3300003383: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 S AM

Overview

Basic Information

• IMG/M Taxon OID: 3300003383
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089079 | Ga0008481
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 S AM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 18458043
• Sequencing Scaffolds: 39
• Novel Protein Genes: 41
• Associated Families: 37

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	18
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1
All Organisms → cellular organisms → Bacteria → Nitrospirae	1
All Organisms → cellular organisms → Bacteria	3
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → Candidatus Nitrospira kreftii	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Phyllobacteriaceae → Hoeflea → unclassified Hoeflea → Hoeflea sp. WL0058	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Hahellaceae → Hahella → Hahella chejuensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Joint Genome Institute, California, USA
• Coordinates
  • Lat. (^o): 37.931388
  • Long. (^o): -122.021761
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F002896	Metagenome / Metatranscriptome	522	N
F005305	Metagenome / Metatranscriptome	405	N
F005683	Metagenome / Metatranscriptome	393	Y
F005950	Metagenome / Metatranscriptome	385	Y
F007651	Metagenome / Metatranscriptome	347	N
F010272	Metagenome / Metatranscriptome	306	Y
F012397	Metagenome	281	Y
F012898	Metagenome	276	Y
F013352	Metagenome / Metatranscriptome	272	Y
F013650	Metagenome / Metatranscriptome	269	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26140J50224_100063	All Organisms → cellular organisms → Archaea	6236
JGI26140J50224_100079	All Organisms → cellular organisms → Archaea	5749
JGI26140J50224_100083	All Organisms → cellular organisms → Archaea	5726
JGI26140J50224_100088	All Organisms → cellular organisms → Archaea	5474
JGI26140J50224_100154	All Organisms → cellular organisms → Archaea	4161
JGI26140J50224_100190	All Organisms → cellular organisms → Archaea	3590
JGI26140J50224_100230	All Organisms → cellular organisms → Archaea	3194
JGI26140J50224_100315	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	2402
JGI26140J50224_100340	All Organisms → cellular organisms → Archaea	2287
JGI26140J50224_100360	All Organisms → cellular organisms → Archaea	2219

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26140J50224_100063	JGI26140J50224_1000635	F057496	MAGVYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGIXTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGXPTVMKNIDAYLRXNLLESEYGLKL*
JGI26140J50224_100079	JGI26140J50224_1000796	F089980	MDLESATELIVMNWLGIFSLAATIFIAIVTINYRNKQHQIQGLLDAFKILNTREHRTSRRKVYELYIEYEKNKDVGIFDNVPEVVDVRADFDVIGTLVKSRNIDEKLFLIEYGPLAYRCWKYLKKHVEAERKKRNFNPFMKNFEDLANKANRFWSKRGYDLSKTLLYQPEQEERS*
JGI26140J50224_100083	JGI26140J50224_1000831	F026602	YAIEQPSKMEGINEEECNKIFNCKIISEDVLKYPDIVNPFTKNEEIAKTLNANDAQIMTEHTCQKLMDVDIVKKKDQKIGEQAPKYLVCLP*
JGI26140J50224_100088	JGI26140J50224_1000885	F100610	MMPVIISLFGNEDMEISEFRLTNKSVFYRCSYGECFRFIADKCMHCCANPIPDTEMHINYLRRLPDIKKAVTDLGI*
JGI26140J50224_100154	JGI26140J50224_1001544	F013352	MKYTLPGKLLTNSIDKXFXEXLXKNXHXASQFSXXPCLSIAIAGFLFSLMXSSTNAQIEVTVDENVSXPIXNSXLSEDAEPRPDILYSXLNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26140J50224_100190	JGI26140J50224_1001902	F026602	MISLTLASMHVFAGRIYAIEQPSKMEGINEEECNKIFNCKIISEDVLKYPDIVNPFTKNEDIAKTLVNNANDSKIMTEHTCQKLMDVDIVKKKDQKIGEQTPKYLVCLP*
JGI26140J50224_100230	JGI26140J50224_1002301	F005950	MTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLQYGLSKVHKVIIRKYTEDDEFIARAQKTRGIKFDYEMELYD*
JGI26140J50224_100315	JGI26140J50224_1003151	F070180	VYSPVFDEIDYRMKSQAKSTLLAIIIPSCIAILLFYIGAYFHPDIFSLLNGLPGVIILSGSVIVVTKLLCYTKLERSEMQKFKPLILGIVCFLIGETFYFYQQYFLQIDIPYPSVADVPYLLASFFFSYFLISCVFSLLDRKNLSPLPIILGSPIAIFPIYVTLSSAYDLAINESTELEFIVNALYYIFDGLMLVTAVIIILNLKKYDPFIFHWICITVGLILLVIGDVGYTYFSIISESLIEEYEWLWSILYAIGYLFLGIGIYWFDRIKNTLEDKKINVFLEKDEMDRLKNSSKNELIADTGTEFSEHIIGYEKFVDKLKDYLERSKEIKILFYDKYWLSDEE
JGI26140J50224_100340	JGI26140J50224_1003401	F005305	DEDFKKEFNELSKYVIEPVMRKFESYLESKDVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKERLIRLIKSCFDKDWQSFYS*
JGI26140J50224_100360	JGI26140J50224_1003603	F002896	MDKMNEDTILHFYRILENSLLESDISKINEEDIDAWSQSFKKVVRESREKSGKGVFVPFLMWKLGEISPVEASKYLVNRKQDECRVSYDHNNVEYILRVMALMFMSWSVTNLKRKTQNGHCQNIDHPHGDTNPRLCKEGTIFHQDLYNECVKTFKDLLIHSDAQHH*
JGI26140J50224_100394	JGI26140J50224_1003944	F005683	MGILLVFXLVVYSIYFGQISFXEGVELKTVGKGAISCGNGEEVKGVXINFFVSYDEETPFAEWNMDHKELGSAGGMITNVKTSSDSFVLKGFEAFDSICDVETPSDVKLSGNCGEGTVRLVSDNGNKGTFASNVKCG*
JGI26140J50224_100419	JGI26140J50224_1004193	F021640	LSPRFGFFKRKTPDYFHDKESQANSVHSVSNKELLEIVENEKKVLQKDLIDNLEPTRNLVLDCLNRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKLKSEFDNLSSLLKTVTKIISTKENQINSCIQCKADLILLDEKMNERRTKKVRLTELIKETQTIDKNIEEGKRQYEDLRKSEEFLNASKILEKIDEKKNEIVVFEKNMINKVSILSRPIT
JGI26140J50224_100461	JGI26140J50224_1004612	F005305	MEDLEKELGPLIENFQXLVKDAKSKKLESLREDEDFKKEFNXLSKXVIEPVMRKFESYLESKXVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKERLIR
JGI26140J50224_100462	JGI26140J50224_1004626	F089131	MLCEQCHTLMXERPVTRKTEDNHDEQAIVLECPQCGQTEYQPVIASFWRRLAA*
JGI26140J50224_100489	JGI26140J50224_1004891	F057496	MAGVYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMKNIDAYLRKNLLESEYGLKL*
JGI26140J50224_100700	JGI26140J50224_1007001	F012397	VSVRIKRNKNNKKGVRWNRILILIVLVTTLSLLSGPSLSFSEIKNEINVTPPLNWEPSPTNNSTTMIWFQNXTKSIFAIXKAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGHSNYGHRYFLNLSSPSILLDSSSGLIPKNEFLSKIPEGYDVPFKGMLILTQKHNELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26140J50224_100772	JGI26140J50224_1007722	F020931	LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKFKSEFDNLSSLLKEVTKILSTKENQIN
JGI26140J50224_100835	JGI26140J50224_1008352	F010272	MYMNHERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKXQAQXKXFXLAQKFXKILKDSNVNLTLPQNGDLSSKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKQEAGADLSKLMQKLQSLRNNSTQ*
JGI26140J50224_100963	JGI26140J50224_1009631	F007651	MLRNHSNYMSNDLNELIARKDKLEGELHHELSSDYNELMKNLSESFRDMHENSVQYYKQKANEELDKMEKNIQSGNKLSAINQKLLADTY
JGI26140J50224_101050	JGI26140J50224_1010501	F070698	MAILNLSETWNNGHNTAFRDSYLDDDNSKILPNGNAPYVIKGNGDCMIIVHADALGASKNFGDGH*
JGI26140J50224_101364	JGI26140J50224_1013642	F005950	SRRKMKMTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLQYGLSKVHKVIIRKYTEDDEFIARAQKTRGIKFDYEMELYD*
JGI26140J50224_101463	JGI26140J50224_1014633	F023903	MVDLMINHEGKKCDNCGDSVDRLVPLNDPTRIGRWWCLKCIYKEGKAKFDADAKNG*
JGI26140J50224_101700	JGI26140J50224_1017002	F012898	MKHMGFHLVAGKKTPFMNGPITVTVASLKANRNKWVRFVKAYLEATQYMTTNKEGSIEVLKRIIPPDDKETLEHAYEEMRTRATVDLMPPEAAVENLVKMMTYIDKRAATLDRSKLADYSILKELAQGKGAPAGR*
JGI26140J50224_101715	JGI26140J50224_1017151	F032685	MVGSKIYIPQDTPLSLALEQRLRSFVEEHRPATIAFVRSGDGELAVIETATPEQAQKVAAXLASSHLSQEPLAAVLDSTPQGRDLERLYGQLKQRELEKNWTNRQW*
JGI26140J50224_101763	JGI26140J50224_1017632	F015943	MGSRAAKLLVVIALGGGCASGVPAGAQTLKTEPAADQLACGQKVLVENNTCPADQILEVTGSCLKTAPEIDVVRTPRGTQYNCVKRKRE*
JGI26140J50224_101921	JGI26140J50224_1019212	F050525	LLAYLAGVSAIFGIGIVGLMALHSPTGRTPSSPPVAAAEPLAKPAKRPLDDKKTAHRNQTHKKVHVTRKQHEAPSIDAGRNAYGYAEELRRIDPNRFLFFGR*
JGI26140J50224_102605	JGI26140J50224_1026051	F018801	MGLTILSIPFIALGVFLKPYALENSRCIGFAGLGPYCFEQASSMPEVIKYGSVAVGFALLYAGRLQIKRQRDGX*
JGI26140J50224_103118	JGI26140J50224_1031181	F085441	YRVNPPEEHQRQLGFEIGLNLQQILFDLKVSRGTWWGYPLHVVADNIRFPFTAVGMRVDLNRGKWHGPNAGNYD*
JGI26140J50224_103251	JGI26140J50224_1032511	F035827	SFFAAASAFAQTYPHSEKYMQQHDGGDRAEYLQEMENSDPWFYVPPVNDVSLSTTDSNVPVN*
JGI26140J50224_103393	JGI26140J50224_1033931	F028049	MSTFHVGSIFLICWALASCANSLTPTIPRASVGDLSDYVLEPLALRVADEKISXASAELKLAHTPKATMQTVASLLNEVPWIGRLLNFRNVSQKAELEEDLAWLETRRIPLKRELLDLFVSRTTQEEEMFIFCVDGIQRRYRALDTNRFTRLPDGPGPCEPIQLYSLKKGRT*
JGI26140J50224_103623	JGI26140J50224_1036231	F033614	TALKLHGPWGTSYWLEFNPSTFKVGDGSSRPTLHPLSFDVKWEWSAVDPNIIYFINGTQLAKYNKSTHVVTNLGGRGVSLKYHVVVVGLDAWVCAAGPGTQNTYRQIFCLNPRNPSQTKFIDILKRTINGVYQSDPNWPTSAPYQTIGIHAMYGSATGTWLDVGFHRASWGAGGDSVFNLSTNKWSLLKAN
JGI26140J50224_103786	JGI26140J50224_1037862	F071761	MRERRIIVRQRSRWTVDEWERGCDLAMTRIDGVPTLVETEPIFQDCLTVLDGAFADGNRLRFELGLGALIDFCTERVNKGDCEQ
JGI26140J50224_103895	JGI26140J50224_1038951	F022740	AGSRNVGFYHRRRAQILAARSNELGGLVSFISVGGQPVNTTRNGTIVAAFTFDDIVWTDIQQKTFAAATAQIRQIRPGSTPVLAATGTITPLADTEIKKLGWKIVQLKPER*
JGI26140J50224_103898	JGI26140J50224_1038981	F077482	MPKWMNWLPHQWHASTLVLPIVILAYPSLRCGEAYELLLDRELSALDQFYAGWGTVIRMDENSEGQGPKDTMQDNEYRPAGGIKKFAEPTIQLRGTAEKIGLDRQSLSSFIGTKFLNEFAFLQSDFVFEKTYQTWEIGIFECETWTVGVNYPIAFHVQCAGGSMDEPREWHYASLGYGPADKTSET
JGI26140J50224_104089	JGI26140J50224_1040891	F099772	ALCQPLLLCACPRRGTNCGWGISHGTVSRLSSRQGGMFRTFGQSFFLLLLTVCAVQLMGTACADDCLRQWSTSPVHAHDQLPGSPDGQTETDPGEGEFEELALAQGEAFRIIHLARACVLDNASCPRTDFAFDWFRPPALP*
JGI26140J50224_104105	JGI26140J50224_1041051	F081899	RQGHQNPLPANERSPMNKGILLITVILFFPAPGLASLSEAHKADELRDYVTAAKEFWPLRSDLERAVDSCTQSVHRDEPDFEAYNEGSSVILFGATPESRFQFHKCMSKKGYPLMKTTK*
JGI26140J50224_104174	JGI26140J50224_1041741	F094081	MRDDQGKILKKEFVERFDKAKGRLQQSVPEIQHLLKTSNVVEAARKIIDPAQSIFKQFADDIQLKDLFAKAEALVANLTVAKSVSRDTPPTETSPSETPASKLPSKKASLKKAPSKGVRSRKPLKKTPLKTRRT
JGI26140J50224_104389	JGI26140J50224_1043891	F079269	GDSQMKKASWFFWAFVGLVWLVISLPFAGDSLKALLEFPDTPPSSQEELGKLLQNIIYAANFSILSVLVLYGLNRGWHKSDGYPKFLRRLDLQTRFTNLFENKPVLAVTNTVLALLAVAFSIFLFLHGRMLVRA*
JGI26140J50224_104660	JGI26140J50224_1046601	F032982	QQYIETRKQQRNDLMQELGLSEEEADQAVSTLELYYHIEASENQWTQAWKAAKRDFLADGERTGIRLADLVVKYVDIARLGGGPESRWT*
JGI26140J50224_104829	JGI26140J50224_1048291	F013650	PFELPKKLTEAYYLSIQGFHVLDKSNVEGAKKYVTFFMKHPDVISWYHAVPLHIIPASRDMLHSAKYQDNPVIQKRMDVLKFLDSVWTKGVPLYYWDGRELNPYIGLYHNENLAGWMLAMRNIKGMKSDQIVDEAAAQVRKKMKRVG*
JGI26140J50224_105033	JGI26140J50224_1050331	F076440	MEKRMQISPGRNWSEGAGDRADQHFEIWYGEEERKDTLVARVWATKDGPHSVELYRKSSLIEPVRVRVLEGLMRELDFXLMKDERDVPRYLMHHCSMASHV