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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 | 3300025250 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0053073 | Gp0061144 | Ga0209026 |
| Sample Name | Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape CL_Col_mCL (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 192092261 |
| Sequencing Scaffolds | 22 |
| Novel Protein Genes | 24 |
| Associated Families | 22 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Xanthomonadaceae → Xanthomonas → Xanthomonas vasicola | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 1 |
| Not Available | 12 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Janthinobacterium → unclassified Janthinobacterium → Janthinobacterium sp. AD80 | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations |
| Type | Host-Associated |
| Taxonomy | Host-Associated → Plants → Roots → Epiphytes → Unclassified → Arabidopsis Root → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Host-associated → Plant → Plant rhizosphere |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | University of North Carolina, USA | |||||||
| Coordinates | Lat. (o) | 35.9082 | Long. (o) | -79.0499 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F023377 | Metagenome / Metatranscriptome | 210 | Y |
| F023612 | Metagenome / Metatranscriptome | 209 | Y |
| F027546 | Metagenome / Metatranscriptome | 194 | Y |
| F031516 | Metagenome / Metatranscriptome | 182 | Y |
| F033107 | Metagenome / Metatranscriptome | 178 | Y |
| F035339 | Metagenome / Metatranscriptome | 172 | Y |
| F036776 | Metagenome / Metatranscriptome | 169 | Y |
| F037289 | Metagenome / Metatranscriptome | 168 | Y |
| F039453 | Metagenome / Metatranscriptome | 163 | Y |
| F040711 | Metagenome / Metatranscriptome | 161 | Y |
| F044583 | Metagenome / Metatranscriptome | 154 | Y |
| F047761 | Metagenome / Metatranscriptome | 149 | Y |
| F058198 | Metagenome / Metatranscriptome | 135 | Y |
| F062899 | Metagenome / Metatranscriptome | 130 | Y |
| F067349 | Metagenome / Metatranscriptome | 125 | Y |
| F068208 | Metagenome / Metatranscriptome | 125 | Y |
| F076649 | Metagenome / Metatranscriptome | 118 | Y |
| F078153 | Metagenome / Metatranscriptome | 116 | Y |
| F080227 | Metagenome / Metatranscriptome | 115 | Y |
| F087885 | Metagenome / Metatranscriptome | 110 | Y |
| F092337 | Metagenome / Metatranscriptome | 107 | Y |
| F101290 | Metagenome | 102 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0209026_1009621 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 1879 | Open in IMG/M |
| Ga0209026_1015848 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales | 1230 | Open in IMG/M |
| Ga0209026_1016034 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Xanthomonadaceae → Xanthomonas → Xanthomonas vasicola | 1219 | Open in IMG/M |
| Ga0209026_1017084 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 1165 | Open in IMG/M |
| Ga0209026_1017977 | Not Available | 1123 | Open in IMG/M |
| Ga0209026_1017980 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium | 1123 | Open in IMG/M |
| Ga0209026_1019112 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales | 1076 | Open in IMG/M |
| Ga0209026_1019298 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Janthinobacterium → unclassified Janthinobacterium → Janthinobacterium sp. AD80 | 1069 | Open in IMG/M |
| Ga0209026_1019846 | Not Available | 1050 | Open in IMG/M |
| Ga0209026_1032203 | Not Available | 775 | Open in IMG/M |
| Ga0209026_1035919 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria | 726 | Open in IMG/M |
| Ga0209026_1036556 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium | 719 | Open in IMG/M |
| Ga0209026_1040924 | Not Available | 671 | Open in IMG/M |
| Ga0209026_1043283 | Not Available | 649 | Open in IMG/M |
| Ga0209026_1047765 | Not Available | 613 | Open in IMG/M |
| Ga0209026_1049044 | Not Available | 603 | Open in IMG/M |
| Ga0209026_1054608 | Not Available | 566 | Open in IMG/M |
| Ga0209026_1056436 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii | 555 | Open in IMG/M |
| Ga0209026_1058070 | Not Available | 545 | Open in IMG/M |
| Ga0209026_1060290 | Not Available | 533 | Open in IMG/M |
| Ga0209026_1060952 | Not Available | 530 | Open in IMG/M |
| Ga0209026_1064262 | Not Available | 514 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0209026_1009621 | Ga0209026_10096212 | F080227 | MQTRHLISSAALALALCAPAAFAAEACRTIVNGIQKCDVVTGQERSSADVAAEVHAKADTSTGCRTIVNGIQKCDVPTGHERSREDVVAELHGGSGDAIAGCRTIVNGIQKCDVPAAYQRGNETAIAGAPAAQRQ |
| Ga0209026_1015848 | Ga0209026_10158483 | F067349 | MPAPNRLSVLICAALAVATPLLAGARAWQLVDESPHAGVGYVLLYWPSLLLEQLPVPAAEAFQRSALPTVLLYFGGYLLLCQLARALWRLIR |
| Ga0209026_1016034 | Ga0209026_10160343 | F047761 | MDAITRLAALLIALLLAVDAFSAERTQTLRIDRHTRIARWHQGDDYRLHFVGGRAESCEVGWTVFNALSDGDLVSVDTSRVFKTCDGIRRGDEVISEARVHRWLLLLPMAVLLAAAFGWIRFERRYDDEPGWWFG |
| Ga0209026_1017084 | Ga0209026_10170842 | F040711 | MPTDSSRDRLASALGSDADHVVMERGFSLAFVGIDGQVRLTQFRLSKNGLDSDRAADDAVFATMLDEFTAVVERLLVARWGGIAMRAAFDGEGELVERLYEVGHLARCDAVDPVSPAGRLVKDGEVVDARELLVRASARLVENWGVFERAPALDDGAHPHEARIRRWIEGTQA |
| Ga0209026_1017977 | Ga0209026_10179773 | F062899 | MNSLAANRTTALPLPLPRGTAKHCSFVEDLNWPGAQPTPDKKPARPTEVWVPGPNGNWEGVTPTLQ |
| Ga0209026_1017980 | Ga0209026_10179802 | F023377 | MTHRPLRSPRALRMAMAAALLLAAAGAQAMTVSYQCTGRRVLTAELTPRKGQLHFEGKDWTVVRVPDKNMARYVSKKDEIEVLTKDRTLTFTHGAETLQCFLYSDALPGDAPLSK |
| Ga0209026_1019112 | Ga0209026_10191122 | F036776 | MNAIVRMLAVYTAFALLLCAMTQMEWSPLPPNGWGQWLALFLLIFPAAIVAELIGERLFGRGVPLDVEESKSHSDCSWARVFTGVAVLLVTVGVVLGAAWWLSHPAANI |
| Ga0209026_1019298 | Ga0209026_10192981 | F101290 | ADLPAAQSNSPEADASLYGQSVTLPRQAAVCAERIADYMPRFQKIYDLWVAQNAAQIAAGNKFIHQQAKVGGVDADAGMAKLGDADSDRLRKTSIELLARHCQLMLESMAPPAVN |
| Ga0209026_1019846 | Ga0209026_10198462 | F027546 | MKVAGESDPAPWQPLGERVARPQPVQPEWKPLAHAPCIEVNRQGQLRTNLPLPK |
| Ga0209026_1032203 | Ga0209026_10322031 | F092337 | ARFTISIRDTSDDELEAAAAAFVCTLHRSGLTPDDALDAWRRMDEWERLNFAADADPGEPWWRAMAIARDAVLAALHAAGIDGQRRPFMIEPASRPH |
| Ga0209026_1035919 | Ga0209026_10359192 | F033107 | MRLINSLALLTIGYLALKQVNKVHAARFEAKPAAKPEEVQTWEGEGGGLPTGGPGPGVKVAPAAVTDPDLAHGGA |
| Ga0209026_1036289 | Ga0209026_10362891 | F076649 | WIEEICSETFPATADANRHAYEVWLVDHGSFVQEIEGQFLIIDKYWGEASSQARKEGLTVEQLKARVDANKAGLRQDFQARGMRSFQARCEAYPEIMLSPQLDLERSQAELVRSVRLGPGATQ |
| Ga0209026_1036556 | Ga0209026_10365562 | F023612 | GLMLRAQEGTYPAHPAAEYALTSSHISTNSIHLLGDYWFFDPAHSNMGPTMSSLVGGFRASTGLVGLAQPLSLYESRPDPLQSLPYIGLGYSHLWFNSQLSLNADFGLASQAHGHGLLTSPSSLDEVTNQLRWAPVMAVNVRYSF |
| Ga0209026_1040924 | Ga0209026_10409241 | F080227 | MQTRHLLTSAALALAFCASGAFAADEGCRTVANGVQHCDVTTGHERTRDDVVADIHASADTATGCRTIANGVQKCDVITGHERSREDVVAELLGRSPSTYTIAGCRTVANGVQKCDVPTAAPRASDTAVAATHH |
| Ga0209026_1043283 | Ga0209026_10432831 | F058198 | FPLDKEAAMFELLLVLLVLAALAVRTFQLRHRIAAWESLWRFRSGPCTVELRRHADLARLGGDSLEFPQPREFRVVSLRIGGIPLWSQQAIISLPAEADARIAAIPASEFDHLFDRHFRMSWPRQATRLAARAHSHSH |
| Ga0209026_1047765 | Ga0209026_10477652 | F044583 | MSQLLTPDQEILRTRIRFALRRATGFVFDIDAMLRKPELRARRIGLWRDVATEELNSLLDQLETEFQHDAADDEDDADRTVVLRRPEAGVAHR |
| Ga0209026_1048191 | Ga0209026_10481911 | F068208 | DLMQPAGVEIYKTSDGHIRAIDLTSWDEPHSQQISNETAATVDDTCSLSGTQVAGAHTDYAGVYFAADLQNPVNSAYFYRLPGADGACNTADDVVHLVRTGMSPTDAPITVSAMPVATVRSASGGITGFVIKSGAQLVLVDNNFANPVTLGTFASTIGVAIALPVGTTQGYPTSQLFLVDGNIVSVNYASPSTSAPLFTIPGW |
| Ga0209026_1049044 | Ga0209026_10490442 | F101290 | EPAATSDSPEAEASLYNQSVTLPRQAAACAERIADYMPRFQRFYDAWRTENATRIANGGKFIHEQAAKGKVNADDGLAKLADQDVERLRKTSIEKLAKHCDLMLESLAPPAAN |
| Ga0209026_1054608 | Ga0209026_10546082 | F035339 | LSAEPLTLAQLRRDRRLVWAWLPIGGGAMFLVVKAWQHWAGEPPPSLYTTLDVVWIAITFSLIARRTTSRCPRCNHRWLRAFPWMSLRKVECGVCGHEMPEG |
| Ga0209026_1056436 | Ga0209026_10564362 | F087885 | RVASAVRKSCGAMISLSVRPGQTRDRATEPPLARASMFRAKRFITSVEIRLR |
| Ga0209026_1058070 | Ga0209026_10580701 | F039453 | MPAILTPLRGDAIRVTHEDVSYEPLERDAALGALLFALDLLGRDAFDVPALRYADRVALAPALDAARQYGLILQRHVARADRARPSLPASVKVDDAHAWVHEAAKAVPEAERDRFCWRLARRLGTNPWCDERPAIALDNQQFGMF |
| Ga0209026_1060290 | Ga0209026_10602902 | F037289 | MSMWISHQSVSLALVVATGWRALHHGATSLARPATLRRAQSGMARLITVVAGH |
| Ga0209026_1060952 | Ga0209026_10609521 | F031516 | DTAQMAAITQAHFFSRVAEFIRDQSGVAAYRHAAMDTTLRTELWAPHWPTLRESSEHDAALFMCFLLACATLGVDAHRAAETVRQATQPEMSMKLFLSERGLLRFSAFDVPDLTRPGAAG |
| Ga0209026_1064262 | Ga0209026_10642622 | F078153 | MGWIVFEAMLALAAMLVAVWWTFRGRAESVDDEAEAEERVER |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |