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 3300026000

3300026000: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_0N_404 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300026000 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0111376 | Gp0116062 | Ga0208143
Sample NameRice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_0N_404 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?Y
Use PolicyOpen

Dataset Contents
Total Genome Size23607217
Sequencing Scaffolds12
Novel Protein Genes13
Associated Families13

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria1
Not Available2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes2
All Organisms → cellular organisms → Bacteria2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium1

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 biome → paddy field → paddy 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

FamilyCategoryNumber of Sequences3D Structure?
F009732Metagenome313Y
F015466Metagenome / Metatranscriptome254Y
F019545Metagenome / Metatranscriptome229Y
F020202Metagenome / Metatranscriptome225Y
F024178Metagenome / Metatranscriptome207Y
F026848Metagenome / Metatranscriptome196Y
F034408Metagenome / Metatranscriptome175Y
F039610Metagenome / Metatranscriptome163Y
F042602Metagenome / Metatranscriptome158Y
F043656Metagenome / Metatranscriptome156Y
F069686Metagenome / Metatranscriptome123Y
F075161Metagenome / Metatranscriptome119Y
F082782Metagenome / Metatranscriptome113Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0208143_100001All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon3744Open in IMG/M
Ga0208143_100880All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium942Open in IMG/M
Ga0208143_101323All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria839Open in IMG/M
Ga0208143_101662All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon783Open in IMG/M
Ga0208143_101946All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium743Open in IMG/M
Ga0208143_102270Not Available709Open in IMG/M
Ga0208143_102548Not Available686Open in IMG/M
Ga0208143_102808All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes668Open in IMG/M
Ga0208143_104511All Organisms → cellular organisms → Bacteria575Open in IMG/M
Ga0208143_104620All Organisms → cellular organisms → Bacteria571Open in IMG/M
Ga0208143_105130All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium552Open in IMG/M
Ga0208143_105711All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes534Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0208143_100001Ga0208143_1000014F069686MSIHLHTTITKKTDNILEELAKTYGTKSRVIEQAVETLLRVDKVGSCDDCVIKTKMSEQMKLRESLDLTSIGRKTLDRLLEVAIGNKTIEAFIQEQKTEAKNIIEILKGS
Ga0208143_100880Ga0208143_1008803F075161LFYGGAFVECARRIASFRQVFRGIRLGLFNRAYGYARRSRLTNLFTIPVEELWDLPVAEARRRLGMPAGGVAADLYREIAIPAGMADALRREWAGFAPTR
Ga0208143_101323Ga0208143_1013232F020202VNRESADELPILTDVVELHATGSFPRPDHIEEAAGPYASGLLSEDDVSALQAALVSRMMNLTDELLHAAAREIEAVMFERVIDRLRAALPELVAAALREHLAPGED
Ga0208143_101662Ga0208143_1016621F009732LKNLSEIKFEELRGKNFEIIRIVEMLCEACEKPLSKKEKFLRKIQIMSKEDFQNLLSRAAVHDRAEVDMENGKIYFYDHDFPGDVHPECIEKL
Ga0208143_101946Ga0208143_1019462F042602VTDRRFVFRWDVDHRVCVTDGLPRIRTVCRDFGVANTFFVNMGRSTNLREWVGKGLVRSRAKLSDREAVHLIKKTGWPRFLLETAL
Ga0208143_102270Ga0208143_1022702F034408WAPRVAYGMVVGVPRAPFTIDVPIVFSSSTVNAPPVVNSFQNNLAQDTWIERVAYNLFQPNSFPGSPFQSLYFSELKQSGQTGVGVQMQVFGAPKYVINDPFTDLGNLMDVFSMAWPNGWLLPKQSNVKVAAILTQTPVSVPFNVTLTFQGWQWVDKALDDLSDAEARARLRKLGIETPDLSILLPTR
Ga0208143_102548Ga0208143_1025482F039610MSRPTTKWIVLASLTLAAITSTACTRNDATGPSEQTAPSFEAQGGNN
Ga0208143_102808Ga0208143_1028082F043656EGKHPWHTRADELMRTRSPVVTPDRELTGFQIRMDLDPSDSHLRPTITVVDAQGCVVGFISHPEQIEGVEIIWG
Ga0208143_103493Ga0208143_1034932F015466MRLKGRHWLTFWLAIFLLVLVAITTRQTAGFQTAQHVRELREERLALEAQRAELERRIRMASSRQVLVPVAERLLGMHEPSDSEFVLFAVPSGPV
Ga0208143_104511Ga0208143_1045111F024178MRRALLLSLALPLMLGTRAAAQTCVGMPSFSSGQMQVAAGSSFADGASGFGGTFGYGAPKALYGKAGIGSTSYDGLDGSSFDFGVGAGYQIPLETTRTAELCPVANLSIGSGPNDIAGSGVDLSSRTFSFGASVGVLVNKSSKVQILPNAAFQFANTRNTVDDGTTSLSGSESYGLLTLGTGFVFH
Ga0208143_104620Ga0208143_1046201F019545AAAEVQASNVLTDAPAKVIVDKWSVDQAIDWEDKKIKEIYDTLRG
Ga0208143_105130Ga0208143_1051301F082782RCLRLSTVQGNYRFILDEAIEQDITYAYDGRTVLAVSETVSRDLWGITVDCAVEDGKRKLIFRKATQGEPFDAIREQPDAVPPAWRASEHERLLAEIAEIGRQIASLRGGSKSALREQLSVLEAAKQEKWDAIRALWAGDGGWHKRNGMVPASTAD
Ga0208143_105711Ga0208143_1057112F026848RRAARAIRPATDRMIRASIGVLLLSLALAGRLAAQTDRWQVTLDGDKYVWDIQLVRLDGDSLVVKQSDSLVRVPVEHINEIRLIRKVEVDLGAGAAGTMNALTGGGDEIYDLSALDLPERLRKVEKILEVHPVGP
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