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 3300003840

3300003840: Avena fatua rhizosphere microbial communities from Hopland, California, USA - H2_Bulk_Litter_50 (Metagenome Metatranscriptome)



Overview

Basic Information
IMG/M Taxon OID3300003840 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0110115 | Gp0093307 | Ga0032355
Sample NameAvena fatua rhizosphere microbial communities from Hopland, California, USA - H2_Bulk_Litter_50 (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size88333158
Sequencing Scaffolds114
Novel Protein Genes128
Associated Families99

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa1
Not Available59
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.6
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes9
All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Salinispira → Salinispira pacifica1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Methylobacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → unclassified Myxococcales → Myxococcales bacterium 68-202
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Actinomycetales → Actinomycetaceae → Actinomyces → Actinomyces graevenitzii1
All Organisms → cellular organisms → Eukaryota → Amoebozoa → Tubulinea → Elardia → Arcellinida → Sphaerothecina → Arcellidae → Arcella → Arcella intermedia6
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Verrucomicrobiae → Verrucomicrobiales → Verrucomicrobia subdivision 31
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Archangiaceae → Cystobacter → Cystobacter fuscus1
All Organisms → cellular organisms → Bacteria6
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → unclassified Terriglobia → Acidobacteriia bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Methylobacterium → unclassified Methylobacterium → Methylobacterium sp. WSM25981
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Treponemataceae → Treponema → Treponema primitia1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Afifellaceae → Afifella → Afifella pfennigii1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales → Gordoniaceae → Gordonia → Gordonia paraffinivorans1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Vibrionales → Vibrionaceae → Vibrio → Vibrio harveyi group → Vibrio diabolicus subgroup → Vibrio antiquarius1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Gemmatales → Gemmataceae → Zavarzinella → Zavarzinella formosa1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Stichotrichia → Urostylida → Pseudourostylidae → Pseudourostyla → Pseudourostyla cristata1
All Organisms → cellular organisms → Bacteria → Acidobacteria1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium1
All Organisms → Viruses → Predicted Viral1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameAvena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies
TypeHost-Associated
TaxonomyHost-Associated → Plants → Rhizosphere → Soil → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies

Alternative Ecosystem Assignments
Environment Ontology (ENVO)grassland biomegrassland areabulk soil
Earth Microbiome Project Ontology (EMPO)Host-associated → Plant → Plant rhizosphere

Location Information
LocationHopland, California, USA
CoordinatesLat. (o)38.97364Long. (o)-123.117453Alt. (m)N/ADepth (m)N/A
Location on Map
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Associated Families

Associated Scaffolds

Sequences


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