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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 | 3300026009 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0111376 | Gp0116050 | Ga0208530 |
| Sample Name | Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_10C_80N_401 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 47811615 |
| Sequencing Scaffolds | 41 |
| Novel Protein Genes | 42 |
| Associated Families | 42 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 14 |
| All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 1 |
| All Organisms → cellular organisms → Bacteria | 6 |
| All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 7 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → environmental samples → uncultured Thermoleophilia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 1 |
| All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Hafniaceae → Hafnia → Hafnia alvei | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 3 |
| 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? |
|---|---|---|---|
| F001212 | Metagenome / Metatranscriptome | 746 | Y |
| F001248 | Metagenome / Metatranscriptome | 737 | Y |
| F001931 | Metagenome / Metatranscriptome | 615 | Y |
| F004686 | Metagenome / Metatranscriptome | 428 | Y |
| F007491 | Metagenome / Metatranscriptome | 350 | Y |
| F007880 | Metagenome / Metatranscriptome | 343 | N |
| F009820 | Metagenome | 312 | Y |
| F009994 | Metagenome / Metatranscriptome | 310 | Y |
| F010008 | Metagenome / Metatranscriptome | 310 | Y |
| F011243 | Metagenome / Metatranscriptome | 293 | Y |
| F011711 | Metagenome / Metatranscriptome | 288 | Y |
| F012266 | Metagenome / Metatranscriptome | 282 | Y |
| F013130 | Metagenome / Metatranscriptome | 274 | Y |
| F024508 | Metagenome / Metatranscriptome | 205 | Y |
| F026365 | Metagenome / Metatranscriptome | 198 | Y |
| F028203 | Metagenome / Metatranscriptome | 192 | Y |
| F032743 | Metagenome / Metatranscriptome | 179 | Y |
| F033082 | Metagenome / Metatranscriptome | 178 | Y |
| F034308 | Metagenome / Metatranscriptome | 175 | Y |
| F035429 | Metagenome / Metatranscriptome | 172 | Y |
| F038329 | Metagenome / Metatranscriptome | 166 | Y |
| F045169 | Metagenome / Metatranscriptome | 153 | N |
| F047144 | Metagenome / Metatranscriptome | 150 | Y |
| F047804 | Metagenome / Metatranscriptome | 149 | Y |
| F053350 | Metagenome / Metatranscriptome | 141 | Y |
| F064065 | Metagenome | 129 | Y |
| F074535 | Metagenome | 119 | Y |
| F076547 | Metagenome / Metatranscriptome | 118 | Y |
| F079119 | Metagenome / Metatranscriptome | 116 | Y |
| F080009 | Metagenome / Metatranscriptome | 115 | N |
| F081174 | Metagenome / Metatranscriptome | 114 | Y |
| F082662 | Metagenome / Metatranscriptome | 113 | Y |
| F083445 | Metagenome / Metatranscriptome | 113 | Y |
| F085485 | Metagenome / Metatranscriptome | 111 | Y |
| F087354 | Metagenome / Metatranscriptome | 110 | N |
| F091808 | Metagenome / Metatranscriptome | 107 | Y |
| F092455 | Metagenome / Metatranscriptome | 107 | Y |
| F097106 | Metagenome | 104 | Y |
| F097920 | Metagenome / Metatranscriptome | 104 | Y |
| F101110 | Metagenome / Metatranscriptome | 102 | Y |
| F101118 | Metagenome / Metatranscriptome | 102 | N |
| F105144 | Metagenome / Metatranscriptome | 100 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208530_1001544 | Not Available | 1462 | Open in IMG/M |
| Ga0208530_1001633 | Not Available | 1433 | Open in IMG/M |
| Ga0208530_1001963 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium | 1329 | Open in IMG/M |
| Ga0208530_1002728 | All Organisms → cellular organisms → Bacteria | 1173 | Open in IMG/M |
| Ga0208530_1002895 | Not Available | 1146 | Open in IMG/M |
| Ga0208530_1003036 | All Organisms → cellular organisms → Bacteria | 1127 | Open in IMG/M |
| Ga0208530_1003752 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes | 1040 | Open in IMG/M |
| Ga0208530_1004000 | Not Available | 1010 | Open in IMG/M |
| Ga0208530_1004379 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 976 | Open in IMG/M |
| Ga0208530_1004503 | All Organisms → cellular organisms → Bacteria | 965 | Open in IMG/M |
| Ga0208530_1004747 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 945 | Open in IMG/M |
| Ga0208530_1005259 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 910 | Open in IMG/M |
| Ga0208530_1005349 | All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes | 904 | Open in IMG/M |
| Ga0208530_1005693 | Not Available | 881 | Open in IMG/M |
| Ga0208530_1005720 | All Organisms → cellular organisms → Bacteria | 879 | Open in IMG/M |
| Ga0208530_1006289 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 847 | Open in IMG/M |
| Ga0208530_1006607 | All Organisms → cellular organisms → Bacteria | 831 | Open in IMG/M |
| Ga0208530_1007542 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 789 | Open in IMG/M |
| Ga0208530_1008669 | All Organisms → cellular organisms → Bacteria → Terrabacteria group | 746 | Open in IMG/M |
| Ga0208530_1008972 | Not Available | 737 | Open in IMG/M |
| Ga0208530_1009664 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → environmental samples → uncultured Thermoleophilia bacterium | 715 | Open in IMG/M |
| Ga0208530_1010741 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 685 | Open in IMG/M |
| Ga0208530_1010743 | Not Available | 685 | Open in IMG/M |
| Ga0208530_1011031 | Not Available | 677 | Open in IMG/M |
| Ga0208530_1011488 | Not Available | 666 | Open in IMG/M |
| Ga0208530_1013463 | Not Available | 624 | Open in IMG/M |
| Ga0208530_1014012 | All Organisms → cellular organisms → Bacteria | 614 | Open in IMG/M |
| Ga0208530_1014360 | Not Available | 608 | Open in IMG/M |
| Ga0208530_1016145 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 580 | Open in IMG/M |
| Ga0208530_1017219 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia | 565 | Open in IMG/M |
| Ga0208530_1017296 | Not Available | 564 | Open in IMG/M |
| Ga0208530_1018150 | Not Available | 554 | Open in IMG/M |
| Ga0208530_1019873 | All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium | 533 | Open in IMG/M |
| Ga0208530_1019954 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 532 | Open in IMG/M |
| Ga0208530_1019971 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Hafniaceae → Hafnia → Hafnia alvei | 532 | Open in IMG/M |
| Ga0208530_1021288 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 518 | Open in IMG/M |
| Ga0208530_1021429 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 517 | Open in IMG/M |
| Ga0208530_1021539 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 516 | Open in IMG/M |
| Ga0208530_1021676 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 514 | Open in IMG/M |
| Ga0208530_1021693 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium | 514 | Open in IMG/M |
| Ga0208530_1022583 | Not Available | 506 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208530_1001544 | Ga0208530_10015441 | F033082 | MPSSPASSSSVAARCLGCGREFETEQVVLLGQTFAAERYCGMCRATEQVNAEEQKVNARWRRVMVPSAYADCSFANF |
| Ga0208530_1001633 | Ga0208530_10016333 | F012266 | LSFCFEVGALSGSLVSPAPEGPCDDMCRLNALSSESDGDAADFLD |
| Ga0208530_1001963 | Ga0208530_10019631 | F076547 | LIRPALEPGEWKERRSGPISLDVGDTFDYVVIEGPSGETVTVSGADEIFALISLANDALPLDDPRKITHGWLARVEAIRDMLLEMAAEGEESLERDRRELAKGWDQMVQVLSAILPPDEPHDERDDYER |
| Ga0208530_1002728 | Ga0208530_10027283 | F001212 | MWEECIRCNEAPAVDEQGYCGHCHWAVRAEIEEGFYALREYLRAWARYADWCDARGLSTV |
| Ga0208530_1002895 | Ga0208530_10028953 | F045169 | VTEWGHNGDLSAPAVVAAPALQLTEADHIDEIPRLTRNQRAVMDWLNEGRDVSMRDLAKQLPRAPVTVKSLFHRGLIGYGQSWEEANGGPDDDRTVRLTPRGRSVMELLQARDHESA |
| Ga0208530_1003036 | Ga0208530_10030361 | F083445 | SAVHELAHLRARLVDLQSELLNRMHERRQIIQRVAEQDLERQQEGGRSSRTAAMQRARASEEVRSFDQNVAALREKIRRLEIEIERDRLSIEVAIAGATDRTSGLVAQRGAA |
| Ga0208530_1003752 | Ga0208530_10037521 | F009994 | MKRVALLCMGLAFGAANVAEAQLTMQMSNGWAFTFSGNVNAFMIYQTSKTAGG |
| Ga0208530_1004000 | Ga0208530_10040002 | F092455 | RPRRGACVNTFHDAFLDARRRIESGADAEQIVPALLKLAEAADEIELAQGLYEDEDKDEEPG |
| Ga0208530_1004379 | Ga0208530_10043793 | F032743 | RMVDGERVRVEVGFEGGQVISGFVDPSSADQLERALHEDGPRVVVLQSEDGPYHVVVPRVAYFKRVVRAGRVGFGSG |
| Ga0208530_1004503 | Ga0208530_10045031 | F011711 | MGDKRQKNQLQMVLAFAVEGRSEAPKARREGTESSTAKRECESPAIPD |
| Ga0208530_1004747 | Ga0208530_10047471 | F091808 | VRVKLGNPAHVGRLLAYLAFDPTVVAHRIADDEIEVSFLGSFNADAQQMQTELRLRAWIAANRE |
| Ga0208530_1005259 | Ga0208530_10052593 | F097920 | LVVPMHYRTGAVNFLEPPDVFLEALGARVERLETSETEVEALLGTAAEPVVALLAPPV |
| Ga0208530_1005349 | Ga0208530_10053492 | F009820 | MRLRLALPAILALLVAGPARAQVQVRVGDPSRATYSELHEALREGSPAADSVRAVLNIRKPARLWDYLGAAIDGTGDWNSGLIALTHLAELRSAAYADSAARLKQRLAAVEGVPFPQNPGLKAEDVEPSLQAILLERRRAVAGDSAVLADILARIPARDYDHGDAWVLGRLGAGAADSVAGRFLSAKDQEFKVRYLTLLSYFTDPTLIPLVSRIYAAPDSFGVPPRMAIRASDALLWIGTRESLQALLDARALAR |
| Ga0208530_1005693 | Ga0208530_10056932 | F101110 | MTEQRRSAASRLLPFLKVERELADERMQRAVAAVCARHPRLAEVEVGWFGHRLQGDAGGRYHALGFLSDPDRGIEDGRGFVVDVVAGHVLRELPLERRRDLPADITALA |
| Ga0208530_1005720 | Ga0208530_10057202 | F024508 | MYTRIQSRAFVALSLGLVPIGSSLNGQSVARADEPSQDNKIQLSYHVKAITRDSAGQYTMSGTVNGEVQGRA |
| Ga0208530_1006289 | Ga0208530_10062892 | F038329 | MTRLEPPYETNGSGIPVSGASPSTAARLIAAWPQTSAVIPAARRLPNGSLQEMASRRP |
| Ga0208530_1006607 | Ga0208530_10066071 | F053350 | VLGLLDLRERGERLEPSRFEIDPTVTDTVRGILADVRDGGDRVLAELALRFDGADLSASGLVV |
| Ga0208530_1007542 | Ga0208530_10075421 | F085485 | GSLDGGVGAVWSARQAWYVSGGLRHTKALPEIYNPAMAQQWAELARIARGRYHRALHFAGVMTQGTSSCNCGLRPPAAHRVLVRALDAQGLGHIPLPVGGTNIIG |
| Ga0208530_1008669 | Ga0208530_10086692 | F047144 | AAGVANVPRSLDPADPLANLTGNPQTGWKRRALETLVERATAALA |
| Ga0208530_1008972 | Ga0208530_10089722 | F035429 | MDAGTERDRDASPFDEQGRVDVPGAPGWRYLPISPSGNDSLAVTVAGPEDVRLSFTVPGFLSRGDELGEVTRVVIRAWERMDRASGLGA |
| Ga0208530_1009664 | Ga0208530_10096641 | F101118 | MQGRDDAYAIRIGLLAVVAFMSWPVWLAIVSGQHTFTTAVGLSALVPLALTLMVPAFAFHAGGHMHRALARLEHRLHIDSFIDHHLHRH |
| Ga0208530_1010741 | Ga0208530_10107411 | F080009 | MATRKQQRRKYQRAVAHARHLDADIADERDEGKTKPERKQQARPVRGAPVPPSALRTAKRAVLFATLFYLVITFTSSAISPGIKLANTAVMFVLFWSMGWMVENFVWRRYQKKHG |
| Ga0208530_1010743 | Ga0208530_10107432 | F026365 | VRRLLASLSAVALTLALPVAAYAADSADTGKPTGHDWTLDSIFVIALSIPAILVILTLIDIARGKHTERHDH |
| Ga0208530_1011031 | Ga0208530_10110311 | F028203 | MTDTTTAKLETGKARVQDMGERTQDYLDRAAQSASSGMDRMTDSARRSVDTAAESAKAGLDWATEKASVLRDRNTALMNTVTDTVTQRPLVAIGVAAAVGYLLGRLMHSSD |
| Ga0208530_1011488 | Ga0208530_10114881 | F013130 | MASKSATEDKRRRTTMVPVTTMEEIPLLSDQERADLLKSLKEAEARAIAGEGVDYDSEAFKARLLEIYRGRKP |
| Ga0208530_1013463 | Ga0208530_10134632 | F001248 | RIRIGVPDDSYVDRRDRDTVDVELWDEGRGEHLAAVSTVLEPDQDGEARELLREVVAGLESGELEPTAAALEPLADRVR |
| Ga0208530_1014012 | Ga0208530_10140121 | F079119 | RVMRLLDRLGFLYNGDGIGGEPRRATATGKPLRHWTIPVTLSGPRTIPFLEYHGARGTPEAEVLRLLDEHLESRELVVLYGHPCYEGVHEALLRKVFAAVIERGFRFVTLQAVAEQLQATAAAR |
| Ga0208530_1014360 | Ga0208530_10143602 | F034308 | MRLSFRQRILLILIGLGAVPTAVAVLGWGFTVRSTTPAAGARRAMEAVGSSGRTLLQTLDSTRLRPQERRALADHAAKLNAAIGSFQRAE |
| Ga0208530_1016145 | Ga0208530_10161452 | F087354 | MTDQTQIRRDPLVEHAVPLVAKAMYLADDANDLWEYFRDRVDAERHRIVEDAIREAIEPLEERFAIDDIARVASAMAAEHRPHGD |
| Ga0208530_1017219 | Ga0208530_10172191 | F081174 | YILSVVPSELPRADSLRFVPQVALRMYDAFWRTFANSSRLEKKLEDGRYHGINVTVLEPSPETGMFDPLAMLNAHPGKSKKLLWEGYRDTERALHGRPAEGTRRPR |
| Ga0208530_1017296 | Ga0208530_10172961 | F011243 | LPSPSPDSRFLALRFAAQEATDFGMNDDAVRRFAELRDRGASDAEIAGELRVPEDVVAALVKADAAQALARRIAAGEEPMYPVPEPEHRVFDTRSGSSAVPLAVLIAVLAGTI |
| Ga0208530_1018150 | Ga0208530_10181501 | F105144 | LSELDVAYFSDEPLREAAGHMRRLLAGEGETEDAERWAPLMAELNAVAAREAPSESALEELYWKLHLYRTEDELKTLRQNADLELSRQQELQRLEELRLRLLATLEAVRAHAPDR |
| Ga0208530_1019273 | Ga0208530_10192731 | F097106 | RIPVARARTNLADACRPPHLRKLMKPGSLRVVTIDDQRWVVRAVRRLDQSVPPLRFFNGAECRYVAEYPEDWPALPESELTSIFQRAHRGA |
| Ga0208530_1019873 | Ga0208530_10198731 | F064065 | FDVLLVRSPERRIDLLPQLDQFGALILDTYDFQDENKALAELQSFAQNHTLILLSSDAPLFSRIKSAVPRAVVIERSREDRGDWIAAQEPAEHYNSSSIRNTWKAIRTVLDRDKVAVASSEQSAPLLIAQTFHPKWVRSDNQPLYAATPFFTFGFFDKKPEMNFQRSRYDRGAVWFS |
| Ga0208530_1019954 | Ga0208530_10199541 | F010008 | VYHAYNDGELVATGRLTLDGPPQVGEEVRLNGRAHVVRDVGYGADAPVLTLEPR |
| Ga0208530_1019971 | Ga0208530_10199711 | F047804 | MRNAGVLAVLVIALSSFSTAQNKTSRPLDVAPEQIQRVEILYFPERVLVRAALTPERLEQLYQYKLELRDIRESPEWERLLPMLRQTAVTASGRNYDLRTAVLLFDKSGRRIASLYFDQFGAGGTINGQSGTISGGIYRWAKSLLKGVAG |
| Ga0208530_1021288 | Ga0208530_10212882 | F082662 | STTSSLAAISREEREALFTMVRPLLEGTYRLPLKHELTWTRLA |
| Ga0208530_1021429 | Ga0208530_10214291 | F007491 | TLAMTLTLLSGCTGGQEGSAAEEQRPRKNPIVTSSAEAQAPQVDVRQQLKSIGHAIPIYAGAKYRDDLTRRDAVMIRDQYGADAQVYTMATDDSYPQVYHYYTTYLSQFRAFQPGPPYPPTQNWRSMEVQLNEAMQDPFIPGDTIKSGEKNVLLQIAETEAEPKTVIRYIV |
| Ga0208530_1021539 | Ga0208530_10215391 | F001931 | ILSSVVQTLLRELKEGNGDKDRRRQVEEWMRVLAEKYPEFKIENGLRDYYLAEANRLRVDFENASDLTEKLSLGRHIESFLDRAAEYDRRIAER |
| Ga0208530_1021676 | Ga0208530_10216761 | F004686 | VDVETEGELTAGATLGYSPVAGDLRRRPGMEQRAGMNFAIRGSAPTLAGTRTSPVIRDKFVPNAKVAVDVDSAKFFELLIGRLSGK |
| Ga0208530_1021693 | Ga0208530_10216931 | F074535 | MGRVDAVTKAGWTRQHLRHGAHMLRYGPHPAATVYDSIGEDFFIALAPGWLNLGLWEGDGSD |
| Ga0208530_1022583 | Ga0208530_10225831 | F007880 | LCRRHLLVGEPARLYQDPSSKRFAKVCPLCYERAERRGWRADGRPIVAVHANPPADQALRERESLIDRLRGQLQSVEFDLDQVRNALAKAEQQAAELRGTKRELKELAGELKRREREIKSLTDDRRRADERAAEAEAAHRAEIARHHAVAAQLDERAAEAGRVNSRMA |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |