3300003398: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co AM

Overview

Basic Information

• IMG/M Taxon OID: 3300003398
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089069 | Ga0008471
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co AM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 11798878
• Sequencing Scaffolds: 17
• Novel Protein Genes: 18
• Associated Families: 18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	10
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Actinomycetales	1
Not Available	2
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	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
F005683	Metagenome / Metatranscriptome	393	Y
F005950	Metagenome / Metatranscriptome	385	Y
F006898	Metagenome / Metatranscriptome	362	Y
F012397	Metagenome	281	Y
F013352	Metagenome / Metatranscriptome	272	Y
F017423	Metagenome / Metatranscriptome	241	N
F021640	Metagenome	218	Y
F024262	Metagenome	206	N
F033614	Metagenome / Metatranscriptome	177	Y
F037482	Metagenome	168	Y
F057496	Metagenome / Metatranscriptome	136	N
F072513	Metagenome / Metatranscriptome	121	N
F075479	Metagenome	119	N
F077360	Metagenome / Metatranscriptome	117	N
F088429	Metagenome	109	N
F098876	Metagenome	103	N
F100610	Metagenome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26130J50248_100039	All Organisms → cellular organisms → Archaea	6739
JGI26130J50248_100073	All Organisms → cellular organisms → Archaea	5007
JGI26130J50248_100080	All Organisms → cellular organisms → Archaea	4781
JGI26130J50248_100107	All Organisms → cellular organisms → Bacteria → Proteobacteria	4040
JGI26130J50248_100221	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	2754
JGI26130J50248_100340	All Organisms → cellular organisms → Archaea	1991
JGI26130J50248_100361	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Actinomycetales	1904
JGI26130J50248_100465	All Organisms → cellular organisms → Archaea	1531
JGI26130J50248_100561	All Organisms → cellular organisms → Archaea	1347
JGI26130J50248_100563	All Organisms → cellular organisms → Archaea	1340
JGI26130J50248_100983	Not Available	892
JGI26130J50248_101671	All Organisms → cellular organisms → Archaea	663
JGI26130J50248_101790	Not Available	642
JGI26130J50248_102147	All Organisms → cellular organisms → Archaea	595
JGI26130J50248_102259	All Organisms → cellular organisms → Archaea	585
JGI26130J50248_102548	All Organisms → cellular organisms → Bacteria	557
JGI26130J50248_103254	All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	504

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26130J50248_100039	JGI26130J50248_1000391	F012397	VSVRIKRNKNNKKGVRWNRILILIVLVTTLSLLSGPSLSFSEIKNEINVTPPLNWEPSPTNNSTTMIWFQNSTKSIFAIIKAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGHSNYGYRYFLNLSSPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLIITQKHKELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26130J50248_100039	JGI26130J50248_1000393	F100610	MMPVIISLFGNEDMDITEFRLTNKSVFYRCSYGECFRFIADKCMHCCANPIPDTEMHINYLRRLPDIKKAVTDLGI*
JGI26130J50248_100073	JGI26130J50248_1000733	F013352	MKYTLPGKLLTNSIDKYFSEYLAKNWHSASQFSRLPCLSIAIAGFLFSLMSSSTNAQIEVTVDENVSNPIFNSILSEDAEPRPDILYSTLNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26130J50248_100080	JGI26130J50248_1000801	F072513	FKRLIPEGRNSVIPNRRWGLDAVGVVVNHIMTAGIAAHAIIVNIMSHTAVIFSAIGYGFSCRYINFQIPPLK*
JGI26130J50248_100107	JGI26130J50248_1001074	F002896	MDKMNEDTILHFYRILENSLLESDISKINEEDIDAWSQSFKKVVRESREKSGKGVFVPFLMWKLGEISPVEARKYLVNRKQDECRVSYDHNNVEYILRVMALMFMSWSVTNLKRKTQNGHCQNIDHPHGDXNPRLCKEGTIFHQXLYNECVKTFKDLLIHSDAQHH*
JGI26130J50248_100221	JGI26130J50248_1002213	F024262	CVFSLLDRKNLSPLPIILGSPIAIFPIYVTLSSAYDLAINESTELEFIVNALYYIFDGLMLVTAVIIILNLKKYDPFIFHWICITVGLILLVIGDVGYTYFSIISESLIEEYEWLWSILYAIGYLFLGIGIYWFDRIKNTLEDKKINVFLEKDEMDRLKNSSKNELIADTGTEFSEHIIGYEKFVDKLKDYLERSKEIKILFYDKYWLSDEEVNLILEKIQQGAFFTQIQVNILLPSSETIFKNLVSXNDNRHILVSFFDRTFSSDSLVFIFEEKYVAIIDRKPTSESVDSDTVFYGLITNXDTIVWPHITTFEKIWVLEKAVNM*
JGI26130J50248_100340	JGI26130J50248_1003404	F098876	QLSKYVIEPVMRKFESYLESKDVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKERLIRLIKSCFDKDWQSFYS
JGI26130J50248_100361	JGI26130J50248_1003611	F088429	PQPETNASLNVPEPQPETNASLNVPEPQPETNASEIVTPRSIDLNITVGKDPIARSENQMVTVVALDPTTGKVLDRVFIKLEIKDPVGILVKNYTGTVGNLTRTFKIGENAIGTFIISATASQAGFQSTKSLPFQVQ*
JGI26130J50248_100465	JGI26130J50248_1004652	F005950	MTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLXYGLSKVHKVIIRKYMKDDEFITRAQKTRGIKFDYEMELYD*
JGI26130J50248_100561	JGI26130J50248_1005613	F005683	SNPMEKSNGTKIMGILLVFGLVVYSIYFGQISFAEGVELKTVGKGAISCGNGEEVKGVRINFFVSYDEETPFAEWNMDHKELGSAGGMITNVKTSSDSFVLKGFEAFDSICDVETPSDVKLSGNCGEGTVRLVSDNGNKGTFASNVKCG*
JGI26130J50248_100563	JGI26130J50248_1005632	F006898	MYLILTTTLLLFSLFSLPGAFGAEMFKGLSFSIDIPNTWAYTETPEAPIERALGVSSYTSVVLVPVQFAELLIQEKGDIGMGNGSTAIVFAKASDYSVKNAPLDLYVKYRMNEDDSLNVTSQQDTTIGKEKAVRIDGNKNNNASNIRXLEYLLLXNDEPYVIRYIASMDDFERNLPAFELMVKSFTFGTNATDSKQT*
JGI26130J50248_100983	JGI26130J50248_1009831	F021640	LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKFKSEFDNLSSLLKEVTKILSTKENQINSCIQCKADLILLDEKMNETRTKEVRLTELIKETQTIDKNIEEGKIQYEDLRKSKEFLNASKILAKIDDKKNEIAAFEKNMINKVSILSRPITKFSYQASK
JGI26130J50248_101671	JGI26130J50248_1016712	F057496	VYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGXPTVMKNIDAYLRXNLLESEYGLKL*
JGI26130J50248_101790	JGI26130J50248_1017901	F077360	ITSIYHMDSAIIMQVYEKSKTTAGLTLSDWTKKFWEWLFQLSDEANPVTVVGPSRPWRYGGRQPTQFQKQCMEKHGECVWFIAPAPYSEPNSVIQLNIPVGNWWFLVGPAIACSSQQLYPSLDSIDKVRKHVNEDISKTNELWTIFDGFSIPWYYIDNTNSFIEIKDVPIKESKNMLHQNLEEDTIQTLQCGYWNFIEPVEPGEHLLTIHSKS
JGI26130J50248_102147	JGI26130J50248_1021471	F017423	IKEKSNKLEEGTEIDVSNKKIGDGKIGIHFYDDLLEGFGSTDLEFAFSDFYKHRITDDLKFEYKTIQPPSLLEIDGHKTGSFHIMFSQKDEIDPISGEVQYWITFVGENGYMIEFLSIPENFDTPDNTEMRDRFISSINFLGLSNTTDTSGRISSVAMSY*
JGI26130J50248_102259	JGI26130J50248_1022591	F075479	MMVDINSEYARAMIRDFIKIQKDILGLPNLTTKQKDDINSXGHXLGTLSSQADDDKIKTGLID
JGI26130J50248_102548	JGI26130J50248_1025481	F037482	SVKLKSWATELPAVQVGFSPTCQMHGYSGLWQTEITYQVWRRIQFKDPDYAALSGKTILQISPDGDGGTGCFFGNFQVQIGSCYAEFEISDRVIDVKVLGDGSMKIRNGLQSRQRIRLEGDPPQRDGFEPDLRGAREIDLTIHCPPDEPGVLRGHLSSDVGGNIYSKATGKWYR*
JGI26130J50248_103254	JGI26130J50248_1032541	F033614	LRVTDAHTHGGDSLIPEYAGFFRTWNADSTALKLHGPHGTSFWLEFHASSFKVGDGSARPTLHPLSFNVKWEWSAVDPDIIYFINGNQLAKYNKATHVVTYLGPHQSVPLAYHVLVVGKDAWICAAAGSAGQNSYTQIYCLNPHDPSQHKFIDILKKTINGIAQHDPH