| Basic Information | |
|---|---|
| IMG/M Taxon OID | 3300003399 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0110179 | Gp0089075 | Ga0008477 |
| Sample Name | Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 PM |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 10787973 |
| Sequencing Scaffolds | 14 |
| Novel Protein Genes | 14 |
| Associated Families | 14 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Archaea | 5 |
| Not Available | 4 |
| All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. KM1 | 1 |
| All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Desulfomonile → Desulfomonile tiedjei | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Hahellaceae → Hahella → Hahella chejuensis | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling |
| Type | Host-Associated |
| Taxonomy | Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Host-associated → Plant → Plant rhizosphere |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Joint Genome Institute, California, USA | |||||||
| Coordinates | Lat. (o) | 37.931388 | Long. (o) | -122.021761 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F005950 | Metagenome / Metatranscriptome | 385 | Y |
| F006408 | Metagenome / Metatranscriptome | 374 | Y |
| F010272 | Metagenome / Metatranscriptome | 306 | Y |
| F020942 | Metagenome / Metatranscriptome | 221 | N |
| F023901 | Metagenome / Metatranscriptome | 208 | N |
| F045401 | Metagenome | 153 | N |
| F057496 | Metagenome / Metatranscriptome | 136 | N |
| F059733 | Metagenome | 133 | N |
| F071574 | Metagenome | 122 | Y |
| F076440 | Metagenome / Metatranscriptome | 118 | N |
| F078854 | Metagenome | 116 | Y |
| F086321 | Metagenome | 111 | N |
| F087425 | Metagenome | 110 | N |
| F087678 | Metagenome / Metatranscriptome | 110 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| JGI26136J50244_100514 | All Organisms → cellular organisms → Archaea | 1324 | Open in IMG/M |
| JGI26136J50244_101018 | All Organisms → cellular organisms → Archaea | 896 | Open in IMG/M |
| JGI26136J50244_101025 | All Organisms → cellular organisms → Archaea | 894 | Open in IMG/M |
| JGI26136J50244_101244 | Not Available | 802 | Open in IMG/M |
| JGI26136J50244_101355 | All Organisms → cellular organisms → Archaea | 765 | Open in IMG/M |
| JGI26136J50244_101673 | Not Available | 688 | Open in IMG/M |
| JGI26136J50244_102054 | All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. KM1 | 634 | Open in IMG/M |
| JGI26136J50244_102491 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 582 | Open in IMG/M |
| JGI26136J50244_102531 | All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Desulfomonile → Desulfomonile tiedjei | 578 | Open in IMG/M |
| JGI26136J50244_102542 | Not Available | 576 | Open in IMG/M |
| JGI26136J50244_102584 | Not Available | 572 | Open in IMG/M |
| JGI26136J50244_102845 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Hahellaceae → Hahella → Hahella chejuensis | 550 | Open in IMG/M |
| JGI26136J50244_103008 | All Organisms → cellular organisms → Archaea | 538 | Open in IMG/M |
| JGI26136J50244_103421 | All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium | 510 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| JGI26136J50244_100514 | JGI26136J50244_1005142 | F023901 | MRSRHNEQGQSCEGGVPLDPXKFGGYEFAIXTKGWDAKREPTHNCHDQHKSGLIPTNLENDKAVRLRQTVKDESGKVHQIGEIDYMDGNGFHKVMDIFDSSPNPWMVDRNLYETKSYFWIRNNGSGYITVRDVSLEILS* |
| JGI26136J50244_101018 | JGI26136J50244_1010181 | F005950 | MTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLQYGLSKVHKVIIRKYTEDDEFIARAQKTRGIK |
| JGI26136J50244_101025 | JGI26136J50244_1010251 | F057496 | MAGVYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMK |
| JGI26136J50244_101244 | JGI26136J50244_1012442 | F078854 | LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLI |
| JGI26136J50244_101355 | JGI26136J50244_1013552 | F010272 | MNHERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKEQAQEKLFELAQKFNKILKDSNVNLTLPQNGDLSSKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKQEAGADLSKLMQKLQSLRNNSTQ* |
| JGI26136J50244_101673 | JGI26136J50244_1016732 | F071574 | MPKMRTNYHYRGRIITLLPRMEGYMWTCQYVILKAGKTEIDGSPAKTYFSREEAESAAFTMAKTFIDQCQ |
| JGI26136J50244_102054 | JGI26136J50244_1020541 | F045401 | MMPLPARVWTSGSVLLPAFAALLVTLSCSQLVYQPGAVVPTASPLPYSAMVRLTEIEAYQVEPGATMVADPRIENKVTGIAQPVSKAKKDWERSIADYLAARKTFTYLSTDSQTDLDLTMRLHIYIDPSVDSDFHHVYVARIDATLAEASGKRALSKYIGF |
| JGI26136J50244_102491 | JGI26136J50244_1024911 | F020942 | PEVHIRKVDALGDRAHAAWRFGEVFLHNFVPRYLVSELFQPYPRGPYMGSLTAFGPGGNAWLSLWDDRARRGLDPGSVRAVKAYDVTLKGRGGFRAFSAIAATLHEAGLDHLLMPIPHDVNARALIDPFVSDLVEFNFCVKRLNGAAPVPSGPIYFDIRH* |
| JGI26136J50244_102531 | JGI26136J50244_1025311 | F087425 | MTCAIYAKNATKQQRIGNVMRYVLILALMVLSHVDTAARAGRVEDRESLRRLPGVEVIVETFLSEEEAAGFSREAIRTGVELVLQSNGIRILSASERLQTSSAPFLYVKVNPLKHSSADTFCLAIEVELHQAVSLLNRPEQKMSARTWNRVQVAMIGDQITGRVTEVVEPLIKQFANDFLTVN* |
| JGI26136J50244_102542 | JGI26136J50244_1025421 | F086321 | MNPSKKEIYKILERFTSQKGGILIILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSGIEGDVIWFGGMLEKSGSEFIGSTYDNGLKSAPV |
| JGI26136J50244_102584 | JGI26136J50244_1025841 | F087678 | LATPPPDQAGFYWFRYDNLSSHVHFKVLLQVIQMQPKATEIGGKFVVRWFNQLVPLEQVPEGLWRGPVRDLR* |
| JGI26136J50244_102845 | JGI26136J50244_1028451 | F076440 | MEKRMQISPGRNWSEGAGDRADQHFEIWYGEEERKDTLVARVWATKDGPHSVELYRKSSLIEPVRVRVLEGLMRELDFYLMKDERDVPRYLMHHCSMASHVYSPYGW |
| JGI26136J50244_103008 | JGI26136J50244_1030082 | F059733 | DDLLEGFGSTDLEFAFSDFYKHRITDDLKFEYKTIQPPSLLEIDGHKTGSFHIMFSQKDEIDPISGEVQYWITFVGENGYMIEFLSIPENFDTPDNTEMRDRFISSINFLGLSNTTDTSGRISSVAMSY* |
| JGI26136J50244_103421 | JGI26136J50244_1034212 | F006408 | GTRRTGGNMAAECLTLHHGGLRGGGRGWRAERCATPESCELHLCIADGDGGFWHPDDPLAFAKWRIRADLDAVPAHVMVNVSRSWDMLRRAAVVTAVGLGGTVAVLGVLWGRQRRFSMKTLSGSGA* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |