3300003396: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M3 PM

Overview

Basic Information

• IMG/M Taxon OID: 3300003396
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089076 | Ga0008478
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M3 PM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 11973419
• Sequencing Scaffolds: 25
• Novel Protein Genes: 25
• Associated Families: 23

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	16
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	2
Not Available	5
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae	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
F007651	Metagenome / Metatranscriptome	347	N
F010126	Metagenome / Metatranscriptome	308	Y
F010272	Metagenome / Metatranscriptome	306	Y
F011965	Metagenome	285	Y
F013352	Metagenome / Metatranscriptome	272	Y
F016054	Metagenome	250	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26137J50245_100031	All Organisms → cellular organisms → Archaea	7517
JGI26137J50245_100136	All Organisms → cellular organisms → Archaea	3392
JGI26137J50245_100225	All Organisms → cellular organisms → Archaea	2502
JGI26137J50245_100273	All Organisms → cellular organisms → Archaea	2244
JGI26137J50245_100288	All Organisms → cellular organisms → Archaea	2158
JGI26137J50245_100299	All Organisms → cellular organisms → Bacteria	2109
JGI26137J50245_100316	All Organisms → cellular organisms → Archaea	2043
JGI26137J50245_100486	All Organisms → cellular organisms → Archaea	1425
JGI26137J50245_100552	All Organisms → cellular organisms → Archaea	1290
JGI26137J50245_100600	All Organisms → cellular organisms → Archaea	1221

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26137J50245_100031	JGI26137J50245_1000314	F081936	LLDRKLDAKKPSPPNVEASVNPKVEQLAHVLEITLIVVPESADLLNFNFRFLIIYRLKFTKIAIRTELIQVKINASIISLGT*
JGI26137J50245_100136	JGI26137J50245_1001362	F013352	MKYTLPGKLLTNSIDKYFSEYLAKNWHSASQFSRLPCLSIAIAGFLFSLMSSSTNAQIEVTVDENVSNPIFNSILSEDAEPRPDILYSTLNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVTDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26137J50245_100225	JGI26137J50245_1002254	F026602	LNNQIIAIGFILISLTLASMHVFAGRLYAIEQPSKMEGINEEECNKIFNCKIISEDVLKYPDIVNPFNKNEEIAKTLNANDAQIMTEHTCQKLMDVDIVKKKDQKIGEQAPKYLVCLP*
JGI26137J50245_100273	JGI26137J50245_1002733	F100606	MLRNHSNYMSNDLNELIARKDKLEGELHHELSSDYNELMKNLSESFRDMHENSVQYYKQKANEELDKMEKNI
JGI26137J50245_100288	JGI26137J50245_1002881	F005683	MGILLVFGLVVYSIYFGQISFAEGVELKTVGKGAISCGNGEEVKGVRINFFVSYDEETPFAEWNMDHKELGSAGGMITNVKTSSDSFVLKGFEAFDSICDVETPSDVKLSGNXGEGTVRLVSDNGNKGTFASNVKCG*
JGI26137J50245_100299	JGI26137J50245_1002993	F010126	MNLFTSRLLTICGLISTALLFQIMISSNLVVAIESSESNTNKISSGSELESIVTNGSSTNQLAYRNSQHGIFMLFPSNWTFSDSGLPEYTQVAAFYGPLQNLSDPIPPRLTITVMNYQQNVSLKDFTNMTLSSLNQTNQVKILSSEPTTLAGXPGYQVVFSTLPNIGNPVSFEIMHSWISMGKKIYVLQYSAESSKFDTYLPTIKQILQSLRIDTTR*
JGI26137J50245_100316	JGI26137J50245_1003161	F007651	MSNDLNELIARKDKLEGELHHELSSDYNELMKNLSESFRDMHENSVQYYKQKANEELDKMEKNIQSGNKLSAINEKLLADTYLSFATTI*
JGI26137J50245_100486	JGI26137J50245_1004862	F006898	MYLILTTTLLLFSLFSLPGAFGAEMFKGLSFSIDIPNTWAYTETPEAPIERALGVSSYTSVVLVPVQFAELLIQEKGDIGMGNGSTAIVFAKASDYSVKNAPLDLYVKYRMNEDDSLNVTSQQDTTIGKEKAVRIDGNKNNNASNIRLLEYLLLHNDEPYVIRYIASMDDFERNLPAFELMVKSFTFGTNTTDSKQT*
JGI26137J50245_100552	JGI26137J50245_1005521	F002896	MDKMNEDTILHFYRILENSLLESDISKINEEDIDAWSQSFKKVVRESREKSGKGVFVPFLMWKLGELSPVEASKYLVNRKQDECRVSYDHNNVEYILRVMALMFMSWSVTNLKRKTQNGHCQNIDHPHGDTNPRLCKEGTIFHQDLYNECVKTFKDLLIHSDAQHH*
JGI26137J50245_100600	JGI26137J50245_1006001	F010272	MYMNHERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKEQAQEKLFELAQKFNKILKDSNVNLTLPQNGDLSSKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKQEAGADLSXLMQKLQSLXNNSTQ*
JGI26137J50245_100883	JGI26137J50245_1008831	F011965	PSLHPLSFAWTWEWSAVDPDIIYFLNGNQLAKYNKVTTLVTNLGGPPNGDTVTMHVAVVGQDSWVCSTAGAGTQNSYTKIYCLNPNNPSQTKFIDVLNKTINGIVQSDPKWPTSAAGQTIGIHSMYGSAAGTWLDVVFLQQSWGANGDSVFNLATNTWSLVTNSDTRWSGHSSMGNGKYVNGSGSINGMDSRGALLRDPNNLMDATKYSFIMQPPSTAGWYDAEHSSWFNSSTNPQAPVLFSRYNCTAPPGPLTWYGEIIAAATDGSNTVWRFAHNHNGGLVGFAGQSFAQISNDGRWALFSSYWDGTLGAAAGDFGF
JGI26137J50245_100910	JGI26137J50245_1009101	F057496	MAGVYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMKNIDAYLRNNLLESEYGLKL*
JGI26137J50245_101175	JGI26137J50245_1011752	F065259	MALALADLLGTPAEGTDLNRNIEIGNKATGASSAIAAGRVVVLDESNGLWGIAGTTSSGRFGIVPKTHPLNVDADDAIQVATGKNSEWYVEAAGTIKPGARCGPYTGGKVIQFVAGDVTATPTEATIEAAIKDFEQAPFVYTGHYGEGSGLFNNPTDGSSGQAVRV
JGI26137J50245_101395	JGI26137J50245_1013952	F057659	MKVFWAFVIIILVFVTTLPVEHRVIPSISGENLSCINSNITKFGNQSINLSIMSEEYFKNXTSDNPQLAQLICPDIINYTTK*
JGI26137J50245_101443	JGI26137J50245_1014431	F065259	MALALADLLGTPADGTDLDRXIEIGIKATGSSSAVAAGRVVVLDESTGVWAIAGSSSTGRFGIVPKLHPLNVDADEAIQVATGKNSAWYVEAQGTIKPGARVGPYTGGKVQQFVAGDVTATPTEATIEAAIKDFEQAPFVYEGHYGEGSGLYNVPTDATTADPVRVRII*
JGI26137J50245_101521	JGI26137J50245_1015211	F033614	TALKLHGPWGTSYWLEFNPSTFKVGDGSSRPTLHPLSFDVKWEWSAVDPNIIYFINGTQLAKYNKSTHVVTNLGGRGVSLKYHVVVVGLDAWVCAAGPGTQNTYRQIFCLNPRNPSQTKFIDILKRTINGVYQSDPNWPTSAPYQTIGIHAMYGSATGTWLDVGFHRASWGAGGDSVFNLSTNKWSLLKANRYSSGHSSIGTRFVNGSGSINGMYSGGACVRNPSNLMDSTQFKFIM
JGI26137J50245_101648	JGI26137J50245_1016481	F005950	MTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLQYGLSKVHKVIIRKYMXDDEFITRAQKTRGIKFDYEMELYD*
JGI26137J50245_101792	JGI26137J50245_1017921	F017423	VTFFLSFTLFIPNVNSSFALEYTNYLSEKYQIAFQYPSDWTIKEKSDKLEEGAEIEVSNKKIGDGKIEINFYDDLLEGFGSTDFDFAFSDFYKHRITEDLKFEYKTIQPPSLLEIDGHKTGSFHIIISQKDEIDPISGEVQYWITFVGENGYIIKFLSIPENFDTPDNTEMRDH
JGI26137J50245_101989	JGI26137J50245_1019891	F048397	HNSTIFRAILEKNKCDKCNLTIHPNFIGNHKCDHQNCPICKNPITPSQYWPHIRSHPGHENDSPPLPKRNMFENRKNENHSGYGNYQRN*
JGI26137J50245_102315	JGI26137J50245_1023151	F016054	MVQSLLENEKEPDVYELGVAEGIKEMLALRGFTKEKILNSTVSNLAETLQIDYYVALIXYNSAKKN*
JGI26137J50245_102712	JGI26137J50245_1027121	F089091	EPCNLLKPLIHLPRFSHKHEVFMYRDLALPLLVVGVMGCTSVQYNEVDCGTLPSDTFWSGNIALQCQEYRRLQAETAYRAEVAQSLRSYRECLSKHEGSLTGAKEQCSVYTQGLRDSPGASPPTK*
JGI26137J50245_102919	JGI26137J50245_1029191	F063100	VLPTTFSDRFQQMMSAKLVELRKESSIEFSKAEADAARRGEVSASSTAGLRSQVDIHLVKKIIAAAVVLLTELISELQIPFSDSLAGELKDQVKAYVSNEQCEDLHRMNRGGISEQHAARLKEELYVNRSFFLKRADAQIDLFVDSL
JGI26137J50245_103042	JGI26137J50245_1030421	F057150	ALIVNSGNMAYAQGNNTQGNVTTTIDADSLIKDLKARHPILAQLVTNEDKDLVVKFKDLDTKEAVKTALALNMLHLLQQYREIDEPQ*
JGI26137J50245_103045	JGI26137J50245_1030451	F010126	PTANINKTNYDYQLEPNVTDGNTINEIAYKNPQHGIFMLFPSNWTFSTSGLPEYNQIAAFYAPLQNLSDPIPARLTIAVMSYEQNISLKDFTNMTISSINQTGQVRISSSDPTTLAGRPGHQLVFSTLPNIGNPISFEILHSWTVVDNKIYVFQYSAESARFNSYLPTVKHILETL
JGI26137J50245_103053	JGI26137J50245_1030532	F087678	MTVITPPDKAGFYWFRYDNLSSKVHYKVLLEVVQMQPQPTEIGGKFVVRWMNQLVPLEQMPEGLWRGPIADLR*