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 3300014296

3300014296: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqC_D1



Overview

Basic Information
IMG/M Taxon OID3300014296 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116110 | Ga0075344
Sample NameNatural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqC_D1
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size255973839
Sequencing Scaffolds184
Novel Protein Genes195
Associated Families186

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium1
All Organisms → cellular organisms → Bacteria34
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria6
Not Available44
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium4
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium34
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium2
All Organisms → cellular organisms → Bacteria → FCB group → candidate division Zixibacteria → unclassified candidate division Zixibacteria → candidate division Zixibacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium RIFCSPLOWO2_12_FULL_62_581
All Organisms → cellular organisms → Bacteria → Proteobacteria3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter marginalis1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae → unclassified Nitrososphaeraceae → Nitrososphaeraceae archaeon5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria4
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. DOA91
All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium3
All Organisms → cellular organisms → Bacteria → Acidobacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Albitalea → Albitalea terrae1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Hyphomicrobium → unclassified Hyphomicrobium → Hyphomicrobium sp. GJ211
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium RIFCSPLOWO2_12_FULL_60_191
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Neisseriales → Chromobacteriaceae → Chromobacterium group → Chromobacterium → unclassified Chromobacterium → Chromobacterium sp. LK111
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Thermomicrobiales → unclassified Thermomicrobiales → Thermomicrobiales bacterium1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Candidatus Acidoferrales → Candidatus Acidoferrum → Candidatus Acidoferrum panamensis1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → unclassified Cyanobacteria → Cyanobacteria bacterium 13_1_40CM_2_61_41
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → asterids → campanulids → Asterales → Asteraceae → Asteroideae → Anthemideae → Anthemidinae → Tanacetum → Tanacetum cinerariifolium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Dichotomicrobium → Dichotomicrobium thermohalophilum1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameNatural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
TypeEnvironmental
TaxonomyEnvironmental → Terrestrial → Soil → Wetlands → Unclassified → Natural And Restored Wetlands → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration

Alternative Ecosystem Assignments
Environment Ontology (ENVO)terrestrial biomewetland areasoil
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: Fairfield, San Francisco Bay, California
CoordinatesLat. (o)38.198971Long. (o)-122.026955Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

Associated Scaffolds

Sequences


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