3300003504: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co S AM

Overview

Basic Information

• IMG/M Taxon OID: 3300003504
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089077 | Ga0008479
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co S AM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 24037369
• Sequencing Scaffolds: 27
• Novel Protein Genes: 28
• Associated Families: 28

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	12
Not Available	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria 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?
F005305	Metagenome / Metatranscriptome	405	N
F006663	Metagenome / Metatranscriptome	367	Y
F007651	Metagenome / Metatranscriptome	347	N
F008973	Metagenome	325	Y
F012397	Metagenome	281	Y
F013352	Metagenome / Metatranscriptome	272	Y
F019548	Metagenome / Metatranscriptome	229	N
F020931	Metagenome / Metatranscriptome	221	Y
F021640	Metagenome	218	Y
F023723	Metagenome / Metatranscriptome	209	Y
F026242	Metagenome	198	Y
F031115	Metagenome / Metatranscriptome	183	Y
F032982	Metagenome	178	Y
F038821	Metagenome / Metatranscriptome	165	Y
F048397	Metagenome / Metatranscriptome	148	N
F057496	Metagenome / Metatranscriptome	136	N
F063993	Metagenome / Metatranscriptome	129	Y
F068543	Metagenome	124	Y
F073997	Metagenome	120	N
F075479	Metagenome	119	N
F080452	Metagenome / Metatranscriptome	115	Y
F084279	Metagenome / Metatranscriptome	112	Y
F089313	Metagenome / Metatranscriptome	109	Y
F089980	Metagenome	108	N
F095927	Metagenome / Metatranscriptome	105	Y
F099772	Metagenome / Metatranscriptome	103	N
F103537	Metagenome / Metatranscriptome	101	N
F104644	Metagenome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26138J51218_100048	All Organisms → cellular organisms → Archaea	5309
JGI26138J51218_100079	All Organisms → cellular organisms → Archaea	4409
JGI26138J51218_100154	All Organisms → cellular organisms → Archaea	3171
JGI26138J51218_100212	All Organisms → cellular organisms → Archaea	2621
JGI26138J51218_100234	All Organisms → cellular organisms → Archaea	2422
JGI26138J51218_100489	All Organisms → cellular organisms → Archaea	1552
JGI26138J51218_100572	All Organisms → cellular organisms → Archaea	1416
JGI26138J51218_100737	Not Available	1231
JGI26138J51218_100820	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1169
JGI26138J51218_100946	All Organisms → cellular organisms → Archaea	1107
JGI26138J51218_101727	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	863
JGI26138J51218_101905	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	835
JGI26138J51218_102104	Not Available	807
JGI26138J51218_103356	All Organisms → cellular organisms → Archaea	684
JGI26138J51218_103523	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	674
JGI26138J51218_105113	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	591
JGI26138J51218_105270	Not Available	585
JGI26138J51218_105390	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	580
JGI26138J51218_105920	All Organisms → cellular organisms → Archaea	561
JGI26138J51218_106108	Not Available	555
JGI26138J51218_106726	All Organisms → cellular organisms → Archaea	537
JGI26138J51218_107057	All Organisms → cellular organisms → Archaea	528
JGI26138J51218_107161	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	526
JGI26138J51218_107294	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	522
JGI26138J51218_107577	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	516
JGI26138J51218_108159	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	502
JGI26138J51218_108289	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26138J51218_100048	JGI26138J51218_1000481	F012397	LILIVLVTTLSFLSGPSLSFSEIKNEITVTSPLNWEPSPTNNSTAMIWFQNSTKSIFAIIKAPDDLVFPLFIAGPFMTGYLKYKGVLESADRLTFGNSNYGYRYFLNLSFPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLILTQKHNELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26138J51218_100079	JGI26138J51218_1000797	F048397	VHNSTIFRAILEKNKCDKCNLTIHPNFMGNHKCDHQNCPICKNPITPSQYWPHIRSHPGHENDSPPLPKRNMDENRKNENHSGYGNYQRN*
JGI26138J51218_100154	JGI26138J51218_1001543	F007651	MXNDLNELIARKDKLEGELHHXLSXDYNELMKNLSESFRXMHENSVQYYKQKANEELDKMEKNIQSGNKLSAINQKLLADTYXSFATTI*
JGI26138J51218_100212	JGI26138J51218_1002124	F073997	MLSSGIESFALINEVGAQISPSERLHSLLEQIVRSEVRKLAISLMFPLLEKSNMPI
JGI26138J51218_100234	JGI26138J51218_1002341	F005305	EDLEKELGPLIENFQSLVKDAKSKKLESLREDEDFKKEFNELSKDVIEPVMRKFESYLESKDVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKERLIRLIKSCFDKDWQSFYS*
JGI26138J51218_100489	JGI26138J51218_1004893	F089980	VNLPNGFMDLESATELIVMNWLGIFSLAATIFIAIVTINYRNKQHQIQGLLDAFKILNTREHRTSRRKVYELYIEYEKNKDVGIFDNVPEVVDVRADFDVIGTLVKSRNIDEKLFLIEYGPLAYRCWKYLKKHVEAERKKRNFNPFMKNFEDLANKANRFWSKRGYDLSKTLL
JGI26138J51218_100572	JGI26138J51218_1005721	F019548	MNPSKKEIYKILERFTSQKGGILIILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSGIEGDVIWFGGMLDKSGSEFIGSTYDDGLKSAPVEQSELVHRVNQAIDKCLEYMLNSVELDKXCIC*
JGI26138J51218_100737	JGI26138J51218_1007371	F026242	MRHEEACLGMFVRLLSDWHGIPKGTVGSIDTVETGMDGSWCFTIFWELHRPLSSAMPGRTRTRTGLQSGSLGLRLWEEDLPRFEXITQEQKAMAALLVAPPADTSNPTTLSLFPPQAVEQLTLPFTDGELVEDDQPQLALASVGA*
JGI26138J51218_100820	JGI26138J51218_1008201	F008973	MSGPTRYPGLAERMRVRVLFFVLTWLTGLLLAASFASAAYGFGRMAAPERTDVISLAIFGAIGLLSQAGLLLAPWAVTRGTTPRTIAALLMGPSGVFLSIFAYEGFTRYAAGAPIWVVAWAAYVCGVFVY
JGI26138J51218_100946	JGI26138J51218_1009462	F057496	VYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMKNIDAYLRKNLLESEYGLKL*
JGI26138J51218_101727	JGI26138J51218_1017271	F104644	VRYRHVWPGLLLLAALGLLLAGLVRWGDHFLSPGPTGGIHRLLQLWAASRPGDELAAAPVSAGTASVDPAAPPPVSLPSMPSTAEA
JGI26138J51218_101905	JGI26138J51218_1019051	F063993	IVTIQLAAPYLRVEVPEERLSAFSVGKSVEVWPQARPDARVRARVVSIRPRSEFATRRNWGLQSRDLRTFSVRLAAEGLPIVSGQTFVVEAGAN*
JGI26138J51218_102104	JGI26138J51218_1021041	F021640	LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKFKSEFDNLSSLLKEVTKILSTKENQINSCIQCKADLILLDEKMNETRTKEVRLTELIKETQTIDKNIEEGKIQYEDLRKS
JGI26138J51218_103356	JGI26138J51218_1033561	F013352	PIFNSTLSEDAEPRPDILYSALNKDTIVGEVLNNFSYPIELVRITATVYDKNGIIVATGDKYVNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEALQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEFSLITDNGQNNTISQQ*
JGI26138J51218_103523	JGI26138J51218_1035231	F084279	MKKTLMTCLAIAALFAIAGSASAITCTIDQRPAATLLVPYFEASFNPDGTPSGTGPNARDTLVTICNASSAPMIAHVNVFNERTELVLDFNIALTGFDCQSMSMARV
JGI26138J51218_104240	JGI26138J51218_1042402	F103537	LRFGSKLEIMPFVLRGRITKSIFAFAAIEYEFPLTVSGQIKHELLKMNDARFKDIVHWRYTEVAKQAAKVFALNKPFINCFKIIHK
JGI26138J51218_105113	JGI26138J51218_1051132	F080452	MMAKRSALLSLLICLAGASAFAQIAPNNQGDIGLFTMPTADNPRGGQLTLGLYGWLERLVAGELPTDADHRTRLYNHWAVAGSVGLGLTDRWSVFASAGWEERESRGGWE
JGI26138J51218_105270	JGI26138J51218_1052701	F032982	QQRNDLMQELGLSEEEADQAVSTLELYYHIEASENQWTQAWKAAKRDFLADGERTGIRLADLVVKYVDIARLGGGPESRWT*
JGI26138J51218_105390	JGI26138J51218_1053902	F023723	KRLKPEQYELKVRWETARQVLEVTPTGVRFDFNAPLKVGTRYPVSLKAPGVAFSTTIEVSRCQLTVDSATGRFFRVTGRFYPYVE*
JGI26138J51218_105920	JGI26138J51218_1059201	F020931	NKELLEIVENEKKVLQKDLIDNLEPTRNLVLDCLNRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLINRFGQVGDSHNRILNEFMRKQINKLKSEFDNLSSLLKTVTKIISTKENQINSCIQCKADLILLDEKMNERRTKKVRLTELIKETQTI
JGI26138J51218_106108	JGI26138J51218_1061082	F099772	QSFFLLLLTVCAVQLMGTACADDCLRQWSTSPVHAHDQLPGSPDGQTETDPGEGEFEELALAQGEAFRIIHLARACVLDNASCPRTDFAFDWFRPPALP*
JGI26138J51218_106726	JGI26138J51218_1067261	F068543	TAETAVVIESAVDEAGNSLSQGDLIIPQKVTFTFSADASGATQAFEEEGSQDYEFECALDDDSFSSCNSPQTINMEDGKHTLVVRLAESD*
JGI26138J51218_107057	JGI26138J51218_1070571	F075479	EYARAMIRDFIKIQKDILGLPNLTTKQKDDINSXGHXLGTLSSQADDDKIKTGLIDMMNRLN*
JGI26138J51218_107161	JGI26138J51218_1071612	F038821	EKEQRARRRRQSGTADGHSLSQLLRTLGDLVGQRSNRLLGIAWQELSIGLVIETAQGRKEVEIFRPDNLYDLWVRMYLKRNHRAFDTPR*
JGI26138J51218_107294	JGI26138J51218_1072941	F006663	VWPLTLRDGLPTTLPGYAAAPRDPLPDSDENEMGTYTEVSRFFQRIESPTSVKQFRLVVQDYGPGKDLAGALKRAVAEASRAPSVEARELKIANLPAFAVTDRSSGNPTTLVTVIASPARLVLAQGANVEREEAVKLLGRVDFQKVIDAK*
JGI26138J51218_107577	JGI26138J51218_1075771	F089313	GEEDLAPLARNVNSEVRKQYILGFSPSGRGELKYRVVFVSVAKKGNWIVRTRRGYRGTAPASTASR*
JGI26138J51218_108159	JGI26138J51218_1081591	F031115	AIARLGSTEEPVFNSVQEEVVEKIIDGFNPPDTEIRQRLAREDPDYDPVAVYAQYAWASGDEFLASMRFLVDFVNVLPTFTRTFSTRYGLPARLELRRFHPVDANRYFLFLRDSNIRALRNIFSGARFIGTAPIYVNEKVTWKAMNYPGPWVRETDGATADLGRTT
JGI26138J51218_108289	JGI26138J51218_1082891	F095927	RKRVAPFMKRYNISLPVYSAAPEDVAQMTAMGIPSTFIIGPDRTLIDMAVGFSPDVEDRWKRVVEKHLKKK*