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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 | 3300026050 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116106 | Ga0208293 |
| Sample Name | Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqA_D1 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 48306687 |
| Sequencing Scaffolds | 15 |
| Novel Protein Genes | 16 |
| Associated Families | 16 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 3 |
| Not Available | 5 |
| 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) | 38.209766 | Long. (o) | -122.033424 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001489 | Metagenome / Metatranscriptome | 686 | Y |
| F005988 | Metagenome / Metatranscriptome | 384 | N |
| F009539 | Metagenome / Metatranscriptome | 316 | Y |
| F011513 | Metagenome / Metatranscriptome | 290 | Y |
| F018543 | Metagenome / Metatranscriptome | 234 | Y |
| F025366 | Metagenome / Metatranscriptome | 202 | Y |
| F027322 | Metagenome / Metatranscriptome | 195 | Y |
| F029547 | Metagenome / Metatranscriptome | 188 | Y |
| F036220 | Metagenome / Metatranscriptome | 170 | Y |
| F046228 | Metagenome / Metatranscriptome | 151 | Y |
| F047144 | Metagenome / Metatranscriptome | 150 | Y |
| F069221 | Metagenome / Metatranscriptome | 124 | Y |
| F070315 | Metagenome | 123 | Y |
| F084199 | Metagenome / Metatranscriptome | 112 | Y |
| F086537 | Metagenome / Metatranscriptome | 110 | Y |
| F091998 | Metagenome / Metatranscriptome | 107 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208293_1000150 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 2032 | Open in IMG/M |
| Ga0208293_1000679 | All Organisms → cellular organisms → Bacteria | 1489 | Open in IMG/M |
| Ga0208293_1002531 | All Organisms → cellular organisms → Bacteria | 1037 | Open in IMG/M |
| Ga0208293_1003683 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia | 921 | Open in IMG/M |
| Ga0208293_1005163 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 819 | Open in IMG/M |
| Ga0208293_1006608 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 747 | Open in IMG/M |
| Ga0208293_1007476 | Not Available | 717 | Open in IMG/M |
| Ga0208293_1007884 | All Organisms → cellular organisms → Bacteria | 702 | Open in IMG/M |
| Ga0208293_1013783 | Not Available | 569 | Open in IMG/M |
| Ga0208293_1014148 | Not Available | 563 | Open in IMG/M |
| Ga0208293_1014333 | Not Available | 561 | Open in IMG/M |
| Ga0208293_1014533 | All Organisms → cellular organisms → Bacteria | 558 | Open in IMG/M |
| Ga0208293_1014918 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 553 | Open in IMG/M |
| Ga0208293_1015698 | Not Available | 542 | Open in IMG/M |
| Ga0208293_1016072 | All Organisms → cellular organisms → Bacteria | 537 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208293_1000150 | Ga0208293_10001502 | F086537 | MSEDGGGEQLAQWLKEAGRRTQAAKAPPATADSDESYNSPASLHHYLEELAGRKLESHAEVLRYLREVAGAQPEGLRAQERRRMVREVSLLVLLAISYLHFYYWEVQLQIAALQSVGVFIPAPPARPHKISS |
| Ga0208293_1000679 | Ga0208293_10006792 | F009539 | VRRSGGSLSVLLFALAVLAAIVGISFALGYILGKLLL |
| Ga0208293_1002531 | Ga0208293_10025311 | F025366 | GLALLMLASTVTPREAGSNVEAWFIYFGMERVPPWATDKSIDTWVFWMAFVGAAVWGARLYTRSNIVEGKLSVLIREDEPWVQLDPGLDRWQAAQSGGSWYRYRIALVNSGDSTLRNVQVKLASLEKKPQNFHAIGSHLQLRLDRAGIMNFDLYPTKDPQWRDAMFVDVFSFCGGPRGCSFLRVTSLPEEANPYIPVDRYDVKIVATSESGEMAIADVAFIPHPGQMPDFRLRNMQSFPG |
| Ga0208293_1003683 | Ga0208293_10036832 | F027322 | VKRPAGITVLAIIFAAAGLSYMMLGFQMTTAVTFGPLPSGQGTWIWGWLIVLTGLAFWAGGLAAWRLAPWGWMLGHVLAILGIIEAVFALLGTGNLSYALASTAFPFIVLWYLNRPSVKKAFGLVEE |
| Ga0208293_1005163 | Ga0208293_10051631 | F047144 | RLVASGVANVPRELDPADPLAGLDGNPQTGWKRDLLAALVERALTALVR |
| Ga0208293_1006608 | Ga0208293_10066081 | F069221 | FGGWAVIRFIRRYHVRGIWRSPTPQESSTYIRLLLIVLLLDIGSKALFFRWDRPEKVEILPNFGLHSVFHVTDFETFHVYLLLYFVYCFLLGPLFFRFANRALDRLWLGSAPFALGGALALSLERLFFGGVHNSFYFAGPLMWICPPCASPSFSSYAWTPADLFVHAAILPFIILLLSYFPPARPSVAEINGR |
| Ga0208293_1007476 | Ga0208293_10074763 | F011513 | ISRSDAAHNASVSSIDAARVHDFRIMVAHGFRSLPIKQL |
| Ga0208293_1007624 | Ga0208293_10076241 | F084199 | MSTTSSSRRKPRTTASSRFGLVLVAAAALAACGGRPRETFVTYFNGDHGVSLRHPAGWRTDQAEQEGVWYRYFLAPPAGPQNRSPVSVTLLAGPAAGSLDEYAERYLAGHNVVAATPEERQGVTGKSWVFAASDGATRYRLLLFAKDDKVVGLYAQGDAAGFEQQAKALDEVWSSLTFERPERYPRREWGAQKTSLG |
| Ga0208293_1007884 | Ga0208293_10078841 | F001489 | AHFEMDCEWRYFLAEHAGTEAGHGWGYIRQANAVYPGRDYARPDPEFEKQYGLTPRTEHHAIMKRDFLSYIFSGNLWPYGHVTAASIQSIEITTPKLLDFEERVVHAEERSHHDAILQKIHDYVWELIDIWGEAPIRKRIGEIERIALNSRPRTIFDPPRREFLRKYFKVPLENVRRFPAWREYLYLNVLGFPPEPVYIGNWPAEIPQPKIGA |
| Ga0208293_1013783 | Ga0208293_10137831 | F018543 | MILENMWIEPSNQGAAANRRPALQSDGSDNLSATLAADGAFPAAVAELDR |
| Ga0208293_1014148 | Ga0208293_10141481 | F091998 | DVAPATHGALRCAPCSGARSTLPRRWRYGMHPQAVGSQIVALGRVELRIGEALRLEMVKTDTESDDMVHLQYYVSTESGGWALWLSCPRNDVAALEAPLQALTPPSVG |
| Ga0208293_1014333 | Ga0208293_10143331 | F005988 | GTQALMESANMRIRTYNMQDEQFAFHRALRSEEVRIQFRGDALDLSEFENVEVSPGEITIIPLGISHSVISIPPEDEDFLRLNFYSKVRWRVPIDPTRHYFDSKFEISTTVHKQAEWREKLAAGR |
| Ga0208293_1014533 | Ga0208293_10145332 | F036220 | VNLGRRRRVVVETPSVVLRLSEASIERLEADEPETAAALHRWLASTLAVRLTAADRAYSASMD |
| Ga0208293_1014918 | Ga0208293_10149181 | F046228 | MKRLRSVLSPMVTTAGILALSGAVLAQSPSESHRAASARAHEIMSSAPCPLPKVTKEKITEDEGRDLAQAFADKNMSGFRVVRPLSYGGGYTTMCYQTVNAAPARPLVLYSVEYSMDLKNPAGETRNLCVDQYGTVSEFCSDFGFAGATGPAGPMGPS |
| Ga0208293_1015698 | Ga0208293_10156981 | F070315 | IRQEESMAKDASGREGFSTGAMAKELEVSPATVKRALTELQIEPDFVKAGCAYYYVERTSAVKKAIKV |
| Ga0208293_1016072 | Ga0208293_10160722 | F029547 | YKELDIRGAYGATHRQYRITMDYLDRKQELLAAVVTHRWPLEQIAEAFETIRSGSGLKMVIVP |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |