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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 | 3300031487 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0132857 | Gp0330685 | Ga0314823 |
| Sample Name | Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_R2 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 22817758 |
| Sequencing Scaffolds | 26 |
| Novel Protein Genes | 27 |
| Associated Families | 26 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae | 2 |
| Not Available | 16 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Freshwater → Groundwater → Unclassified → Soil → Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → land → biofilm material |
| Earth Microbiome Project Ontology (EMPO) | Unclassified |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Pennsylvania | |||||||
| Coordinates | Lat. (o) | 40.7997 | Long. (o) | -77.8629 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F000817 | Metagenome / Metatranscriptome | 879 | Y |
| F001418 | Metagenome / Metatranscriptome | 698 | Y |
| F001519 | Metagenome / Metatranscriptome | 679 | Y |
| F001633 | Metagenome / Metatranscriptome | 660 | Y |
| F003158 | Metagenome / Metatranscriptome | 504 | Y |
| F004323 | Metagenome / Metatranscriptome | 443 | Y |
| F009606 | Metagenome / Metatranscriptome | 315 | Y |
| F011643 | Metagenome / Metatranscriptome | 288 | Y |
| F013934 | Metagenome / Metatranscriptome | 267 | Y |
| F017060 | Metagenome / Metatranscriptome | 243 | Y |
| F030637 | Metagenome / Metatranscriptome | 184 | Y |
| F033437 | Metagenome / Metatranscriptome | 177 | Y |
| F035161 | Metagenome / Metatranscriptome | 172 | Y |
| F038822 | Metagenome / Metatranscriptome | 165 | Y |
| F053640 | Metagenome / Metatranscriptome | 141 | Y |
| F055474 | Metagenome / Metatranscriptome | 138 | Y |
| F059087 | Metagenome / Metatranscriptome | 134 | Y |
| F061584 | Metagenome / Metatranscriptome | 131 | Y |
| F067982 | Metagenome / Metatranscriptome | 125 | Y |
| F071145 | Metagenome / Metatranscriptome | 122 | Y |
| F072008 | Metagenome / Metatranscriptome | 121 | Y |
| F072453 | Metagenome / Metatranscriptome | 121 | Y |
| F076984 | Metagenome / Metatranscriptome | 117 | Y |
| F099956 | Metagenome / Metatranscriptome | 103 | Y |
| F100898 | Metagenome / Metatranscriptome | 102 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0314823_101253 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1927 | Open in IMG/M |
| Ga0314823_104094 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae | 956 | Open in IMG/M |
| Ga0314823_104408 | Not Available | 918 | Open in IMG/M |
| Ga0314823_104490 | Not Available | 908 | Open in IMG/M |
| Ga0314823_104586 | Not Available | 897 | Open in IMG/M |
| Ga0314823_104826 | Not Available | 870 | Open in IMG/M |
| Ga0314823_105224 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 831 | Open in IMG/M |
| Ga0314823_105270 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 827 | Open in IMG/M |
| Ga0314823_105589 | Not Available | 801 | Open in IMG/M |
| Ga0314823_105745 | Not Available | 789 | Open in IMG/M |
| Ga0314823_105800 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae | 785 | Open in IMG/M |
| Ga0314823_106870 | Not Available | 717 | Open in IMG/M |
| Ga0314823_107164 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 702 | Open in IMG/M |
| Ga0314823_107232 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 698 | Open in IMG/M |
| Ga0314823_107409 | Not Available | 689 | Open in IMG/M |
| Ga0314823_107507 | Not Available | 684 | Open in IMG/M |
| Ga0314823_107519 | Not Available | 684 | Open in IMG/M |
| Ga0314823_110415 | Not Available | 578 | Open in IMG/M |
| Ga0314823_110447 | All Organisms → cellular organisms → Bacteria | 578 | Open in IMG/M |
| Ga0314823_110870 | Not Available | 567 | Open in IMG/M |
| Ga0314823_111869 | Not Available | 541 | Open in IMG/M |
| Ga0314823_111897 | All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium | 541 | Open in IMG/M |
| Ga0314823_112126 | Not Available | 535 | Open in IMG/M |
| Ga0314823_112189 | Not Available | 534 | Open in IMG/M |
| Ga0314823_112567 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium | 525 | Open in IMG/M |
| Ga0314823_113769 | Not Available | 501 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0314823_101253 | Ga0314823_1012534 | F059087 | MGVHISFTHPPSAIRSPMGAVAFAIGLKLLVPTPGKHGFRAVKDFIE |
| Ga0314823_104094 | Ga0314823_1040941 | F001633 | VGVGVRHTLFPGGTRLDTLAFAGVVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDAPCRERRAGRGADTPATFIVARRHPYHGDGTGFWPIVGPALRV |
| Ga0314823_104408 | Ga0314823_1044081 | F035161 | GTGSISPGLPGNQTGTPGVVLIQVQCVPSNLAGNNGGTVTIRKVDQFGQPLMASFSIQQGPFWVEVARVNLGSTLAQNPCATDGTQGTFNITGAGTSCANVGVISPAVFASGLPAGQYRIVEVAGPNSYCTLVQVYNGNQGQNQSGVLPFSGSLLTQPVTVNLPTANPLDVQLTFVNSCIVPGGASTATSQIAVVIGGSTPGLVNTSNIEIVPAPGSDDDARLDIRIRDSASIIIPNAHVTVLIDKGALALRRDLSGVSPASGYDVIEPNPGSNFASPFAGDTCDQSTNGWWQQSATTGSYTWPF |
| Ga0314823_104490 | Ga0314823_1044902 | F061584 | LTHRFPFGGSRTWCGIPRPRRRAAVTSHEVGRSTECCERRSCKRIGLLAPSMTSLFPASLSGVTSPPAPVLLRVRVHPPMSFTSPTEYEPLQTCPARFRAKRLPWGFPPHRGISIQSPLPTELPRSRSHVPPSAFLAPSTVCSSAHLAGLFHPTATSGIHLPGVISRCQAESPRR |
| Ga0314823_104586 | Ga0314823_1045861 | F030637 | MRCPVLCRQNAGTSHEVGCSPEFYERRPCGPIGLSAATSTLRFLARPGGSTSCVVPRSLAKTGSSSPELGLLFRVRTASNLPHARMRRAPSLGFRSQSRHQLRRSTCERGSQPRPMFRPRCFAHPRRFALSTALWACFIPLPRPGFTFQGFVPAAWPARLVDESFPHVVGRRHLPSSFLGGSSSGSLAFRALIRAAIRSNRRSV |
| Ga0314823_104826 | Ga0314823_1048261 | F072453 | REERVEISGWTLIALACVVLVNTVFIIGLAVALFMLNKKIDEALDKAGPLLQKATETLNQVEETTSQLQQRVDRVLDKTTRLVDQVSERVDTTTAIAEEAVTEPLIGAASIMAGINRGLRVYSERTSEKGNGK |
| Ga0314823_105224 | Ga0314823_1052242 | F000344 | MRPKHLHAAESGVGKHIARESERVQACAAGKERVTNAHPHKLAP |
| Ga0314823_105270 | Ga0314823_1052701 | F000344 | MRPKHPHAVESGVGKHITRESERVQACAAGKERVTNAHPHQLAS |
| Ga0314823_105589 | Ga0314823_1055891 | F009606 | PNVIRTKAKPKVNPVSGANFEYANEPRIGDSFVVVVAGPNGVQSFTFHHPIGHADVDVDDWVCTPVGDIPSLLSRREDPDEADRKAKRDKFRLDLAVDAGLLKRTGKDGQLVYPDTEINRQDALGVARAAAKEAVKSEKGTPPPDLYIRFLDQKIQEKESAIRKFLADPQTIQKAENKFPASGFRTRGGPLADREQVGVDYLSGLSRTQATDAVVKRIYGSGDDDD |
| Ga0314823_105745 | Ga0314823_1057451 | F033437 | PGGTRLDALAFAGGVLPDATLRGMRMFRSHGGTVPAVTSWNLSSEASAPGSDAPCRERRAGRGADTPAIFLSRVGTFTAGTAPAFGWPFALRYGSDLLPLRLLSLLQ |
| Ga0314823_105800 | Ga0314823_1058002 | F053640 | TVAAQRSEMVAESTTGIIPGDRGKAGGNWCRPPLMPAKAVMRHISPVPLAGVVSGQSTHELGTEPQAAIRNRVEWSQATQGVSTCASTQLPQRLRLLLRRPERHRVSRRDDPAKRPHSPHEWGAQGTYGGGERTDLGKVREPPHRGGVKHTSPSCKRQRSLRGKRSDP |
| Ga0314823_106870 | Ga0314823_1068702 | F017060 | MSRSAESNVQLASGGREDLRQLFALSFSEPTRDDEDLRHAVMDYVRTAKAERRTPEMVIVSLKRAIIDAAAARISYRAANELTDRVVRWFIDGYYGGDGPASDRSLDLRMGPAPRPS |
| Ga0314823_107164 | Ga0314823_1071641 | F004323 | MPLVGFRRQEGRAAPAATNLSPVARDYPSRALSDVFQAAALRL |
| Ga0314823_107232 | Ga0314823_1072322 | F001519 | VNSLCAEISVFQGVGESTGVFVERSAIRGKKGLCMSMRDLAIKSRVLGDGYYYIPADLWPKAKEPIVVHKHDWTVISSIPRTVRVPKKRAEAK |
| Ga0314823_107409 | Ga0314823_1074091 | F072008 | VLIDKGALALRRDLSSFPNSGFDPIEPVPAAANFASPFSGDTCDQANNGWWQQSTTSGGYTWPFLSSSRQQADGYTNSEGVISACVYVDTTLAPGTTPGKINVQAIIESPTQGGLYNPGLGTNPYYPLGNNLSLPNYFGVPNIVLTASITVVGPPASITVAAAPTSLNCGEKATITVTVKDSAGQNVSDRTRVELVTNFGGVIGGTTATLGPVSVAGGNVYPVSSSSAE |
| Ga0314823_107507 | Ga0314823_1075071 | F001418 | QRPEAGFTSSSGSVRALSVNAKKELSGQKRLETVSNRVK |
| Ga0314823_107519 | Ga0314823_1075191 | F000817 | SRIIPGDWGKAESGWLAWPLLSRIVRFGSGGRIHQFL |
| Ga0314823_110415 | Ga0314823_1104151 | F013934 | MDKANVERIHLLLKRHEQMLEEKRINPEEFLRQNEQFQETFGRLMRSTVVPVLEEVKDILVGKVESASIFHKRTAAGLRVKLDRWEDFERSFLFFGDDAAQCVRVTHEGVGFGLLSRKIGLHQVTPELVEEEAMKFLKRLIGQEQLRRPMHAADPFERRRPAGTSASSSPSSQYRGERGDYDLVRI |
| Ga0314823_110447 | Ga0314823_1104471 | F099956 | LPHFEEKPDRNRNPGSASTFTLRPGVRLEPLGDGSAVLYSRDLDQSLSLNHTAALLCSF |
| Ga0314823_110447 | Ga0314823_1104472 | F038822 | MGNYNSLSDRRAFLKRTIQGAGLAFAAPAILSSLGSGALHAQASGPTAAVAGRPYGSDGGAMQ |
| Ga0314823_110870 | Ga0314823_1108702 | F011643 | ETRYGSVARDKPLKGKPWTWQRDETSPQTQVAEQAVEDVRNVEGGT |
| Ga0314823_111869 | Ga0314823_1118692 | F100898 | RSSRVLPSGSGSRRSGVGGARRDTTSMVRIPVGIGAGYRFPIGPTRSIAAYASPFFVWSRLSEKGMRAQGDNAMRGSVAGDLVLTRNIGITAGYEFGAKTSDGAFGTTSGVFGAAVSYAF |
| Ga0314823_111897 | Ga0314823_1118971 | F003158 | MVASQAETLRKAIENLIDAKLHDALARPGGLERLTAHRLTGVASFDIRTAERKLQQSLA |
| Ga0314823_112126 | Ga0314823_1121261 | F071145 | MRKLASIAGAAILAVTALATPANAQGNMMAGGSCGTSAGAYGMTDLNSTAYGTGSHGVPALFYTVNYSNVPAPTTVGVIVRYNGELESQTAVASFTAQNAGGT |
| Ga0314823_112189 | Ga0314823_1121891 | F067982 | MRPRTAIHAALLTLAAATTLPAQVTLKTTGNELRDALGDVVHIWVSPFRSEKRDWLGVLGVAAGAGALLPVDDQIDSWIVRHPNAAIVRATDPWNEDHPELGDLSTGQRLLPISGVLIVSGMISDNRKLREAGWGCLSAWQSSSTIREALYATVSRERPSLDNHDQYA |
| Ga0314823_112567 | Ga0314823_1125671 | F076984 | MFVENYRRDNAESIMAGGEARPMPYPRISEKDWNVWATFLPVRSHNLDRAAASKFSTISLDEGIPLQVAVEIQKASQHFDRVEVWRKNQVEKDPIAVGMLGQERFLIARWGMEKLIPFEAIKKSMPLILAWKYATSPLGVLVELASLSLLAWNLVL |
| Ga0314823_113769 | Ga0314823_1137691 | F055474 | MPLQIKAFSRFSFPQAHLRNPPDFPSLPVARLHVNDDDLGSLFQVRYVLRGS |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |