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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| Taxon OID | 3300033179 Open in IMG/M |
| Scaffold ID | Ga0307507_10000018 Open in IMG/M |
| Source Dataset Name | Populus trichocarpa ectomycorrhiza microbial communities from riparian zone in the Pacific Northwest, United States - 7_EM |
| Source Dataset Category | Metagenome |
| Source Dataset Use Policy | Open |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Sequencing Status | Permanent Draft |
| Scaffold Components | |
|---|---|
| Scaffold Length (bps) | 224203 |
| Total Scaffold Genes | 110 (view) |
| Total Scaffold Genes with Ribosome Binding Sites (RBS) | 70 (63.64%) |
| Novel Protein Genes | 15 (view) |
| Novel Protein Genes with Ribosome Binding Sites (RBS) | 10 (66.67%) |
| Associated Families | 11 |
| Taxonomy | |
|---|---|
| All Organisms → cellular organisms → Eukaryota → Opisthokonta → Fungi → Dikarya → Ascomycota → saccharomyceta → Pezizomycotina | (Source: UniRef50) |
| Source Dataset Ecosystem |
|---|
| Host-Associated → Plants → Roots → Unclassified → Unclassified → Ectomycorrhiza → Soil And Ectomycorrhiza Microbial Communities From Populus Trichocarpa Stands In Riparian Zones In The Pacific Northwest, United States |
| Source Dataset Sampling Location | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location Name | USA: Oregon | |||||||
| Coordinates | Lat. (o) | 44.5508 | Long. (o) | -123.25 | Alt. (m) | Depth (m) | Location on Map | |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000630 | Metagenome | 971 | Y |
| F002220 | Metagenome | 581 | Y |
| F004318 | Metagenome / Metatranscriptome | 443 | Y |
| F005943 | Metagenome | 385 | Y |
| F008074 | Metagenome | 339 | Y |
| F014479 | Metagenome / Metatranscriptome | 262 | Y |
| F016255 | Metagenome | 248 | Y |
| F020829 | Metagenome | 221 | Y |
| F037003 | Metagenome | 168 | Y |
| F041034 | Metagenome | 160 | Y |
| F094694 | Metagenome | 105 | Y |
| Protein ID | Family | RBS | Sequence |
|---|---|---|---|
| Ga0307507_10000018100 | F020829 | AGGA | MPLVSSKLITNIIFSIYGTPLTLGLYTLIIYTGPLYIWIIITTISRLTTCYNYKDRLTALLIIKHTYIAAFSLYRSWNP |
| Ga0307507_10000018107 | F004318 | N/A | VLSGLRLSLVSYIVLGLVLGLVLDIELVLDLGLGSLSILFIVEYQFF |
| Ga0307507_10000018109 | F041034 | AGCAG | MWFGIISRFLVDVGGILMLVEFGGILGLVELGGLFRYRVDFSRNFRLVDFSRFFRFRFRV |
| Ga0307507_1000001850 | F005943 | AGG | MLRDGGNSYRAYVFEESTRRCAIDRKGRGRKEVIYLRVADVSCTRGVRGSMGLSHGGPYGGVP |
| Ga0307507_1000001854 | F041034 | N/A | VDVGRNLILVEFGGILGLVELGGLFRYRVDVGRNFKLVDFGRFFKFRFRA |
| Ga0307507_1000001857 | F004318 | N/A | VLSKLKLSLVSYVVSYLGLGLVLSIELVLDLGSGSLSILFIIEY |
| Ga0307507_1000001858 | F002220 | AGG | MHPLKSNSVVKLSFSFSFAIRFAFTSSSSLRAENWLSPKIIILLVCMLTIPNGVPMVVIKKYRLNIKVVIKSFSL |
| Ga0307507_1000001859 | F008074 | AGAAG | LEYWLAAKIHNVNDDIEVKVVVIFKGKLESAKGLLVYLAVIVVLYKMLNCLNLDFMACLLKNPKQLVNGWVAKMMV |
| Ga0307507_1000001866 | F016255 | N/A | MPFFIPLNTSNSCLVKELNMRNVNNKIIKDAFKDALSFTNPLGSLLKELAF |
| Ga0307507_1000001867 | F000630 | GGAG | MGVKGTEANLSKRNLSRGIVNAIGGKHLRALKRPNKGRKYNSNTLKNRDNRTKRLALLDRCPSRQPKM |
| Ga0307507_1000001869 | F000630 | GGAG | MGVKGIEANLGKKNLSYSIVNAIGGRHLRALKRPNKGRKYNSNTFKNRNNRTKRLALLGKCTSR |
| Ga0307507_1000001877 | F094694 | AGCAG | VVSVLKVGLVYIVCKVLSKYIYLLTLTCIVAVVDFIGKFKCQLFYL |
| Ga0307507_1000001880 | F037003 | GAG | MEEIRKEQMVEGEIKEYVIKDEITEETVEVKRNYLSVPVMHYLQTIPSIERACKDIL |
| Ga0307507_1000001881 | F014479 | N/A | VGPEGFRLLSSSVVTVIEGVYVFLSVANNHRCIRVFKLLVHLGVRAYLAVLPKGLYCRNLLLLEGPSCLSATAVYKVFVEFPFRSSQDFKGG |
| Ga0307507_1000001898 | F000630 | GGA | MLKRRIGVKGTEANLGKRNLSHGIVNAIGGKHLRAPRRPNKGRKYNSNTLKNRDNRTKRLALLGRYSSRQPKMRI |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |