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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 | 3300026019 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116041 | Ga0208528 |
| Sample Name | Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_5C_80N_305 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 76502321 |
| Sequencing Scaffolds | 29 |
| Novel Protein Genes | 32 |
| Associated Families | 31 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 9 |
| Not Available | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales → Thiobacillaceae → Thiobacillus → Thiobacillus thioparus | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 4 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptosporangiales → Treboniaceae → Trebonia → Trebonia kvetii | 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 → Rice Paddy Soil → 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 → paddy field → paddy field soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Saline → Water (saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Twitchell Island, California | |||||||
| Coordinates | Lat. (o) | 38.1087 | Long. (o) | -121.653 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000776 | Metagenome / Metatranscriptome | 895 | Y |
| F001075 | Metagenome / Metatranscriptome | 786 | Y |
| F001212 | Metagenome / Metatranscriptome | 746 | Y |
| F001931 | Metagenome / Metatranscriptome | 615 | Y |
| F003606 | Metagenome / Metatranscriptome | 477 | Y |
| F003716 | Metagenome / Metatranscriptome | 472 | Y |
| F006565 | Metagenome / Metatranscriptome | 370 | Y |
| F007038 | Metagenome / Metatranscriptome | 359 | Y |
| F007380 | Metagenome / Metatranscriptome | 352 | Y |
| F007672 | Metagenome / Metatranscriptome | 347 | Y |
| F008145 | Metagenome / Metatranscriptome | 338 | Y |
| F009686 | Metagenome / Metatranscriptome | 314 | Y |
| F009704 | Metagenome / Metatranscriptome | 314 | Y |
| F010182 | Metagenome / Metatranscriptome | 307 | Y |
| F010692 | Metagenome / Metatranscriptome | 300 | Y |
| F017338 | Metagenome / Metatranscriptome | 241 | Y |
| F017543 | Metagenome / Metatranscriptome | 240 | Y |
| F025775 | Metagenome | 200 | Y |
| F027599 | Metagenome / Metatranscriptome | 194 | Y |
| F030357 | Metagenome / Metatranscriptome | 185 | Y |
| F035341 | Metagenome | 172 | Y |
| F038660 | Metagenome / Metatranscriptome | 165 | Y |
| F040296 | Metagenome / Metatranscriptome | 162 | Y |
| F041464 | Metagenome / Metatranscriptome | 160 | Y |
| F049183 | Metagenome / Metatranscriptome | 147 | Y |
| F058404 | Metagenome | 135 | Y |
| F065245 | Metagenome / Metatranscriptome | 128 | Y |
| F068194 | Metagenome / Metatranscriptome | 125 | Y |
| F085523 | Metagenome / Metatranscriptome | 111 | Y |
| F086043 | Metagenome / Metatranscriptome | 111 | Y |
| F097472 | Metagenome | 104 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208528_1000301 | All Organisms → cellular organisms → Bacteria | 5272 | Open in IMG/M |
| Ga0208528_1001154 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales | 2542 | Open in IMG/M |
| Ga0208528_1001163 | All Organisms → cellular organisms → Bacteria | 2531 | Open in IMG/M |
| Ga0208528_1001355 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 2307 | Open in IMG/M |
| Ga0208528_1001731 | All Organisms → cellular organisms → Bacteria | 2012 | Open in IMG/M |
| Ga0208528_1002406 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 1694 | Open in IMG/M |
| Ga0208528_1003397 | Not Available | 1418 | Open in IMG/M |
| Ga0208528_1003927 | All Organisms → cellular organisms → Bacteria | 1317 | Open in IMG/M |
| Ga0208528_1004134 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 1287 | Open in IMG/M |
| Ga0208528_1004885 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1193 | Open in IMG/M |
| Ga0208528_1005287 | Not Available | 1150 | Open in IMG/M |
| Ga0208528_1007408 | All Organisms → cellular organisms → Bacteria | 986 | Open in IMG/M |
| Ga0208528_1008208 | Not Available | 943 | Open in IMG/M |
| Ga0208528_1008936 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 907 | Open in IMG/M |
| Ga0208528_1012741 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 776 | Open in IMG/M |
| Ga0208528_1013235 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 763 | Open in IMG/M |
| Ga0208528_1017182 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales → Thiobacillaceae → Thiobacillus → Thiobacillus thioparus | 682 | Open in IMG/M |
| Ga0208528_1017292 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 680 | Open in IMG/M |
| Ga0208528_1018263 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 664 | Open in IMG/M |
| Ga0208528_1019895 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 641 | Open in IMG/M |
| Ga0208528_1026472 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes | 568 | Open in IMG/M |
| Ga0208528_1028956 | Not Available | 546 | Open in IMG/M |
| Ga0208528_1029141 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 545 | Open in IMG/M |
| Ga0208528_1029544 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 542 | Open in IMG/M |
| Ga0208528_1031073 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 530 | Open in IMG/M |
| Ga0208528_1032164 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 523 | Open in IMG/M |
| Ga0208528_1032935 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptosporangiales → Treboniaceae → Trebonia → Trebonia kvetii | 518 | Open in IMG/M |
| Ga0208528_1033205 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 516 | Open in IMG/M |
| Ga0208528_1033977 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 511 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208528_1000301 | Ga0208528_10003014 | F007038 | MTRRIFLDTEWTKPPWSMQSELMWIGLADEDGRSWYGISSEVDINPSTNDFISGVFRLITPDEPRLTNEKIAASVIDFCGDVDEFWAWIPTMERFAEGFRLGEEAAELYAKYWDVDLQMVRSLVQPWPDGWPDRLLDLNAAAVEAGVELPPRAVNHLHPRVHAEWNRELFKLIRMSRER |
| Ga0208528_1001154 | Ga0208528_10011544 | F010692 | AACFLTEINNILPLFQQPTEYADMAIGALILFALLLYQAPELIGRARAARGRVGGLGTVAPGEAPAA |
| Ga0208528_1001163 | Ga0208528_10011631 | F049183 | MLRRMPTDASVTTRLEPPYETNGSGIPVSGASPSTAARLIAACPQTSAV |
| Ga0208528_1001355 | Ga0208528_10013551 | F003716 | AGAAFAGNGNGKRHAHTIHYAFVGKLTAVPGNGGVSITVEGGNHAALRAMLGQPVTQTFAYGDGTEFLQWSHGAPTVVQPGNLAAGDYVRVNVRAARGSSLSDVEQQDATIVGDHGTELYTAAQPLYLFRGRLASVGSAGVTVDVRGGNRHALRLLVGQSSTQTFATGDQTIFLLWQGRVPSVIALSQLKVGDRIVVRVRAARGSTLAQVESTPAVHVGDREPANASS |
| Ga0208528_1001731 | Ga0208528_10017313 | F058404 | MTRVWTVVLSVWAMLAIVAVLAWSQRPAPAAAPQPAAQTLVVKGANGKQQLVLVQPGTATAPHATTSTSGVVKP |
| Ga0208528_1002406 | Ga0208528_10024061 | F038660 | HSWRLQAVVDRYRIASNGEIILVLYDIPTGKYMDAYLPNRRCLGARARDRTGMIAARAQFTEHCPRVTAEWQLLGATVDVSGIGFWNPVRTTRGALPNGAELRPLTNLHIVAGCGVG |
| Ga0208528_1003397 | Ga0208528_10033973 | F040296 | MTTDDIVRAEESKIERFMALGLGRYAAIGMVEDGVDWHTVEALVKTGRPLAVALEASRGGSSPR |
| Ga0208528_1003927 | Ga0208528_10039271 | F009704 | VLVSMRFSRVEADATDERPLQSRRSYLLGRYAAIVHTRQGRVVRVEEHPHLASALEAVGLEDEQA |
| Ga0208528_1004134 | Ga0208528_10041341 | F086043 | VRATYEVRPPEWAETLAILQSVSLADGPAGVRARVVAADGARVTIEFPSLAEERDPAQLLAACVAGE |
| Ga0208528_1004885 | Ga0208528_10048852 | F000776 | VGEVDPLGMRRDALDAFLDQKVAEGYVIETRTDTHAIVSRRPKGLKRFTSGPDPGRYVVEVDESGCATMRPAEPRRA |
| Ga0208528_1005287 | Ga0208528_10052871 | F009686 | MTEREMFERSFMRPSNYFKLHPLDQFNIDTELGILNWQGEDLTPEDRARFDAHYED |
| Ga0208528_1005770 | Ga0208528_10057702 | F001075 | LPLTAQHTVFSESFVVFGFGAANDEMLQDVVSTEHLRTGFVLEGERETYLHRIAFQMLSEASLDPAASRELILETAKKHWSGE |
| Ga0208528_1007408 | Ga0208528_10074082 | F003606 | VRPRSANEWRDFWRDGGERELAAQLDEFEPHSARIATLLGSAAPMRAVVAELGRIRRHELQLEPDPARDADVAARIYDWFPGT |
| Ga0208528_1008208 | Ga0208528_10082081 | F001212 | RCNSAPAVDDLGYCGHCHWAVRAEVEEGFYQLREYLRPWARFSEWCEARGLLAR |
| Ga0208528_1008936 | Ga0208528_10089362 | F010182 | MDVTASFLAGSILSWALPIALLVSVCIWWGAILRRRSGSDASL |
| Ga0208528_1012741 | Ga0208528_10127411 | F085523 | VIASIGTLLIPLWILLGLLVLMGVLALLGRIQGGRYLRPLIQLIAKVPLFRRWLEKASNAALERSNPELASAMKKMQRHAKHLHDPQRAQAAMSQLTRQERAAL |
| Ga0208528_1013235 | Ga0208528_10132352 | F041464 | AGYVPAEVAPAVRGDEQAVSLWEFRGEDGRRVGLRVLLAPAGAWIQEPRA |
| Ga0208528_1014851 | Ga0208528_10148512 | F068194 | VQARKSVWKTSSYLVYAGGLTVLVSAVAALGYLSGHYGNGALTGWALLILVVLYGIAHALRRRGRWVAAGIFAFASVIAWGAFVATAWHWFGWLDSPGSFSHFSFARLSLELLILVSARYHRRVFAFPFISLISTVVGWLFVIDLISSGGTWTKVVTLFVGLAYLVAG |
| Ga0208528_1017182 | Ga0208528_10171822 | F025775 | TNKLKLINFNGVRAMKQLLTFQGFPMVVVVGLIVWAWISILSVLIGSFF |
| Ga0208528_1017292 | Ga0208528_10172921 | F006565 | VSCGQAHSSARDLVAQGQEVKLVAETVGISRSSLYYKRRPHGSRADRRFDSIIVKTCGAKPAYGYR |
| Ga0208528_1018263 | Ga0208528_10182632 | F007672 | VDVTAGLSLEDVPARGAGDKIGRLLREIESLIAADEAADRQITGGWRTFADILAAAHIHTWDAYSVDLSADAESFRQLSRRQQEAVKRIFGTLYRAESIVDDWMGRIVAALPRGPEYESMRAALMTQEHDERMHRGSLLRVASEVLGIPAADTDR |
| Ga0208528_1019895 | Ga0208528_10198951 | F001931 | MKILEGVVQTLLHDIESGSGDKDRRRQVEEWMRTLAEKYPEFRIETGLRDYYLAEAERLRADFEKSPEMAEKLSLGRAIESFLDRAA |
| Ga0208528_1023563 | Ga0208528_10235631 | F097472 | MKQDTTVVIVLSAMILFVSGCVSGPGIDKEKFSELNRTARELKTSLQKNKPCDVPNALIQRLAAGTAALQDRTASKAERDLLAAYSNLLTTYQDGLLLCQYQAQMNKYPFVPAGRIYVFQELDPVVDKYGFSTESHLYPPTGVLFRSIAGNSITVIWENAVIQTRVIDNMTNYN |
| Ga0208528_1026472 | Ga0208528_10264722 | F027599 | MLGVVKLVPVPKLDPPVATEYQLIVPAEAVAPKTTVPVPQRLFGVVPVIVGTGFTVAVTAVLVPVVHPVAVAST |
| Ga0208528_1028956 | Ga0208528_10289561 | F030357 | MSDQVVVPLRPRTRVGYTDTAALNDIHTLLTTTEPGIAALADIAVVLACTGRPMVAVRDIEITTTETALGWPVACAQAGDTSVYIRQEPAGPGLLIEICTKSVAEHDALTVTLDGHRLHPAPRPTGRTA |
| Ga0208528_1029141 | Ga0208528_10291411 | F065245 | RSTGWERSPAFVRAFRAMQPTIPAALVTLGSAKAPYVLPIDFAAWRNGGFDLLPEAYYNQYPGYRPDLAVAHAQRAGWPLSRVHPVIGVYDHYPASAYVPLLSNLGTRGFSVFLGDQMTQADYAALSGVAAQTLAAG |
| Ga0208528_1029544 | Ga0208528_10295441 | F086043 | VRATYEIAPPAWGETLAILQSVSLPDGPAAVRARVVDVSGARVTVDFPALDGDCTAEQLLATCIAGEWADRGDVDSCRLVEVDWPRGL |
| Ga0208528_1031073 | Ga0208528_10310731 | F008145 | MAVRGEEVANSIDAHVRSAVEKMVEEIHSSIDDIREVVDQQLKAALQSVRADVNSLAVLPQIQKFITEFEESILASRPPAPAAADASRVKKAIQAIERGKSQVDILNALLDQCLEFGSRAALLILRGETFSGWKGVGFSGHGGSDDLIKRFNAAPGL |
| Ga0208528_1032164 | Ga0208528_10321641 | F035341 | PWPGGMGTLDSVARRFPPRQGNEASVQLMARANALPKNEAVDAFMRREIERGALAIGEPPALPDVSAIRELLLREPLVWERNEGIGGDNEMPARRAAQMTLARTLVASALARARADDPVAWEDLRAVWTLARSLDGQPQMMMQTAAFSMARMINAVAWKMPLPAPAWFGEMQQ |
| Ga0208528_1032935 | Ga0208528_10329352 | F017543 | MTAVQPTAMMAGRYQRAFTIAVLFLVAGWHLAGAGGQLLHNRPAYGSFAFQGAMWLIMALAIAAGSVL |
| Ga0208528_1033205 | Ga0208528_10332051 | F017338 | CRYTIEGGLLALRAGGSVTLAQRPEGDQRELSVTVKGYLPRLAARAGAPPWTGMLYAKGQSPFHAAVSRRYFELLLRSRDS |
| Ga0208528_1033977 | Ga0208528_10339771 | F007380 | TARLIEEAPEERQARPVFLDVEDSPELLRVVSTYNDMFGRLYEALQNSVGEEQAHDIFMSALQQSGGEELWNGVFFDQYGRFDENMLIANISELPFEKRKIVLDEGLNTLLSVQLFEVSQHLDAAGKVEVFRFISDQKATLERVGA |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |