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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 | 3300013042 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0127392 | Gp0191749 | Ga0164268 |
| Sample Name | Enriched backyard soil microbial communities from Emeryville, California, USA - RNA 3rd pass 37_C BE-Lig BY (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 17601338 |
| Sequencing Scaffolds | 8 |
| Novel Protein Genes | 8 |
| Associated Families | 7 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 5 |
| All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea | 1 |
| All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata | 1 |
| All Organisms → cellular organisms → Eukaryota | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Unclassified → Soil → Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Emeryville, California | |||||||
| Coordinates | Lat. (o) | 37.83 | Long. (o) | -122.29 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F003009 | Metagenome / Metatranscriptome | 513 | Y |
| F005470 | Metagenome / Metatranscriptome | 399 | Y |
| F012845 | Metagenome / Metatranscriptome | 276 | Y |
| F024692 | Metagenome / Metatranscriptome | 204 | Y |
| F028375 | Metagenome / Metatranscriptome | 191 | Y |
| F069541 | Metagenome / Metatranscriptome | 123 | Y |
| F071833 | Metagenome / Metatranscriptome | 121 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0164268_103439 | Not Available | 561 | Open in IMG/M |
| Ga0164268_104047 | Not Available | 562 | Open in IMG/M |
| Ga0164268_114364 | Not Available | 956 | Open in IMG/M |
| Ga0164268_122500 | Not Available | 671 | Open in IMG/M |
| Ga0164268_122962 | All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea | 1642 | Open in IMG/M |
| Ga0164268_126020 | Not Available | 885 | Open in IMG/M |
| Ga0164268_129587 | All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata | 988 | Open in IMG/M |
| Ga0164268_129876 | All Organisms → cellular organisms → Eukaryota | 706 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0164268_103439 | Ga0164268_1034391 | F012845 | FWVWSFSFLASMKNHYLGLLLSFEETFLEGGLILKWKNTESWVNNFIAFCYEKGIGTRKNLAKAAQLYKKDIDQMPRVLYSRYRKVLVVKEKRAHGLQLSQEEENINVDEQAEDLKLKIEERLEDTTRMDCYLFYVYGKIYEKIDEDNDRAIEWYQKGVDVDTDSCLKNHLLCNEAWRLKCKKRLLK |
| Ga0164268_104047 | Ga0164268_1040471 | F071833 | TFQKPLPMNFAFEGTQDPQQKINFAQVLIKRKLIEPFEKLSRENVECYNLEKDAKEGNGQYIERVNKCLDAWQRHFEHVEEKTNKYLVSLREKEAHHFSKLFHCTNAINEPEIQACRREENERFANELKETFSQL* |
| Ga0164268_114364 | Ga0164268_1143641 | F028375 | LNKNFFIFIDPILNMMDISVTCEKWLASYPKFNWKSTFGFLQAPEVLKAIEFCDNGIACFVKGLQYEHDKDYHEALNCYENGAMQLDSLCLFRLHEIYSGDTNFGVEYNERQAMCHLAYSALLSQFETFDHKVTFWAKLEACWKKDAAHKDYLMELLNNPPADYLQSTGPLFAKLFTFYNNKETFIDLLPELKALSIDVTKNKFFAILNAIFDFMAYTYNSGFSKTDLEKYVETILDMLTNDILFENFFQNYVAHLRIIRAKKKFAFLFQRRLETDCFWVWSFSFLASMKNHYLGLLLSFEETFLEGGLILKWKNTES |
| Ga0164268_122500 | Ga0164268_1225001 | F069541 | KAFTMNLAAECKIWLNTYPKFNWKHTFDFLLSGESTKAVGFTDYGIACFVKGLQAELVDKDYNEAFSWYENGAMQLDALCLFRLHEIYIGDNNFKIEYNEEQAIVHLAYSALLCQFEVFDQKVSFWQKFDAFWKKDSAKTSYIQKLLLDPPAHYLIPTGPLFSKLLAFYNNKNSFLDVLPELKELSIDTMKNKFFPIVNALFDFLAYTYNSGFSKIDLEKYVE |
| Ga0164268_122962 | Ga0164268_1229622 | F003009 | LVWFQRNYFNLSILNLVKYFSTLTVAFHDIHSLFGFFIILVVMSQLVSGTMLSFSLVPEAMMVPIVRDEEDIEDLYTDDFF* |
| Ga0164268_126020 | Ga0164268_1260202 | F024692 | RFSGGCFRYSLPEFDSMGLCNSKAVDDEAPGTSAAQKSGGGAVSEAKDAATNDFRETLRTVILLILNRLATALEYEQEGFSELATKLEMKNYMQLCAPQHFEAVIKETWDLDKTPPEKPDVPADHISFAQNKFIKLLEAAEKADWRDPSISPQELTDRIQEAVKATQKILRDSAIASNSSDLKIHLFFFAKCLEVVDGDIATHHELLYSNIEDMTEPK* |
| Ga0164268_129587 | Ga0164268_1295871 | F003009 | TIFNLVRYFAVLSVSFHDVNSLFGFFILLTVFSQLVSGTMLSFSLIPEPMLVPIVRDEEDLEDLYTDDFF* |
| Ga0164268_129876 | Ga0164268_1298761 | F005470 | MSSIKLRKEGQLITEFPPEMVARSRLLTKLVEEFNSTEVDLEPAPGKDFSPATINKVKEFLEKFDKGLTKMPKKPLLIFVTYNDWLDNNFDEKLREWLEEFLKPKSFYDLVELFNAAFYLQIDDLREICAARIAHSIILERKAPEDFLRDFGIVTQYQDFFTPEEEAKFIEKEFINKNDFEGVAAEDEEELNKE* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |