3300003792: Arabidopsis rhizosphere microbial communities from North Carolina, USA - plate scrape MF_Cvi_mMS_r2

Overview

Basic Information

• IMG/M Taxon OID: 3300003792
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101313 | Ga0055540
• Sample Name: Arabidopsis rhizosphere microbial communities from North Carolina, USA - plate scrape MF_Cvi_mMS_r2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 278948068
• Sequencing Scaffolds: 11
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium URHA0028	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Ideonella	1
All Organisms → cellular organisms → Bacteria	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: 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?
F026918	Metagenome / Metatranscriptome	196	N
F027546	Metagenome / Metatranscriptome	194	Y
F033107	Metagenome / Metatranscriptome	178	Y
F044538	Metagenome / Metatranscriptome	154	Y
F053537	Metagenome / Metatranscriptome	141	Y
F071622	Metagenome / Metatranscriptome	122	Y
F073010	Metagenome / Metatranscriptome	120	Y
F074001	Metagenome / Metatranscriptome	120	Y
F089269	Metagenome / Metatranscriptome	109	Y
F094368	Metagenome	106	Y
F105520	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055540_1005750	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	5107
Ga0055540_1006330	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis	4722
Ga0055540_1008144	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	3820
Ga0055540_1008244	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3782
Ga0055540_1010570	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3060
Ga0055540_1011122	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	2934
Ga0055540_1011290	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → unclassified Comamonadaceae → Comamonadaceae bacterium URHA0028	2891
Ga0055540_1016130	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	2140
Ga0055540_1016599	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	2088
Ga0055540_1021462	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Ideonella	1676
Ga0055540_1078742	All Organisms → cellular organisms → Bacteria	634

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055540_1005750	Ga0055540_10057504	F053537	MKYMHKAIWQADGNLVIRGNTRALLFRALQDVRADLAARGEEADPLKRTLAALQDVLGEYDGPVPSAVDLLGDPVKERVSRNLLKG*
Ga0055540_1006330	Ga0055540_10063303	F074001	MRRKPSHAPLEKARTKTDQVQRDLEVASAELGLTHGALERELPPDVKQGDVAWAIHQNKKLEKKVQQAAEELEEVTDLLDQAKTGTPGGGGTRGDPH*
Ga0055540_1008144	Ga0055540_10081443	F094368	MAQPIPFLDPEVKPPDYRVPRGRSGHGAKSALETLLKDLDRVRRAKEAYGDLPKRPDSSLRY*
Ga0055540_1008244	Ga0055540_10082445	F033107	MKTLSALALLGLGFVALSRVANVHKGRNHGRPAAKPEEVQTWEGEGGGLPTGGPGPGVKVSTPVSDPDLAHGTTH*
Ga0055540_1010570	Ga0055540_10105704	F073010	MNGWLLRPRVLAVLACATFACILLYQLPWSPAASAHFTARTGQLPFDERPAGYTLSGALRDFQRLGPEGLQDYRAYRVLDLLFPWLLCALVAGVMLRLEAARATMWPWLAALADSAENVALWAMFLTRDDLSPRLVPVASFLTQLKFCLYAAMLLMLLAVGVRYVLRERRRARMAG*
Ga0055540_1011122	Ga0055540_10111222	F044538	MRLIARFVVLMVAVFGVSLAFAWAWDRSDTPPATTPVRGS*
Ga0055540_1011290	Ga0055540_10112903	F105520	MTLPVMDALSRTELDFLHRLLLDLQRESEDHGDAAGVAALELALAILRWDGETPPALDAQVGLGAAIQSRLGLDALCAWQQWRTERRRRPALTP*
Ga0055540_1016130	Ga0055540_10161302	F026918	MDSKQLFIEHLAGELQAMEVGRVPMNPLRYRVHAKMLKKALGDLPAPLVMSRPGGAHPQVLHEMANRFFEDTGHLPRPDAAAHKARSLLERTLAQCRAPRPL*
Ga0055540_1016599	Ga0055540_10165993	F071622	MKDGKPNYAGEPEGRRPASAGRKGSGGGTMRQRSFVERATATGHSGHGSESVRPHLRDQLRLKSLLPQPYPTPEPESPKDDSHR*
Ga0055540_1021462	Ga0055540_10214622	F089269	KQQIRAGVLPPHDLNTLYMIYFPVDVTITLDGITSCVDFGAYHFATNDLEMKKNNIFYTVEPDCHSSMASIEFAASHEFAEATTDNIPTPGSNPDFPQAWNDANGFEVADICGGSGQLTRGGKSYTVTQFFLNSTNACSTGNYTSP*
Ga0055540_1078742	Ga0055540_10787421	F027546	MKTAGETDPAPVQPLGDRVQAPKPVRPEWQPLAHAPCIEVNRQGQLRTNLPLPK*