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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 | 3300023021 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0132900 | Gp0272157 | Ga0233354 |
| Sample Name | Soil microbial communities from Shasta-Trinity National Forest, California, United States - GEON-Q76 |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 38554106 |
| Sequencing Scaffolds | 36 |
| Novel Protein Genes | 39 |
| Associated Families | 37 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 6 |
| All Organisms → cellular organisms → Bacteria | 7 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 12 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia → Blastocatellales → Pyrinomonadaceae → Pyrinomonas → Pyrinomonas methylaliphatogenes | 1 |
| Not Available | 8 |
| All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Spiralia → Gnathifera → Rotifera → Eurotatoria → Bdelloidea → Rotaria → unclassified Rotaria → Rotaria sp. Silwood1 | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Soil And Plant Litter Microbial Communities From Temperate Forests In California, United States |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Unclassified → Forest Soil → Soil → Soil And Plant Litter Microbial Communities From Temperate Forests In California, United States |
| Alternative Ecosystem Assignments | |
|---|---|
| Environment Ontology (ENVO) | forest biome → solid layer → forest soil |
| Earth Microbiome Project Ontology (EMPO) | Free-living → Non-saline → Soil (non-saline) |
| Location Information | ||||||||
|---|---|---|---|---|---|---|---|---|
| Location | USA: California | |||||||
| Coordinates | Lat. (o) | 40.2197 | Long. (o) | -122.985 | Alt. (m) | N/A | Depth (m) | 0 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000236 | Metagenome / Metatranscriptome | 1499 | Y |
| F000265 | Metagenome / Metatranscriptome | 1420 | Y |
| F002204 | Metagenome / Metatranscriptome | 584 | Y |
| F006090 | Metagenome | 382 | Y |
| F008640 | Metagenome | 330 | Y |
| F009712 | Metagenome | 314 | Y |
| F012052 | Metagenome | 284 | Y |
| F014784 | Metagenome / Metatranscriptome | 260 | Y |
| F017152 | Metagenome | 242 | Y |
| F017410 | Metagenome / Metatranscriptome | 241 | N |
| F020517 | Metagenome | 223 | Y |
| F021060 | Metagenome | 220 | Y |
| F024393 | Metagenome / Metatranscriptome | 206 | Y |
| F024882 | Metagenome / Metatranscriptome | 204 | Y |
| F026727 | Metagenome / Metatranscriptome | 197 | Y |
| F028303 | Metagenome | 192 | Y |
| F038402 | Metagenome | 166 | Y |
| F038723 | Metagenome | 165 | Y |
| F041828 | Metagenome / Metatranscriptome | 159 | Y |
| F043999 | Metagenome / Metatranscriptome | 155 | Y |
| F046479 | Metagenome | 151 | Y |
| F049310 | Metagenome / Metatranscriptome | 147 | Y |
| F051828 | Metagenome | 143 | Y |
| F053496 | Metagenome | 141 | Y |
| F054123 | Metagenome / Metatranscriptome | 140 | Y |
| F060318 | Metagenome | 133 | Y |
| F061723 | Metagenome | 131 | Y |
| F068443 | Metagenome | 124 | Y |
| F070480 | Metagenome / Metatranscriptome | 123 | Y |
| F077644 | Metagenome | 117 | Y |
| F081682 | Metagenome / Metatranscriptome | 114 | Y |
| F083844 | Metagenome | 112 | Y |
| F084606 | Metagenome | 112 | Y |
| F087640 | Metagenome / Metatranscriptome | 110 | Y |
| F094582 | Metagenome | 106 | Y |
| F101406 | Metagenome / Metatranscriptome | 102 | Y |
| F105718 | Metagenome / Metatranscriptome | 100 | Y |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0233354_100006 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 13364 | Open in IMG/M |
| Ga0233354_100122 | All Organisms → cellular organisms → Bacteria | 5370 | Open in IMG/M |
| Ga0233354_100168 | All Organisms → cellular organisms → Bacteria | 4797 | Open in IMG/M |
| Ga0233354_100326 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 3760 | Open in IMG/M |
| Ga0233354_100495 | All Organisms → cellular organisms → Bacteria | 3214 | Open in IMG/M |
| Ga0233354_100597 | All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia → Blastocatellales → Pyrinomonadaceae → Pyrinomonas → Pyrinomonas methylaliphatogenes | 2982 | Open in IMG/M |
| Ga0233354_100617 | All Organisms → cellular organisms → Bacteria | 2924 | Open in IMG/M |
| Ga0233354_101986 | Not Available | 1511 | Open in IMG/M |
| Ga0233354_102113 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1454 | Open in IMG/M |
| Ga0233354_102293 | All Organisms → cellular organisms → Bacteria | 1369 | Open in IMG/M |
| Ga0233354_102859 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1194 | Open in IMG/M |
| Ga0233354_103499 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1058 | Open in IMG/M |
| Ga0233354_103701 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 1024 | Open in IMG/M |
| Ga0233354_103788 | Not Available | 1009 | Open in IMG/M |
| Ga0233354_103922 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 990 | Open in IMG/M |
| Ga0233354_104049 | All Organisms → cellular organisms → Bacteria | 972 | Open in IMG/M |
| Ga0233354_104452 | All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Spiralia → Gnathifera → Rotifera → Eurotatoria → Bdelloidea → Rotaria → unclassified Rotaria → Rotaria sp. Silwood1 | 919 | Open in IMG/M |
| Ga0233354_104758 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 884 | Open in IMG/M |
| Ga0233354_105143 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 848 | Open in IMG/M |
| Ga0233354_105947 | Not Available | 784 | Open in IMG/M |
| Ga0233354_106592 | Not Available | 743 | Open in IMG/M |
| Ga0233354_106907 | All Organisms → cellular organisms → Bacteria | 725 | Open in IMG/M |
| Ga0233354_107209 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 709 | Open in IMG/M |
| Ga0233354_107839 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 678 | Open in IMG/M |
| Ga0233354_109417 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 620 | Open in IMG/M |
| Ga0233354_109578 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 615 | Open in IMG/M |
| Ga0233354_110153 | Not Available | 598 | Open in IMG/M |
| Ga0233354_110405 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 590 | Open in IMG/M |
| Ga0233354_110683 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 583 | Open in IMG/M |
| Ga0233354_111394 | Not Available | 565 | Open in IMG/M |
| Ga0233354_112003 | Not Available | 552 | Open in IMG/M |
| Ga0233354_112338 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 544 | Open in IMG/M |
| Ga0233354_112393 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 543 | Open in IMG/M |
| Ga0233354_112458 | All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia | 542 | Open in IMG/M |
| Ga0233354_112993 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 531 | Open in IMG/M |
| Ga0233354_113378 | Not Available | 524 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0233354_100006 | Ga0233354_10000615 | F049310 | MSQWNVTPHDQAERARETAEARADLEQRAAEQGVKPFTSLEDFAGDPELTADFDVDEFLRMVRETRDTPSNRSMS |
| Ga0233354_100122 | Ga0233354_1001226 | F020517 | LKARKLIGRDIRHYLVKRPNHILTSSLSWNQVQAELKERGTEADEAMLFRGIVTLDGTEYRDKYADSRTHITEHVNEELG |
| Ga0233354_100168 | Ga0233354_1001685 | F000265 | MPELRGVQATPETKAEWKLAYSYYQEAPGDPYDKKNDRTERISYVARMMKLTRKQAKRRVRNFEAWQRNLKKGLVED |
| Ga0233354_100184 | Ga0233354_1001845 | F000236 | MQRKIFWITFLVLGLVADLTLPLWVSVAATIPIGVFSWWLAYRSEWFE |
| Ga0233354_100326 | Ga0233354_1003264 | F051828 | MENNQPVDLITTSEARLLLGVSAVKMAQLIKDGVVRHFPNPLDKRVKFISKREVLSLRPKRAEAA |
| Ga0233354_100495 | Ga0233354_1004951 | F002204 | MDEQERKPNISYQVRVTPGRLGQDPDAPDWEVCELEDGEIQDNSDIFDNMTQAEAKHIANMWTKKKEEAEAGKKEEAEAGG |
| Ga0233354_100597 | Ga0233354_1005975 | F094582 | GHSQHQGQLIGVETTAKPRYLPGNRQFYGTTYGHDAAADPFAAYLGRAGMVNGTRYAHNYPSLREFIRVVNEDWRGRSLLPDGYRVTVCPPAVFNLVGTIFHPEWSQTETLELGFYRDEQGNATCYAVGSNAPGDFSYIREVEGEDEWSLAGFRVALVPE |
| Ga0233354_100617 | Ga0233354_1006172 | F021060 | VWDTKRQIIWLVAGLALGTFVVYQDAHDEAGKFVPRFFAFMEMLLIIIIIVLFYIYSRKGRG |
| Ga0233354_101986 | Ga0233354_1019862 | F024393 | MPVKESSATALVRFTGLGIICFNKELRRGEIAAIRDQKHVLTIKIQQPVYQDGGGNDLIVYQDIATYQQLPKEDVQIEIKALHNPSIEGYEIYQSGDFDRLDSADVNDFRWLVNMNALHDDSELSPTGEQHYPLTKMYIGNGLFYTHKLDTNLFFEKVEKDAGGTAKQREVFGNVAETIGVKIEGDEVSFTIRIGGQEKTHTLRRVEGLPFKIEIINMDYSENAVYSDMADYYKYLSCPTGTRFDFTPMVEDADGQPTEGGSINQKTYCHPVVADDLSSIDEL |
| Ga0233354_102113 | Ga0233354_1021131 | F053496 | SGLLTFSVPGAAISVSVNGSVAWSSMKSVDPSTYRTGVFIDEKPELLRLAIGHLCEIGRASLDTISLALKLKVIRARARQLAPSYPAAETSGVPTEQYLLIQCVREELRLNPDEAMHWYRRARLMIADPATRTTAPAIANHPDALAVWEYLDRSIDPSIIGRTFQLP |
| Ga0233354_102293 | Ga0233354_1022933 | F008640 | MTAADLLGFTLKELKREIEDGAIVAVWTALGERMTREELVAVAMQKWEQSVIEAALGKDALSVLPEAIRLVELRARVPRYERDVLRALARREGTSVDAVLTRELEGVASAHAEELAGVPGLAMAMRWPETGVTG |
| Ga0233354_102859 | Ga0233354_1028591 | F068443 | RMLRAVRHVHRYPATDTKRGRPSQWKREDLLQVGTQLTALLERETTSHLSLSSFIDHYLRLLDFPADVIQALADGDINLFEAEQLARITPERLGVSSGQARHTRTDLLSTHLRTRLSGERLRQRVAELFRTSSAEAEDSVENDADFDLEDFDPYDPTHLFWDQIKQLGFALRDIRREDVEDEEIDELLIASESVLTILARIQKRKERKTVKLQI |
| Ga0233354_103499 | Ga0233354_1034991 | F054123 | LHSAPAPTVVCHSGTVSYKFVGAPGATFTYAGAKYSLPKSGWIELLSGHDDKAYLAANGRTLPLDVWPIDAFGTRTVPLQDASAVPATQNDSGPISTINN |
| Ga0233354_103701 | Ga0233354_1037012 | F041828 | LKLIEARGAYPDDLSLRGYTEILRTTIVRDFLAHPKAMQAVPKLTAEFLSNFDRFNLTAQEGYLISLIDGRLDLQKLLILSPFDPFTTLFNLAKLQEERAITVPK |
| Ga0233354_103788 | Ga0233354_1037881 | F070480 | MKRAFVAFAVLVVFTSMLLPSTAAASEAWILDIPTRGIPNQESGMVRVILELSAAPAGSQLVVNGTTLNLGGSANVAGDSVTYEALAGNNARITYIPLSNFGADFCAGTFSIEKQINMRFVGAQDITAYRMSTYIVAAPMAECSQVSKHTGDTPASLIPNDDGVAPALDATYKGRNTFDVALVLDKSGSMNDLPPGALNGPKKIDILKSAVQNF |
| Ga0233354_103922 | Ga0233354_1039221 | F043999 | ETTSRRRSGFGEIGGRGSGVGQRTPYSASRLPTPDSRLQDIIWNNEPPLNVELCAMEKPVRRTLLPGVTDAGAPPLVIIDSRAVVSRARRRAIVRDVIDLLLLVGVDGLFLRWPLAHVPFLDRYDSLLVLLGLNAMLVGYVWLARALPRWTARRVATTWSLPERARFFRRS |
| Ga0233354_104049 | Ga0233354_1040491 | F012052 | MPLTELEPQTLAQMPFKVLDETLRQLRSTRNDIIRYGVWNTRNLTDDEFNHADDRKLLGYFRQDLLETRFLSKGRRIDLIQLWHWFDDQMTGTEPMLINGEELFVNVQDKDLDKVRKRIAEIQSFLPTLRGD |
| Ga0233354_104452 | Ga0233354_1044521 | F105718 | MLLRWLVPISRFGLAALFLFTAGAKLAIVRAFALNVAELLSAAGINYSRWMWPATIAVIVAEIIAAALLLMPRTVRLGAVLAGLLLVGFSGFALYYVYALHGEPLEC |
| Ga0233354_104758 | Ga0233354_1047582 | F061723 | MSEETTQNIPGVDGRSFEERVFARFDAIDSRFDGVDSSLRALDSRLQTLESRAYDTKPIWEQALKEIMDTRRELSKRLDRIEAIAHETRADLRDAEDRIERLESKPAQ |
| Ga0233354_105143 | Ga0233354_1051431 | F014784 | YFNIEWHIIPSAAALPLDDAYMARLYPSAPRHFKRTREHAPSYRDQLVKGHEKLQGRVVGVETTVKPRYLPGNRQFYGTAYGHDASADPFAAYMGRAGMENGTRYAHNYISLRAFLRVVNDDWRARALLPAGYRVTVCPPAVFNLVGTVFHPEWSETETLELGFYRDEQGNATCYAVGSNAPGDFSYIAEVEGEGEWSLTGFRLALVPPE |
| Ga0233354_105865 | Ga0233354_1058651 | F017152 | PMTPEILRNAVAAALSRQPRVSEITATSTQDVSAGPLIQTMTMNGFTIFDSESAAQEPDVRRFIVKSPGGDEHAVLVRIDEEAVGYAERMTKRRLPPESSFWTTQALRLLSDYLWKEGRVPPTRKLTVKDIDRDELPIAARW |
| Ga0233354_105947 | Ga0233354_1059472 | F081682 | MVEGEMAIMSVETVDDGVLRAYFRRQGATDWCYVDGKNLGKLSQVTLPKFDPNEEIEYYFIVLDNDGKRVVAKSPRIYNARNDHRCDAAYARHATMVTLECLPPGTNPISRSLAAGYAIKTTIGKDPSLPQSPEKPGEPPRPGAGQD |
| Ga0233354_106592 | Ga0233354_1065922 | F087640 | MALETWPLHQIEAALGADADGVLPRAIRTKELRVRLPRHHVDMLEYRAEQGRTTVSGVLARELDGIASSQADELSAAIPGFAEALAWPDGELTMRPC |
| Ga0233354_106907 | Ga0233354_1069071 | F009712 | MSALVGRLFQLIGMIILPIGLLTGLLKDNVSMEVRLLFIGGAIFLIGWLMAKKTAS |
| Ga0233354_107209 | Ga0233354_1072092 | F084606 | MKKMIPLFLFLTVTLTVTNVFAHAGHIHTYMGTVTMLHTDTQFMMKTSDGKDLAIDTTAATSWLDAKGHAAKKNDLAVGSRVVVKMNIDGKTAASVTMASPPKAQAR |
| Ga0233354_107839 | Ga0233354_1078393 | F038402 | MAMLITFPDESTELIPQAVTVDQQNFHEGMYDFYDERGVLLRQIDMHGRIRWALVDEPEGETQQSK |
| Ga0233354_108670 | Ga0233354_1086701 | F028303 | MAKVTAEIPGELSRQIDRVIRDGWFPDQDTLVREALSHFVDAKSFLGDSPRMLHRFA |
| Ga0233354_109417 | Ga0233354_1094172 | F024882 | MPCDHVGPTELIEMAETHLRERALPPANGMRFRWSENPAGGMWASVVTEIERRGEQWVVTRIDRNREPVSDGETGFRPL |
| Ga0233354_109578 | Ga0233354_1095782 | F026727 | PTVAGIIKWAKRAPDQCPLPHAYMGDLLRFNRDEANQWAKEEAERRRVHSERRRLKIA |
| Ga0233354_110153 | Ga0233354_1101531 | F017410 | PKKPQAKIQTVKKQIPVKKIAPDRVEELVKKHLGNIGEAENAFKSASALLEKHKTNYPELEQYIEHVSPSDRSIQMLDDVKDPRRSHYVFKILLTGVEPAYQIAHPGEKDHTNVDRAAWISTFEEALAKTIVHIVLSRQAEQTSQAVGVGALKE |
| Ga0233354_110405 | Ga0233354_1104051 | F046479 | MIERLGMLSLLLLSTLVASALAADVTGTWRVTISTSDGAITGKASLKQTGEVVTGWVGPDENDPIPVTGILKGNKLTIKTSPQPGRTAAFDRCDLIVNGDKMVGTIDTNKGKIEFVRVRP |
| Ga0233354_110683 | Ga0233354_1106831 | F006090 | KEVLVGPNPDAAKVKGVMFGGRKQLLNDVAGEEGFAAIVAKLSPRTASYTKTPLASSWCEFASIIELDRTIHETLKQKHPNILALIGASSAELGIGRVYKSLDSTELVNFLESQALFHNQFQKFGNVRFEKTPNGGRMICSDYPVYSPIYCASGVGFYLESILRHGGSDPSVVETKCQTLGDAFCSFEMAWR |
| Ga0233354_111394 | Ga0233354_1113941 | F083844 | NTISRLSLRKKLTILAAVGVFLPVLLLTYMQYQSLTELQNKTKGAFKDNLRQGFTILQRQMKQRLEEVAAQTLNPAGSPQLSSGSSLSSLGGAEELEKHFANVKRSHPEIEEIFAFVYPDGKQETKAQAYFYSDKFVKTAGSEFTPAQSHLLSLFEKARMAQSFLDDNRNYLLLYDSCPTCPPDMREG |
| Ga0233354_112003 | Ga0233354_1120031 | F038723 | MSDDVTKVQRFDLLSSSESGLSYVREKRGGTMRVLTESELADFNDPPPCPQCAEQFGCEHFNCAGEPMLAEDDIEASAPPEWLAFAKACGISREDLDRLKLIEQHEGEYRVAAGADMRTQELALLLNEE |
| Ga0233354_112338 | Ga0233354_1123382 | F077644 | TDEQSLAGRGITSALEKIAEDARAMRDSLDRQLQETDRIADASKAMLEIAQVNDGIAREFNTTVQSLVTSGRDFESEVSKFRFTRDS |
| Ga0233354_112393 | Ga0233354_1123932 | F101406 | TDRMLKVSRGFVASLFGIGMTLLAWFGSWAWPGWPASLALDVLGKYADFPDLPRPVKGTVVVLLIIINVGTWAALIRAAMLLIPRRAEA |
| Ga0233354_112458 | Ga0233354_1124582 | F060318 | LLRIAAYLSQPQQFMAVADARAEMRRTLEMTAKGSVVLTTHGEPEAAVVPFTTLEDMRSALMQLLVTEIEGSFTRTQEQARLDADAAPTTSDEELESLVGDAIRTARQRGKNSSERKASR |
| Ga0233354_112993 | Ga0233354_1129931 | F017152 | ATGTSASQGVSTEPLIEIITMNGFTILESEGARQVPDERHFTVKSPNGDEHEVLVQINEEAVGYVERMTKRRLPPENSFWTLQAQRLLSDYLWKEGKVPPTKRLMVKDVDRDEIPIAARW |
| Ga0233354_113378 | Ga0233354_1133781 | F087640 | EIWPMHVIEEALGDDADGILPQAIRSAELRVRLPRHHIDMLHYRADQQETTVSGVLERELDGIASAHIEELSAALPGFAEAMAWPG |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |