3300005515: Combined assembly of arab plate scrape MF_Cvi (Combined Assembly)

Overview

Basic Information

• IMG/M Taxon OID: 3300005515
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0061145 | Ga0077122
• Sample Name: Combined assembly of arab plate scrape MF_Cvi (Combined Assembly)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 2131587156
• Sequencing Scaffolds: 36
• Novel Protein Genes: 36
• Associated Families: 30

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium URHA0028	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Variovorax → unclassified Variovorax → Variovorax sp. S2	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Reyranellaceae → Reyranella → Reyranella massiliensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	3
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Acidovorax → unclassified Acidovorax → Acidovorax sp. Leaf73	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Achromobacter → Achromobacter arsenitoxydans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae → Curtobacterium → unclassified Curtobacterium → Curtobacterium sp. S6	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1

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: University of North Carolina, USA
• Coordinates
  • Lat. (^o): 35.9082
  • Long. (^o): -79.0499
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001574	Metagenome / Metatranscriptome	669	Y
F006808	Metagenome / Metatranscriptome	364	Y
F007245	Metagenome / Metatranscriptome	355	Y
F012265	Metagenome / Metatranscriptome	282	Y
F015908	Metagenome / Metatranscriptome	251	Y
F024880	Metagenome / Metatranscriptome	204	Y
F025373	Metagenome	202	Y
F027546	Metagenome / Metatranscriptome	194	Y
F030808	Metagenome / Metatranscriptome	184	Y
F031609	Metagenome / Metatranscriptome	182	Y
F034624	Metagenome / Metatranscriptome	174	Y
F037437	Metagenome / Metatranscriptome	168	Y
F039184	Metagenome / Metatranscriptome	164	Y
F044538	Metagenome / Metatranscriptome	154	Y
F044594	Metagenome / Metatranscriptome	154	Y
F044595	Metagenome	154	Y
F052711	Metagenome	142	Y
F053413	Metagenome / Metatranscriptome	141	Y
F053537	Metagenome / Metatranscriptome	141	Y
F060695	Metagenome	132	Y
F071622	Metagenome / Metatranscriptome	122	Y
F074001	Metagenome / Metatranscriptome	120	Y
F075003	Metagenome / Metatranscriptome	119	Y
F076420	Metagenome / Metatranscriptome	118	N
F083928	Metagenome	112	Y
F092682	Metagenome / Metatranscriptome	107	Y
F092690	Metagenome / Metatranscriptome	107	Y
F094127	Metagenome / Metatranscriptome	106	Y
F094368	Metagenome	106	Y
F105520	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0077122_10015725	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	10411
Ga0077122_10025303	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium URHA0028	7454
Ga0077122_10083569	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	3125
Ga0077122_10087057	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	3034
Ga0077122_10089699	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Variovorax → unclassified Variovorax → Variovorax sp. S2	2968
Ga0077122_10094083	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Reyranellaceae → Reyranella → Reyranella massiliensis	2867
Ga0077122_10143682	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium	2092
Ga0077122_10144880	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2080
Ga0077122_10145144	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	2077
Ga0077122_10150602	Not Available	2020
Ga0077122_10153688	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1989
Ga0077122_10181385	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1754
Ga0077122_10198698	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1636
Ga0077122_10201876	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1616
Ga0077122_10226855	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1477
Ga0077122_10232545	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1448
Ga0077122_10256408	All Organisms → cellular organisms → Bacteria → Proteobacteria	1343
Ga0077122_10290956	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	1217
Ga0077122_10324522	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1117
Ga0077122_10329903	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Acidovorax → unclassified Acidovorax → Acidovorax sp. Leaf73	1102
Ga0077122_10367719	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1012
Ga0077122_10402878	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium	942
Ga0077122_10436098	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	885
Ga0077122_10535719	All Organisms → cellular organisms → Bacteria	752
Ga0077122_10568173	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Achromobacter → Achromobacter arsenitoxydans	718
Ga0077122_10572198	Not Available	714
Ga0077122_10590788	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	696
Ga0077122_10603896	All Organisms → cellular organisms → Bacteria → Proteobacteria	684
Ga0077122_10636259	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	657
Ga0077122_10638477	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	655
Ga0077122_10673607	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	628
Ga0077122_10692153	All Organisms → cellular organisms → Bacteria	615
Ga0077122_10699346	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae → Curtobacterium → unclassified Curtobacterium → Curtobacterium sp. S6	610
Ga0077122_10768207	Not Available	567
Ga0077122_10771619	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	565
Ga0077122_10859574	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	519

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0077122_10015725	Ga0077122_100157253	F044538	MRLIARFVVLMVAVFGLSIAFAWAWDRSDAPKTAQHA*
Ga0077122_10025303	Ga0077122_100253032	F071622	MKDGRPNSTGDPERWRPGSAGRKGGGPKKQRGFVERATATGHSGYGSESVRPHLRDQLQLKALLPQPFPTPEQDNRKDEHHR*
Ga0077122_10083569	Ga0077122_100835693	F053537	MKYMHKAIWQCDGNLVIRGNTRALLFRALEDARAGLAQREDAGELQRTLAALQQALGSYDGKLPSVVELLGDPVRDRISRNLLKG*
Ga0077122_10087057	Ga0077122_100870572	F092690	MSTYVAVRHGALQARVMLGAPHENDAVNDSSFPEDRKARLVRNLLALRAVLAMEQMQTGRWSERIEELDQELASLGHDMKSTAAFATECLRRTFLLPRLVSRRKRAAHGLAKQPQPQE*
Ga0077122_10089699	Ga0077122_100896992	F044595	LESVIVKSAYVVTANRPMNGLVAFVRAAAMKSIGGCASALHPSLPTSYQRLDRNEDQVHPGEGSA*
Ga0077122_10094083	Ga0077122_100940834	F053413	MFLSPLGERLGEGAATDGARGTPSPNLSPKGERSKRRGRSC*
Ga0077122_10143682	Ga0077122_101436822	F015908	MRYMMIAAVLGMLASQAQAESKKYRSVLIPEKSVQACSGWGQTYTVDVSNGVLTLGVNYARRLFSAPVDSDGKIAASYKDPSGGILKFIALGNGEYELSNPLVPCYYRLVPSASPPWNS*
Ga0077122_10144880	Ga0077122_101448802	F030808	MNLNLSAFQSQEFIVGIAVAAILVSALIASSMFRNIALAVAAGGVVLLYLQGGVPALLATSAMLEKEIRALPEFSNGLIVGFAVAAVFLFGMQKRST*
Ga0077122_10145144	Ga0077122_101451442	F001574	MTSLRLGTGALDFLNPNGLARPALEKFLGAWFACFVVMAHGDFANAVSLDHARIASICGTIGALVAVVLLTQMDRTTISLPKQMTVSAFATFIGDVFAHPSHFPPQWGEPLVTAAVSAAIAAALWQARRLLKSL*
Ga0077122_10150602	Ga0077122_101506021	F037437	MMRRTTVCVVVLGVLALGVLALGIMAAAQTAAADVSIIGKWQIVEAVPAPWAPADQQAALAAQGKNLLKTEVTFAQGSLASKFKPFNCKSKVLYEPNSIEVDALFQGNLPEPNPAAAAARLGFPRADIPGVDVRCLKAQYTFHFRDPNTALINLDRVIYTFKRQ*
Ga0077122_10153688	Ga0077122_101536881	F027546	MKTAGEPDPAPFQPLGDRVQAPKPARPEWQPLAHAPSIEVNRQGQLRTNLPLPK*
Ga0077122_10181385	Ga0077122_101813852	F094368	MEPIAYLDPEVRPPEYRVPRGRSGVGAQSALETLLRDLERIRRAKEAYGDLARTQENSQFLF*
Ga0077122_10198698	Ga0077122_101986982	F092690	MNTESEVDRNARLVRNLLALRMVLCMDQMQTGKWGDRIEEIDQELATLGHDMKSTAACATESLRRTFLLPRLVSRRSRAAHRPPARAVPRG*
Ga0077122_10201876	Ga0077122_102018762	F060695	MRASASLLWLGAAVTLSAFVSAYVVAMFVADRLADCTTPAVLPVAYCVMLGYAIMGAQIGINDLVNSGRPPPYLEELQWASFILIGLGIVWVGFAYSIWVVVGFLMLFFVPLGAVYLIVGMPVFAAVMRLYERAVPDLDAAAAWPATVLAVAPFVVFSLHDIEARCGVLQ*
Ga0077122_10226855	Ga0077122_102268551	F006808	MPIIDIHTHCAPPRPPGDRFGVAEALRGVPVGRNTITNYRGLPAVSYYEMGDFELQQEACAKAGVTHRLISTPFAAEVMAAISKSPSLDICKAVNDGIAGIVARAPNNWGMGTLNPLDKEHIAEGERCLKELKFKGLLICSSWHGRFLDGE
Ga0077122_10232545	Ga0077122_102325452	F039184	MDEDFSFMRACDLARTADENFKLAWIAEIEASWQVSDLDHGDFGFILVMADGRRLYWRYTSDDPGAGRVEDLVVSELAAGEVPEGDAPWSRPELLNKRLAVLRRLA*
Ga0077122_10256408	Ga0077122_102564083	F012265	DGVGGPLKGGAVDPPEFARQIAAALHERKGTVGKAILRELVTEFVKPTVADPQILSTDRAIAILEQLLTTVLPQLKESEEFNRLAKTVLGEEIEQRRNLRARRLEDTAT*
Ga0077122_10290956	Ga0077122_102909562	F074001	MNQLPSQPVIDQAKSKTDQVQRDLEVASAELGLTHGALERELPPGVKKGDVAWALHQNKVLEKKVQQAAEELEEVTELLDQAKDDPA*
Ga0077122_10324522	Ga0077122_103245221	F007245	MRALRTAAIALVLAAVATAPAFGVASVSVFGLKAPEEISGFTLNDSTNFEKLKPGDGYGLDYSQSGWKLDVYIYDLKRAAIPDDVKSAIVRAEFERARADTFLAQPRGIYAQVYLKRNFTIDDSAKRTRFQCAAFHLRRDGAKPQDGYLCVTSWNNKFVKFR
Ga0077122_10329903	Ga0077122_103299033	F083928	MNILAWLNSLRPAIPMSVERPCELMSTSELRRHIQQGAVLINGERVAWGDPVVFPVLSLVFFPKSPTRRTTII*
Ga0077122_10367719	Ga0077122_103677192	F074001	MSQVPSQPAIDNARSKTDQVQRDLEVASAELGLTHGALERELPPDVKKGDVAWAIHQNKILERKVQQAAEELEEVTELLDQARGDPS*
Ga0077122_10402878	Ga0077122_104028782	F105520	MDASSVQLARTELDFLQRLLLDLQRQLEHGEPETAAALELALAMLQWNGEAPPELDQQVGLGAAIEMKLGLDALCAWRQWRDQCRKRAALTP*
Ga0077122_10436098	Ga0077122_104360982	F034624	QPSEVDRAAVAHMGATAPKAVYVVKVKLQAKPPVTSMAWALYIDDERIPKYWEYTDGIYFTVPDSQFFSRHKGKQLRFSRNGTDFFDTGVKLAPAPSVAHGSAARLPLQADVLK*
Ga0077122_10535719	Ga0077122_105357192	F025373	MADEGFPRIYAVAKWVVIGSLAVLAILAGAFWTLLLGGFAESGFRAEQPRGGREEAVEITPECAWPYSVHDEKAKAVCRMFYHLTPEQRAQVLKARQ*
Ga0077122_10568173	Ga0077122_105681731	F001574	MTSLRLSADARDFLNPNGLARPALEKFAGAWLACFVVMAHGDFANALSLDNARIASICGTIGALVAVALLTQMDRTTISLPRQMTISAFATFIGDVFAHPSHFPPQWAEPLVTAGVSAAIAVALWQARRLIKSL*
Ga0077122_10572198	Ga0077122_105721982	F030808	MNLNLSAFQSQEFIVGIAVAAILVSALIASSMFRNIALALAAGGVVLLYLQGGVPALLATSAMLEKEIRALPEFSNGLIVGFAVAAVFLFGMQKRSA*
Ga0077122_10590788	Ga0077122_105907882	F052711	MVRGGRAALVAAMMAATGTPVAGQVLDATYRGTMVCEKLPFTSGQMREAIEVTISGGAARYSHVVRLRNAAVEAAAEQGTGTVSGTKIDLQGGWKGGSQQYEAKYSGSFVRR
Ga0077122_10603896	Ga0077122_106038961	F075003	MLRLSIACVLVLAVSLPASANWTRAQRAQFLGQCVESCQSTLNLPDSKRRVCDATCGCVADQAETLVTPADMYALDEAAAAGRTTETMQKI
Ga0077122_10636259	Ga0077122_106362592	F092682	MHGRRQHTTAQKVRSSAAWRVCACIIDRSFVVIRLKHLAV*
Ga0077122_10638477	Ga0077122_106384771	F044594	MSVLAHTSAIAYRLAPRAARQPGQLRQLLDRFLQWRQHRAEQDIAIHLGLTGGHITDEIERRISEHLMSRGGFRG*
Ga0077122_10673607	Ga0077122_106736072	F053537	MKYMHKAIWQADGNLVIRGNTRALLFRALDDARSQLGDGADQQLVRTLQALQDVLGRYDGHLPSAVELLGDPQREQLSRNLLKG*
Ga0077122_10692153	Ga0077122_106921531	F031609	PHIEKNLADEVFRDLFIPDEPKPETEHPDMVPSVKHLHGEPVALSDPSDQNFI*
Ga0077122_10699346	Ga0077122_106993461	F024880	TSEQGLVDFFAKARVDAGNGQTAEATNSVASSGEMLGKLREFVEKAHHVDAKNQATRAKQRVAAAEAKTDLASLDTLGSLGKFNSLAQFNPIGQSGSFGQLASLNQFTSAGLPPGPASASLGPGPGLESKGRLSAMADKMTNDLMDSAIHHMWTQVVVHGTTSVTKSVMTLLKGQ*
Ga0077122_10768207	Ga0077122_107682071	F094127	AIVRAEFERARADTFFAQPRGIYAQVYLKRNFTIEDSAKRTRFQCAAFHLTRDGAKPQDGYLCVTSWNNKFVKFRLTTLADSTTEAAARNYVNAWVPVLWGSGSKVEVEKPKVKKSAAARLGRAPRRAQ*
Ga0077122_10771619	Ga0077122_107716192	F039184	RTADADFKLAWIAEIEVSWQVTDLDHGDFGFILVMADGRRLYWRYTSEDTGAGRPEDLVASELAPGEIPEGDAPWSRPETLNKRLAVLRRLT*
Ga0077122_10859574	Ga0077122_108595742	F076420	DRAVDPPEFARQIAAALHERKGTVGKAVLRELVSEFVKPIVSDPQILSSDRAIAILEQLLTTVLPQLKESEEFNHLAKTVLGEEIEQRRQLRARGLEDTAT*