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 3300005878

3300005878: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_80N_104



Overview

Basic Information
IMG/M Taxon OID3300005878 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)
Gs0111376 | Gp0116063 | Ga0075297
Sample NameRice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_80N_104
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?Y
Use PolicyOpen

Dataset Contents
Total Genome Size197711891
Sequencing Scaffolds188
Novel Protein Genes205
Associated Families191

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria10
All Organisms → cellular organisms → Bacteria54
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria2
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria10
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium14
All Organisms → Viruses → Predicted Viral1
Not Available36
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium4
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium URHD00171
All Organisms → cellular organisms → Bacteria → Acidobacteria7
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium7
All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia → unclassified Blastocatellia → Blastocatellia bacterium2
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes5
All Organisms → cellular organisms → Bacteria → Acidobacteria → Blastocatellia → Chloracidobacterium → Chloracidobacterium thermophilum1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → Herpetosiphonales → Herpetosiphonaceae → Herpetosiphon → Herpetosiphon aurantiacus1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae → Niastella → Niastella yeongjuensis1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium8
All Organisms → cellular organisms → Bacteria → environmental samples → uncultured bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Archangiaceae → Archangium → Archangium gephyra1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Methylobacterium1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Candidatus Koribacter3
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Oscillatoriales → Oscillatoriaceae → Oscillatoria → unclassified Oscillatoria → Oscillatoria sp. PCC 108021
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfovibrionales → Desulfovibrionaceae → Desulfovibrio1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Acidobacterium1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium 13_1_40CM_4_65_81
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales → Tannerellaceae → Parabacteroides → unclassified Parabacteroides → Parabacteroides sp. ASF5191

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 → Rice Paddy Soil → 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 biomepaddy fieldpaddy field soil
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: Twitchell Island, California
CoordinatesLat. (o)38.1087Long. (o)-121.653Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

Associated Scaffolds

Sequences


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