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 3300027695

3300027695: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Rhizosphere soil Co-N PM (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300027695 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0110179 | Gp0089067 | Ga0209966
Sample NameArabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Rhizosphere soil Co-N PM (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size403242281
Sequencing Scaffolds460
Novel Protein Genes496
Associated Families485

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → Nitrospira japonica1
All Organisms → cellular organisms → Bacteria66
All Organisms → cellular organisms → Bacteria → Nitrospirae2
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → Candidatus Nitrosocosmicus1
All Organisms → cellular organisms → Archaea7
All Organisms → cellular organisms → Bacteria → Proteobacteria14
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root14625
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales9
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria8
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria7
Not Available122
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → Rhodospirillaceae → Hypericibacter → Hypericibacter terrae1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium6
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi7
All Organisms → Viruses → Predicted Viral1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria14
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium RIFCSPLOWO2_12_FULL_60_191
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. ST-bin51
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium19
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium3
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → unclassified Gemmatimonadaceae → Gemmatimonadaceae bacterium2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium30
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium8
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium16
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium21
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria6
All Organisms → cellular organisms → Bacteria → Terrabacteria group2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes11
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC68601
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium → unclassified Methylibium → Methylibium sp. T291
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium11
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium7
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → Gemmatimonadaceae → Gemmatirosa → Gemmatirosa kalamazoonesis1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → unclassified Actinobacteria → Actinobacteria bacterium 13_1_20CM_4_69_91
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Bryophyta → Bryophytina → Bryopsida → Funariidae → Funariales → Funariaceae → Physcomitrium → Physcomitrium patens1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon3
All Organisms → cellular organisms → Bacteria → Acidobacteria6
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → Nitrososphaera1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Deinococcus-Thermus → Deinococci → Deinococcales → Deinococcaceae → Deinococcus → Deinococcus geothermalis → Deinococcus geothermalis DSM 113001
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Thermomicrobiales → unclassified Thermomicrobiales → Thermomicrobiales bacterium1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. AUGA SZCCT04311
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameArabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling
TypeHost-Associated
TaxonomyHost-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling

Alternative Ecosystem Assignments
Environment Ontology (ENVO)Unclassified
Earth Microbiome Project Ontology (EMPO)Host-associated → Plant → Plant rhizosphere

Location Information
LocationJoint Genome Institute, California, USA
CoordinatesLat. (o)37.931388Long. (o)-122.021761Alt. (m)N/ADepth (m)N/A
Location on Map
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Associated Families

Associated Scaffolds

Sequences


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