Sample 3300003392

Basic Information
IMG/M Taxon OID	3300003392 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0110179 \| Gp0089073 \| Ga0008475
Sample Name	Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co PM
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Basic Information

IMG/M Taxon OID

GOLD Reference
(Study | Sequencing Project | Analysis Project)

Sample Name

Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co PM

Sequencing Status

Permanent Draft

Sequencing Center

DOE Joint Genome Institute (JGI)

Published?

Use Policy

Open

Dataset Contents
Total Genome Size	13940539
Sequencing Scaffolds	25
Novel Protein Genes	27
Associated Families	26

Dataset Contents

Total Genome Size

13940539

Sequencing Scaffolds

Novel Protein Genes

Associated Families

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	13
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	3
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	1
Not Available	6
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → Nitrospira japonica	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1

Dataset Phylogeny

Taxonomy Groups

Number of Scaffolds

All Organisms → cellular organisms → Archaea

All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon

All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium

Not Available

All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → Nitrospira japonica

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium

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

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

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
Location on Map

Zoom:	Powered by OpenStreetMap^©

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

Location on Map

Zoom:

Family	Category	Number of Sequences	3D Structure?
F005683	Metagenome / Metatranscriptome	393	Y
F006898	Metagenome / Metatranscriptome	362	Y
F009776	Metagenome / Metatranscriptome	313	Y
F012388	Metagenome / Metatranscriptome	281	Y
F012397	Metagenome	281	Y
F013352	Metagenome / Metatranscriptome	272	Y
F017423	Metagenome / Metatranscriptome	241	N
F019548	Metagenome / Metatranscriptome	229	N
F020931	Metagenome / Metatranscriptome	221	Y
F033614	Metagenome / Metatranscriptome	177	Y
F033996	Metagenome / Metatranscriptome	176	N
F037804	Metagenome	167	N
F041299	Metagenome	160	N
F048397	Metagenome / Metatranscriptome	148	N
F062531	Metagenome	130	N
F068109	Metagenome / Metatranscriptome	125	Y
F068551	Metagenome	124	N
F071574	Metagenome	122	Y
F073212	Metagenome / Metatranscriptome	120	Y
F073748	Metagenome	120	N
F076440	Metagenome / Metatranscriptome	118	N
F077482	Metagenome	117	N
F079269	Metagenome	116	N
F081936	Metagenome / Metatranscriptome	114	N
F099265	Metagenome / Metatranscriptome	103	N
F103537	Metagenome / Metatranscriptome	101	N

Family

Scaffold	Taxonomy	Length	IMG/M Link
JGI26134J50242_100085	All Organisms → cellular organisms → Archaea	5056	Open in IMG/M
JGI26134J50242_100112	All Organisms → cellular organisms → Archaea	4519	Open in IMG/M
JGI26134J50242_100209	All Organisms → cellular organisms → Archaea	2727	Open in IMG/M
JGI26134J50242_100215	All Organisms → cellular organisms → Archaea	2701	Open in IMG/M
JGI26134J50242_100334	All Organisms → cellular organisms → Archaea	1995	Open in IMG/M
JGI26134J50242_100394	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1768	Open in IMG/M
JGI26134J50242_100538	All Organisms → cellular organisms → Archaea	1375	Open in IMG/M
JGI26134J50242_100565	All Organisms → cellular organisms → Archaea	1334	Open in IMG/M
JGI26134J50242_100602	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1289	Open in IMG/M
JGI26134J50242_100782	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1083	Open in IMG/M
JGI26134J50242_100988	All Organisms → cellular organisms → Archaea	932	Open in IMG/M
JGI26134J50242_101002	All Organisms → cellular organisms → Archaea	923	Open in IMG/M
JGI26134J50242_101027	All Organisms → cellular organisms → Archaea	913	Open in IMG/M
JGI26134J50242_101070	All Organisms → cellular organisms → Archaea	896	Open in IMG/M
JGI26134J50242_101081	All Organisms → cellular organisms → Archaea	890	Open in IMG/M
JGI26134J50242_101406	All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	789	Open in IMG/M
JGI26134J50242_101543	All Organisms → cellular organisms → Archaea	758	Open in IMG/M
JGI26134J50242_101868	Not Available	695	Open in IMG/M
JGI26134J50242_102187	Not Available	651	Open in IMG/M
JGI26134J50242_102248	All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → Nitrospira japonica	642	Open in IMG/M
JGI26134J50242_102269	Not Available	639	Open in IMG/M
JGI26134J50242_102288	Not Available	637	Open in IMG/M
JGI26134J50242_102620	Not Available	603	Open in IMG/M
JGI26134J50242_102909	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	579	Open in IMG/M
JGI26134J50242_103406	Not Available	544	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26134J50242_100085	JGI26134J50242_1000855	F012397	VSVSIKRNKNNKKGVRWNRILILIVLVTTLSFLSGPSLSFSEIKNEITVTPPLNWEPSPTNNSTTMIWFQNSTKSIFAITKAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGHSNYGYRYFLNLSSPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLIITQKHKELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26134J50242_100112	JGI26134J50242_1001121	F081936	NAKKPSPPNVEASVNPKVEQLAHVLEITLIVVPDSADLLNFNFRFLIIYRLKFTKIAIRTELIQVKINASIISLGT*
JGI26134J50242_100209	JGI26134J50242_1002091	F013352	QFSSLPCLSIAIAGFLFCLMTSTTYAQIEVTVDENVSTPISDSTLSEDAEPRPDILYSALNKDTIIGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEVLQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVTYTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26134J50242_100215	JGI26134J50242_1002154	F019548	MNPSKKEIYKILERFTSQKGGILFILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSGIEGDVIWFGGMLDKSGSEFIGSTYDDGLKSAPVEQSELVHRVNQAIDKCLEYMLNSVELDKNVYVDASNRMSGYVKLTRIGEHIREKHPDLFRDNTKSE*
JGI26134J50242_100334	JGI26134J50242_1003341	F048397	VHNSTIFRAILEKNKCDKCNLTIHPNFIGNHKCDHQNCPICKNPITPSQYWPHIRSHPGHENDSPPLPKRNMDENRKNENHSGYGNYQRN*
JGI26134J50242_100394	JGI26134J50242_1003941	F041299	VYSPVFDEIDYRMKSQAKSTLLAIIIPSCIAILLFYIGAYFHPDIFSLLNGLPGVIILSGSVIVVTKLLCYTKLERSEMQKFKPLILGIVCFLIGETFYFYQQYFLQIDIPYPSVADVPYLLASFFFSYFLISCVFSLLDRKNLSPLPIILGSPIAIFPIYVTLSSAYDLAINESTELEFIVNALYYIFDGLMLVTAVIIILNLKKYDPFIFHWICITVGLILLVIGDVGYTYFSIISESLIEEYEWLWSILYAIGYLFLGIGIYWFDRIKNTLEDKKINVFLEKDEMDRLKNSSKNELIADTGTEFSEHIIGYEKFVDKLKDYLERSKEIKILFYDKYWLSDEEVNLILEKIQQGAFFTQIQVNILLPSSETIFKNLVSYNDNRHILVSFFDRTFSSDSLVFIFEEKYVAIIDRKPTSESVDSDTVFYGLITNNDTIVWPHITTFEKIWVLEKAVNM*
JGI26134J50242_100538	JGI26134J50242_1005384	F009776	MTRQKKLFNKTGDSVEIKKDGKDVIVTVQYTTKVEPTXXATEDNFNDIVSVYERTGFTEEPRQ*
JGI26134J50242_100565	JGI26134J50242_1005654	F068551	MQLGVIVIFIFVILGIVFFIVFGIGYFKTENPQNENLQNRSAAVFPNPDSIPPECKYTPNDLLCQFQLEKQKMKLSQNE*
JGI26134J50242_100602	JGI26134J50242_1006023	F099265	MDKMNEDTILHFYRILENSLLESDISKINEEDIDAWSQSFKKVVRESREKSGKGVFVPFLMWKLGEISPVEARKYLVNRKQDECRVSYDHNNVEYILRVMAL
JGI26134J50242_100782	JGI26134J50242_1007822	F037804	MDDIEHDLEEFANYILEAIKQSEGEISNWDEIIRKWKEIEKKKDLALXKKLK*
JGI26134J50242_100988	JGI26134J50242_1009882	F017423	FALQYTNYLSEKYQIAFQYPSDWTIKEKSNKLEEGTEIDVSNKKIGDGKIGIHFYDDLLEGFGSTDLEIAFSDFYKHRITDDLKFEYKTIXPPSLLEIDGHKTGSFHIMFSQKDEIDPISGEVQYWITFVGENGYMIEFLSIPENFDTPDNTEMRDHFISSIDFLGLSNNTDASGRISSVAMSN*
JGI26134J50242_100995	JGI26134J50242_1009951	F103537	EIMPFVLRGRITKSIFAFAAIEYEFPLTVSGQIKHELLKMNDARFKDIVHWRYTEVAKQAAKVFALNKPFINCFKIIHKLSKQIFNIILATKFSR*
JGI26134J50242_101002	JGI26134J50242_1010021	F006898	MYLILTTTLLLFSLFSLPGAFGAEMFKGLSFSIDIPNTWAYTETPEAPIERALGVSSYTSVVLVPVQFAELLIQEKGDIGMGNGSTAIVFAKASDYSVKNAPLDLYVKYRMNEDDSLNVTSQKDTTIGKEKAVRIDGNKNNNASNTRLLEYLLLHNDEPYVIRYIASMDDFERNLPAFELMV
JGI26134J50242_101027	JGI26134J50242_1010271	F013352	GLQTSQKDGMKYTLPGKLLTNSIDKYFPECLTKNSHFASQFSSPPCLSIAIAGFLFSLMASSTNAQIEVTVDENVSTPISNSTLSEDAEPRPDILYSALNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEVLQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26134J50242_101070	JGI26134J50242_1010702	F062531	KAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGHSNYGYRYFLNLSSPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLIITQKHKELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26134J50242_101081	JGI26134J50242_1010812	F033996	MELNLTAKDKHALKSLSVDLRDMLRMKKVDDRTGNPEYRRVFDATFFKVTDGNYLDEMLNWVEDFSNRMADAESEQSKDELNLETKRLIDAGWIT
JGI26134J50242_101406	JGI26134J50242_1014061	F033614	NSTALKLHGPWGTSYWLEFNPSTFKVGDGSSRPTLHPLSFDVKWEWSAVDPNIIYFINGTQLAKYNKSTHVVTNLGGRGVSLKYHVVVVGLDAWVCAAGPGTQNTYRQIFCLNPRNPSQTKFIDILKRTINGVYQSDPNWPTSAPYQTIGIHAMYGSATGTWLDVGFHRASWGAGGDSVFNLSTNKWSLLKANRYSSGHSSIGTRFVNGSGSINGMYSGGACVRNPSNLMDATRYTFIMQPPSAATGWHDGEHSSWFNASTN
JGI26134J50242_101543	JGI26134J50242_1015431	F005683	VFGLVVYSIYFGQISFAEGVELKTVGKGAISCGNGEEVKGVRINFFVSYDGGTPFAEWNMDHKELGSAGGMITNVKTSSNSFVLKGFEAFDNICDVETPSDVKLSGNCGEGTVSLVSDNGNKGTFASNVKCG*
JGI26134J50242_101868	JGI26134J50242_1018681	F077482	MSIMPKWMNWLPHQWYASTLVLPIVILAYPSLRCGEAYELLLDRELSALDQFYAGWGTVIRMDENSEGQGPKDTMQDNEYRPAGGIKKFAEPTIQLRGTAEKIGLDRQSLSSFIGTKFLNEFAFLQSDFVFEKTYQTWEIGIFECETWTVGVNYPIAFHVQCAGGSMDEPREWHYASLGYGPAGKTSETVR
JGI26134J50242_102187	JGI26134J50242_1021871	F073748	NFLLNRRGCVLFTCLIAGLQICLTAPGWSEEVHFGCEYDEEKTHETSTSNSGPERRSTHGEARYTIDWQSKRVQGFSGEYELKFSDAELRIQRKTQNSSGEWLNKASESIIINRYTGEYVFSEKVEGESVKGISRYWYTYKTRKGICKKIDKSLF*
JGI26134J50242_102248	JGI26134J50242_1022481	F076440	MEKRMQISPGRNWSEGAGDRADQHFEIWYGEEERKDTLVARVWATKDGPHSVELYRKSSLIEPVRVRVLEGLMRELDFYLMKDERDVPRYLMHHCSMASHVYSPYGWIQVNPGR*
JGI26134J50242_102269	JGI26134J50242_1022692	F071574	MPKMRTNYHYRGRIITLLPRMEGYMWTCQYVILKSGKTEQGTEIDGSPAKTYFSREEAESAAFTMAKTFIDQCQLDKARYEVEQW
JGI26134J50242_102288	JGI26134J50242_1022881	F012388	HANGHPAKRWLVVVARGQTDLYAHLVQAFSRDGKVKVILDRRKDDSRNSPQVTHRLRTHGAVIIRQAG*
JGI26134J50242_102620	JGI26134J50242_1026201	F020931	LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKFKSEFDNL
JGI26134J50242_102909	JGI26134J50242_1029092	F068109	MIEALQQAGFHDVRACHFFDSFAGTNKERVAKKYGVRGTNFTAVK*
JGI26134J50242_103146	JGI26134J50242_1031461	F073212	SDSKILLYGYFETNSTGGFNDVTFADDLKQDHYKLYFADDVNTDGTFDIGAKRIYSNVTIPCGQ*
JGI26134J50242_103406	JGI26134J50242_1034061	F079269	MKKASWFFWAFVGLVWLVISLPFAGDSLKALLEFPDTPPSSQEELGKLLQNIIYAANFSILSVLVLYGLNRGWHKSDGYPKFLRRLDLQTRFTNLFENKPVLAVTNTVLALLA

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300003392: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co PM

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences