3300005511: Combined assembly of arab plate scrape MF_Col (Combined Assembly)

Overview

Basic Information

• IMG/M Taxon OID: 3300005511
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0061137 | Ga0077121
• Sample Name: Combined assembly of arab plate scrape MF_Col (Combined Assembly)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 2241371899
• Sequencing Scaffolds: 57
• Novel Protein Genes: 64
• Associated Families: 53

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	2
All Organisms → cellular organisms → Bacteria → Proteobacteria	4
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	2
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. sBnM-33	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. SRL28	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Variovorax	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 200	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium	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 → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Rhizosphere → 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
F002233	Metagenome / Metatranscriptome	580	Y
F003272	Metagenome / Metatranscriptome	496	Y
F007178	Metagenome / Metatranscriptome	356	Y
F008003	Metagenome / Metatranscriptome	341	Y
F009763	Metagenome / Metatranscriptome	313	Y
F012265	Metagenome / Metatranscriptome	282	Y
F014281	Metagenome / Metatranscriptome	264	Y
F016724	Metagenome / Metatranscriptome	245	Y
F019503	Metagenome / Metatranscriptome	229	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0077121_10010491	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	12637
Ga0077121_10012866	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	11115
Ga0077121_10028868	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	6445
Ga0077121_10031420	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter	6074
Ga0077121_10046358	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	4645
Ga0077121_10049571	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	4431
Ga0077121_10056780	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	4031
Ga0077121_10066132	All Organisms → cellular organisms → Bacteria → Proteobacteria	3622
Ga0077121_10067627	All Organisms → cellular organisms → Bacteria	3564
Ga0077121_10086698	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	2977

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0077121_10010491	Ga0077121_1001049112	F012265	MDNRRIDRTQLDRTESRTPDGVGGPAQDRAVDSPEFARQIAAAIHERKGTVGEAVLRELVTEFVKPIVSDPQILSTERAIVILEQLLTTVLPQLKESEEFNNLAKTVLGEEIEQRRNLRARSLEDTPT*
Ga0077121_10012866	Ga0077121_1001286613	F092690	VSDTRFPDDRKARLVRNLLALRTVLAMDQMQTGRWSERIEEIDEELAGLGHDMKSIAAFATESLRRTFLLPRLVNRRKRAAHRRLGREAPQE*
Ga0077121_10018874	Ga0077121_100188741	F094025	ILASRPPINLGSQVGQQGAPSQAGSAPAAQGAQIEERRLEAKISDDPKKAQDGKNTGKPADTTLQTVLTNSGMKNVSNPPSEADLKTYYSKNGPAHELIAKGSYQEAAAEYRKLADKAADPAEQKRLTTAADQLEVAQKMKTAKVGSLQFPPTETNVTDYFKTMKGKPISEIKDAFQSYANAFYVHSEKKGVDRGDVVYSEHKYKEGTIVYNSHAPVSWKEVTDDREVHSDGRRIIDCEGYAHMGQQIFKAAGFQNVNFGVVARKDDPHTSQNESLTDQHIMVSGSRTIMVDGKPKTEMAVISNNRIDSKIADDNLKPADLKNFQTGLFARTFQQTYVDKVPGLIRVGPEAWREEFKLEDDIKAWQKK*
Ga0077121_10028868	Ga0077121_100288682	F057637	MTETLVVRELAVRELDPKLGNLGGADGARLGRLRATAADLEKTKMMTFDQIEQPQPRSDFEIAKISAWCRKHGYACHVSSRGQLELRTKSSAMATRGRTTALAM*
Ga0077121_10028868	Ga0077121_100288683	F060793	MIARNHIRAARYRALALTETDQERANLLDRLAAEAEHGVLCTLRHHLRLVYSADEAVCAKAA*
Ga0077121_10031420	Ga0077121_100314206	F074001	MTRNTSPAPLEQARSKTDQVQRDLEVASAELGLTHGALDRELPPDVKQGDVAWALHQNKKLERKVQQAAEELEEVTDLLDQAKAGGSGGDGRSRDPH*
Ga0077121_10046358	Ga0077121_100463581	F094368	MAQPIPFLDPEVKPPDYRVPRGRSGHGAKSALETLLKDLDRVRRAKEAYGDLPKR
Ga0077121_10049571	Ga0077121_100495715	F094368	MSQPIPFLDPEVKPPDYRIPRGRSGHGSKSALETLLKDLDRVRRAKEAYGDLPKRPDSSLRY*
Ga0077121_10056780	Ga0077121_100567802	F038811	MHPAFWPMHAFVFWSDVFMIPWKMLMAPVSSSMKEATAATDPAAVAGLDPVSPEEIGTSATDFRTNSDTSH*
Ga0077121_10066132	Ga0077121_100661325	F080119	MRRLIFLWLVLPACLLGPGAVAQSDPRQAVCQASWERCLGSGGDGKNWKPIYDRCMKARVACLGGRAYLPTVPQNFSSGAILEQGAGASADPANADPATQDAQCQNGGRRGARSNCVLAMAGEGYGQSFSLLGPGVPMARIQRVSSVVKCAGGKPASFYSNGRIESCTLDNSGMATVALTDTSGKTANCAARAVVRFDPEGRLAACDRP*
Ga0077121_10067627	Ga0077121_100676277	F080316	MVIEEEILARIRAAKTWDSSARVEDFQVQAADNGFVLINLKTRRAQLLYDEDSELSDLEQLFPENEKRYRGLL*
Ga0077121_10086698	Ga0077121_100866984	F105520	MDALSRTELAFLHRLLLDLQRQGEERGDAQGVAALELALAVLRWDGETPPPLDAQVGLGAAIQSRLGLDALCAWHQWRAERRRHPTLTT*
Ga0077121_10129254	Ga0077121_101292542	F003272	MARVGHMMLAAAMLAAMNKPVAAQVLDATYRGTMVCDKLPSISQQTREAIEVTVSGGAVRYSHVVRLHNSAVEATAEQGTGTLDGQNINLQGSWKSGSRQYEAIYSGSFVRRSARLKGTQAWNDGGKTVTRACAGAIKRPLKPFLPRDRR*
Ga0077121_10138473	Ga0077121_101384733	F066929	ACRTSKSLDLAAYQKLARTMIVAVGDNMREFSASVQDAPKAEAQFAAQAGRGAAGELQRLANDPVVKEFLNRNRKRAAVELTQTYLENIERALLLRRVQARQASPLATGDDILLEIEKVSSSPLDYADANNKKRAMNRFLELMAIAERAVSETSNQTELLKWGPVRLMVVLEGPLKEHCVMKG*
Ga0077121_10144465	Ga0077121_101444654	F003272	MVRVGPVMLAALAVTATPAAAEVLDATYRGTMVCDKLPFTSDKMREAIEVTITGGAARYSHVVRLRNLAVEATAEQGTGTVDGQKIDLQGTWKGGSRDYAAKYSGSFVRRSARLKGTQTWTDGGKTVVRACAGAIKRPFKPFLPRNKKQAAAR*
Ga0077121_10159883	Ga0077121_101598832	F070258	MMARRAIGLLLMAICIAGLLAFNIHPPEGDDSNLLNKLVVTAVLGGGAFAAWKFLVRTRRA*
Ga0077121_10173379	Ga0077121_101733792	F001574	MTSLRLSADARDFLNPNGLARPALEKFAGAWLACFVVMAHGDFANALSLDHARIASICGTIGALVAVALLTQMDRTTISLPRQMTISAFATFIGDVFAHPSHFPPQWAEPLVTAGVSAAIAVALWQARRLIKSL*
Ga0077121_10187702	Ga0077121_101877022	F073708	MYVVFVEEVGGPQDPIHTARTLEQAFAQIVCRCGYSYRFEPADEHGWCLFLTDVERPERSPDPIHSSCIKPRDAQHDLMSQAVDGRLRGHVALHIDVYRRAQVLRAGNGSKVLLEAYG*
Ga0077121_10190512	Ga0077121_101905123	F086200	MERIPDVFEIPEPMRGKPLPWLTAIAMTAIVVVATLALVVANEVPSENPQVMVDR*
Ga0077121_10204792	Ga0077121_102047923	F071622	MKDGKPSNAGEPQGWRPASAGRKGGPARQRGFVERATASGHSGHGSESVRPHLRDQLRLKSLLPQPYPTPEPEGPKDDQAY*
Ga0077121_10218515	Ga0077121_102185152	F002233	MEDKEMRQVRSLLSSASSRIVRRFAQIVAIAAASLPAVGA*
Ga0077121_10221850	Ga0077121_102218503	F099462	MSAQTQIVYLEYLITVIEEAGRFTSRVTRDGGLIEHDGHFSEGWKTASCASLNRAVQVAKTAIDNDQIR*
Ga0077121_10223669	Ga0077121_102236692	F057616	MNGGDGWVNDKAVPLLSGAPPQIRERDHGDSHAADIDQVSEESKPA*
Ga0077121_10227091	Ga0077121_102270911	F092520	MRRIIQANIDRFRDLLKTETDATKRAMEVRLLAEEEAKLEQLPAYDKKEPQAY*
Ga0077121_10239262	Ga0077121_102392622	F092261	MAYKIQYFRDGKPYAEVYWDQPLPQTRETAKKGLKRNRAESATILDMDQGLKPVETLTASP*
Ga0077121_10271463	Ga0077121_102714631	F025057	LRARSDRFGGGGTCSGSSAARGLRGEMGGLSLIEAT*
Ga0077121_10295754	Ga0077121_102957541	F002233	MQQVRSLLRGASSRIGRRLSQIVAIAAASLPEAGA*
Ga0077121_10303186	Ga0077121_103031862	F103484	MKLVPHVAKVALVGLAMAGLTAPVFAAGLMPGNGGTIKLPTVLPPSVKESLSLLPSSGGTSGFDVLGQKFGVQNGALDFFSVRPSEGGEFKPLFRGGFGEGGLKLQLKW*
Ga0077121_10317612	Ga0077121_103176123	F089476	MKKAFLTAVIVEIAFLGVATTASLADDLPALNSKWREPQHRTCLEITQISDALPGPAGCAQIAGRMKDDLMIGYACKSGSDISFFSGLQTDNSIKPDIFIGRYSAEAIIAQYCTRITNDWPPEYDCRNEMTFKSVSSCTP*
Ga0077121_10319606	Ga0077121_103196062	F068795	MGIDMTKETKPLWVWLSLALLAIGSVAYITTVFLFEYIIGLF*
Ga0077121_10324928	Ga0077121_103249281	F007178	VKMIKRGDRVKLTARVAAAFNNNKRPGKVDWTDRRGVIERISANKVHAFVLWDGRKTPDELPINGIEPG*
Ga0077121_10342597	Ga0077121_103425972	F059087	LKSRMSVHISFTHHPIGKPLPVGAVAFAIGLKLLVPTPGKHGLVAVKDLHE*
Ga0077121_10344695	Ga0077121_103446952	F044594	MSVLAHTSHIAYRTAPRAARQPGQFRRLLDRFLEWRQRRVEQDIAIHLGITGGYITDEIERRIFERLMTRGGFRG*
Ga0077121_10354301	Ga0077121_103543012	F019855	MLQAVSSDATFGRAPTFNTDTGFTLALSPDKKAFTATFSGLEAILEAKSTPIVTRTFSFAIPLVDTEPGDEIPFFVQGTAEFENGANVHMVFTVNDQSTTAYFPAQSKDGFLHRLDYKVTDAKEARVTVLLLASRDSKAGVEAYLNVSTIDTDIAKH*
Ga0077121_10367958	Ga0077121_103679582	F053537	MKYMHKAIWQADGNLVIRGNTRALLFRALEDVRADLAARGEEADPLKRTLAALQDVLGEYDGPVPSAVDLLGDPAKERVSRNLLKG*
Ga0077121_10381434	Ga0077121_103814342	F008003	MIFSDLPAPAEASVLPTRICRGFAQAGNRDTLFGIMLAGS*
Ga0077121_10383152	Ga0077121_103831523	F052711	MVRGGRAALAAAMMAATGTPVAGQVLDATYRGTMVCEKLPFTSGQMREAIEVTISGGAARYSHVVRLRNAAVEAAAEQGTGTVSGTKIDLQGSWKGGS
Ga0077121_10388599	Ga0077121_103885991	F019503	RDIFKQRGWYDDRRSLQIAASIAVAVVVIGLIVWGLVWAWHYIKRYRLAMGFMSLTLGFAIIRFISLHEVDAWNANAPWARTAVDLIAAAGVALIAIARLWQLRAFALQRATEKS*
Ga0077121_10390922	Ga0077121_103909222	F059087	LKNSVCVHISFTHPPSANHPPMGAVAFAIGLKLLVPTPGNNGFRAVKDFIE*
Ga0077121_10391969	Ga0077121_103919693	F092690	AVRQGTHQARVMLGASTENDAVTDSSFPEDRNARLVRNLLALRAVLAMEQMQTGRWSERIEELDQELASLGHDMKSTAAFATECLRRTFLLPRLVSRRKRAAHGLAKQPQPQE*
Ga0077121_10404869	Ga0077121_104048692	F098177	MTNETEKTVAPGTTKVEPAVTPAPQQNQGDAKPSADKPANQQQK*
Ga0077121_10467399	Ga0077121_104673991	F012265	MDNRRIERSQLDRTESRAPEGFAGPVNDRAVDSPEFARQIAAAIHERKGTVGQAVLRELVSEFVKPTVSDPQILSTDRAIAILEQLLTTVLPQLKESEEFNQLAKTVLGEEIEQRRNLRARSLEDTPT*
Ga0077121_10480300	Ga0077121_104803001	F020707	QMCLIHRDFKHFATANAIQFRRWRKVSSIMCAKVLSIMREDPARVTSP*
Ga0077121_10500467	Ga0077121_105004672	F009763	MFRKTVHPLDLVLAVLVAVAPGMAVFYWLAINGRLPFDLLTGLSYLLVAASVMLAAVGSIVWFAVWFCSPRRG*
Ga0077121_10518317	Ga0077121_105183171	F051218	SAQEDRDPLFFAEFLIAEQAQIVGGDPFDRSAPPAPAFTSYMMCQPPELDALATQLGKELCVQSTIVADLTATGPALATAAAAPAQVSPEDIVSSDPGAISCRLDPKRSDAQLPAVACARGSYWAWYKAKWSDPLLATPAPP*
Ga0077121_10521025	Ga0077121_105210251	F027578	MDRRKFFGLSVAAGGLLAARPLYAQPTGPAYAGSPKMEVQTFRPQQQQFRIGYTTNTRGGWEGSPFVGISEGRDVGFRYFEIFGSSFCATKDGFEPAPRDTQPMKAWPDGYSWKYPTGARLKREVYYPDRWEAL
Ga0077121_10531945	Ga0077121_105319452	F075015	MAEKLSDKEIERRKKQAEMNAAAPKPHENFQQFGGKGKSGPKQAKARIQRHQGR*
Ga0077121_10561199	Ga0077121_105611992	F012265	MDNRRIERTQLDRPDQHAPDGVGGPARDRAVDPPEFARQIAAAIHERKGTVGKAILRELVSEFVKPTLADPQILSTDRAIAILEQLLTTVLPQLKESEEFNRLAKTVLGEEIEQRRNLRARRLEDTAT*
Ga0077121_10601205	Ga0077121_106012051	F105520	FLHRLLLDLQRRLGDGGAQGDPELVAALELALAVLHWDGEAPPELDAQVGLGAAVQMRLGGDGMVAWRQWRDQRRKRCALTP*
Ga0077121_10603500	Ga0077121_106035001	F012265	MDNRRIERTPLDRPEARGLEGVAGTLKDRAVDPAEFARQIAAALHERQSKFGKTILHELVSEFVKPIVADPQILSTDRSIAILEQLLTAVLPQLKETEEFNRLAKTVLGEEIEQRRHLRARRLEDTAT*
Ga0077121_10617955	Ga0077121_106179552	F072533	MLDTVQSVSLLTLVEIVGPVLLAAGLIYGIWHSRRRRSQQPKSKAGTIYAQDD*
Ga0077121_10619188	Ga0077121_106191882	F066965	RLNGQSTAKIAATVISANTNHSVIKQFPGDATPLFASADAPIYTTGGKPGN*
Ga0077121_10654761	Ga0077121_106547612	F073708	GQEPQHIARTLDQAFAMIVCRCGYSYRFEAAQEQGWLLFLIDVERPERSPDPLHSTCIKPRDAQHDLMSQAIDGRLKGHVALHGEAYLRARVARTGEGSKVYLEAAE*
Ga0077121_10713571	Ga0077121_107135712	F016724	MRTKKSILGLVYAGSEVRRAPLIGMQFLHQGAVRPADVVTPRPRLQAKDLIGLLVRHF
Ga0077121_10722829	Ga0077121_107228291	F014281	RLLHCRRYGCNGAAETDMKIYLLILLIGSLLAAIHFTSAPKQQSETLPQ*
Ga0077121_10757374	Ga0077121_107573742	F101930	GVAEMPNARLITKGSWKLITDPKRPAAVIYELDSEAPSELRDFWEVDKSTLLVLDKDLRVRRSGFGDPDTVAYALYGYHCNPGQRMRDCLHE*
Ga0077121_10762632	Ga0077121_107626321	F084157	MVIRIVAIVIWTVCIYGFLGGSFVYRENLPTGQYNLYILTMYKTLPPPPKGPSYCNFFNAGPYALALPCNLKPPFIGWLQGGKY*
Ga0077121_10765914	Ga0077121_107659142	F060073	TNMPKKSGYVSSSSGMTGLADYSRLVPSAAVGGTPGTLIGIGTQGNRTCFGLLRRSACD*
Ga0077121_10797075	Ga0077121_107970751	F047261	LPVYRYDGLEPLLAALAEKVIAPAERKVKALEERRRMIEAELIKSQ*
Ga0077121_10824090	Ga0077121_108240902	F096718	AFPAFSAVLSAKSMKEGAFKPRIIARNLLVAPPSARVNTGFA*
Ga0077121_10852910	Ga0077121_108529101	F085924	ILELPVVHNLANGRIVVRRNLDEIHACLKRHLDGNHGLDRSVVEAGLIDQLDLCVADFIVGARPVFGCSGRGSVGTANG*
Ga0077121_10869979	Ga0077121_108699792	F019507	MDARELVDIACEDDPRAPCLWLPSDLFPEFCEAIRQRPNLIGAVIYRNKTIRDGGPYSDITT
Ga0077121_10938937	Ga0077121_109389371	F052711	MVRATIAVLALAITIMTDAPAAAQVLDATYRGTMVCDKLPSTSQQTREAIEVTISGGAVRYTHVVRLRNAAVEATAEQGTGTIDGQKINLEGGWKSGSRQYEAKYSGSFVRRSARLKG
Ga0077121_10942990	Ga0077121_109429901	F095729	MKTSLRTFAFASTLLVTAAFPLLSHAQDVRREDRVTHYLEADIIDSNKDHLVSKKEFMDAMSKSWDMHMSDAQKMAPDAKAPKDKMTLQQYLEFSKMFGLNIGG*