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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 | 3300026858 Open in IMG/M |
| GOLD Reference (Study | Sequencing Project | Analysis Project) | Gs0075432 | Gp0054322 | Ga0207729 |
| Sample Name | Tropical forest soil microbial communities from Luquillo Experimental Forest, Puerto Rico - Sample 69 (SPAdes) |
| Sequencing Status | Permanent Draft |
| Sequencing Center | DOE Joint Genome Institute (JGI) |
| Published? | N |
| Use Policy | Open |
| Dataset Contents | |
|---|---|
| Total Genome Size | 17478707 |
| Sequencing Scaffolds | 35 |
| Novel Protein Genes | 39 |
| Associated Families | 37 |
| Dataset Phylogeny | |
|---|---|
| Taxonomy Groups | Number of Scaffolds |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 139 | 1 |
| Not Available | 16 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 2 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia → Escherichia coli | 1 |
| All Organisms → cellular organisms → Bacteria | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → unclassified Spartobacteria → Spartobacteria bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium liaoningense | 1 |
| All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 2 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Bryobacteraceae → unclassified Bryobacteraceae → Bryobacteraceae bacterium | 1 |
| All Organisms → cellular organisms → Bacteria → Acidobacteria | 1 |
| Ecosystem Assignment (GOLD) | |
|---|---|
| Name | Tropical Forest Soil Microbial Communities From Luquillo Experimental Forest, Puerto Rico |
| Type | Environmental |
| Taxonomy | Environmental → Terrestrial → Soil → Loam → Forest Soil → Tropical Forest Soil → Tropical Forest Soil Microbial Communities From Luquillo Experimental Forest, Puerto Rico |
| 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 | Luquillo Experimental Forest Soil, Puerto Rico | |||||||
| Coordinates | Lat. (o) | 18.0 | Long. (o) | -65.0 | Alt. (m) | N/A | Depth (m) | .1 | Location on Map |
| Zoom: | Powered by OpenStreetMap © | |||||||
| Family | Category | Number of Sequences | 3D Structure? |
|---|---|---|---|
| F000466 | Metagenome / Metatranscriptome | 1105 | Y |
| F000628 | Metagenome / Metatranscriptome | 973 | Y |
| F001962 | Metagenome / Metatranscriptome | 611 | Y |
| F002851 | Metagenome / Metatranscriptome | 526 | Y |
| F002925 | Metagenome / Metatranscriptome | 520 | Y |
| F003090 | Metagenome / Metatranscriptome | 508 | Y |
| F004961 | Metagenome / Metatranscriptome | 417 | Y |
| F007624 | Metagenome / Metatranscriptome | 348 | N |
| F010636 | Metagenome / Metatranscriptome | 301 | Y |
| F011271 | Metagenome | 292 | Y |
| F012657 | Metagenome | 278 | Y |
| F014442 | Metagenome / Metatranscriptome | 263 | Y |
| F014678 | Metagenome / Metatranscriptome | 261 | Y |
| F015159 | Metagenome / Metatranscriptome | 257 | Y |
| F018039 | Metagenome / Metatranscriptome | 237 | Y |
| F020122 | Metagenome | 225 | Y |
| F027165 | Metagenome | 195 | Y |
| F044096 | Metagenome / Metatranscriptome | 155 | Y |
| F045257 | Metagenome / Metatranscriptome | 153 | Y |
| F045461 | Metagenome | 152 | N |
| F048477 | Metagenome / Metatranscriptome | 148 | Y |
| F054241 | Metagenome | 140 | Y |
| F055065 | Metagenome | 139 | Y |
| F056355 | Metagenome / Metatranscriptome | 137 | Y |
| F057789 | Metagenome | 135 | N |
| F059050 | Metagenome / Metatranscriptome | 134 | Y |
| F062053 | Metagenome / Metatranscriptome | 131 | Y |
| F062933 | Metagenome / Metatranscriptome | 130 | Y |
| F063348 | Metagenome | 129 | N |
| F064014 | Metagenome / Metatranscriptome | 129 | Y |
| F066902 | Metagenome / Metatranscriptome | 126 | Y |
| F069413 | Metagenome / Metatranscriptome | 124 | Y |
| F069475 | Metagenome / Metatranscriptome | 124 | Y |
| F069634 | Metagenome | 123 | Y |
| F075781 | Metagenome / Metatranscriptome | 118 | Y |
| F086002 | Metagenome / Metatranscriptome | 111 | Y |
| F096166 | Metagenome | 105 | N |
| Scaffold | Taxonomy | Length | IMG/M Link |
|---|---|---|---|
| Ga0207729_100120 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 3261 | Open in IMG/M |
| Ga0207729_100287 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 2551 | Open in IMG/M |
| Ga0207729_100327 | All Organisms → cellular organisms → Bacteria → Proteobacteria | 2454 | Open in IMG/M |
| Ga0207729_100498 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales | 2111 | Open in IMG/M |
| Ga0207729_100945 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 139 | 1653 | Open in IMG/M |
| Ga0207729_100956 | Not Available | 1642 | Open in IMG/M |
| Ga0207729_100988 | Not Available | 1625 | Open in IMG/M |
| Ga0207729_101052 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 1590 | Open in IMG/M |
| Ga0207729_102276 | Not Available | 1124 | Open in IMG/M |
| Ga0207729_102624 | Not Available | 1047 | Open in IMG/M |
| Ga0207729_103119 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium | 942 | Open in IMG/M |
| Ga0207729_103648 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia → Escherichia coli | 852 | Open in IMG/M |
| Ga0207729_103767 | All Organisms → cellular organisms → Bacteria | 835 | Open in IMG/M |
| Ga0207729_103783 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 832 | Open in IMG/M |
| Ga0207729_104064 | Not Available | 796 | Open in IMG/M |
| Ga0207729_104602 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria | 742 | Open in IMG/M |
| Ga0207729_104852 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → unclassified Spartobacteria → Spartobacteria bacterium | 719 | Open in IMG/M |
| Ga0207729_105075 | Not Available | 700 | Open in IMG/M |
| Ga0207729_105593 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium liaoningense | 656 | Open in IMG/M |
| Ga0207729_105672 | Not Available | 650 | Open in IMG/M |
| Ga0207729_105743 | All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium | 645 | Open in IMG/M |
| Ga0207729_106179 | Not Available | 614 | Open in IMG/M |
| Ga0207729_106526 | All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium | 591 | Open in IMG/M |
| Ga0207729_106689 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 581 | Open in IMG/M |
| Ga0207729_106736 | Not Available | 578 | Open in IMG/M |
| Ga0207729_107275 | All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Bryobacteraceae → unclassified Bryobacteraceae → Bryobacteraceae bacterium | 550 | Open in IMG/M |
| Ga0207729_107413 | All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium | 544 | Open in IMG/M |
| Ga0207729_107619 | All Organisms → cellular organisms → Bacteria → Acidobacteria | 535 | Open in IMG/M |
| Ga0207729_107904 | Not Available | 522 | Open in IMG/M |
| Ga0207729_108013 | Not Available | 517 | Open in IMG/M |
| Ga0207729_108041 | Not Available | 517 | Open in IMG/M |
| Ga0207729_108045 | Not Available | 516 | Open in IMG/M |
| Ga0207729_108052 | Not Available | 516 | Open in IMG/M |
| Ga0207729_108124 | Not Available | 513 | Open in IMG/M |
| Ga0207729_108417 | Not Available | 501 | Open in IMG/M |
| Scaffold ID | Protein ID | Family | Sequence |
|---|---|---|---|
| Ga0207729_100120 | Ga0207729_1001204 | F057789 | MSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITVNGKLYASHDLRKVAALLPDEDLQRHHQALVNVMFAKKQRGYRKTAYNLADRVNSWRTEEQKLAPRQAAKMSALAVAEPAPFRNRGFSERTIKALLDCSIDQPERLLFMQSADLKKIPGVGKASFDEIMRYRAKFIRSSVMKKNP |
| Ga0207729_100287 | Ga0207729_1002873 | F002851 | MRSFIEAGAVIAACGSAIFWFTSAMCRLPSINRGTNELDKVTELSKALQRMNRWNFWAAGLMGVTALLSALGRFLGLIF |
| Ga0207729_100327 | Ga0207729_1003274 | F012657 | MAWLKIIEKKRLLSASPVMIAASLHQMAEKYDPQVAPTTLHLPEAVHADFREKVFLYREANVLLALVDRVNPSSDGRDSLFEPVFWEYERIIFRESSDHFGELSDHPILRAARRQSVMAAFQDLKVRIHPPMGNKFDIARDWSRNWFAGIGHDEMNPARLEHFSWFWSDEYSAVQKALEATIVRSRRSILSGGNAEPGRYGRKI |
| Ga0207729_100352 | Ga0207729_1003521 | F059050 | IAGWERRRCRNYGDFAAGSGVDVVERGGKVGNFATRHVRELNCERITDRLCNAILRF |
| Ga0207729_100498 | Ga0207729_1004982 | F069634 | MKIGIHAPDKPPVVVSLLLAILALIAYFVNTPAAFWIAMFAYIVGAVGVITEI |
| Ga0207729_100945 | Ga0207729_1009452 | F069413 | MQSSLPAGWLAFTGRESNPLDHYKRFQITLSSPSSGFILAQRTAGFPQYGWKAG |
| Ga0207729_100956 | Ga0207729_1009561 | F054241 | TENEPITAERIRKKKFVALLGQCLDCGQPVIEGQAFFRSDHGIRHALCEFDPAYAKRAREPKVKTE |
| Ga0207729_100988 | Ga0207729_1009881 | F063348 | MTGFDQTVRLPDRQGVPSERWCAQERKTIVNVKKAEIEDLAFRFRDEVKAEILQHRGSNAVGVVGSFVVNIEAHRARYAKKLDAIRAGADAATVFLADEVGREIDALATKEIKRVRDAGRVEFEPGAADHQIPLEIHKIGLSDNQLEVIMRTAEPLAEEKCQEFLQRLAAILPMRGQISDDDVSVAVHRALSDIIRNSAVWKEWNQNSPPTLQDGQVSDAA |
| Ga0207729_101052 | Ga0207729_1010522 | F000466 | MAHLLTYMTTPEAWQRWKKLPSQGVVKRDWVPTGRIDFATRFYGNLEDSDQPSEFKLIVEERRIVESITGNENLEIQWRLATLNEAKVVVAQYHKYLLENSLIKSVFDEPASLPPPKRIQKIQESTAA |
| Ga0207729_101988 | Ga0207729_1019882 | F014442 | MVLNHRRSNFMKSPSAFDEDDLFTYEVSDEALETAGGHELAGNYTLGSCTGLSVCPG |
| Ga0207729_102276 | Ga0207729_1022761 | F014442 | MMNFQSTLNEEDDLLTLDISDEALETVGGNEVVGNFTLGACTGLSVCPA |
| Ga0207729_102624 | Ga0207729_1026241 | F062933 | MHLVSKIGIAIFAAAAVAAVIVDTMRPIAARRLFALVAALIAGVTAFYLVPEPLPELTRAEFMTEVRAGHVRRVEIEDQQVIIGESSTRGEFRTEFDRYKDVDLPAELRALGIEV |
| Ga0207729_103119 | Ga0207729_1031192 | F044096 | MRSAIPIFLAILVLATTPARAQGTWLETRMTRAICSSEATPVANTDRLARRLNLTEPQKAALKDLTD |
| Ga0207729_103648 | Ga0207729_1036482 | F055065 | VNPAKAGINSERAIAEKLTVAWLPCQESSALQWPAQSNYRLKAEDFGSTVLKLQNP |
| Ga0207729_103767 | Ga0207729_1037671 | F062053 | QQKRKANLQWRTKNPDYFGGAYLQQKAKYGTRAEYMRHYRQQHPDYVRRNAASVRKWRQQPRLEPVSHTSRDLHVTIESERTSLRIAHVSHTSRDIFVTLETA |
| Ga0207729_103783 | Ga0207729_1037831 | F045257 | MKRYPCFIAALSMCFFASMGAACAEVKADTGGIAIGGSVTGSTLNIGIPQQKVDELVRDAKRPLEELTAQQRDNILLLK |
| Ga0207729_104064 | Ga0207729_1040641 | F069475 | VSQRVVSIALNSATIARLASAARPLVAVLDEQQKRAAGQLAQEMGLGEVVMAALN |
| Ga0207729_104481 | Ga0207729_1044811 | F057789 | MSATSAYAGTTIAIPTAVREEMSETALQFTGTDLRGLLDVLLEALKVIRRTGRRPTITINGKLYANHDLRKVAALLPDEDLQPHHQAAADVMFAKKQFGYRRTAYNIAERINSWRTEEQKQVALKAGRTSALPVLEPFPFRHRGFSERTIRALMDC |
| Ga0207729_104602 | Ga0207729_1046021 | F002925 | MKTCPDCNGEGVIEKGTDDEQQCPTCGGSGFVPDDDDDEEVTRTASW |
| Ga0207729_104852 | Ga0207729_1048522 | F001962 | MILKSETYHFLGLDLTRHAGFIVTIHDEDGLRLASTPPMPTPAQAFEEARKIVDNKVEGPRKLKVPPSIMPP |
| Ga0207729_105075 | Ga0207729_1050751 | F010636 | MKVLSGLLLTPTFAAALLLACTQTNAAHRGGGSAYDGTWSVAIYTLRGD |
| Ga0207729_105593 | Ga0207729_1055932 | F014678 | MIGSFRVERQGASSKIGFDHVGDDGARFGKIERCDSRIHLVETLAATQKLGIDRANLV |
| Ga0207729_105672 | Ga0207729_1056722 | F020122 | IKLKTMLILKRNPDAEYSESYNILFEGRHVGRIYKAVSHAPREAPWFWGLNFFEWQGSDGPQYGNAATLEAAKQAFRAAWDRRPKASGNL |
| Ga0207729_105743 | Ga0207729_1057431 | F007624 | FHGPRPTCPKHPKQRVHRHGFYVRFENCDSQRRLRIERFVCPRCGRTLSVLPKNRLPYVAVNTTILESDFDARASGTDPPSCSEKERGCLGRAFERFADRVAPLCALLGQMIRGIKPSVSECWRALRQLDNLEGILLLLGTKFNTSLLADYRCLQPGF |
| Ga0207729_106179 | Ga0207729_1061792 | F064014 | MNRSSVESHLRVEVKHRCAAPKRYTWEIFSEGKTLPLKESTDQFRSWEEASWAGKKALKKLLANTP |
| Ga0207729_106526 | Ga0207729_1065262 | F003090 | EKMTVIDYKGYRIEVGPVGKGWRASIFSPGSIRPWPNSPANLEKSSSEELVAEAKRIIDVRLGPRSL |
| Ga0207729_106689 | Ga0207729_1066891 | F000628 | RYQGDLSASINDALLAVNLNTVKLVTLQGKKKQTARETQVVLLRRLIQRLHHVAEARGCSINQLVNSGLAAYYSKEQAGKRGPSSRPTRPVASATYDKMSPDERQQLVEELAGLAGLQEGPKDAFPDGTRYEYDSRLKTTFEITPSGKRFPVALVAGRFRRDLANAIARKTAR |
| Ga0207729_106736 | Ga0207729_1067361 | F048477 | MEELNAFRKVARKHGFVDGEETEDGTVLWMWRPNADAEDRICIDNVTNSATVFWETIPWKIHSKTFRVAFALEEWFVSTSRQAAIPGNPKLVG |
| Ga0207729_107275 | Ga0207729_1072751 | F066902 | SAAELELIEQLRKYPELFERVRKILEISASAEGPIRKADEIEALLIEEMRRLGHATMETWAGRAEQTLADELKQKDASASVRKKKR |
| Ga0207729_107413 | Ga0207729_1074131 | F096166 | MPVFSQTSDGFSIFRSAPVRAGTYAGVCLSSIFVLWVYVANRVPELEIFARERNMAAVALLVFFASVPVMRFYRSPLNLVASGMLGWSLLTITYLLLCVKFVELGQNYSSFHIFMLGTVAYFIF |
| Ga0207729_107619 | Ga0207729_1076191 | F056355 | DWEFCPDCQWTSELNLEQVPIEGLQKLAGWNYPLKGLVTGQFHGRGTRQEPSLTGLLDVADGEAYTVPFNRLRGQLNVTPDEVRFSNAELRFFAPGSEKAHGAGIVTGTAGYRYADQSLGLDLVGASLPLANFRRVRAANLPLGGQISFRLKSSGPATKPEAEGSFRVVDLVVSNEV |
| Ga0207729_107803 | Ga0207729_1078032 | F075781 | PDQPAAETPRGQARPTEERFWLRVDGQMKRSFSSKEPAMTAGREIKKAFPVVVVTLEDTKDGSIETVK |
| Ga0207729_107904 | Ga0207729_1079041 | F015159 | MTEEESALVPADTRYRALLDVSRAMVEQPTVKAVLHSLREVLSSSCRLHGAHLYVLGSDQESLHLLEFDREADAPAIKIGTKISRIGEPARVLEDLEPVFLPDVSQEMLKHPELAPFATQSV |
| Ga0207729_108013 | Ga0207729_1080131 | F045461 | MLCGAVFIIMLVAAVIVDLAALLQFSGLISGLPANILKTSTLEIGGILTALTIFPLLAMGMSISIDQNRSEDK |
| Ga0207729_108041 | Ga0207729_1080411 | F027165 | MGYNARNDEIHENLERMRREREDYEDSLAIVRQFNARLSAKKTAWFWPTVGAALASKHHWLVIACDACDTVIDLDLTVKRRDPDAPIRVALNDVRCPRCD |
| Ga0207729_108045 | Ga0207729_1080451 | F018039 | MARTLREVIAAVPAERRAKTAAAHRQKLIAEEQKLIEEKKKRQLVEAKRVLELDRNLIVIAVLIIALPLIAALAVMLAALAVGDQ |
| Ga0207729_108052 | Ga0207729_1080521 | F011271 | IDLQSEAKEKQALKLAEIRETLVAAGYDTTAKQAAILGIGRSTAWVLLNRDKRAGPSAKVIKRILSSPQVPARARRKVEQYVEQKARGLYGHCESATRTFGNQFQHL |
| Ga0207729_108124 | Ga0207729_1081241 | F004961 | MSDLAKKFLAKWEFEHIEVVARSHREDQARHLALRCREDAAKAGISGQDLEAAVEGNLIGNMLQALDAAEFRQMYRDQVAEQEED |
| Ga0207729_108417 | Ga0207729_1084171 | F086002 | MRELMGKIPTKDPNITDVVYLSEIVRCLECQKTVPMGIEVVTVKKGG |
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Bioinformatics & Integrated Biology Lab Institute for Fundamental Biomedical Research Biomedical Sciences Research Center "Alexander Fleming" |