3300003761: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mTSA_r2

Overview

Basic Information

• IMG/M Taxon OID: 3300003761
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101308 | Ga0055535
• Sample Name: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mTSA_r2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 124390723
• Sequencing Scaffolds: 42
• Novel Protein Genes: 43
• Associated Families: 36

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	22
All Organisms → cellular organisms → Bacteria → Proteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Erythrobacteraceae → Erythrobacter/Porphyrobacter group → Erythrobacter	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Paucibacter → Paucibacter toxinivorans	1
Not Available	9
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Leptothrix → Leptothrix cholodnii	1
All Organisms → cellular organisms → Bacteria	2

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Roots → Endophytes → Unclassified → Arabidopsis Root → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations

Alternative Ecosystem Assignments

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

Location Information

• Location: USA: North Carolina
• Coordinates
  • Lat. (^o): 35.6667
  • Long. (^o): -78.5097
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F012876	Metagenome / Metatranscriptome	276	Y
F023377	Metagenome / Metatranscriptome	210	Y
F023378	Metagenome / Metatranscriptome	210	Y
F026918	Metagenome / Metatranscriptome	196	N
F028856	Metagenome / Metatranscriptome	190	Y
F031516	Metagenome / Metatranscriptome	182	Y
F034241	Metagenome / Metatranscriptome	175	Y
F035339	Metagenome / Metatranscriptome	172	Y
F036775	Metagenome / Metatranscriptome	169	Y
F036776	Metagenome / Metatranscriptome	169	Y
F039453	Metagenome / Metatranscriptome	163	Y
F040130	Metagenome / Metatranscriptome	162	Y
F040670	Metagenome / Metatranscriptome	161	Y
F040711	Metagenome / Metatranscriptome	161	Y
F040712	Metagenome	161	Y
F044564	Metagenome / Metatranscriptome	154	Y
F044583	Metagenome / Metatranscriptome	154	Y
F044585	Metagenome / Metatranscriptome	154	Y
F047761	Metagenome / Metatranscriptome	149	Y
F049682	Metagenome / Metatranscriptome	146	Y
F049748	Metagenome / Metatranscriptome	146	Y
F049749	Metagenome	146	Y
F050419	Metagenome / Metatranscriptome	145	Y
F053329	Metagenome / Metatranscriptome	141	Y
F055847	Metagenome / Metatranscriptome	138	Y
F056275	Metagenome / Metatranscriptome	137	Y
F058198	Metagenome / Metatranscriptome	135	Y
F062899	Metagenome / Metatranscriptome	130	Y
F067349	Metagenome / Metatranscriptome	125	Y
F073010	Metagenome / Metatranscriptome	120	Y
F076251	Metagenome / Metatranscriptome	118	Y
F076649	Metagenome / Metatranscriptome	118	Y
F077376	Metagenome / Metatranscriptome	117	Y
F078153	Metagenome / Metatranscriptome	116	Y
F090602	Metagenome / Metatranscriptome	108	Y
F092337	Metagenome / Metatranscriptome	107	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055535_1000047	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	139836
Ga0055535_1000056	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	128204
Ga0055535_1000073	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	112778
Ga0055535_1000088	All Organisms → cellular organisms → Bacteria → Proteobacteria	102543
Ga0055535_1000097	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	95927
Ga0055535_1000123	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	83521
Ga0055535_1000179	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	67830
Ga0055535_1000252	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	56714
Ga0055535_1000272	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	54297
Ga0055535_1000306	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	49813
Ga0055535_1000433	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	38884
Ga0055535_1000459	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	37599
Ga0055535_1000467	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	37033
Ga0055535_1000508	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	34490
Ga0055535_1000550	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	32223
Ga0055535_1000620	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	28873
Ga0055535_1001370	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	12742
Ga0055535_1001601	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	10728
Ga0055535_1001717	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae	9913
Ga0055535_1001877	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	8896
Ga0055535_1005331	All Organisms → cellular organisms → Bacteria → Proteobacteria	2851
Ga0055535_1005865	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Erythrobacteraceae → Erythrobacter/Porphyrobacter group → Erythrobacter	2601
Ga0055535_1006961	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Paucibacter → Paucibacter toxinivorans	2214
Ga0055535_1007601	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	2048
Ga0055535_1007842	Not Available	1988
Ga0055535_1009346	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Leptothrix → Leptothrix cholodnii	1696
Ga0055535_1010532	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1511
Ga0055535_1010658	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1496
Ga0055535_1011050	All Organisms → cellular organisms → Bacteria → Proteobacteria	1448
Ga0055535_1011441	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1402
Ga0055535_1012649	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1278
Ga0055535_1013792	Not Available	1181
Ga0055535_1015314	Not Available	1076
Ga0055535_1016852	All Organisms → cellular organisms → Bacteria	987
Ga0055535_1017581	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	950
Ga0055535_1020990	Not Available	801
Ga0055535_1021105	All Organisms → cellular organisms → Bacteria	797
Ga0055535_1023609	Not Available	717
Ga0055535_1026726	Not Available	637
Ga0055535_1028407	Not Available	602
Ga0055535_1031860	Not Available	539
Ga0055535_1033395	Not Available	515

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055535_1000047	Ga0055535_1000047143	F028856	MDNFSAGQSHDAKFEAGMLFDMDNPLALLRPDDNLGDEAAFPSTWQLLASGDAPND*
Ga0055535_1000052	Ga0055535_100005289	F077376	MTTTYVLSLTGDEEKAANATHWATFRKAKLVSISRRTPEMPPAAAGKDSIVVTAHGELDPLDAERAAATRHPQALAALLVRTLDIQDGAGVVLADFDSEQFAADVVAEIAALGRDVVCPGRASNFAFGSRVGARAWRA*
Ga0055535_1000056	Ga0055535_100005689	F050419	MSNASRPTFLRNFGRGTAARRAPDLADMGTAFALDEALEQGSYDTLAPGESPPPMRAVVPVAPWRLWLGRKLGA*
Ga0055535_1000073	Ga0055535_100007360	F023378	MKFDAALWPVPPGVEIHFYFQCMREPQFYKTRTILDKLMLDVGMFPDRVATTGEMIPSHFVWAHATEQPPSGVFRRQTGNLAMDLSGSDATHPVALSHVVKTLAAERSRSTTIIHWIVREDESPADPASLDCLYPTRLRNGVYDSEESAQVPLAEVPAPTQPAPLSAAGLGPVQEWPGVRRRANTR*
Ga0055535_1000088	Ga0055535_100008826	F092337	MSALQTATFTISIRGVSEDELEAAAAAFICTLHRAGLTPHDALAAWGRMDAWEQRDFAPDAEPGPAWWRTMRVARDAAMAALDAAGLDGQQRPFTIEAVSPSC*
Ga0055535_1000097	Ga0055535_100009795	F012876	MTKTTHHFTALALSALMALGIVAGMNGLATAQYAAADSQEMARYGQAHVAVQHVTIVGHRANA*
Ga0055535_1000123	Ga0055535_100012359	F053329	MPPDLENPSAHEPALSRNHAAGVPRETASPAERALAPDGDAPMQSASATADDGTYVGQAGGYMGGPLPAVESGHAEVDKANVRGDGAYGFPAGPGVGVPGGEHQPAAQKPDVVPNPYPER
Ga0055535_1000179	Ga0055535_100017916	F026918	MDSKQLFIEHLAGELQAMEVGRVPMNALRYRVHAKMLRKALIGAATPALLERQGGAHPQVVHALSNRFFEETGHLLQPNATAHKARSVLERTLATCRQARQK*
Ga0055535_1000252	Ga0055535_100025230	F067349	MAAPDRPSILISAALAVATPFLGGAMAWRLLDDDGRSGLVYVLVYWPSILLDALPPVVADAFTVSALPTVLLYFAGYLLLCQGVRAAWKRIAAIRFYRRHA*
Ga0055535_1000272	Ga0055535_10002728	F036775	MYDQLDQMPDVPEIEDRPGQRRQARLSNAVFYAGCFALALLPASLAGILLHDFIGEPMLFLAAVVLSTWVVTTVALVKIAGPMLRCRAIVAAGGLVSVAMCSLFLIE*
Ga0055535_1000306	Ga0055535_100030612	F023377	MTHRPVCSPRAIRMAMVAALALAGAAAQAMTVSYQCTGRRLLTAELAPRQGQLHFEGQDWTVSRVPGGHEAHYVNKKDGIDVVTRERNMTFTHGSETLQCFLYSDALPGDAPQKTN*
Ga0055535_1000433	Ga0055535_100043336	F055847	MNRRYAYRDYEILVSARPAGGQPGWRPEICVIAPDDRWEFVPTHHSLVANDPGWCLEIGRLCAESAIQSMDPARERATRAGPLH*
Ga0055535_1000459	Ga0055535_100045912	F040711	MSHDAPRDQLASALGRDADHVVMERGWSLAFVGVDGQVRLLQFRLSKKGFDADRAADDAVFATMLDEFAAVVERLLAARWGGIAMRAAFDGEGELVERLYEAGHLARCDAVDPVSPAGRLVKDGEVVDARELLVRASARLVENWGVFERAAARDDGAYAHEARIRHWIEGTSA*
Ga0055535_1000467	Ga0055535_10004675	F040670	MNPLVNRNTATADNGRPPPADAPMQALPWAEDSSRSIGAEDANTRYQGELFLPGWLKIELQPTAEQGPGA*
Ga0055535_1000508	Ga0055535_10005084	F031516	MVDNRINPSSTMLHFDTAQMAAITQAHFFSRVAEFIRDQTGVAAYRQAAMDTMLRTELWAPHWPTLRNASEHDAALFMCFLLACATLGVDANRATEAVRQSTQPETSMKLFLSERGLLRFSAFDVPDLTRPGAAA*
Ga0055535_1000550	Ga0055535_100055020	F056275	MDWHCINFKRGGAHEAEAADLVLALEDAYDSAGEPPAAEVFLARGRVGDYAFYLSPEAASMAPSVLQRFHAVMCDPPQDLHRCTPMIL*
Ga0055535_1000620	Ga0055535_10006203	F073010	MNRWLLRPRVMGWIAAGVFLCIALFQWPSSPAASSRFAALAGAPPFDERPAGYTLSGVLAAFHSLGPQGLADYTAYRALDMVFPWLLCALVAAVMLRLDAPRATLWPWLAAIADTIENVLQWRILVTRDDLSPELVQWASGATQVKFAFYGGMLLMLLVVGVRALWRQHRALR*
Ga0055535_1001370	Ga0055535_10013702	F039453	MPATLTPLRGDAIRVTHEDVHYEPLQRDAALGALLFALDLLGRDAIDVPAMRYADRVTLGPALDAARQYGLILQRHVARIDRGSPLLPAAVKVDDVHAWVHEAARAVPEAERDRFCWRLARRLGANPWCDERPAIALENQQFGMFEEGFEEIEAAKAGALEEAVAEAGDGATPA*
Ga0055535_1001601	Ga0055535_10016015	F035339	MPTTGAELTRAQLRRDRVVLWCWLPVGGLAMFLVVKAWQFVAGAAPPALYTVLDVAWIAVTFALISRRSTSRCPKCDHRWLRAFPWMSLKKVECGVCGHEMPED*
Ga0055535_1001717	Ga0055535_10017177	F047761	MDVITRLAALLIALLLAIDAFSAERTETLRVDRHTRLTRWHQGDDYRVHFAGGRVESCEVGWTVFNALADGDLVAVDTSRVFKSCDGIRRGDEVISGGRAHRWLLLVPMAVLLAAAFGWIRFERRYDDEQGWWFS*
Ga0055535_1001877	Ga0055535_10018773	F049749	MKFFGRKRASVMLVRAWCSPFGEDGPAGELLALVDQVLAAIAAKPLEGAINHGDVQPMSSLRRALAKMKPAQLDTLTVQDESGDVICSFGAEGASVGDRSRAFEIFALLPPAAEAQQDKLLRMLLGYGLHYGYARSLGPDFNPLSEVRVKRGFFDTAIQVDGGRADWLVPEMDVRAGAVRGVYPANVFSAIGLARLAGSGLRLPPSAPTLGETLWRPSAAERAEILRLNPTYRDYLHFGDA*
Ga0055535_1005331	Ga0055535_10053313	F077376	MTTYVLSLTGDEEKAANATHWARFRRAKLISVSRQADQRMPDAGRDSIVIAEHGAGDRRATSCNPSTHDPAALAALLVRTLDIQDGTGVVLADFDNEEFAADVVARIAALGRRVTCTGQLRDFSFGARVRPLFARAA*
Ga0055535_1005865	Ga0055535_10058653	F031516	MLHFDTAQMSAITQAHFFSRVAEFIRDQTTVAAYRQAAQDTSLRTALWAPHWSTLRDASEHDAALFMCFLLACDTLGVDATRAAEAVRQSSQPETSMKLFLSERGLLRFSAFDVPGLTRPGAQV*
Ga0055535_1006961	Ga0055535_10069613	F034241	MSQANPRQYIGALRAAVSAAKAVNKARAAAYHLLPDGISCKMDWAGWSDPWYDATPRQQALLDVLQDLLDGGETEVPMIALKTALRLEIPESEILRSRDNVGTDGEPGYFFDDVLHGLYVLDAQETEQVFYSLIDRLMQPQCVRAGPGDR*
Ga0055535_1007601	Ga0055535_10076014	F078153	MGWMLFEAMLALGVMLAVVWWTFRGRAENDDEADADEPDRPQ*
Ga0055535_1007842	Ga0055535_10078421	F023378	MSKTYVVSGCGMKFDAALWPVPANVEIHFYFQCMREPQLYKTRTILDKLMLEVGMFPDRVAVAGDMIPSHFVWAHAGEQPVSGVFRRQSGQLAMDLGDTDASRPVALSHIVKTLSADRARSNTAIHWIVRESEDLAELSGLDCQYPPRLRSGGTDDGDESREMPLSGQMPLRPSQRMPLSPMGMGPTEAWPGVRRR*
Ga0055535_1009346	Ga0055535_10093461	F049682	MEQREFEAVVDEFGADVQDLVELVETARYEQATAVEISRLLDAREDLLVLVNKLPALRAAEAPASMSVPLASLRTRIAHAREALRSSHDSKEILQMVAETGETFSSIVAPLQAAGRWPKGRSR*
Ga0055535_1010532	Ga0055535_10105322	F044583	VDQLLTPNQEILRNRIRFALRRATGFVFDIDAMLRKPELRAKRIGLWRDVADHELSSLLDQLETEFQADAADEEEAERTVVLRRPEAGATPR*
Ga0055535_1010658	Ga0055535_10106581	F076251	MTTPPRSPFWRVLQLIAGVALFLYALRLLSPMPGDRAGFILLVAILAAGSMALADSIIGLVVAGLDKMHKKGNE*
Ga0055535_1011050	Ga0055535_10110502	F023377	MTHRPVCPPRAIRMAMAALLLLAAAGVQAMTVSYQCTGRRLLTAELNPRKGQLHFEGHDWTVLRVPDKNMARYVSKKDDIEVITKERAMTFTHGGETLQCLLYSDALPGDAPRTRPAN*
Ga0055535_1011441	Ga0055535_10114412	F036776	MNAIVRLLAVYTGLSLLLCAFTRLEWSPLQPNGFGQWLALFLLIFPAAAAAEFLGERLLGKTPAVEAAESRTHSDCSWGRIVTGVGVLLVTFGVVLGVAWWLSHPAATL*
Ga0055535_1012649	Ga0055535_10126491	F050419	MTNASRPTFLRNFGRGASSSRRPPDLADMGTAFALDEALESGSIDSIVPGDPSPPPVRAAGRVAPWRLWLGRKLGA*
Ga0055535_1013792	Ga0055535_10137922	F040712	MAARPAAGQNGVLLIRLPASMSLRCFIVRRCLHASLEAVGLRAVNLPLVVDARRHVHPPVPLDAGYLVVDRRAFARITFPRADGSAAATMQTIGFASLSGVLRAICAERIGLAGRAAIPGPRRALELRREGRWSEVLEASERVEAPMRARLDAWLRSWRFATWRFALQAFKRL*
Ga0055535_1015314	Ga0055535_10153141	F044585	MTPAEIDHQALTALRLLPDEPERAMRVWDDAFARATAAGLDRTLLRLRIVKMHHQARFGDRHALGPKMLAATVEARAHGWRTESLLVDLLEVFLATLSANHADGMGDVEAIRAEAEAHLDPIELSWMELMAGHFRGYMLGWALEPERTYRALNRLIACPDSPPGLVAN
Ga0055535_1016852	Ga0055535_10168522	F062899	MNPLAANRTAAPVLPPPPRAKHCSFVEDLNWPAHMPTPDKKTVRPTEVWVPGPNGQWEGVTPTLQ*
Ga0055535_1017581	Ga0055535_10175811	F090602	MHPQPTSAASARVEWELLPSLMTRLGGRRPRSQPAWRETMPSEIDLQEPSDPFEEVLPGLEVREVREPDIFQIFFG*
Ga0055535_1020990	Ga0055535_10209901	F036775	MYDQLDQMPAIDEIEDRPGQRHPRGMPDPVFYACCCALALLPASLAAVLLHRLIGDPFAFLAAVVVAVWVITTVALVKIAGPLLRCRAIVAAGGIVSVAMCSLFLLD*
Ga0055535_1021105	Ga0055535_10211051	F040130	MPGSVKRALAIVAGVVLGMAIAAGASPWRELFRRTEPVQPAPIQREPAPDTRV*
Ga0055535_1023609	Ga0055535_10236091	F076649	ASAITTIVLPPRSAFAAARANGGLATGDYFHDFAELIVRVRSVKWIEEICSETFPATAEANRHAYEVWHVDNGPLVDEVEGQFLVIAKYWGDESPAARKEGLTVDQLKAKVDANRAGLRQDFLSRGMKSFQTRCEAYPEILLSPQLDFERSQADLLRSVRMGPGQRQ*
Ga0055535_1026726	Ga0055535_10267261	F058198	VNELLLVSLVLVALALRTFVVRHRIARWECLWRFRSGPCTVELRRRAGMARLGGDSCEYPQPREFRVMSLRVGGIPLWSQRAIVSLPTDADSRIGEIPASEFDHLFDRHFRLSWPRQAKAMRRLAARAH*
Ga0055535_1028407	Ga0055535_10284071	F044564	MTTQPDTTPRAIRIDGPLSARAVLDHFNEKGRALLGAGQEDAAGRIAQLLAHEADLSAAWGGLPGTDHPRHWQPDVGDEAALSDRRSEHRRLDVHLPLWWALPLAVRDRQPQRVVLPLAATREGLAALVRRHMPGAWWNQRVHVTLDVETRVYWGARGAVHPHAAARHACAQRGDAGHPSMKL
Ga0055535_1031860	Ga0055535_10318601	F049748	MDIKQDPNAIPNFNAGGRVGELQRNEPEQTQSSVELDPTAGGDGGTSEAAEHESLLGDGSGKSARPDGPAKGGRDPSSTGPGAVDGLVGAP*
Ga0055535_1033395	Ga0055535_10333952	F092337	MRATDSAMRSLRTATFTISIRDSSEDQLEAAAAAFTCTLHRAGMTPEDALLAWRRMDEWERRNFAADADPGPQWWRTMAIARDAVLAALRAAGLDGQRRPFMIEPATRPH*