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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 | 3300027437 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0095510 | Gp0072108 | Ga0207476 |
| Sample Name | Soil microbial communities from Kellog Biological Station, Michigan, USA - Nitrogen cycling UWRJ-G05K2-12 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 33318367 |
| Sequencing Scaffolds | 36 |
| Novel Protein Genes | 42 |
| Associated Families | 42 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 13 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462 | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae | 1 |
| All Organisms → cellular organisms → Bacteria | 5 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia | 2 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium erythrophlei | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Acetobacteraceae → Craurococcus → environmental samples → uncultured Craurococcus sp. | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Soil Microbial Communities From Arlington Agricultural Research Station In Wisconsin And Kellogg Biological Station In Michigan, Replicating The Bioenergy Cropping Systems Trials (Bcsts) |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Agricultural Land → Soil → Soil Microbial Communities From Arlington Agricultural Research Station In Wisconsin And Kellogg Biological Station In Michigan, Replicating The Bioenergy Cropping Systems Trials (Bcsts) |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → agricultural field → agricultural soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Michigan | |||||||
| Coordinates | Lat. (o) | 42.4 | Long. (o) | -85.37 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000268 | Metagenome / Metatranscriptome | 1411 | Y |
| F000411 | Metagenome / Metatranscriptome | 1170 | Y |
| F000569 | Metagenome / Metatranscriptome | 1018 | Y |
| F001033 | Metagenome / Metatranscriptome | 799 | Y |
| F001554 | Metagenome / Metatranscriptome | 672 | Y |
| F002315 | Metagenome / Metatranscriptome | 572 | Y |
| F002603 | Metagenome / Metatranscriptome | 544 | Y |
| F003059 | Metagenome / Metatranscriptome | 510 | Y |
| F003758 | Metagenome / Metatranscriptome | 470 | Y |
| F006629 | Metagenome / Metatranscriptome | 368 | Y |
| F017538 | Metagenome / Metatranscriptome | 240 | Y |
| F017759 | Metagenome | 239 | N |
| F018256 | Metagenome / Metatranscriptome | 236 | Y |
| F020078 | Metagenome / Metatranscriptome | 226 | Y |
| F022740 | Metagenome / Metatranscriptome | 213 | Y |
| F024176 | Metagenome / Metatranscriptome | 207 | Y |
| F025530 | Metagenome | 201 | Y |
| F034172 | Metagenome / Metatranscriptome | 175 | Y |
| F035451 | Metagenome / Metatranscriptome | 172 | Y |
| F037759 | Metagenome / Metatranscriptome | 167 | N |
| F038225 | Metagenome / Metatranscriptome | 166 | Y |
| F038480 | Metagenome | 166 | Y |
| F039800 | Metagenome / Metatranscriptome | 163 | Y |
| F041921 | Metagenome / Metatranscriptome | 159 | N |
| F045439 | Metagenome / Metatranscriptome | 153 | Y |
| F049507 | Metagenome | 146 | N |
| F053375 | Metagenome | 141 | N |
| F053859 | Metagenome | 140 | Y |
| F057709 | Metagenome | 136 | Y |
| F058768 | Metagenome | 134 | N |
| F063961 | Metagenome / Metatranscriptome | 129 | Y |
| F065229 | Metagenome / Metatranscriptome | 128 | Y |
| F067789 | Metagenome / Metatranscriptome | 125 | Y |
| F078804 | Metagenome | 116 | N |
| F082749 | Metagenome / Metatranscriptome | 113 | Y |
| F084203 | Metagenome / Metatranscriptome | 112 | N |
| F089374 | Metagenome / Metatranscriptome | 109 | Y |
| F099660 | Metagenome / Metatranscriptome | 103 | N |
| F100558 | Metagenome / Metatranscriptome | 102 | Y |
| F105281 | Metagenome / Metatranscriptome | 100 | Y |
| F105318 | Metagenome | 100 | N |
| F105656 | Metagenome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0207476_100189 | Not Available | 1958 | Open in IMG/M |
| Ga0207476_100417 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 1564 | Open in IMG/M |
| Ga0207476_100583 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462 | 1397 | Open in IMG/M |
| Ga0207476_100614 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae | 1359 | Open in IMG/M |
| Ga0207476_100818 | All Organisms → cellular organisms → Bacteria | 1235 | Open in IMG/M |
| Ga0207476_100961 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 1162 | Open in IMG/M |
| Ga0207476_101275 | All Organisms → cellular organisms → Bacteria | 1047 | Open in IMG/M |
| Ga0207476_101641 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 952 | Open in IMG/M |
| Ga0207476_102184 | Not Available | 853 | Open in IMG/M |
| Ga0207476_102572 | All Organisms → cellular organisms → Bacteria | 802 | Open in IMG/M |
| Ga0207476_102619 | Not Available | 795 | Open in IMG/M |
| Ga0207476_102867 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia | 771 | Open in IMG/M |
| Ga0207476_102926 | Not Available | 765 | Open in IMG/M |
| Ga0207476_102994 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 758 | Open in IMG/M |
| Ga0207476_103191 | Not Available | 740 | Open in IMG/M |
| Ga0207476_103321 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 729 | Open in IMG/M |
| Ga0207476_103832 | Not Available | 692 | Open in IMG/M |
| Ga0207476_103909 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium erythrophlei | 687 | Open in IMG/M |
| Ga0207476_104333 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes | 662 | Open in IMG/M |
| Ga0207476_104920 | Not Available | 633 | Open in IMG/M |
| Ga0207476_105025 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria | 628 | Open in IMG/M |
| Ga0207476_105132 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 623 | Open in IMG/M |
| Ga0207476_105137 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 623 | Open in IMG/M |
| Ga0207476_105200 | All Organisms → cellular organisms → Bacteria | 620 | Open in IMG/M |
| Ga0207476_105346 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 615 | Open in IMG/M |
| Ga0207476_105591 | Not Available | 603 | Open in IMG/M |
| Ga0207476_105877 | All Organisms → cellular organisms → Bacteria | 593 | Open in IMG/M |
| Ga0207476_105982 | Not Available | 589 | Open in IMG/M |
| Ga0207476_106738 | Not Available | 564 | Open in IMG/M |
| Ga0207476_106892 | Not Available | 560 | Open in IMG/M |
| Ga0207476_106930 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia | 558 | Open in IMG/M |
| Ga0207476_106966 | Not Available | 557 | Open in IMG/M |
| Ga0207476_107126 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Acetobacteraceae → Craurococcus → environmental samples → uncultured Craurococcus sp. | 552 | Open in IMG/M |
| Ga0207476_107285 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 548 | Open in IMG/M |
| Ga0207476_107517 | Not Available | 543 | Open in IMG/M |
| Ga0207476_108638 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 517 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0207476_100189 | Ga0207476_1001892 | F034172 | MRTIFVFLVAGLIVLFGGASYAADLRLDHERTHARGAGTFDQRMRVVEQKPYCGDCEAPIGRTHSANVARLRFINWPFWQERCAVGACGVYYPVMRSCAFWGLGCT |
| Ga0207476_100417 | Ga0207476_1004171 | F003059 | MMRAGITAGMLAGAVIVTAAVPAAAQVRDAVYRGTLVCDKLPFSAGKGREAIEVTIAGGTVRYSHVVRLRDAAEPVSEQGKGSLNGQDIELQGSWKAGNRQYEAKYSGAFVRRHADLKGTQTWTDGGKSFTRACTGTIKRPFRVFLPGEKK |
| Ga0207476_100583 | Ga0207476_1005831 | F017538 | SLTLVRASRNRDGEWSSDDYDVFEGKQLVGRVTLTPQAPEGRPWFWMITARPESSQNQGYAVSREQAMLEFNARWLNPARL |
| Ga0207476_100614 | Ga0207476_1006141 | F024176 | MTRSHVFAIAAGLLLAVSGPSFAAKRMSDTKSGLKSQSRAEESNGLANSGSAIRPYGRDPYLYSRDDPY |
| Ga0207476_100818 | Ga0207476_1008181 | F022740 | YHRRRAQILAARSNELGGLVAFISVGGQPVNTTRNGTIVAAFTFDDIVWTDIQQKTFAAATAQIRQIRPGSTPVLAATGTITPLADTEIKKLGWKIVQLKPER |
| Ga0207476_100961 | Ga0207476_1009611 | F099660 | MRLRIRTLLCGTAIFSAVSFFTITFAETNPFSKAQVADSIRKVE |
| Ga0207476_100961 | Ga0207476_1009612 | F001033 | MNFVSRTKSMALPHQILGASTNEKRELLMCGHSLIARLTIAVFVFQMLGVTSVVHAEGPDSTAGTSSADTRKLVIDPSSASVALWKASLIVSPLTHRDGSYVGDYQLKVKPYFFKSEKGSLVLAASDDAVGKLQAGTAMNFTGQAVTHKDGRTHIVLGRATPSSRDRGSVTFSIVTDDAKIVFNTSYHFPAPRP |
| Ga0207476_101275 | Ga0207476_1012751 | F037759 | MKSRGLLRPATLAAAIVAGGLLGGAARAQPPELGASSIGILPPPDILESVRYLGLDPKGEPVRRGAYYVLHAYDRAGIELRVVADAQFGDVLFMAPALNTSLTPPYVRAARIIQVEPPESGGQQ |
| Ga0207476_101449 | Ga0207476_1014494 | F105318 | MEEFIHQQNLERHRKMLSEQTHEPQRQTIVRLLADEENRDDPLSKLDS |
| Ga0207476_101452 | Ga0207476_1014521 | F100558 | VAEILALVAAFFFALAATLQQKGALGMGEVSLGSP |
| Ga0207476_101641 | Ga0207476_1016412 | F063961 | HATCTQKIKSLGIAPLVERPVRTLNQSTLCLDDQSERGHATTADAAKKVISKLGHWPNLEGLPMGCNAGWAIG |
| Ga0207476_102184 | Ga0207476_1021842 | F105656 | MSIVSRRTFTKGLLASALVPGTSAFGQPNDPASIAIIDTPQNAAKVAAKLAAQ |
| Ga0207476_102484 | Ga0207476_1024842 | F017759 | MLSGAVIVHGCNPLLLFGVVVGLLNSECPQQYGAYESKYGAHGQHIELQGKVHGSASLVDALRLARNDPAPKAPVTRPAFPAGGIAYRTCAIDNRLIERLKKSE |
| Ga0207476_102572 | Ga0207476_1025721 | F000268 | MLMRVVAVMLLLSAGIAAEAVSYSFVSKASGRLGGPIRFEFYRDSTTRPKTDIKSFTVSTRTADDRWKAMWSILSGRGLTQPIEYGVTPPGFTTMIQPQKLIPGRVYAGFATDGHGGSSGVTFGFDKDGTMIFPDSFDR |
| Ga0207476_102619 | Ga0207476_1026191 | F035451 | EARKMTMSKMAFLGVAVVAAVVIGSGTLAWVHNGAATADHENATHYVVGPDGRLIGAAPNPSIRSQWERDGLPN |
| Ga0207476_102867 | Ga0207476_1028671 | F006629 | MVNVMGMLTLDIVPGLNFHCRNALVAALSRIEFPVLDETLQPLTLPLPESTVQTITPLPVTCRERASYGYWGRGAYVARAFAR |
| Ga0207476_102926 | Ga0207476_1029261 | F089374 | MTNILDSARASHEGPRLIVRKASHAPIWSVWAVLEGTPSEEIFE |
| Ga0207476_102994 | Ga0207476_1029942 | F053859 | VKIRTVFKWAICVLAIVVLVGVGAVGWIAFVSLEKGEQHRRQFQAELDSGRWDFGDQPALLAVAQGI |
| Ga0207476_103191 | Ga0207476_1031912 | F020078 | MHSATRFCWQSGVIALATIIFAFLVPGIALCKVVSLTSIASAIAITTLVAGFGLYLAGQLIEKRTPQSERVDHYLQASILVTAAGLLWGHVVLQTGPWRDRSIEPGVAFAIVAGCGVAGALLLIRRARRLAAN |
| Ga0207476_103321 | Ga0207476_1033211 | F053375 | MHMHVTGFSAATILVFAIASPLHAQGIEVFGGYSVNADYVQNRPAILVADQKVSPFFSHGSGPTGFEASFKHAVRNGLGIKVDVSGYSDTFPPGPAAYCQP |
| Ga0207476_103832 | Ga0207476_1038323 | F038225 | MKRLSLALLGAVGAFFVLTPAQAADYRVVQYNDTKICQVVDMAGPFKPILSNYTVLTKKSVATFDAAVKARADVGAKAKCT |
| Ga0207476_103909 | Ga0207476_1039092 | F084203 | MRARVRRAMWMLGALALAVPASAQESTDVAPLTPEDSALLANALVFDPAALVTAPKKPLRLPGYRNNEYDITRTQKVDGSTTVVVKQPVQTEWSNSVGADLAPSKPTAYPLPLSTERNNGMPA |
| Ga0207476_104333 | Ga0207476_1043332 | F038480 | IVLYFAATAAHSMPISVLNANGLSATIPISDQCGDRCGSSRSYVKDRRSGVGGYSGGYVLVRDPLIQRRPFCPFGSYVACVVSGTYCVDLCH |
| Ga0207476_104920 | Ga0207476_1049201 | F067789 | MDTVISLLELFVYIAGILGLSMFVTWAVVKVSPSESAKEQRAQEKGEAKA |
| Ga0207476_105025 | Ga0207476_1050252 | F058768 | MRELEPEFDAQWRGLDASGQKTLRAIVLGDGSPYRTAALRRLELTKDVVRRALPRLSATAEIEERDAGGYAIVDPLFAAWVDRLNDRPGDGDPGDADQTEPGR |
| Ga0207476_105079 | Ga0207476_1050791 | F082749 | MDGESVDAAGKLGRKRLINHAMTLDAGLSLKGVRHDIDPVVSLPARPVPGMALMLVRFINHFEVLRRESLGQLFCDEIGGSHIARLGERSLPVNGYKQVLKASPVKAH |
| Ga0207476_105132 | Ga0207476_1051321 | F001554 | DNRKMGFISEEFRSLMLEIWRVKYLQMPRFREVISSIPMEIRLSHFLNDGDSPDIPIPIYVGYLNQIREMARSSAR |
| Ga0207476_105137 | Ga0207476_1051372 | F002315 | MKHVAVLSMAMLATVTFAADKKTYRYTCKGGAFTVTAAVEASGRWSKAEPVVLQIDSEPPQTLIADPDVPDADSFTNKDYEFYALKTFITLTRKSHGVVVKTYNACWVE |
| Ga0207476_105200 | Ga0207476_1052002 | F041921 | MSVRPPVIRDQDKIDVRLTGEAEYLIPFTFIEALNEGTLFDRPAHAFLDAARERRLFHVLNRTTDNIIGTGIIQGSGDERSTKQAEVGGLMFHPAARGFGLCSLLVKIMMVYAVKESGRDSPDEKYLAHVIDGNGAPLHALLEAGFRPIGPVDVRRGDIDAVIDYMI |
| Ga0207476_105346 | Ga0207476_1053461 | F002603 | MTAIEIRFPDESVELDNVEEHRVLTTLEVIYEGGSLHGKTADFPTRDVERVVVGLHLPNWHFFETYKRTICVDIRSQRTIFGYAGTFKPQQPAVWWKRLLTVLRIRKVKP |
| Ga0207476_105591 | Ga0207476_1055911 | F018256 | ISKLSQMPSFEGLLEWLTGPTWKFAALVLGSVGASYLILAHRLWWAYAVIMLAQVVYFFSAGSAELAVMRASVLFAYGVITLPPMRPLAPLATDIAVMVICFCYIMIVLCLYSAAWVASGGRVPQGAYGRRPTPLEPLRPSRLLDTFLPGHRSQDVTLWEGAVFALSSLLFVAASMALSLYTGAYVTEAIRSGVATVGTG |
| Ga0207476_105877 | Ga0207476_1058771 | F000411 | KATLTSPLCAAGKKNRCDEAESCECGAFSAICLLVSVRALQIFLSLATVLLLAGMPARGALSIGDTYSISFVDIDGNKHSTADGHVTIVVWTTSADREQARTVGDHVPDFCLGNPAYRMITVVHFTRRHMALGRRLATGLIRHRVREEAKRLQARYDAQKIVRDAKSDIFVVIDFDGTSASQLGQSASATDFCVFVF |
| Ga0207476_105982 | Ga0207476_1059821 | F025530 | MSDMRISTSTTMQIGEAARDNIAAGIWFAVLAGSLFLTAHGQSILMTAGLMLELTAAYSTFVLCGKGARSLFVHAVPYAFALAGAVFLCLAPDFPNAVQASLVFLGVTALMHGSVVYSALKNSPESEDP |
| Ga0207476_106738 | Ga0207476_1067382 | F000569 | MDLHIKKVWLPGAASCLLFFGFYWVLIWLPFDKTRFQFLAIPYLVLPFVGALAAYGSRRMKGSVLERILSALFPVFAFVALFAVRIVYGLFFEGHPYTLPHFLGGLSVTLVFIVVGGLL |
| Ga0207476_106892 | Ga0207476_1068921 | F045439 | MSRSSFSRRTFLQGSVGLTVANFVPGTTPFAHAATMEEQTIAAAK |
| Ga0207476_106930 | Ga0207476_1069301 | F049507 | PDGADEAAGRTEDEHKVSWQLAKTDYGTVFIKADEKERITYIAAYLRPGKEMPFDKIGQLEKAPVLSDHVVAWDVVRPNRPLIRVVARGSERKANSITMFIVKRPRAD |
| Ga0207476_106966 | Ga0207476_1069661 | F078804 | MNFVYATLCSVAVLVLCGATAPAFGYVKKAPTNQSAGKAIKKQASVFDSDGYRLVSPNSTMRCAQTLRSTLDCKE |
| Ga0207476_107126 | Ga0207476_1071262 | F003758 | PRLSPNVLRAFENAEDEILMNTLKGAPRLDVPSLFRPQFMAEVQKEHPEYFADLPPLK |
| Ga0207476_107285 | Ga0207476_1072852 | F065229 | LLIRFAISIFALTLLGLAISLSVAQSEQEASAAKAATLTHQ |
| Ga0207476_107517 | Ga0207476_1075171 | F057709 | MSEFDLKVALIIFVTKFIDPFAAVPALVAGYFCRTWWQVVIA |
| Ga0207476_108121 | Ga0207476_1081211 | F105281 | GGRRVKRVLLAAAAVGAWLLLRRRRSGDERNVVVGWADGSELELGEGPSRERLASIAEGALR |
| Ga0207476_108638 | Ga0207476_1086382 | F039800 | MSAADPTRSKEIASFRARLFTAIMVIVATLTALGFYLAQRRVTDDAERNL |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |