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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |
| Basic Information | |
|---|---|
| Taxon OID | 3300021320 Open in IMG/M |
| Scaffold ID | Ga0214544_1005990 Open in IMG/M |
| Source Dataset Name | Root nodule microbial communities from cowpea collected in UCLA plant growth center, Los Angeles, California, USA - CNSS3 |
| 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) | 22934 |
| Total Scaffold Genes | 29 (view) |
| Total Scaffold Genes with Ribosome Binding Sites (RBS) | 21 (72.41%) |
| Novel Protein Genes | 7 (view) |
| Novel Protein Genes with Ribosome Binding Sites (RBS) | 6 (85.71%) |
| Associated Families | 7 |
| Taxonomy | |
|---|---|
| All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fabales → Fabaceae → Papilionoideae → 50 kb inversion clade → NPAAA clade → indigoferoid/millettioid clade → Phaseoleae → Vigna → Vigna unguiculata | (Source: UniRef50) |
| Source Dataset Ecosystem |
|---|
| Host-Associated → Plants → Rhizosphere → Unclassified → Unclassified → Root Nodules → Root Nodule Microbial Communities Of Legume Samples Collected From Usa, Mexico And Botswana |
| Source Dataset Sampling Location | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location Name | USA: California | |||||||
| Coordinates | Lat. (o) | 34.06 | Long. (o) | -118.44 | Alt. (m) | Depth (m) | Location on Map | |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F005662 | Metagenome | 393 | Y |
| F007299 | Metagenome | 353 | Y |
| F019604 | Metagenome | 228 | Y |
| F026490 | Metagenome | 197 | Y |
| F044323 | Metagenome | 154 | Y |
| F046863 | Metagenome | 150 | Y |
| F053100 | Metagenome | 141 | Y |
| Protein ID | Family | RBS | Sequence |
|---|---|---|---|
| Ga0214544_100599010 | F053100 | GAG | VWYTSPPALSDMSCRSRVICVGMLAELARCDTLVPQPLSVMNSVKAKKW |
| Ga0214544_100599012 | F019604 | AGG | VKEEGKPYFLDADGSTKFPFSWTSSPSRYKDMGMDELSAGDKEVVEILMKFVDKLPTKGLISVYNSVHLIIDIEGICLLLKLC |
| Ga0214544_100599013 | F007299 | AGG | VQSGKKNLALFQSLRKEMAAKAKVARNTDVPNLQESMVEVHVHGGTKRKVELPPRHGKGKDVKRARAVLLGTGSASGAGLASGDKGPESNLIELPERSVRKDIAINLPDTIINSIDNMEADHIVRTMVEFGSKALILSHRVGSLYRREVKEGGREKMEEL |
| Ga0214544_100599022 | F044323 | N/A | VEVDVAAGGNLFAREAKYWFIIRDHSGVQKLEFLVGGPVEDVNGATLVNRDFLNGVVFDFNRDDHGVILLVVEAMKVVLYEDDGRHVASVVGMGDMVDGLDMTKVSLSGKRGGSSTSEATRDGVDGAT |
| Ga0214544_100599025 | F046863 | AGG | VVGKALQNTASWDVYRATWVIDFEVLIRVGFASIAIQGEGFPLGRKRGVGDEVGEWVATSALVGREQMGWDGMVDHSGEGGDKVVRGDVGCWKVLRVVWWDMCGV |
| Ga0214544_100599029 | F026490 | GGA | MKCSGNEDKSKKNSRQWRFLVKMKSKSGAMVWKVARGDEREG |
| Ga0214544_10059904 | F005662 | AGG | MCLVVGHMMGMELVEFPSTTNGRGVLSMVITCVGHTMGKELLCSRRLLLGEESIVW |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |