NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
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Sample 3300025273

3300025273: Arabidopsis root microbial communities from North Carolina, USA - plate scrape MF_Col_mMS_r2 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300025273 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0053073 | Gp0101301 | Ga0209673
Sample NameArabidopsis root microbial communities from North Carolina, USA - plate scrape MF_Col_mMS_r2 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size371181494
Sequencing Scaffolds12
Novel Protein Genes12
Associated Families7

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae6
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter1
All Organisms → cellular organisms → Bacteria → Proteobacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium → unclassified Methylibium → Methylibium sp. T29-B1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameArabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations
TypeHost-Associated
TaxonomyHost-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
LocationUSA: North Carolina
CoordinatesLat. (o)35.6667Long. (o)-78.5097Alt. (m)N/ADepth (m)N/A
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F013935Metagenome / Metatranscriptome267Y
F053537Metagenome / Metatranscriptome141Y
F071622Metagenome / Metatranscriptome122Y
F074001Metagenome / Metatranscriptome120Y
F092690Metagenome / Metatranscriptome107Y
F094368Metagenome106Y
F105520Metagenome / Metatranscriptome100Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0209673_1009097All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae4338Open in IMG/M
Ga0209673_1011421All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter → Ramlibacter tataouinensis3663Open in IMG/M
Ga0209673_1011876All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter3554Open in IMG/M
Ga0209673_1014991All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae2969Open in IMG/M
Ga0209673_1016223All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae2795Open in IMG/M
Ga0209673_1018537All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae2528Open in IMG/M
Ga0209673_1027755All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae1836Open in IMG/M
Ga0209673_1030687All Organisms → cellular organisms → Bacteria → Proteobacteria1687Open in IMG/M
Ga0209673_1032431All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae1609Open in IMG/M
Ga0209673_1034635All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales1522Open in IMG/M
Ga0209673_1046859All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium → unclassified Methylibium → Methylibium sp. T29-B1176Open in IMG/M
Ga0209673_1078720All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae761Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0209673_1009097Ga0209673_10090973F071622MKDGKPSNAGEPQGWRPASAGRKGGPARQRGFVERATASGHSGHGSESVRPHLRDQLRLKSLLPQPYPTPEPEGPKDDQAY
Ga0209673_1011421Ga0209673_10114213F074001MTRNTSPAPLEQARSKTDQVQRDLEVASAELGLTHGALDRELPPDVKQGDVAWALHQNKKLERKVQQAAEELEEVTDLLDQAKAGGSGGDGRSRDPH
Ga0209673_1011876Ga0209673_10118763F074001MRRKPSHAPLEKARTKTDQVQRDLEVASAELGLTHGALERELPPDVKQGDVAWAIHQNKKLEKKVQQAAEELEEVTDLLDQAKTGTPGGGGTRGDPH
Ga0209673_1014991Ga0209673_10149912F092690VSDTRFPDDRKARLVRNLLALRTVLAMDQMQTGRWSERIEEIDEELAGLGHDMKSIAAFATESLRRTFLLPRLVNRRKRAAHRRLGREAPQE
Ga0209673_1016223Ga0209673_10162233F094368MAQPIPFLDPEVKPPDYRVPRGRSGHGAKSALETLLKDLDRVRRAKEAYGDLPKRPDSSLRY
Ga0209673_1018537Ga0209673_10185372F053537MKYMHKAIWQADGNLVIRGNTRALLFRALEDVRADLAARGEEADPLKRTLAALQDVLGEYDGPVPSAVDLLGDPAKERVSRNLLKG
Ga0209673_1027755Ga0209673_10277553F105520MTLPVMDALSRTELDFLHRLLLDLQRESEDHGDAAGVAALELALAILRWDGETPPALDAQVGLGAAIQSRLGLDALCAWQQWRTERRRRPALTP
Ga0209673_1030687Ga0209673_10306872F053537MKYMHKAIWQADGNLVIRGNTRALLFRALQDVRADLAARGEEADPLKRTLAALQDVLGEYDGPVPSAVDLLGDPVKERVSRNLLKG
Ga0209673_1032431Ga0209673_10324314F094368MSQPIPFLDPEVKPPDYRIPRGRSGHGSKSALETLLKDLDRVRRAKEAYGDLPKRPDSSLRY
Ga0209673_1034635Ga0209673_10346353F071622MKDGKPNYAGEPEGRRPASAGRKGSGGGTMRQRSFVERATATGHSGHGSESVRPHLRDQLRLKSLLPQPYPTPEPESPKDDSHR
Ga0209673_1046859Ga0209673_10468592F092690VSDTRFPDDHTSRLVRNLLALRTVLAMDQMQTGRWSERIEEIDQELATLGHDMKSTAASATESLRRTFLLPHLVNRRKRATHRPSGRAAPQE
Ga0209673_1078720Ga0209673_10787201F013935LGIVPEVGIFCELVQLGEACRRFLDVKDASSAARLTA
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