| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300003289 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0110115 | Gp0061291 | Ga0006776 |
| Sample Name | Avena fatua rhizosphere microbial communities - H4_Rhizo_Litter_19 (Metagenome Metatranscriptome, Counting Only) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 7043118 |
| Sequencing Scaffolds | 21 |
| Novel Protein Genes | 23 |
| Associated Families | 21 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 16 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 1 |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp. | 2 |
| All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies |
| Type | Host-Associated |
| Taxonomy | Host-Associated → Plants → Rhizosphere → Soil → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → rhizosphere → soil |
| Earth Microbiome Project Ontology (EMPO) | Host-associated → Plant → Plant rhizosphere |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Hopland, California, USA | |||||||
| Coordinates | Lat. (o) | 38.97364 | Long. (o) | -123.117453 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000203 | Metagenome / Metatranscriptome | 1619 | Y |
| F000237 | Metagenome / Metatranscriptome | 1498 | Y |
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F000360 | Metagenome / Metatranscriptome | 1232 | Y |
| F000817 | Metagenome / Metatranscriptome | 879 | Y |
| F001418 | Metagenome / Metatranscriptome | 698 | Y |
| F004796 | Metagenome / Metatranscriptome | 423 | Y |
| F005082 | Metagenome / Metatranscriptome | 412 | Y |
| F022652 | Metagenome / Metatranscriptome | 213 | Y |
| F024042 | Metagenome / Metatranscriptome | 207 | Y |
| F026580 | Metagenome / Metatranscriptome | 197 | Y |
| F033437 | Metagenome / Metatranscriptome | 177 | Y |
| F034200 | Metagenome / Metatranscriptome | 175 | Y |
| F034588 | Metagenome / Metatranscriptome | 174 | N |
| F054015 | Metagenome / Metatranscriptome | 140 | Y |
| F065302 | Metagenome / Metatranscriptome | 127 | Y |
| F070802 | Metagenome / Metatranscriptome | 122 | Y |
| F076910 | Metagenome / Metatranscriptome | 117 | N |
| F076940 | Metagenome / Metatranscriptome | 117 | Y |
| F083053 | Metagenome / Metatranscriptome | 113 | N |
| F096396 | Metagenome / Metatranscriptome | 104 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0006776J48906_100036 | Not Available | 585 | Open in IMG/M |
| Ga0006776J48906_100038 | Not Available | 706 | Open in IMG/M |
| Ga0006776J48906_100062 | Not Available | 974 | Open in IMG/M |
| Ga0006776J48906_100127 | Not Available | 553 | Open in IMG/M |
| Ga0006776J48906_100128 | Not Available | 730 | Open in IMG/M |
| Ga0006776J48906_100150 | Not Available | 670 | Open in IMG/M |
| Ga0006776J48906_100539 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 648 | Open in IMG/M |
| Ga0006776J48906_100658 | Not Available | 552 | Open in IMG/M |
| Ga0006776J48906_100680 | Not Available | 548 | Open in IMG/M |
| Ga0006776J48906_101333 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila | 818 | Open in IMG/M |
| Ga0006776J48906_101362 | Not Available | 562 | Open in IMG/M |
| Ga0006776J48906_101644 | Not Available | 582 | Open in IMG/M |
| Ga0006776J48906_102012 | Not Available | 514 | Open in IMG/M |
| Ga0006776J48906_102618 | Not Available | 576 | Open in IMG/M |
| Ga0006776J48906_103103 | Not Available | 535 | Open in IMG/M |
| Ga0006776J48906_103952 | Not Available | 586 | Open in IMG/M |
| Ga0006776J48906_105753 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp. | 850 | Open in IMG/M |
| Ga0006776J48906_105929 | Not Available | 632 | Open in IMG/M |
| Ga0006776J48906_107282 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp. | 725 | Open in IMG/M |
| Ga0006776J48906_107344 | Not Available | 1039 | Open in IMG/M |
| Ga0006776J48906_108660 | All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes | 676 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0006776J48906_100036 | Ga0006776J48906_1000361 | F001418 | GLKAEAEFTSSSGSVRALSVNAKKGLRDEERLETVPNSVK* |
| Ga0006776J48906_100038 | Ga0006776J48906_1000381 | F000817 | AAVNRLKPEVSRIIPGNWGKAESGWLARPLLRRIARFDGGGRIHQFL* |
| Ga0006776J48906_100062 | Ga0006776J48906_1000621 | F034588 | LPRWRLHPPASPLIRTSGCPSFRISGFTGDRSSSRLDSLSFGGAGCESSRSPLRFASPVSPTISFWVAPDPHPPVPADFRSESPRSSVPSGRPLRISGLLRLFASGFVAQTFPKSPWFLLAQRRRFRLSRVAPKLPSSADPYLPPQVAPASASTAGSMITPWLNRTLHPRLAPRMNLRYQSGTSIPDLISSALLISIHRSQSADHEL* |
| Ga0006776J48906_100127 | Ga0006776J48906_1001271 | F026580 | RSELNQVARGSFELERIAVTQRVNGCYCASARADDSGGLAHKKRVVSQTKEAERQDKVSIRTGKETGSRQGP* |
| Ga0006776J48906_100128 | Ga0006776J48906_1001281 | F000817 | AAVNRLKPEVSRIIPGDWGKAESGWLARLLLSRIARSGSGGRIHRFL* |
| Ga0006776J48906_100150 | Ga0006776J48906_1001501 | F083053 | LDGNSGLTGDAGLMETGSTLDAKAEGERPKEIETASSVGQGKLDPLDAKIHPRRKPEDAKFEDSRGFNIDPTVDAEAGQPGEA* |
| Ga0006776J48906_100539 | Ga0006776J48906_1005391 | F033437 | RMFRSHGGTVLTVAGRDLLSEVFAPSSVAPCRERHAGRGADTSAILLRVGTVTAGTAPAFGWSLALRYGSDLLPLRLLSLLQCGGVVFTLPH* |
| Ga0006776J48906_100658 | Ga0006776J48906_1006581 | F065302 | DSATRLHADVRFAARCSG*IACHSPSPLFSM*RVTVASALNGHNTLPEPESRYGLSLAHNDAFATIARSTFLACTFVSPSDTFANPFDSRLLRSVRFRGRTGALSMPGTRFPRRSPTFPIDPRSPLPFRSSCENLPDQSVQPVPFQEARLA*RSIASYSPPLPLSIPLQINV*NSLRPARLSFR |
| Ga0006776J48906_100680 | Ga0006776J48906_1006801 | F004796 | MNSTSLPLPLQLTKPVLLAGDLDTQVREGLSDAYDSKAQLCSHTQSSAQSKTLNVLGIQVDVNADIVVDDVIA* |
| Ga0006776J48906_101333 | Ga0006776J48906_1013332 | F000344 | MRPKHPHAAESGVGKHTARESERVQACAAGKERVTNAHPHIW |
| Ga0006776J48906_101362 | Ga0006776J48906_1013621 | F022652 | SRVHGTIERTTRMLSVRSAAKCAFSFVCCSPLLLFSLPRVNTANAVFGYRTLPEPASRCGLSLTRNDAFAPFRGQGSRPAPSIPRQTPSRIRSIPGSIAPFGFEADPGRHPRPKPVFRADFRRSRDFFQPPLPFGLFRALRIKAFNRLLPHEARPARLRSPFCSPSRSLSIPLRIDACGSLRPA* |
| Ga0006776J48906_101644 | Ga0006776J48906_1016442 | F034200 | VALGQRIVKSDGRPKAKGQDAKPQLQACLDLVRKPASANASRSEPRGLTRNSAT |
| Ga0006776J48906_102012 | Ga0006776J48906_1020121 | F054015 | LCASTVPMTLAVARKRDLPNERRPTAGQSEHTHREGHAIAAGSVKTFHHVGDVEMNTAGL |
| Ga0006776J48906_102618 | Ga0006776J48906_1026181 | F076910 | PRCQARSVQTYQVFRAQAGECRAVATVPYVPKSSRTAGPLMVSRCVSTGAPPVLGGHGDRQLAGSVHTYRVCRGTETLGPSSEVTRLRRSRNPARAILLDLANDTDEHVRPGNPAPANGSPSSNRGRLEEKPITLKARPHRSTVAPITGPRLGGRGSKEAHQKWPDLGVAPRGEGSVLPNVLGAVTEQAIA |
| Ga0006776J48906_103103 | Ga0006776J48906_1031031 | F076940 | HRTEQRNRKCRAFRLLAPRLAFSPPAGSKPPGTPRAAFDQDRSLVTAFRSPVTVAPSRSHHPGVNASSLLLRVQPLVCTARSDLPLHHRYRFAPASGDFVASIPLQRLRAARVAAPAISTPLQDYYFLPDQSVQSRWPPLGPPSEFARFPLAPWCRLLLGLAPDHRSWFATFPAACCS |
| Ga0006776J48906_103761 | Ga0006776J48906_1037612 | F000203 | RQALFPVLALGAPQGRAASFPTLFSTASGVFGLVAGPFSASQRLNFE* |
| Ga0006776J48906_103952 | Ga0006776J48906_1039521 | F000360 | IIPENIHFHLESDSDLSLKDLEAKRSHTHLVVTLDKFRTELKNMNFYYNKKTFPALTDSGVVTFRIGGAGARLKMVFTVEQHTGDKHPRLTEGYADFHIYHMDINFDKSTLTHDVLLPMMTNMWKLQIQNEIERAVEKNLTNVVQKLSEQLTTTLGEVNRPFLSGLETARKTVKKSDLAQVYQNRREKLE* |
| Ga0006776J48906_105753 | Ga0006776J48906_1057531 | F005082 | RRMVRLDFTKISPDPFRPAENVELSMSVYMVVDLPPAGFTNAEALAVYTGFKTLISASSDALVVKLLGGES* |
| Ga0006776J48906_105929 | Ga0006776J48906_1059292 | F024042 | MIEPVTRTHESGLVPRSSLSAEGKLRRAETALWGTSFRDEGKHGEPQDRQQGATPLHGRGGETVEVVRNHAGGTRGGLAAHPRRETRRRGSRASDSSASYDGGAIFG |
| Ga0006776J48906_107282 | Ga0006776J48906_1072823 | F096396 | MKSLMSLWSVTANELAVRCCTSATLDIRTVGRRVEHEGLSFLAITLANYGKAIEKWLDQGFVVPSDCPSFKKDRLSGLPVFLRGFLGRVFHAHSG |
| Ga0006776J48906_107344 | Ga0006776J48906_1073441 | F070802 | MKQYSSILLCMLVAISGHAFGAPVDGSNGDCPGGLANGAQIERGRSVFECRNGNVVAKACVADDLKHIDIGSTTDRKTTRLQCTLNSDGSATLEPTACLFQGQEHKVDEQFEDANNFYTCKKSETDLKIVNSGCIDQGKRVPMNQEVTRGDSVMVCTETVNNGAKMVQSGCAQDGKSYKVGDSFESGKNWFNCTRLGREKVSAKLAGCVNNGKRLNDGDRFTENEVISECTIENGQSNIRVISCAQRDDKGEVVERRIGCTWVEGPEPFQYEWACRQDGATAKKVQVRCNYKVGGGVYNIEPGCYRVIDKAAHGC |
| Ga0006776J48906_108660 | Ga0006776J48906_1086601 | F005082 | TSKLAPDVFRPAENVDVSMAVYIVFDVPRRGGYTAAEQLGVYTGFKNQFSATSDALITKLLAGES* |
| Ga0006776J48906_113638 | Ga0006776J48906_1136381 | F000237 | HES*DSDSGESTYEDKSGSYIS*FYDAFLKEIQDA*YWTMFVFIYF*LHHFNASTVNYFFFER*NISELDEIRFYGVAPH*YFRPLMGLLVISPTHYEGLM*MGLFFILLAFLPIIYN*YNPFHKHLPAIPMQNSLLQTSAFIIFMLSMFCAASMLPCGRYYYEPEGGYVGNP*VKFSF |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |