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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 | 3300020602 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0116272 | Gp0236372 | Ga0213500 |
| Sample Name | Leaf-associated microbial communities from Abies magnifica in Yosemite National Park, California, United States - Redfir_Yose_2 |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 727303767 |
| Sequencing Scaffolds | 37 |
| Novel Protein Genes | 39 |
| Associated Families | 5 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| Not Available | 28 |
| All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta | 4 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Pseudoalteromonadaceae → Pseudoalteromonas → unclassified Pseudoalteromonas → Pseudoalteromonas sp. CR1 | 1 |
| All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Staphylococcaceae → Staphylococcus → Staphylococcus aureus | 1 |
| All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Acrogymnospermae → Pinopsida → Pinidae → Conifers I → Pinales → Pinaceae → Picea | 1 |
| All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Bacteroidaceae → Bacteroides → Bacteroides uniformis | 1 |
| All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Above-Ground Endophytic Microbial Communities From Plants In Different Locations In The United States |
| Type | Host-Associated |
| Taxonomy | Host-Associated → Plants → Phylloplane → Unclassified → Unclassified → Leaf → Above-Ground Endophytic Microbial Communities From Plants In Different Locations In The United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | Unclassified |
| Earth Microbiome Project Ontology (EMPO) | Host-associated → Plant → Plant surface |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: California | |||||||
| Coordinates | Lat. (o) | 37.6622 | Long. (o) | -119.6197 | Alt. (m) | N/A | Depth (m) | N/A | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F011735 | Metagenome / Metatranscriptome | 287 | Y |
| F023843 | Metagenome / Metatranscriptome | 208 | Y |
| F034461 | Metagenome / Metatranscriptome | 174 | Y |
| F065766 | Metagenome / Metatranscriptome | 127 | Y |
| F078199 | Metagenome / Metatranscriptome | 116 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0213500_10011094 | Not Available | 1200 | Open in IMG/M |
| Ga0213500_10013440 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta | 1128 | Open in IMG/M |
| Ga0213500_10016904 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Alteromonadales → Pseudoalteromonadaceae → Pseudoalteromonas → unclassified Pseudoalteromonas → Pseudoalteromonas sp. CR1 | 1049 | Open in IMG/M |
| Ga0213500_10022942 | Not Available | 957 | Open in IMG/M |
| Ga0213500_10026033 | Not Available | 922 | Open in IMG/M |
| Ga0213500_10031090 | Not Available | 876 | Open in IMG/M |
| Ga0213500_10043300 | All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Staphylococcaceae → Staphylococcus → Staphylococcus aureus | 796 | Open in IMG/M |
| Ga0213500_10046828 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Acrogymnospermae → Pinopsida → Pinidae → Conifers I → Pinales → Pinaceae → Picea | 779 | Open in IMG/M |
| Ga0213500_10049766 | Not Available | 765 | Open in IMG/M |
| Ga0213500_10052038 | Not Available | 755 | Open in IMG/M |
| Ga0213500_10058759 | Not Available | 730 | Open in IMG/M |
| Ga0213500_10065848 | Not Available | 708 | Open in IMG/M |
| Ga0213500_10067095 | Not Available | 704 | Open in IMG/M |
| Ga0213500_10070651 | All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Bacteroidaceae → Bacteroides → Bacteroides uniformis | 694 | Open in IMG/M |
| Ga0213500_10071793 | Not Available | 691 | Open in IMG/M |
| Ga0213500_10076476 | Not Available | 679 | Open in IMG/M |
| Ga0213500_10090755 | Not Available | 648 | Open in IMG/M |
| Ga0213500_10097215 | Not Available | 636 | Open in IMG/M |
| Ga0213500_10107881 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta | 618 | Open in IMG/M |
| Ga0213500_10119950 | Not Available | 600 | Open in IMG/M |
| Ga0213500_10120334 | Not Available | 599 | Open in IMG/M |
| Ga0213500_10122068 | Not Available | 597 | Open in IMG/M |
| Ga0213500_10125360 | Not Available | 592 | Open in IMG/M |
| Ga0213500_10134549 | Not Available | 581 | Open in IMG/M |
| Ga0213500_10134638 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta | 580 | Open in IMG/M |
| Ga0213500_10135624 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta | 579 | Open in IMG/M |
| Ga0213500_10162961 | Not Available | 550 | Open in IMG/M |
| Ga0213500_10172464 | Not Available | 541 | Open in IMG/M |
| Ga0213500_10176763 | Not Available | 537 | Open in IMG/M |
| Ga0213500_10181589 | Not Available | 533 | Open in IMG/M |
| Ga0213500_10182073 | Not Available | 532 | Open in IMG/M |
| Ga0213500_10191338 | Not Available | 525 | Open in IMG/M |
| Ga0213500_10211881 | Not Available | 510 | Open in IMG/M |
| Ga0213500_10214297 | Not Available | 508 | Open in IMG/M |
| Ga0213500_10215450 | All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta | 507 | Open in IMG/M |
| Ga0213500_10217386 | Not Available | 506 | Open in IMG/M |
| Ga0213500_10222077 | Not Available | 503 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0213500_10011094 | Ga0213500_100110942 | F034461 | LEQQLLSKEKIWVTKIIGYDFEIIYKKWKQNVVANAFSMNYEDVEELLFVISL |
| Ga0213500_10013440 | Ga0213500_100134403 | F011735 | MWHGPYIISEVLGKGAYELVNHNGTYLGEPQNGIYLKCYYAWT |
| Ga0213500_10016904 | Ga0213500_100169042 | F011735 | LWLGPYVVKRVLQKGAYELVDFEGIPLVEPINGLYLKKYYA |
| Ga0213500_10022942 | Ga0213500_100229422 | F011735 | MWLGPYIVNHVLGKGAYELINYEGNILKRPRNGLYLKK |
| Ga0213500_10026033 | Ga0213500_100260332 | F011735 | IIKWELQKGAYELVDFEGIPLAEPKNGLYLKKYYV |
| Ga0213500_10031090 | Ga0213500_100310901 | F065766 | MAEEKRDKEAGDPIKMFLEEAFVRQQNKIMDSFAQILR |
| Ga0213500_10043300 | Ga0213500_100433001 | F078199 | MLGYDFEIIYKKEKHNLVAYTLSKKNEDVGGLLCAISLP |
| Ga0213500_10046828 | Ga0213500_100468283 | F011735 | MWLGPFIISKVLKKGAYELIDYEGNKLVEPRNGIYLKNYFA |
| Ga0213500_10049766 | Ga0213500_100497661 | F065766 | MAEETRYDEAGDPIKMLLEEALAQQRNEMMDNFTQIL |
| Ga0213500_10052038 | Ga0213500_100520381 | F065766 | MEDENRDDGAGYLIKMFLEEALTQQRNEMMDNFTQILRRMLAATKE |
| Ga0213500_10058759 | Ga0213500_100587591 | F011735 | IIKRVLQKGAYELVDFEGIPLNEPRNGLYLKRYYA |
| Ga0213500_10065848 | Ga0213500_100658481 | F011735 | MWLGPYIVSKVLKKVAYKLTDYEQNKLSEPRNGLDLKKYYA |
| Ga0213500_10067095 | Ga0213500_100670951 | F011735 | MWLVPYIVSKVLKKGSYELTNYEGDKLVEPRNGLYLKKYY |
| Ga0213500_10070651 | Ga0213500_100706511 | F011735 | MWLVPYIVKRVLGKGAYELIDYEGNVMKKPKNGLYLKKYFS |
| Ga0213500_10071793 | Ga0213500_100717931 | F011735 | MWHGPYIVDKLLEKGAYELVNYDGTSLGEPRNGIYLKR |
| Ga0213500_10076476 | Ga0213500_100764761 | F011735 | GPYIIKIVLQKGAYELVYFEGLPLAKPRNGLYLNKYYA |
| Ga0213500_10090755 | Ga0213500_100907551 | F011735 | IGLYIISKVLKKGAYEFMDYKGNKLVEPRNGLYLKKYYA |
| Ga0213500_10097215 | Ga0213500_100972152 | F011735 | LWLGPYIIKRALEKGAYELVDFDRIPLAEAINGLYLKKYYA |
| Ga0213500_10107881 | Ga0213500_101078812 | F011735 | MWIGMYIVSKVLKKGAYELTDYEGNKLAEPRNGLYLKKYYA |
| Ga0213500_10115027 | Ga0213500_101150272 | F023843 | VNDFRVDIEKFNGQNFELWKLKMEDLVVEKEQWSYVDLDTKPIVMSKDDW |
| Ga0213500_10119950 | Ga0213500_101199501 | F011735 | LLGPYIVKRELQKEAYELLDFEGIPLAEPRNGIYLKKYYA |
| Ga0213500_10120334 | Ga0213500_101203341 | F011735 | MWIGPYIVSRVLKKGAYELTDYEGKKLVEPRNGLYLKKYYP |
| Ga0213500_10122068 | Ga0213500_101220682 | F011735 | PYIVNKVLEKGAYELVDYDGISLGEPQNGLYLKRYYA |
| Ga0213500_10125360 | Ga0213500_101253601 | F011735 | IIGKVLEKGAYKLINHDGTSLGEPQNGLYLKRYYA |
| Ga0213500_10134549 | Ga0213500_101345492 | F011735 | SESMWHGPYIIKQVLKKRAYELVDYDGIPMGEPWNELYLKNYYA |
| Ga0213500_10134638 | Ga0213500_101346381 | F034461 | MLGYDFEIIYKKGKKNVVADALSXKDEDVEVLLHAMSILQPSWITEARDEWQN |
| Ga0213500_10135624 | Ga0213500_101356243 | F078199 | MLGYDFEIIYKKGKQNLVAYALSRKHEDIEGFLCAIS |
| Ga0213500_10162961 | Ga0213500_101629611 | F023843 | MESSSRIKIEKFNGQSFELWKLKMEDILVDREQWIAIDPCTMSTGMVKEDWEQLDRKEKSTI |
| Ga0213500_10172464 | Ga0213500_101724641 | F011735 | MWHGPYIVDKVLEKEAYELVKYDGTSLGKLGNGLYLKRYYA |
| Ga0213500_10176763 | Ga0213500_101767632 | F011735 | FQSMWLGPYIIKWVLQRGAYELVDFEGIPLNEPRNGLYLK |
| Ga0213500_10181589 | Ga0213500_101815891 | F011735 | MWHDPYIVDKVLEKGAYELVNYDGTSLGEPCNGLYLKQYYA |
| Ga0213500_10182073 | Ga0213500_101820732 | F011735 | MWIGPYIDSRVLKKGAYKLTDYEGNRLDEPRNGLYLKKYYA |
| Ga0213500_10189496 | Ga0213500_101894962 | F011735 | LGLGKFKSMWLGSYIMSRVSKKGDYELTDYEGNRLDEPRNGLYKKKYYV |
| Ga0213500_10191338 | Ga0213500_101913381 | F011735 | MWLGPYIVKHVLGKGAYELVDYEGNAMKRPINGLYLKKYFS |
| Ga0213500_10211881 | Ga0213500_102118811 | F011735 | GKFVSMWLGPYIVKRLLGKWAYELVDYEGNVLPRPRNGLYLKKYFA |
| Ga0213500_10214297 | Ga0213500_102142972 | F078199 | MLGYDFEIIYNKGKQNVVANALLRKHEDIEGFLYAISLPQS |
| Ga0213500_10215450 | Ga0213500_102154501 | F011735 | MWIGPYIVSKVLQKGAYELTDYEGNKLEEPRNGLYLKNYYA |
| Ga0213500_10217386 | Ga0213500_102173861 | F023843 | VSSSRVEIEKFNGQNFESRKLKMEDLLVDKKRWVVVDLGTKPTAMSQEEWNK |
| Ga0213500_10222077 | Ga0213500_102220771 | F011735 | LGPGKFKSMWIGLYIVSKVLKKGAYELTDYEGNKLAEPRNGLYLKKY |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |