWSRPRSIEGGACYATGLKYLML |
| Ga0208292_1000531 | Ga0208292_10005311 | F041286 | MSETDKDLQKAVDEHLKRLHERYKSNAKVFTATHIGHISLSIVFVLSILFPFLYLQIDARETNSELEHLSLGIAQLDQRAATYRQAMTGLKKVFGAVEDTPKPLEGYIQALEKEAAGGPVVPLPEGLKPVQESCGSPSDKDPWMECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQ |
| Ga0208292_1001139 | Ga0208292_10011391 | F063813 | EILPIIHKDALMSLVRWSQAHGQKLKPSECESKFQPLAEPSHPSKKPSDQLGSGTGSAPIDETNSIERGLS |
| Ga0208292_1001241 | Ga0208292_10012414 | F053088 | MDQPIEYFLTQAKRISGASPTTKIHGVLFNVTIGVVAAGTVYGHKSARNGSDIRTSLIVDAYVINGFYIIGTRTGSNYLLARVGPSRIFRDQWGILQEHLGKNHKALAGLPKSDFSTFGPGFMHATCPAQIKDFDRLRREAA |
| Ga0208292_1001859 | Ga0208292_10018595 | F073723 | MSGMTLLERLLLPLVRRFVSFWVRPSILPDSLAERFQQGRPVVYVLEKRSII |
| Ga0208292_1002557 | Ga0208292_10025572 | F009010 | MPEVPKFLYLLVDAPLLIAIPIVIFAALAFWSRSKTAAVAAIAWNLYLIYELGMKAEEFCSGLNCVKRTPLYGVYPLLALVSMLALVQGYVHVRDNRRSGRLR |
| Ga0208292_1005538 | Ga0208292_10055381 | F016687 | IALCAGSASAWDTRWQFKQEAPSNSYGSGTRDIEMQKRFDYNSMNKFKGTIETSSGYTIMRNLNGDTMRGYIDKDGSGLLRDQNGNFHNVNTRW |
| Ga0208292_1005984 | Ga0208292_10059843 | F024001 | MFTGTVFIVDAKGSRKNKFAILGVEALAWQGAKTQEYLDIPSFRNAARRDASASKM |
| Ga0208292_1006128 | Ga0208292_10061282 | F031716 | MSRYTPGHWHVKEENGSYGVFSDDDALLAVTLPDDIKDKNAVKANAILMASAPLLLKLIIEIKEHLDNNMIVTQEGLKINDSHLRDSIIDAILRAEGYRL |
| Ga0208292_1006147 | Ga0208292_10061471 | F049598 | MKKLLLVALVAGAVLAFCAPALAWPVALPWWQPSQHFTCVGKIQAVDTTTSAVTVRVHLASRGAADYLGEDLTVAVAANARIYKAVGARLTPIALGDLVVGEKLRVEGAIEYATGSAVYVGKRLVMRRLPLNQIKRFAFRGPVTQIDADARTLTATMNRVTRALSPYYHRTCDFAVAPDARVWVMKDGWPVRATLADVVVGDRVYAQGGADRSTPSAPVFTIRWMVVRHAVPAPVTP |
| Ga0208292_1007656 | Ga0208292_10076561 | F087857 | TMKRNFIVVPLLVIAFVAIQIVPPAHAEPITLTIMAIAGITTVMTAACTDMAVHGEHIVQANSPNEKPAEVFASERSADSSNNHDVQVTTAR |
| Ga0208292_1010642 | Ga0208292_10106421 | F069000 | LSVPLALLLWSLRSAGEDVRTSVAIVAVLLALPWVVPAMVLVAALSVPVYMWLHTQGPVPPVLQWLGGTVLVAAVIGAHVNAALGWVWMHRGKAVPEPGIGDFLKRHSAGAQQRTDDAR |
| Ga0208292_1012166 | Ga0208292_10121661 | F093898 | MMRFLVARAVNPQLGLFDGLRQWNGIAAALRESPRKRTYQTDDLDQFLS |
| Ga0208292_1012812 | Ga0208292_10128122 | F087402 | MARAKVVEFDYYQFLRIMQRAGNAGQRIDKTDSRWGEYVRENKINEVAATAIARQKFENATPVIIAEGGDADGLYFFSKDDEACLRLTALE |
| Ga0208292_1015803 | Ga0208292_10158032 | F037791 | LVLLRMEVAAFHPLPCDRKRLVSVALFLAFIGRANGDL |
| Ga0208292_1017213 | Ga0208292_10172132 | F047153 | SALVYDFEKSRWASLLTSINYGQVIGLWDHKWRPNVEAGYDFKDDAGNQRWVFRAGITLLLPQ |
| Ga0208292_1017690 | Ga0208292_10176901 | F000982 | LHYQIRGKAYPAPRYWERLSQMLDEEAEKRGKTPPPPPLTHGLESDPTDEDKTERLREQIAWADRNQLLHRVQMFFEAMPPSGWVRGEKR |
| Ga0208292_1018196 | Ga0208292_10181962 | F016687 | MKTPKYLAGLVIISMIALCAGSAFTWDTRWQFKQDAPPNNYGSGTRDIEMQKKHDYNSMNKFKGTTDSSNGYTVMRNLNGSTMRGYFDKDGSGLLQDQNGNFYRVNTHW |
| Ga0208292_1019159 | Ga0208292_10191592 | F007038 | MTRRVFLDTEWTAPPWSDRTELMWIGLADEGGRSWYGISSEVVIDPSTNAFISGAFGLIDPAEPRLSRAQLAAAVMDFCGAVDEFWVWIPTLESFSAWSGLGDGAPESYAKCRDIDLRMLRALLNPWPAGWPKSVHDLNAAAVAAAVEIPPRASNHLHPQVHADWNRRLFDLIQAAPRS |
| Ga0208292_1020360 | Ga0208292_10203601 | F000690 | FAVPGITFEQEYLKALLLMRLDSGNFTPDQVEWVAGHLDDWVPSLSLVPPPGEGAGFYVDLTGSQGLRRREKRALAGRVQMLDTGPAYTRVVEQLRWLPEQDDAVPKAGELPAREQRLLLMRLASLFGPEAIAHAPRAERIAVDGQVRVVVGLIALTHAVAEIDQPAAGERPPRAPSFDEPTHAPDPTADAESVARRIQGFTWRIADRSETGCRLIAPAREAPTHLGELLAIRDGEAWILGVVRRMQRGPAEEVTVGVEIVARRLVRVLMRTWSAPADDGR |
| Ga0208292_1026647 | Ga0208292_10266472 | F049078 | MKVHVKHSLKADVASVFKLCTEQKSQEAIYAGLGGSDVKIKREGRAPNVKLKISRREPANPPAAIRRIVPS |
| Ga0208292_1027705 | Ga0208292_10277051 | F076224 | QKVKEFTLNLKYDSTFKYYSELNSGHPFTVVIDSNICRVDIPDFPNPEISIPEIASIDPLIEQATNNIHFYAYKIPKIEKSKSEIKIEYYNDDSVYSYVVNYNMLDIDSIVQANAGTDFYNLERLKETRPFDDTMLIKYQFDRDYYNRYYSDDEFKKQMEELQKELQQLSKEVKNQKIRVHSEVTKSPKK |
| Ga0208292_1028972 | Ga0208292_10289722 | F033859 | MLPRFQKLLAPLAISAAIAAPGAASAQDLSPPASEWRSYCQTYLKALDGDTTASDLDVTYCLGVTKGLLNGMRVGSQIGALSFASRVAVQYKLDPDEVFQLFQTQEPSRLLGICSPAASAAPEFVRAVLAHLEKNPGNLQRPIAEVFYEGLQ |
| Ga0208292_1031206 | Ga0208292_10312061 | F026705 | MLDALKTRYEAFANRVLCSLSEIEREDVRSFDRWFYQGGGWRWLVGIIALTTGVAFVASKLPWNMRFIEAAVLFNVVVLTLLWSGLTAWFGYRKFSGKLFRYIVVGPLLALVGAFAGASIAGLVTGVDPLAWLQDSTKVRHIVTAGLV |
| Ga0208292_1032067 | Ga0208292_10320671 | F089119 | MSPRAAAGMMEGQAPIALVGLLAIGVIIAVNYFARPQPGAANRAPVATDCRQCGTVVAVRRSAHSIPVTFVEVQMTDGSVRTLRAPARQFSVGDAVEV |
| Ga0208292_1052478 | Ga0208292_10524781 | F047753 | MKKIIGILEELRIDDAWLRVAPFALAGCRKESYGKLTRLCRRKETLMAVVVAGVIGLYSAKKHIGLCKKAVKAGKNAYRDSDRELNKYLDAIWRVYILDNSIDKQRLIEKAIGCLSGKLDQELSHSLTEAKKEYKAMIQQIIGAVQADTGHSENAVH |
| Ga0208292_1053862 | Ga0208292_10538621 | F103189 | GDDATFTLLQRTTGRKVELPADPKLSPDRARLVTADFCASRCSNELALWRVTRDGVRKESTWRPRASWSDVVATWKDAETVIVEYSVAGTQARSRISRRLADAEWVRAQAP |
| Ga0208292_1055771 | Ga0208292_10557711 | F077451 | GLGGLFGRNSPGRWAGLAASFTELGVDLDTAKKFGPIVIDYVAHHGGEDLVDKIRSALKI |
| Ga0208292_1056121 | Ga0208292_10561211 | F043793 | MLALRTLTVKMTVNFGGAASGALQINSLEGSLMIEWE |
| Ga0208292_1057134 | Ga0208292_10571341 | F076231 | MERTMMHSKSGRTGTANMSEFSGFVSTKQSGIISITKVVILISVLLAVLMVVSK |
| Ga0208292_1058736 | Ga0208292_10587362 | F044151 | MFLSVAFAGVLYFLEPMLFEQGLGTSLGGRDRLASDEPEAKLTSPT |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |