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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 | 3300031490 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0132857 | Gp0330687 | Ga0314825 |
| Sample Name | Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_R4 (Metagenome Metatranscriptome) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 23427689 |
| Sequencing Scaffolds | 15 |
| Novel Protein Genes | 17 |
| Associated Families | 16 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales → Prochloraceae → Prochloron → Prochloron didemni | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 2 |
| Not Available | 10 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States |
| Type | Environmental |
| Taxonomy | Environmental → Aquatic → Freshwater → Groundwater → Unclassified → Soil → Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | terrestrial biome → land → biofilm material |
| Earth Microbiome Project Ontology (EMPO) | Unclassified |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: Pennsylvania | |||||||
| Coordinates | Lat. (o) | 40.7997 | Long. (o) | -77.8629 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000203 | Metagenome / Metatranscriptome | 1619 | Y |
| F000344 | Metagenome / Metatranscriptome | 1257 | Y |
| F001633 | Metagenome / Metatranscriptome | 660 | Y |
| F004178 | Metagenome / Metatranscriptome | 449 | Y |
| F015651 | Metagenome / Metatranscriptome | 253 | Y |
| F017654 | Metagenome / Metatranscriptome | 239 | Y |
| F023352 | Metagenome / Metatranscriptome | 210 | Y |
| F029638 | Metagenome / Metatranscriptome | 187 | Y |
| F033437 | Metagenome / Metatranscriptome | 177 | Y |
| F053640 | Metagenome / Metatranscriptome | 141 | Y |
| F067982 | Metagenome / Metatranscriptome | 125 | Y |
| F070547 | Metagenome / Metatranscriptome | 123 | Y |
| F072453 | Metagenome / Metatranscriptome | 121 | Y |
| F080474 | Metagenome / Metatranscriptome | 115 | Y |
| F098003 | Metagenome / Metatranscriptome | 104 | Y |
| F099464 | Metagenome / Metatranscriptome | 103 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0314825_103430 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales → Prochloraceae → Prochloron → Prochloron didemni | 1027 | Open in IMG/M |
| Ga0314825_104994 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 823 | Open in IMG/M |
| Ga0314825_105166 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei | 808 | Open in IMG/M |
| Ga0314825_105305 | Not Available | 796 | Open in IMG/M |
| Ga0314825_105310 | Not Available | 796 | Open in IMG/M |
| Ga0314825_105530 | Not Available | 779 | Open in IMG/M |
| Ga0314825_106144 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia | 739 | Open in IMG/M |
| Ga0314825_107978 | Not Available | 648 | Open in IMG/M |
| Ga0314825_109111 | Not Available | 607 | Open in IMG/M |
| Ga0314825_110147 | Not Available | 577 | Open in IMG/M |
| Ga0314825_110747 | Not Available | 561 | Open in IMG/M |
| Ga0314825_112469 | Not Available | 519 | Open in IMG/M |
| Ga0314825_112565 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 517 | Open in IMG/M |
| Ga0314825_113115 | Not Available | 504 | Open in IMG/M |
| Ga0314825_113151 | Not Available | 504 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0314825_103430 | Ga0314825_1034301 | F033437 | VALSSRSLALDVIQQVWSFGSPDFPQTSRHSLFPGGTRLGALAFAGCVLPDATLRGMRMFRSHGGTVLTVTGRDLLSEASSPSSVAPCRERRAGRGADTSAILLRVGTLTTGTAPAFGWPLALRYGSGLLTLRLRSLLQCGGVVFHAAP |
| Ga0314825_104994 | Ga0314825_1049941 | F001633 | WGWAFVTRSFPAAHAWTRSLFAGGVLPDATLRGMRMFRSHGGTVLTVAGRELSSEASAPGSDAPCRERRAGRGVDTPATFIFRVGTFYRGVGISLWLIVGPALRV |
| Ga0314825_105152 | Ga0314825_1051522 | F000203 | GMGVRQTLFPAPTLGANKLAAGFPTLFSTASGVFGLVAGPSSASRSLDY |
| Ga0314825_105166 | Ga0314825_1051661 | F000344 | MRPKHPRDAESGVGKHTARESERVQACAAGKERVTNA |
| Ga0314825_105305 | Ga0314825_1053051 | F004178 | MRPRPPHAAESGVGEHTARESESAKQCAKEGARGER |
| Ga0314825_105310 | Ga0314825_1053101 | F023352 | MRPKHPLAAESGVGKHTARESEAPNCVPSGKSAWRTP |
| Ga0314825_105509 | Ga0314825_1055091 | F000203 | EFATLSFPMPALGAIQAAGFPTLFSTASGVLGLVAGPSRPLRELDY |
| Ga0314825_105530 | Ga0314825_1055301 | F029638 | VVLIQVQCVPSNLAGNNGGTVTIRKVDQFGQPLQASFSIQQGPFWVEVARVNLGSTLAQNPCATDGTQGTFNITGAGTSCANVGVISPAVFASGLPAGQYRIVEVAGPNSYCTLVQVYNGNQGQNQSGVLPFSGSLLTQPVTVNLPTANPLDVQLTFVNSCIVPGGASTATSQIAVVIGGSTPGLVNTSNIEIVPAPGSDDDARLDIRIRDSASIIIPNAHVTVLIDKGARALRRDLSGVSPASGYDVIEPNPGSNFAS |
| Ga0314825_106144 | Ga0314825_1061441 | F053640 | VAAQRSEMVAESTTGIIPGDRGKAGGNWCRPPLMPAKAVMRHISPVPLAGVVSGQSTHELGTEPQAAIRNRVEWSQATQGVSTCASTQLPQRLRLLLRRPERHRVSRRDDPAKRPHSPHEWGAQGTYGGGERTDLGKVREPPHRGGVKHTSPSCKRQRSLRGKRSDP |
| Ga0314825_107978 | Ga0314825_1079781 | F099464 | TPPPPAIRLIMSLHMLTRVAAAVALTVGIGAYVTADIKGDYNLEFVVQEAPYAGTLKTTAGAKGAFTGKLDFTSPSKVLSDVTGKTVGDSVTFEGKYEDQGRGCTGTLVARGTAEKDGSKASGVVDINDSCGGALAGTFRMWK |
| Ga0314825_109111 | Ga0314825_1091111 | F072453 | VIVLLNTLFIGGICVVLFLLNKKLNDALAKAEPVLIRATETLGRVEETTVRLQHKVDEVLDKATELVEQVSERVDTTTAIAEEAVTEPLIGAASLMAGINRGLRAYAERSHEKGDGRS |
| Ga0314825_110147 | Ga0314825_1101472 | F080474 | WQPIGSPFGLRLDLAYARLNGREASETGLGAQPDDPNIWSATANATLDLVRWGESRRGALYLVGGGGFFRFTDFYNFDRSDNDPESAFEGDPVTKGGLTGGAGLAFPIGRTSFFVESRYTTVDTEGTNTKWVPVVIGLKWR |
| Ga0314825_110747 | Ga0314825_1107471 | F015651 | KSSNLMALLDMAPSAFSGGEVSPLPKIKSLAALKAEVQKHFGKLSGQEVDALVGWFNRNFFRLDR |
| Ga0314825_112469 | Ga0314825_1124691 | F067982 | MRLRPTIAHGVLLALATGATSLPAQVTFKTTGYEIRDALSDVVHIWVSPFRSEKRDWLGVLGVAAGTAALVPIDDQIDSWIVRHPSAAIVQATNPWNEDHPELGDLSTGQRLLPISGVLIASGMVSGNRKLREAGWGCLSAWQSSSTVRQVLYATVSRERPS |
| Ga0314825_112565 | Ga0314825_1125652 | F017654 | LANRTNLKLNDIVVSQVEDGHHLLIVTAMPNDEMSLVYRGDGWNVQYAVAKGARLAAGKGGDLWYTADQLSTLEYLETFRAERSL |
| Ga0314825_113115 | Ga0314825_1131151 | F098003 | LLERYMSRTIRYAVLALAVAAISACSSSVTEPTVPKCTANSKNAPQSCVSLDYINPVV |
| Ga0314825_113151 | Ga0314825_1131512 | F070547 | MDNTSRRAFAARYTEPSGRRWVAEEVARLEMVVASIDGPAPRLVLRFTSEDSLCEQRFARCGPIGWTSPEIVEALFLSARPIRAVPEPQPPGGPRRRVTRPNR |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |