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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 | 3300021289 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0131209 | Gp0238800 | Ga0213903 |
| Sample Name | Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hobet_Cave_3 |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 26157464 |
| Sequencing Scaffolds | 34 |
| Novel Protein Genes | 34 |
| Associated Families | 33 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 29 |
| All Organisms → cellular organisms → Bacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| Not Available | 2 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Unclassified → Soil → Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → land → soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: West Virginia | |||||||
| Coordinates | Lat. (o) | 38.083 | Long. (o) | -81.98 | Alt. (m) | N/A | Depth (m) | .1 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000265 | Metagenome / Metatranscriptome | 1420 | Y |
| F001519 | Metagenome / Metatranscriptome | 679 | Y |
| F001750 | Metagenome / Metatranscriptome | 642 | Y |
| F002338 | Metagenome / Metatranscriptome | 569 | Y |
| F002548 | Metagenome / Metatranscriptome | 549 | Y |
| F006775 | Metagenome | 365 | Y |
| F007336 | Metagenome / Metatranscriptome | 353 | Y |
| F008145 | Metagenome / Metatranscriptome | 338 | Y |
| F011178 | Metagenome / Metatranscriptome | 294 | Y |
| F013424 | Metagenome / Metatranscriptome | 271 | Y |
| F013826 | Metagenome / Metatranscriptome | 268 | Y |
| F014455 | Metagenome / Metatranscriptome | 263 | Y |
| F018610 | Metagenome | 234 | Y |
| F018786 | Metagenome | 233 | Y |
| F021377 | Metagenome / Metatranscriptome | 219 | Y |
| F021852 | Metagenome / Metatranscriptome | 217 | Y |
| F032404 | Metagenome / Metatranscriptome | 180 | Y |
| F043096 | Metagenome / Metatranscriptome | 157 | Y |
| F043603 | Metagenome | 156 | Y |
| F051251 | Metagenome / Metatranscriptome | 144 | Y |
| F057405 | Metagenome | 136 | Y |
| F061194 | Metagenome | 132 | Y |
| F061696 | Metagenome | 131 | Y |
| F062146 | Metagenome / Metatranscriptome | 131 | Y |
| F065095 | Metagenome / Metatranscriptome | 128 | Y |
| F066812 | Metagenome | 126 | Y |
| F068101 | Metagenome / Metatranscriptome | 125 | Y |
| F068102 | Metagenome | 125 | Y |
| F068443 | Metagenome | 124 | Y |
| F081525 | Metagenome | 114 | Y |
| F092133 | Metagenome | 107 | Y |
| F094358 | Metagenome | 106 | Y |
| F105755 | Metagenome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0213903_100403 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 2323 | Open in IMG/M |
| Ga0213903_100456 | All Organisms → cellular organisms → Bacteria | 2220 | Open in IMG/M |
| Ga0213903_100619 | All Organisms → cellular organisms → Bacteria | 2005 | Open in IMG/M |
| Ga0213903_100704 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1921 | Open in IMG/M |
| Ga0213903_100726 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1901 | Open in IMG/M |
| Ga0213903_100792 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1849 | Open in IMG/M |
| Ga0213903_101061 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1657 | Open in IMG/M |
| Ga0213903_101243 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1561 | Open in IMG/M |
| Ga0213903_102098 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1242 | Open in IMG/M |
| Ga0213903_102226 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1211 | Open in IMG/M |
| Ga0213903_102346 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1184 | Open in IMG/M |
| Ga0213903_102466 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1161 | Open in IMG/M |
| Ga0213903_102747 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1106 | Open in IMG/M |
| Ga0213903_103520 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 985 | Open in IMG/M |
| Ga0213903_103670 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 964 | Open in IMG/M |
| Ga0213903_104045 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 915 | Open in IMG/M |
| Ga0213903_104292 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 885 | Open in IMG/M |
| Ga0213903_104452 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 870 | Open in IMG/M |
| Ga0213903_104791 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 839 | Open in IMG/M |
| Ga0213903_104827 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 836 | Open in IMG/M |
| Ga0213903_106014 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 744 | Open in IMG/M |
| Ga0213903_106542 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 709 | Open in IMG/M |
| Ga0213903_106961 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 685 | Open in IMG/M |
| Ga0213903_107502 | Not Available | 657 | Open in IMG/M |
| Ga0213903_108869 | Not Available | 598 | Open in IMG/M |
| Ga0213903_109580 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 572 | Open in IMG/M |
| Ga0213903_109855 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 563 | Open in IMG/M |
| Ga0213903_109859 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 563 | Open in IMG/M |
| Ga0213903_110593 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 539 | Open in IMG/M |
| Ga0213903_110687 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 536 | Open in IMG/M |
| Ga0213903_111050 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 525 | Open in IMG/M |
| Ga0213903_111615 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 511 | Open in IMG/M |
| Ga0213903_111675 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 509 | Open in IMG/M |
| Ga0213903_112013 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 500 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0213903_100403 | Ga0213903_1004031 | F068443 | LRATRRRPRKADPLASAQAVRSIIEHLRSALPEIIPHKDKELIRLLRAARHIQRYRATDTNRGRPGKWKREELLSVVARLEHILDRETSSHISLASFVDHYLRLIDFPADVVEVLEKGEINLFEAEQLARVTAGRLEVTSGQAKRTRAELLSSHLQTKASGDRLRKRVNELLRTSKANAGDGTVDNPLANSEDLEDFDPYDSTHLFWEQLKQLGFAFRSIRREDVTDEEIEELLKASEPILATLNRIQRRREQMKVIKVEL |
| Ga0213903_100456 | Ga0213903_1004563 | F013424 | MAQAAGKAPKQITWIICLILYIVALLAHFGMVHVSGDIASWSWIIGFGLLLVAVQVRGL |
| Ga0213903_100619 | Ga0213903_1006193 | F057405 | MADEAPLDDGQTSRAVLRRIRRTALGAWLGFAVFLAFSGGFRDVLGLTCSAAVTMICFLWLEEIVETLLQPTAHLHARRLTLRTLARYALLGMALTVTIIIARFNAVSLLLGFSVIVVGICGEALYSLYRSFIEG |
| Ga0213903_100704 | Ga0213903_1007041 | F051251 | MTEPRNTTVVALNGEPLTPEAVIAQLRTLRSQIEDVAPLSKDQRRLVKQRLRVHPQPILDASINVIGVLDNVSQALGQPLDDVRRLQDDVLRWDAAVDEARAFLKSIEGSTLNRRDRLAVIATQAYAIGTQLAKDPAKAVLLPHIEEVKRLKGVSRRKKPAPAPKPPAPANDTSTPRKA |
| Ga0213903_100726 | Ga0213903_1007263 | F000265 | MTELRGASAPPEIKAEWVRAYEEYRRAPGVPHNQKLDRTERISYVAQKLNLTRKQAKRRIRNYEAWQRNISKGLVEG |
| Ga0213903_100792 | Ga0213903_1007923 | F043603 | MNNIAQTRTTRIESALSTAYVLPAMLAVNTVALLALDQIGGIPQWVKAAAALFLAF |
| Ga0213903_101061 | Ga0213903_1010612 | F018610 | MIEVAVIVAMAGLDPEEHFLYLAPYSDRRDGQETVADYVNGRRRFFPMLAGGVPKMVNRDQVLWVRYEKLPAVVDLDETIVERLTILELVDGARIEGVVPTTDRPRELSRLSDVLNDATEEFLRIDDDEETYFVNKAFIRRVIPR |
| Ga0213903_101243 | Ga0213903_1012432 | F032404 | MLEGEISEINLIERLVELWREQFTGAIRFENDGIIKIIYFKGGDILSASTNDRSDSIDEILMRAGKVSREHVKQALAK |
| Ga0213903_102098 | Ga0213903_1020982 | F001750 | MPKLITEIPSDLSRQIDRIIRDGWFPDQESVVREALSQFVDAKSFLGDSPRMLHRFAADALNDSKPEVALKFVSRALSLMVGQDITDFTLYQSLVELRVQILLVLGRDDEALASAEEAKEKLPNNPAIARWIEKLQKNRPRGEA |
| Ga0213903_102226 | Ga0213903_1022262 | F011178 | MTGTAREAMKINIADLGPGMRERLSERLDRAAQLRCTEHDQPVVSVTIYGRENGWFDARWTTCCEALERQAVAIVKERC |
| Ga0213903_102346 | Ga0213903_1023462 | F008145 | MAVRGEEVASSIDAQVRESIEKMVAEIRSSVEDVRVLVDQQLKAALQSVQADVNSFTFLPQIKKSIAELEEQIETERPAVAAVAASPASAGALRVKSAVQIIERGRSQVDVLNSLLEQCLEFGSRAALLILRGETFSGWKGVGFSAQGGNDEMIKRFNAAPGLIPELDRVLREEKVVSWDGTNLSTRF |
| Ga0213903_102466 | Ga0213903_1024662 | F062146 | MPFVSATREDGATLLVNLDRIQYVAYQDTEGQEVLSIVFDTNPPAGGRNGTNEVVVHGEE |
| Ga0213903_102747 | Ga0213903_1027471 | F092133 | KMPVDMHYGRFLFPLAEEIRQMIGIHSWARVHDMNLRQSMQYNRFKDTIADRLGDYLKNHGLVRQRPHPFPLHKKWEAARNSTEADLFRALAFVADLEIKRKSGGLPVDIGIETFMLSRLRA |
| Ga0213903_103520 | Ga0213903_1035202 | F001519 | MTLVNSLCAEISVFQGVGETTGVMVERRAIRGKKGLCKSMRDLAIKSRVLGDGIYYIPIDLWPKSQEPIVVHKHDWTVISSIPRTSRATKKRALAE |
| Ga0213903_103670 | Ga0213903_1036701 | F007336 | MKPLASVLTQIQQHQPPRVILVGGNSEFLSENAFHQLRDALVADNPALSVESYEPGTDLTAILDSFRTMSLFGGARLLIVPEVNAFVSAKEIASLYDKAVADWKSAKTDRKRATASAKLLHVLGLAGCDLDMKDRPIADAMGVTLDATLTDMLAFCRATGKKAGRGEDDAALLMEAIARGGAAGTILLMRTGDVPRDSATIDLIDKVGAVVVADLTRDGFTSALDQAITSIAAE |
| Ga0213903_104045 | Ga0213903_1040452 | F006775 | MQLGKDACACGHIIDQHDGGRGGPCNSCACSSGELPTAFQVGVIHSMHEMTITLMRLVKEIQLARGGGTQHQG |
| Ga0213903_104292 | Ga0213903_1042921 | F065095 | PLMAETDQKQNIERAILRARDGVGDRIDELDRHLRTNLDPKVLASNYAPQLVAGGAVLGVVLGFGMPKVFRRLITWGVPLAIVAATIKNAKERHDRNDLTGLS |
| Ga0213903_104452 | Ga0213903_1044521 | F081525 | CIWVRLCRKPLPTMSIKIRFSAFVAACLLVANAASAACVNRFVSRTERPRQVVTLLTGKLTFQEAQALAAAINKKASPPVEWVGDDGKSISKQFGELKVVRPMPVGCDGKTSGVVMIVTFATSTIPAKKMIVKLNPETTVAFDQQAE |
| Ga0213903_104791 | Ga0213903_1047912 | F061696 | FAWGSEMRFRELVADIYLLTIAYQSEMGADLRSTSYTTMDKTIQLAGRLASIPTAISGLPAAITSLNYLKQIVVTKGLSMRFARLIEEIRPGFIGDDRR |
| Ga0213903_104827 | Ga0213903_1048271 | F061194 | KRKAVLDEGLNTLLSVQLFEVSQHLDQAGKVDVFRFISDQKASLEKATA |
| Ga0213903_106014 | Ga0213903_1060141 | F051251 | MTEPKNTTVVLLDGEPLTPEAVIAQLRTLRSQIEDVAPLSQQQRRLVKQRVRLHTKPVLDASINVIGVLDNVSQALGQPLSEVRQLQDDVLRWEAVVEEARSFLKSIEGSTLNRSDRLTLIATQAYAIGKQLAKDPAKAVLLPHIEEVKRLKGISRRKRPAPAPNPPAPANDTSTPTKA |
| Ga0213903_106542 | Ga0213903_1065421 | F021377 | MATQNPTNPNGAAELAQALTTLEPEAVVEMLRALRAQLGEVTPLTTAERRLLRRRAKTTNPVLQASINMIGAHDQVSQAVAQPADGVRRMYDEANRWTAVEDELRTLLEGVAGANLVRRQRITLIAGQAYNIGTQLARDPANAVLRPHVEEIKRLKRSTRRKKAGEATQSPPPAPSSVTPGSPKP |
| Ga0213903_106961 | Ga0213903_1069612 | F094358 | RYHHPSTMLDLDGLQVAYLGVALAHYLDLETGDIVDLPLDAEAPGEDDRFLRIPTRTPESETEDRRLFVETMPPSAMRDQLERTIDNWNAFRHVLLEDRKTERHFFNFKNDQATRAIEEWLTSEGIDPSS |
| Ga0213903_107502 | Ga0213903_1075021 | F013826 | MAVCWRCPRCKEVSCEDDVNAQGRPLACDHCERPFLPHETECTVCDATNPWVRRDSLHFWCRQCGNTQTFYGRTA |
| Ga0213903_108869 | Ga0213903_1088691 | F018786 | MSRPQVLKRFVAVAVLFSLCSALFLSSNTSVRAAGNTLPSTATGKISPDLQKLILSGSNPRVKVIVQSNSTSATLLGGLLNMVGGLLVTVLATLNIRIVDVEANSVQTLAADPSVSYISLDAPVLSSGHITNTTGTQQ |
| Ga0213903_109580 | Ga0213903_1095801 | F002338 | MQELKAEKPPESPEGSDPVARLMERLGEEGFTTEQGAEWWDEYGEIIYRRAEKLPLAAGETIFIFTRIPDLNERILRQTSDSVVQTYRAQTVTQKALSVLQSTTVYHCLVCTSDQPHNESLSEYITRLGGATFIPVVIVPGINEVNYPNLEEKVGVLRPRIEYLQYLLGERRENVD |
| Ga0213903_109855 | Ga0213903_1098551 | F021852 | MTDFEDRIRRMTREAMGEIGREADEIEDVLEPPGADYCVITFRDPALKPIEISKPLGAGESQEQDEIRRALQYRFHT |
| Ga0213903_109859 | Ga0213903_1098591 | F002548 | MPKFEYESHTEPDSAFFERRRLRRVRMIVELTLNLISSDRTVSHREARCLVDCARKAILELFPGFDVRYERIVQPSFSRVL |
| Ga0213903_110593 | Ga0213903_1105932 | F068101 | MAERDPDDYERSAAGLDFDGGTIRDKAEELGAKMLEGPEALLDEIENLLPEAWREQIRAYPVVAMALGLGIGLWLGMKKSDEIIAAGSSLVSAAAMANVSAVMDKVKG |
| Ga0213903_110687 | Ga0213903_1106871 | F068102 | GCSKPEPLTEEKAKEIVASWMFKREPVYAEVPQRVWWNPKAPKDDYDEKAVRTLRNLERAGLVTVTEKLTADSGEYVAKVTKKGFPILGTAPSNRGPVYRATICQKVYDGLRNFVRHPHEPTVGHAELVWHYDNPTWLYPLFETKIDKPLKAPYLSNVSFWYAKHQWRFEINVKKTKA |
| Ga0213903_111050 | Ga0213903_1110501 | F066812 | LLSVLVLPWVVGEIEHEEAKRHGGPSNEVEPGEIEVHTDAEADSAAARMRLGEVILFIRDLIQPLCARLSLAAGTRHQMEQALETFWRLLEPPSDRRAQFRAVYRDPFSDALSLLELYALSSGRYVDVFRQWQAFAVRVKRAQEEVEGTVKKRRRRRRH |
| Ga0213903_111615 | Ga0213903_1116151 | F043096 | ALLVGADHPGLRQAAKLVGFMPVYTATAPEAREYFNQEFPPLVMLHPGQITPPPLEAMAPIISLTPQDRRKSFFILFSDSLRTLDGNAAFLYGVNLVVALKDLGSFQQIYRDAFSYHERLYAPMNAVAKALAAH |
| Ga0213903_111675 | Ga0213903_1116751 | F014455 | LMFRVGQKASRGFAKQIGLRGMANVLGVVGGVKYMRRHS |
| Ga0213903_112013 | Ga0213903_1120131 | F105755 | VRRLQRAAVLAAALLLPRCTVSVSRYAFETALKNQANVDRIRIGQTLAEVQKIMGKPPERRSAHVRFDGISIEEWSYITDYVRRMDTTITFVGGKVDEIHAAKWD |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |