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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 | 2124908004 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0056628 | Gp0051177 | Ga0025758 |
| Sample Name | Poplar biomass bioreactor microbial communities from Brookhaven National Lab, NY - total biomass decay community |
| Sequencing Status | Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | Y |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 422235325 |
| Sequencing Scaffolds | 23 |
| Novel Protein Genes | 24 |
| Associated Families | 21 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 8 |
| All Organisms → cellular organisms → Bacteria | 6 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 3 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → unclassified Bryobacterales → Bryobacterales bacterium | 2 |
| All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Verrucomicrobiae → Verrucomicrobiales → Verrucomicrobia subdivision 3 → unclassified Verrucomicrobia subdivision 3 → Verrucomicrobia subdivision 3 bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Poplar Biomass Bioreactor Microbial Communities From Brookhaven National Lab, Ny |
| Type | Engineered |
| Taxonomy | Engineered → Solid Waste → Wood → Composting → Bioreactor → Poplar Biomass Bioreactor → Poplar Biomass Bioreactor Microbial Communities From Brookhaven National Lab, Ny |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | na → na → na |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | Upton, NY | |||||||
| Coordinates | Lat. (o) | 40.869444 | Long. (o) | -72.886667 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000911 | Metagenome / Metatranscriptome | 840 | Y |
| F001564 | Metagenome / Metatranscriptome | 670 | Y |
| F002247 | Metagenome / Metatranscriptome | 578 | Y |
| F004207 | Metagenome | 448 | Y |
| F006161 | Metagenome / Metatranscriptome | 380 | Y |
| F011112 | Metagenome / Metatranscriptome | 295 | Y |
| F012889 | Metagenome / Metatranscriptome | 276 | Y |
| F020087 | Metagenome / Metatranscriptome | 226 | N |
| F024403 | Metagenome / Metatranscriptome | 206 | Y |
| F029666 | Metagenome / Metatranscriptome | 187 | Y |
| F030027 | Metagenome | 186 | Y |
| F032176 | Metagenome / Metatranscriptome | 180 | Y |
| F044406 | Metagenome / Metatranscriptome | 154 | Y |
| F045708 | Metagenome / Metatranscriptome | 152 | Y |
| F046796 | Metagenome / Metatranscriptome | 150 | Y |
| F048052 | Metagenome / Metatranscriptome | 148 | Y |
| F056624 | Metagenome | 137 | Y |
| F063615 | Metagenome / Metatranscriptome | 129 | Y |
| F067044 | Metagenome / Metatranscriptome | 126 | N |
| F085858 | Metagenome / Metatranscriptome | 111 | Y |
| F094351 | Metagenome / Metatranscriptome | 106 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| PBDC3_contig11870 | Not Available | 775 | Open in IMG/M |
| PBDC3_contig12383 | Not Available | 1468 | Open in IMG/M |
| PBDC3_contig17320 | All Organisms → cellular organisms → Bacteria | 845 | Open in IMG/M |
| PBDC3_contig20969 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 857 | Open in IMG/M |
| PBDC3_contig21573 | All Organisms → cellular organisms → Bacteria | 529 | Open in IMG/M |
| PBDC3_contig31267 | All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia | 820 | Open in IMG/M |
| PBDC3_contig32960 | All Organisms → cellular organisms → Bacteria | 521 | Open in IMG/M |
| PBDC3_contig38816 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi | 507 | Open in IMG/M |
| PBDC3_contig73468 | Not Available | 1087 | Open in IMG/M |
| PBDC3_FIDWTPW02P9HH9 | Not Available | 506 | Open in IMG/M |
| PBDC3_FIDWTPW02PR0R3 | Not Available | 518 | Open in IMG/M |
| PBDC3_FIDWTPW02QIA0F | All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → unclassified Bryobacterales → Bryobacterales bacterium | 506 | Open in IMG/M |
| PBDC3_FIDWTPW02RBNCB | Not Available | 508 | Open in IMG/M |
| PBDC3_FIDWTPW02RM943 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 512 | Open in IMG/M |
| PBDC3_FIDWTPW02RMT7N | All Organisms → cellular organisms → Bacteria | 511 | Open in IMG/M |
| PBDC3_FISUTAU01BNWQ5 | All Organisms → cellular organisms → Bacteria | 507 | Open in IMG/M |
| PBDC3_FISUTAU01DI46C | All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon | 555 | Open in IMG/M |
| PBDC3_FISUTAU01EW7EF | Not Available | 542 | Open in IMG/M |
| PBDC3_FUFP16391_g1 | All Organisms → cellular organisms → Bacteria | 750 | Open in IMG/M |
| PBDC3_FUFP4423_b7 | Not Available | 661 | Open in IMG/M |
| PBDC3_FXFY4337_b1 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Verrucomicrobiae → Verrucomicrobiales → Verrucomicrobia subdivision 3 → unclassified Verrucomicrobia subdivision 3 → Verrucomicrobia subdivision 3 bacterium | 690 | Open in IMG/M |
| PBDC3_FXFY5848_g1 | All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → unclassified Bryobacterales → Bryobacterales bacterium | 748 | Open in IMG/M |
| PBDC3_scaffold01175 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 4386 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| PBDC3_contig11870 | PBDC3_05139340 | F046796 | MDILENILERISQTQEQRDVYLRQAEAEEGKIAKLESMYYLLEDPTTQELMKDMVVGLAVQNGVAVPNGNKGDGAEKHYVGMQRVREYVKQIAAGQTFTAHEVYTLSIAHRGHGDPKYQHPEFERQRIASISLALTSMTKGGDLEIVKQGRGRECTVYRRAEGK |
| PBDC3_contig12383 | PBDC3_03191840 | F011112 | VPAKPSWYSKIDEVIRQLEALPRPFVDRATVEFLLGVGRRRAQQIMAPCITDRVGANGLADRHALIERLRRFAVADDGYYERQRRRKMAEILAQLQKDRLERPQLLVEAPVEIINQDIEKLPAGVRLERGRITVEFDHAQQALEKLLALAMAIGNDFDWFERVTRHG |
| PBDC3_contig17320 | PBDC3_02065680 | F006161 | MALDSSFVAGVLAGMEGTLVELIDRVDIAELKASLDVLHSRVTALRVSIEPPAREPETEEESEPVAAETA |
| PBDC3_contig20969 | PBDC3_01402740 | F029666 | LGVSAYSFLDPGSSFPLPRSFDFAAYIETEREFWALFPETEGKRVNFCQTGLTAQIFIESRDDGSDLRPEETYFLMPCPDSTLRPIRMAPCRRLTLDEFRMSHLTALKLIDKLHDTARVMDEVHLRILGPEILDESEL |
| PBDC3_contig21573 | PBDC3_06652330 | F067044 | MKNSHLRMATLRFTKTVRDTMIDITVTVDRMIAEAGAKSEGAARCHLLSVIGGDQEVAAIAAAIADNGRFSV |
| PBDC3_contig31267 | PBDC3_04781920 | F012889 | MNMLQRHTQGLAHCPMCTHTVPAEIDIKGKIPRVARGAKCPRCGSSLEVAVVVQVPEAA |
| PBDC3_contig32960 | PBDC3_00785250 | F001564 | LCEPGLCPDAPEGGRCDHCPQDKLDAAQTSEAGLLIRRALDLRAALNLGVHIRLDDIPANEFYAMVILDEERDQLDRERTNPNGRQ |
| PBDC3_contig34470 | PBDC3_05658400 | F094351 | METPAESLNVEQLLNLHTLTKDVAKVCQKQLRSHLDTIALLFRPRRILGDAMEGAERES |
| PBDC3_contig38816 | PBDC3_07770610 | F085858 | QLAKPFPKNEKAEDPLIMRTDDMKEFSEVIRSKIIPTTFVFQCTLCGLEISDYDRHFGLIKMNQHVMSEHANQVKSLDMEDLYSRKPTVVLESF |
| PBDC3_contig73468 | PBDC3_00140860 | F030027 | QLDRLPLPGDPPIQPGVEHDNIRGAGYFDSPPEAEPPVIQ |
| PBDC3_FIDWTPW02P9HH9 | PBDC3_01467650 | F044406 | MLATALPVAAAGWAFLVWLFGGGFGLALVVFFVLKFWAGNADRR |
| PBDC3_FIDWTPW02PR0R3 | PBDC3_02268190 | F048052 | VSSVHRISEALAERVHSLHVEKKGSGGQAFLDVHVKRDLQPAELRSSQFYKMGDVVEFKDKGSGSVMRSPVTAVLPNAVVVARNDQPKQIPLTQVRAVFDSSRIERGSGETLLLQEKIKQGDRVFEKGSRQVIAEIKSSTVYFKSGLEL |
| PBDC3_FIDWTPW02QIA0F | PBDC3_01584980 | F002247 | IRELSGIGNVYLGTELVDIAEYELEVYEENPEDHEHHGSNWIPGTKKIRGTVTGELPIRKDLKLVTEEGYTLSFFLRDSMGSAVIVDSKLETTGNPVQ |
| PBDC3_FIDWTPW02RBNCB | PBDC3_04765720 | F044406 | MLATALPVAAAGWAFLVWLFGGGFGLALVVFFVLKVLGRYADRR |
| PBDC3_FIDWTPW02RM943 | PBDC3_07763530 | F029666 | PLIHLGVSAYSFLNPGSSFPLPRSFDFAAYIETEREFWALFPETEGKRVNFCQTGLTAQIFIESRDDGSELRPEETYFLMPCPDSTLRPIRMAPCRRLTLDEFRMSHLTALKLIDKLHDTARVMDEVHLRILGPEILNESEL |
| PBDC3_FIDWTPW02RMT7N | PBDC3_06389320 | F001564 | VGEWPEKPSLHYLVHWALRREELCDPGLCPDAPEGGRCDHCPQDKLDAAQTSEAGLLIRRALELRAALNLGVHIGLDDIPANELYAMLILEEERDQLDRERANAERR |
| PBDC3_FISUTAU01BNWQ5 | PBDC3_00021450 | F000911 | MSISMDRFVSKGGFASYDPHQNQPQRVAIFQLQCRCCGYEPEDPVVAPRVCPKCHSTSWERFARPGSILDNAQRY |
| PBDC3_FISUTAU01DI46C | PBDC3_01601130 | F032176 | MFAWSAQLKGSGKAQGVNATVNVTAKSMTPPKGVAASKDKAMLFTMTGDMAVARGMDLMKMVPGENPSSVGLWTFMSMSDKLGWLNDVIAVVTFE |
| PBDC3_FISUTAU01EW7EF | PBDC3_03161700 | F056624 | MSENTDQLHELERHCELCREDVRERIALVDRRLLALEIVVRGEDGRNGIKSQLNSLCLRFDAFEKKAIRWIAIGTALPGIVVAVLGILKFIGKL |
| PBDC3_FUFP16391_g1 | PBDC3_07378010 | F004207 | STLEDPTTLFEKTPILQALQASGSNNNLLDPGKQLILFDF |
| PBDC3_FUFP4423_b7 | PBDC3_08639750 | F063615 | MVLAFLMMRFLISMTRGWMMAVGITLPKPEQEKAVALIWVAAFVVMALIVVGVGWAVLSSMSGSVNYR |
| PBDC3_FXFY4337_b1 | PBDC3_03151080 | F045708 | MTELTKPIHRRTKDPFMHYRRRIVVSLEPGDVLSVRLEGTRTRYTAEIADVFRQLCTWHATAERRRKAEERKARRAK |
| PBDC3_FXFY5848_g1 | PBDC3_01538870 | F020087 | MPMTTVQNMYGRPFEILEGDDLRALCEQAIEAGGGALATNTAMMCRPFCASGAGNPIISAHRSPIPGFEWDEVWFGFEDFTSEEEFLRQHGYYGSGRCYIVVKVDGRKKLVALKDFIAHCPDIILGPALRALGHGMFRYSKFFINKNRLPHHTHDVKEEAYWIEPTMIVDYDLFDERCFMTLGLHQDFGPEQLRQYLTAGAWDDPAKALKQHARWFYMRPGNAMIMKTQNLHGPAALLPHYEPQF |
| PBDC3_scaffold01175 | PBDC3_00766340 | F024403 | MRILLRLDVFVYAAELALNALDLMPCGFRLLGIQLRSSGARQPPLRSIHNRHHYLQIA |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |