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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 | 3300026721 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0053063 | Gp0054416 | Ga0208841 |
| Sample Name | Forest soil microbial communities from Willamette National Forest, Oregon, USA, amended with Nitrogen - NN395 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 18950396 |
| Sequencing Scaffolds | 35 |
| Novel Protein Genes | 36 |
| Associated Families | 35 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria | 6 |
| Not Available | 13 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 4 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium erythrophlei | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Ktedonobacteria → Ktedonobacterales → Ktedonobacteraceae → Ktedonobacter → unclassified Ktedonobacter → Ktedonobacter sp. | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Soil Microbial Communities From 10 Grassland Sites In Ca, Co, Ks, Ky, Mn, Mo, Nm, Sc, Tx, That Have Been Nitrogen Fertilized |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Loam → Forest Soil → Soil → Soil Microbial Communities From 10 Grassland Sites In Ca, Co, Ks, Ky, Mn, Mo, Nm, Sc, Tx, That Have Been Nitrogen Fertilized |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | forest biome → land → fertilized soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Willamette National Forest, Oregon, USA | |||||||
| Coordinates | Lat. (o) | 44.20517707 | Long. (o) | -122.1284473 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000410 | Metagenome / Metatranscriptome | 1170 | Y |
| F001819 | Metagenome / Metatranscriptome | 630 | Y |
| F001854 | Metagenome / Metatranscriptome | 626 | Y |
| F002233 | Metagenome / Metatranscriptome | 580 | Y |
| F002784 | Metagenome / Metatranscriptome | 530 | Y |
| F003369 | Metagenome / Metatranscriptome | 491 | Y |
| F003614 | Metagenome / Metatranscriptome | 477 | Y |
| F005924 | Metagenome / Metatranscriptome | 386 | Y |
| F008837 | Metagenome / Metatranscriptome | 327 | Y |
| F008956 | Metagenome / Metatranscriptome | 325 | Y |
| F009926 | Metagenome / Metatranscriptome | 311 | Y |
| F010418 | Metagenome / Metatranscriptome | 304 | Y |
| F012680 | Metagenome / Metatranscriptome | 278 | Y |
| F014546 | Metagenome / Metatranscriptome | 262 | Y |
| F015378 | Metagenome / Metatranscriptome | 255 | Y |
| F016327 | Metagenome / Metatranscriptome | 248 | N |
| F019720 | Metagenome / Metatranscriptome | 228 | Y |
| F020075 | Metagenome / Metatranscriptome | 226 | Y |
| F025182 | Metagenome / Metatranscriptome | 203 | Y |
| F025548 | Metagenome / Metatranscriptome | 201 | Y |
| F026382 | Metagenome / Metatranscriptome | 198 | N |
| F027917 | Metagenome / Metatranscriptome | 193 | Y |
| F028611 | Metagenome / Metatranscriptome | 191 | N |
| F029122 | Metagenome / Metatranscriptome | 189 | N |
| F040663 | Metagenome / Metatranscriptome | 161 | Y |
| F041945 | Metagenome / Metatranscriptome | 159 | Y |
| F045294 | Metagenome / Metatranscriptome | 153 | Y |
| F050559 | Metagenome / Metatranscriptome | 145 | Y |
| F056188 | Metagenome / Metatranscriptome | 138 | Y |
| F061090 | Metagenome / Metatranscriptome | 132 | Y |
| F070498 | Metagenome / Metatranscriptome | 123 | Y |
| F080445 | Metagenome / Metatranscriptome | 115 | Y |
| F087829 | Metagenome / Metatranscriptome | 110 | N |
| F092562 | Metagenome / Metatranscriptome | 107 | Y |
| F092649 | Metagenome / Metatranscriptome | 107 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0208841_100065 | All Organisms → cellular organisms → Bacteria | 1965 | Open in IMG/M |
| Ga0208841_100106 | Not Available | 1757 | Open in IMG/M |
| Ga0208841_100259 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 1351 | Open in IMG/M |
| Ga0208841_100279 | All Organisms → cellular organisms → Bacteria | 1328 | Open in IMG/M |
| Ga0208841_100288 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 1321 | Open in IMG/M |
| Ga0208841_100306 | All Organisms → cellular organisms → Bacteria | 1296 | Open in IMG/M |
| Ga0208841_100359 | Not Available | 1231 | Open in IMG/M |
| Ga0208841_100421 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria | 1150 | Open in IMG/M |
| Ga0208841_100433 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 1141 | Open in IMG/M |
| Ga0208841_100456 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1125 | Open in IMG/M |
| Ga0208841_100536 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1061 | Open in IMG/M |
| Ga0208841_100693 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium erythrophlei | 982 | Open in IMG/M |
| Ga0208841_100855 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 924 | Open in IMG/M |
| Ga0208841_100870 | Not Available | 917 | Open in IMG/M |
| Ga0208841_100969 | Not Available | 884 | Open in IMG/M |
| Ga0208841_100981 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 881 | Open in IMG/M |
| Ga0208841_101191 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium | 828 | Open in IMG/M |
| Ga0208841_101416 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 781 | Open in IMG/M |
| Ga0208841_101550 | Not Available | 758 | Open in IMG/M |
| Ga0208841_101603 | All Organisms → cellular organisms → Bacteria | 750 | Open in IMG/M |
| Ga0208841_101635 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Ktedonobacteria → Ktedonobacterales → Ktedonobacteraceae → Ktedonobacter → unclassified Ktedonobacter → Ktedonobacter sp. | 746 | Open in IMG/M |
| Ga0208841_101835 | Not Available | 718 | Open in IMG/M |
| Ga0208841_102247 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 674 | Open in IMG/M |
| Ga0208841_102381 | Not Available | 660 | Open in IMG/M |
| Ga0208841_102414 | Not Available | 657 | Open in IMG/M |
| Ga0208841_103012 | Not Available | 611 | Open in IMG/M |
| Ga0208841_103190 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium | 600 | Open in IMG/M |
| Ga0208841_103444 | All Organisms → cellular organisms → Bacteria | 584 | Open in IMG/M |
| Ga0208841_103719 | Not Available | 567 | Open in IMG/M |
| Ga0208841_104669 | Not Available | 525 | Open in IMG/M |
| Ga0208841_104789 | All Organisms → cellular organisms → Bacteria | 520 | Open in IMG/M |
| Ga0208841_104823 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 519 | Open in IMG/M |
| Ga0208841_104898 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae | 517 | Open in IMG/M |
| Ga0208841_104930 | Not Available | 515 | Open in IMG/M |
| Ga0208841_105021 | Not Available | 512 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0208841_100065 | Ga0208841_1000652 | F000410 | MSRKLVWIDQERFRGFGCSECGWRFKPAGRPPGTSLDEVMNNFELQRDKEFKSHVCADHAADKNPG |
| Ga0208841_100106 | Ga0208841_1001061 | F003614 | MKPSELPGARRLYRLTNRALAQIRELWQYAGEDELPPDSLLQTQVEALRILHIDVPLSAKRQFQLFCSEHFPGLADILDCLAADQLWALLSMRVQLADSDQPHAQSAAVRFGGLGRRYVLVAFDDRPVGLLSHADGSGILP |
| Ga0208841_100259 | Ga0208841_1002591 | F029122 | MLIRPAIGDTDPIRYRRPTPDGQFSGNIIDEAMRPP |
| Ga0208841_100279 | Ga0208841_1002792 | F001854 | MKTFLLVIVSLCFALSVAALTPDATNQTPRKTQAIAGARLTTIMGTIYEDGDQLRLVTDQRAWRVDNPEILKGHEGHYVHANAYVYPETNSIHITEVKLPTPSETEKDDIK |
| Ga0208841_100288 | Ga0208841_1002882 | F003369 | MSKWNFVAMGQAGLTGRAQDIAQPVARGVARRTGQPEADILSLIGAASLTIALIGFLRQVDTVIKAGRTGRQPATDARPLVLRKGNGER |
| Ga0208841_100306 | Ga0208841_1003061 | F092562 | MNKRKAGLVFIALITCALAGQALAQGQEIEFKSNADDLAKIRSVLEEFRQDIIHKDGYAITKLMLNPNVLFH |
| Ga0208841_100359 | Ga0208841_1003592 | F014546 | MSESPTGRAEAEGKEMTEQEELVQDIRERLGEMPKRALPFNLLAFTTTIGQRYSMTQNEIIRLVMQEAEALGVNYRIGSSSR |
| Ga0208841_100359 | Ga0208841_1003593 | F008956 | GSPWTPEKDGLLRSMGAAGESAAAIATLLKRTPDAVRKRAHLLKIKLARSQPGPKAKGNAAKTATPA |
| Ga0208841_100421 | Ga0208841_1004213 | F002784 | MNEFTAKNEQAFLDACGAIGVEPNAMVNTQKERYLVSEFLKNPVSWLKTELLYHSYTTRGEAQEVANGIDRMISEGAPVGQSKLFPRSKHSSALSDTAFGS |
| Ga0208841_100433 | Ga0208841_1004332 | F050559 | IVLTVDHRFALSHPALVSAPSKKLCAALRSPCGIETGRR |
| Ga0208841_100456 | Ga0208841_1004562 | F087829 | LKPWHFVREPSYSPRSLSAGSHTPRLRMVCSQLSSISCARLLSALSPTTALKMESPSTQSLFARSWRYLDQGDVNRLLRGHYSPVLALTDSCVDPTRSPLLRPKPRSRSLCRLLPAPAAGGTFPTLSLRILPCVPGPLSRRSRGVHLPVSSSTSSAFPRTLSRSASRVNPSKRFHDGSHFRDCSHFVMFRPSGLLASQIVPTAATYRRRAAEAFTSEQNMRRCLRMHRIC |
| Ga0208841_100536 | Ga0208841_1005362 | F045294 | KDMGIDDESRHPKMCSEVAGGVTRNMVCLFREPDAGNLPVRFDERLQRC |
| Ga0208841_100693 | Ga0208841_1006932 | F040663 | MAKRRRNGRFSLKEDRQLIQMAAVSTTLEEAAAIFRTSVETIERKAERLGIKLKRKRLS |
| Ga0208841_100855 | Ga0208841_1008551 | F061090 | MTPWFRLTLICCVLLCLFLGLTQAVDWNYQPVVSSGSSSDRGTKATSDSPTSSVVGSMAFHLARARPFGSLVLDCGLTVGNIGPPGQENHGPPKPMDLGKLPARAGNSNQSHRATLSKKLLVFSR |
| Ga0208841_100870 | Ga0208841_1008702 | F028611 | MSGGTKAVLDDLKHAGEFTKIENTAIVYVLRGWFGSLSAIPGALEAGDDAWAFTTLQEHFDSKLNPDPTKRTPEQVNILGELQKKAKETQDRVDEILGAKSDEDERINKLVDAFVEQLVKNPPERAIPAT |
| Ga0208841_100969 | Ga0208841_1009691 | F016327 | MCQRHSQKLPCLTHMKPNREKIEAEDLVKERLPLTKWELTPKEKEDFDRVMRLMFDAASILRYDLELGEDAIGKTLKELADWATN |
| Ga0208841_100981 | Ga0208841_1009812 | F020075 | MERYKFEIRFRLAAELKQSYSYVEMVRCLGNSGLRDIVLERGGFLNYKDTTLALRLPSDMGSEEAESIGHGLIRRLGEALGWDPRHFSGTLVLWGQGRANEEDAQQARQMLIKQGFTVFLERLSAS |
| Ga0208841_101191 | Ga0208841_1011912 | F012680 | FSVVSCTLLPLEVGKDKKHLRSILEPLDLGAWLDLGPRGLRLIPHDPVLPPTYFNPDGSVDLVNKDLYLDDVMSHMERIAAALGCELEWDF |
| Ga0208841_101416 | Ga0208841_1014162 | F008956 | MSPKFPWTSEKDELLRSMGAAGESTAAIATLLKCIPEAVRGRARLLKIKLARSPPGLKGKGK |
| Ga0208841_101550 | Ga0208841_1015501 | F056188 | AAANPEISPLEFLLGIMRDPNVSSEFRIKVAQATLPFVHAKPGSARPGDPAGTAKLIDGTGAFAIDNAVAKALRDDYHRLGELLRKKCGDPLSAAEVEEESKLGECIADRARAIGCQAGYGLKQAQKDSNRLHQLYCKRISPPSCGGGALPDAEDAEEAQLRARVAAFDESPVGCARHRIRDLEMQDFRGGRSADEQNELDSLRTLYPDLPLDPDDPLTEAFEAWRRERARLQHRT |
| Ga0208841_101603 | Ga0208841_1016032 | F001819 | MKGKTAILLPSTNFYATNFELGSISPLFIHHLSRSRWRIDTEVFQTITTDCHLKHPAVHQTTALVVLTMIRFLAYTLALVFYHRQVRSHARRKCDTFHALAKRFAYWFLAVSPNTS |
| Ga0208841_101635 | Ga0208841_1016352 | F015378 | EKEKMTDTKQVERNMQNIHTSNEHSSYCECIWCLEKDTQLFGRPDLGKQEIEQEMAAMLKDLPLPITIKQQGDHYGDEYIWHCMGTTGKAYSFVDATRQALQSFIAISR |
| Ga0208841_101835 | Ga0208841_1018351 | F070498 | MVDTTNTQAEQTQTTEMPGTETPTPDEKSDRDELKEASQQFFRTLFQAGVHLARTSVNMLPEEPREHIVSAGREFTRGLATFAHEIADNFEK |
| Ga0208841_102247 | Ga0208841_1022471 | F025548 | PFQCAGINRHEAENAKFLRVRSSDPLGPEFCVGYREVHDEA |
| Ga0208841_102381 | Ga0208841_1023812 | F027917 | LLQPRGASVPLPEKSAVLVVEENAVIRSANAKRLRAAGFEVLEAANSAEAELILKSTTVDALFVPVRRG |
| Ga0208841_102414 | Ga0208841_1024141 | F026382 | VPDDLAELVRHYGLSVSEVAQAALREAVNESGRHFRRELAYVVLEHVKWREVVAGNYPDDPRNRQAVAALRALAEYILALEPDDSRLVHLRDSAEHARQLDSYVPETGEACGNWGRTLGSYGFYQDCTPEEGLRKLTEASDKDDAEWAALGGDVLAEVTRSVARSLGFADQDATADADPEEATRIVRGRRRGTYMYKSA |
| Ga0208841_103012 | Ga0208841_1030121 | F019720 | MKLLAWIRAPFAWKVVRQHDGYTYFENAVTGRRRCYWDGSGWGHVDYSFMRLGDVSYGPFGREVIGGQNN |
| Ga0208841_103190 | Ga0208841_1031901 | F010418 | MKKFEDQSDGGISITGNEVQIHLAPNEAYALWQWLSARKDAFQAHSSEKQLELKIHLYQEDLSHLDELKSVIPDLHERGPVAKILDARLGTVSEQALHLLKEYEIEYHIHPLLEDDDVYAQG |
| Ga0208841_103444 | Ga0208841_1034442 | F009926 | KFGIDRADFVEHLAQFAEVGEELADFGVGRIRNVTDPRALAGSTDCGKISLGAMPSSVDTVAVGPPAAFVGLDQRAAQYLFDRRQAARKVVATLAKSCR |
| Ga0208841_103719 | Ga0208841_1037191 | F080445 | VEHVGEKGTKINMETTNEQTPERVTVNSVKIDDEVLALDVVKRGEKRFVFEITRDNGNRMVASSDEHKKAKRAARAGKPIWKRTVKAALKEKLDQ |
| Ga0208841_104669 | Ga0208841_1046691 | F025182 | VQIIVEVEVEAGAYASEQYQSRISAPSVCPNCGIAQSLEAHGYYWRWVSEALCGKVLRMAVRRFFVGAAQ |
| Ga0208841_104789 | Ga0208841_1047892 | F041945 | FETIRQLQKENEYLKRQREILKKAMSIVGEEPNPGMR |
| Ga0208841_104823 | Ga0208841_1048232 | F002233 | MRQLRSLLRTAPARIGRRFAQIVAIAAASLPSAGA |
| Ga0208841_104898 | Ga0208841_1048983 | F092649 | VRLRTGSVEEGGLGAGRTLLNKTARRSEQFVSTSVAYLFVGRRSAGRPGLDLAF |
| Ga0208841_104930 | Ga0208841_1049301 | F008837 | GLIESAIRKEATEILLTPVQELDMVRMDFGRLHCYYRQPEITRAQFAYLAIYFVLIGNVAAGEAPTERLFRGSDERLYSLQFGKTRLPDSEPAVVIYIEPVRLASGRRR |
| Ga0208841_105021 | Ga0208841_1050212 | F005924 | MTDKITYDIYRGTADRTLRLATMPGAGLPAHLKRKEWVLMPRGKSPVHSDAVRDVGMRGYCFFQVVESQ |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |