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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 | 3300003704 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0103008 | Gp0088348 | Ga0008088 |
| Sample Name | Tropical rainforest soil microbial communities from the Amazon Forest, Brazil, analyzing deforestation - Metatranscriptome F II A1 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 4297753 |
| Sequencing Scaffolds | 25 |
| Novel Protein Genes | 25 |
| Associated Families | 20 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 20 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Flavobacterium → Flavobacterium antarcticum | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylosinus → unclassified Methylosinus → Methylosinus sp. C49 | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Geminisphaera → Geminisphaera colitermitum | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Tropical Rainforest Soil Microbial Communities From The Amazon Forest, Brazil, For Analyzing Deforestation At Different Spatial Scales |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Tropical Rainforest → Tropical Rainforest Soil → Tropical Rainforest Soil Microbial Communities From The Amazon Forest, Brazil, For Analyzing Deforestation At Different Spatial Scales |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | forest biome → tropical forest → forest soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Amazon Forest, Brazil | |||||||
| Coordinates | Lat. (o) | -10.0 | Long. (o) | -62.0 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F001633 | Metagenome / Metatranscriptome | 660 | Y |
| F001975 | Metagenome / Metatranscriptome | 609 | Y |
| F003787 | Metagenome / Metatranscriptome | 468 | Y |
| F015442 | Metagenome / Metatranscriptome | 254 | Y |
| F015698 | Metagenome / Metatranscriptome | 252 | Y |
| F017604 | Metagenome / Metatranscriptome | 239 | Y |
| F019442 | Metagenome / Metatranscriptome | 229 | Y |
| F021919 | Metagenome / Metatranscriptome | 216 | Y |
| F029031 | Metagenome / Metatranscriptome | 189 | Y |
| F031389 | Metagenome / Metatranscriptome | 182 | Y |
| F037756 | Metagenome / Metatranscriptome | 167 | Y |
| F044324 | Metagenome / Metatranscriptome | 154 | Y |
| F054015 | Metagenome / Metatranscriptome | 140 | Y |
| F056191 | Metagenome / Metatranscriptome | 138 | Y |
| F061003 | Metagenome / Metatranscriptome | 132 | N |
| F081396 | Metagenome / Metatranscriptome | 114 | Y |
| F082737 | Metagenome / Metatranscriptome | 113 | Y |
| F083351 | Metagenome / Metatranscriptome | 113 | Y |
| F098815 | Metagenome / Metatranscriptome | 103 | N |
| F099818 | Metagenome / Metatranscriptome | 103 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0008088_100190 | Not Available | 537 | Open in IMG/M |
| Ga0008088_100302 | Not Available | 583 | Open in IMG/M |
| Ga0008088_100594 | Not Available | 582 | Open in IMG/M |
| Ga0008088_100753 | Not Available | 553 | Open in IMG/M |
| Ga0008088_100901 | Not Available | 780 | Open in IMG/M |
| Ga0008088_101010 | Not Available | 750 | Open in IMG/M |
| Ga0008088_101083 | Not Available | 746 | Open in IMG/M |
| Ga0008088_101221 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia | 591 | Open in IMG/M |
| Ga0008088_101314 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 784 | Open in IMG/M |
| Ga0008088_101347 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Flavobacterium → Flavobacterium antarcticum | 545 | Open in IMG/M |
| Ga0008088_101387 | Not Available | 705 | Open in IMG/M |
| Ga0008088_101409 | Not Available | 511 | Open in IMG/M |
| Ga0008088_101655 | Not Available | 584 | Open in IMG/M |
| Ga0008088_101829 | Not Available | 601 | Open in IMG/M |
| Ga0008088_102176 | Not Available | 578 | Open in IMG/M |
| Ga0008088_102340 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylosinus → unclassified Methylosinus → Methylosinus sp. C49 | 611 | Open in IMG/M |
| Ga0008088_102351 | Not Available | 575 | Open in IMG/M |
| Ga0008088_102357 | Not Available | 616 | Open in IMG/M |
| Ga0008088_102482 | Not Available | 784 | Open in IMG/M |
| Ga0008088_103287 | Not Available | 562 | Open in IMG/M |
| Ga0008088_103296 | Not Available | 693 | Open in IMG/M |
| Ga0008088_103335 | Not Available | 533 | Open in IMG/M |
| Ga0008088_103597 | Not Available | 550 | Open in IMG/M |
| Ga0008088_103805 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Geminisphaera → Geminisphaera colitermitum | 577 | Open in IMG/M |
| Ga0008088_104354 | Not Available | 544 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0008088_100190 | Ga0008088_1001901 | F054015 | MRNRFEPSEDLRLVSGLANRSYPEGKRLPLRASTALVTLAVAPKRNLPNERRPTAGQSEHQRWEGHALEAGGVKTFRDVGDVEMNTAGL* |
| Ga0008088_100302 | Ga0008088_1003021 | F021919 | VPSDPISQPTPRRHATAQSYATRIAGRRPFGSPLPLFKDNGSTLPGSPASFSGWNRHLEATFRSPETTARFQATISRSKLPTCFFDTPPFAGQARSNSGSPTRYGSPRCARDRYRSPVARLAPDAPDPSSNLHSPLGSFGPCRIKAFDPIPGQEVHLLSAPDCPLLPAIDSILLVPMTDHRARLAKRSAACCSS |
| Ga0008088_100594 | Ga0008088_1005941 | F029031 | VQGTANLVSGSEPGTLIRWQTYKTERWRGAKGNRAEHKGELLKR* |
| Ga0008088_100753 | Ga0008088_1007531 | F029031 | HGTANLVSGNGPGTLIRRRTNKTERRRGAKGNRAECQGEPFEWQLG* |
| Ga0008088_100901 | Ga0008088_1009012 | F056191 | LCEARFRHALTAEMSETFPSGGSMHASVKLEGIDGRAPQERVEHVA |
| Ga0008088_101010 | Ga0008088_1010101 | F081396 | ERGLVAGSQGLEAGQEPRAGRSISGENDQASDRETLEIIAERDCDELDARSRAERTTTPSAGFEERHLEEAKPRRGSGPVGG* |
| Ga0008088_101083 | Ga0008088_1010832 | F017604 | MSKGCGGTAGDTSDDNPDPETPARSRGQVSRKGGWERGRLDEETRSPTRREAGDGRAEDQNRGRGQSPAGVVAWD |
| Ga0008088_101221 | Ga0008088_1012211 | F001975 | MAMASTSTSTQQDLQDQFLSIVSKSQEMALDAIKSMVDTVQTITPKIPAVDVPFADRLPKPQDVVANGYDFAQKLLSSQRKFADEVVKAAAPLLPGNGDSK* |
| Ga0008088_101314 | Ga0008088_1013141 | F001633 | GGTRLGTLAFAGGVLPDATLRGMRMFRSHGGTVLTVAGRDLSSEASAPGSDAPCRERHAGRGADTPATFVVARRHPYHGDGTGFWPIVGPALRV* |
| Ga0008088_101347 | Ga0008088_1013471 | F061003 | MSAREALVEGAKKATDASREQVYWYVGANDYWYEQLRRQPAALQELSSKVGKLSEVRLDSLRTTVSDTSKNVVNVLQEQLKVARDRRTELAARGEAITHDWYTSVAAQDASAFAAAVREAKNPVDLANAVRTWYWNFDAVTPGSPQPAAETKSDEPKVDEPKASPRKAAPTA* |
| Ga0008088_101387 | Ga0008088_1013871 | F044324 | GKLEREDHLGIDGLAGDGDTLWIIAAGHTQHRREKIVNGAGGNDIGEVIRAEPEGAGTHEGTRTVVGGNTTAVVADPGSDESFEVDASSAGARGNSGRTAAPTARKHRIVMSDRG* |
| Ga0008088_101409 | Ga0008088_1014091 | F019442 | TLRLLAPRYPLWAGTGSMPPDASQQVSRVGPDARDGLSLAHNDFRFHGCHSGVSAPGLPLRFLARWLDCPFGLSAPPPDPVRPSSGNFVASGPLQLLQLAWLTASPSSASLRGFYPLGINALLVLLPAGPPSEPARSPLAPRSLILLLVFQLRIIVPGPLRFRRLTVPQ |
| Ga0008088_101655 | Ga0008088_1016551 | F021919 | FQVTGFHSQTPRRHATAQSFAARITGHHPFRSPPRSLSRDGSILPGSPASFPGQDRYLEAAFHSPGTTARLRAAIPRSKLLTYFFDAPPDDHPARSNPGSPARSGSPRYARVLCLDSVA*LSLGGSSPSPDLHSPSGPFEPLRIKAFNPIPDRKVHLPSAPDCLSLPDLDSILLVSMPDHRSRLAKRSVARCSS |
| Ga0008088_101829 | Ga0008088_1018291 | F098815 | MRGQSLACSVVETLPVCSPLRLLSRIGSVRPSPSAVFLPARSHRLGTAFPLPCSSPATTVPFREPPRRGQSSWPIPSASISNLSSSPFGLELRPSAPFITSPGAFLAQNPLPAGRPKTLKRPSNVRSPLGLSSLRLSALGQRLNLRSLPLCPARFSFAPHKR* |
| Ga0008088_102176 | Ga0008088_1021761 | F029031 | GTASLASDSELGTLIRRRTNKIERRRGAKGDRVERKGEPSSGRLG* |
| Ga0008088_102340 | Ga0008088_1023402 | F099818 | MPMERRGWVIVVERGPTGSTGRSPQFQRKAAAFVRWHEPDDARVSRPESVRGS |
| Ga0008088_102351 | Ga0008088_1023511 | F082737 | FQVTLGASSLPNLHARFEPVTSSTPDPFRLAPRPRCFSVGASLLSARPASLPVRSQNLEAAFHSPTTTGLLPDDRGGVRVPALPLRLCDKVSVGPFRSDLHPWQVSRIAWDFCNQNPLPSDPMPLLPAALNRRSPSGFLALPDQSTRSRWPTGNLPSITPDHPSLPTGGLIRYQPADHRSGFATLLSARCS |
| Ga0008088_102357 | Ga0008088_1023571 | F083351 | MPGGALDSVGRPRSESCEREPGTREVRVHIVRLGGRHRSDASRVFSTGRSQGLLVNREGASQEEVR* |
| Ga0008088_102482 | Ga0008088_1024823 | F037756 | LFPVPTLGAHLAVAAGFPTLFSTASGVFGLVAGPFNVSRR* |
| Ga0008088_103287 | Ga0008088_1032871 | F003787 | K*SDFQHCSPPACTVLNIAIQSAGRLASPLPDNRFSITGSMLQDAPRTFS*LGPDARNGLSLVRYGSSLRSLHCGVNVPGLLLRFQLAASSARSALLLHYPCRLAPVRAASMLLARCSFRDSYEDRYFRPPLPFGTVTSLQINATARLTISRPAFRIRPISLRSPPPVSISSVSAADHRSRSATSSK |
| Ga0008088_103296 | Ga0008088_1032961 | F081396 | ERGLVTDSQESEAGQEPRAGRSISGENDQASDRETLKIIDERDCDELAERSRAGWMVTPSTGSEELHLEEVKPKRGSSPVGG* |
| Ga0008088_103335 | Ga0008088_1033351 | F015442 | MVAPGRGQSFQASERPLRGVSSKQELAAGGLGSVNPQPSKGGGGESTKSRSEILFAKLSAGHAGGERGCESD |
| Ga0008088_103597 | Ga0008088_1035971 | F015698 | PACTALSLVSRSAVRFCLSAPLVAFSRSPPGSRLPGAPLASSQTGPVARNGLSLPFNSRRSRGFHSRIHVPGLLLRHRRGYSPARSAFRSTALGGSPRSRPLPRFSPWPACCRARSAFAPASAPLWDSYLPLDRCVRLEPMPISPPSECARLLLAPHPRLPITSPGKRINARSSLRFRRLLFL |
| Ga0008088_103805 | Ga0008088_1038051 | F031389 | LTWLRGLAVRLVFAVGERKAASRNGLLPETEFADARRSFDPQPGKTGGGERRAYVTPSLDATLWPCMPAGEQAD* |
| Ga0008088_104354 | Ga0008088_1043542 | F054015 | MTLAVARKRNLPNERRPTAGQSEHQHREGHAIEAGFVKTFRHVGDVEMNTAGL* |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |