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

Overview

Basic Information

• IMG/M Taxon OID: 3300026000
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116062 | Ga0208143
• Sample Name: Rice paddy soil microbial communities from Twitchell Island, California, USA - SF_Rice_25C_0N_404 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: Y
• Use Policy: Open

Dataset Contents

• Total Genome Size: 23607217
• Sequencing Scaffolds: 12
• Novel Protein Genes: 13
• Associated Families: 13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
Not Available	2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	2
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
• Type: Environmental
• Taxonomy: Environmental → 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

• Location: USA: Twitchell Island, California
• Coordinates
  • Lat. (^o): 38.1087
  • Long. (^o): -121.653
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F009732	Metagenome	313	Y
F015466	Metagenome / Metatranscriptome	254	Y
F019545	Metagenome / Metatranscriptome	229	Y
F020202	Metagenome / Metatranscriptome	225	Y
F024178	Metagenome / Metatranscriptome	207	Y
F026848	Metagenome / Metatranscriptome	196	Y
F034408	Metagenome / Metatranscriptome	175	Y
F039610	Metagenome / Metatranscriptome	163	Y
F042602	Metagenome / Metatranscriptome	158	Y
F043656	Metagenome / Metatranscriptome	156	Y
F069686	Metagenome / Metatranscriptome	123	Y
F075161	Metagenome / Metatranscriptome	119	Y
F082782	Metagenome / Metatranscriptome	113	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208143_100001	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	3744
Ga0208143_100880	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium	942
Ga0208143_101323	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	839
Ga0208143_101662	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	783
Ga0208143_101946	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium	743
Ga0208143_102270	Not Available	709
Ga0208143_102548	Not Available	686
Ga0208143_102808	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	668
Ga0208143_104511	All Organisms → cellular organisms → Bacteria	575
Ga0208143_104620	All Organisms → cellular organisms → Bacteria	571
Ga0208143_105130	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	552
Ga0208143_105711	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes	534

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208143_100001	Ga0208143_1000014	F069686	MSIHLHTTITKKTDNILEELAKTYGTKSRVIEQAVETLLRVDKVGSCDDCVIKTKMSEQMKLRESLDLTSIGRKTLDRLLEVAIGNKTIEAFIQEQKTEAKNIIEILKGS
Ga0208143_100880	Ga0208143_1008803	F075161	LFYGGAFVECARRIASFRQVFRGIRLGLFNRAYGYARRSRLTNLFTIPVEELWDLPVAEARRRLGMPAGGVAADLYREIAIPAGMADALRREWAGFAPTR
Ga0208143_101323	Ga0208143_1013232	F020202	VNRESADELPILTDVVELHATGSFPRPDHIEEAAGPYASGLLSEDDVSALQAALVSRMMNLTDELLHAAAREIEAVMFERVIDRLRAALPELVAAALREHLAPGED
Ga0208143_101662	Ga0208143_1016621	F009732	LKNLSEIKFEELRGKNFEIIRIVEMLCEACEKPLSKKEKFLRKIQIMSKEDFQNLLSRAAVHDRAEVDMENGKIYFYDHDFPGDVHPECIEKL
Ga0208143_101946	Ga0208143_1019462	F042602	VTDRRFVFRWDVDHRVCVTDGLPRIRTVCRDFGVANTFFVNMGRSTNLREWVGKGLVRSRAKLSDREAVHLIKKTGWPRFLLETAL
Ga0208143_102270	Ga0208143_1022702	F034408	WAPRVAYGMVVGVPRAPFTIDVPIVFSSSTVNAPPVVNSFQNNLAQDTWIERVAYNLFQPNSFPGSPFQSLYFSELKQSGQTGVGVQMQVFGAPKYVINDPFTDLGNLMDVFSMAWPNGWLLPKQSNVKVAAILTQTPVSVPFNVTLTFQGWQWVDKALDDLSDAEARARLRKLGIETPDLSILLPTR
Ga0208143_102548	Ga0208143_1025482	F039610	MSRPTTKWIVLASLTLAAITSTACTRNDATGPSEQTAPSFEAQGGNN
Ga0208143_102808	Ga0208143_1028082	F043656	EGKHPWHTRADELMRTRSPVVTPDRELTGFQIRMDLDPSDSHLRPTITVVDAQGCVVGFISHPEQIEGVEIIWG
Ga0208143_103493	Ga0208143_1034932	F015466	MRLKGRHWLTFWLAIFLLVLVAITTRQTAGFQTAQHVRELREERLALEAQRAELERRIRMASSRQVLVPVAERLLGMHEPSDSEFVLFAVPSGPV
Ga0208143_104511	Ga0208143_1045111	F024178	MRRALLLSLALPLMLGTRAAAQTCVGMPSFSSGQMQVAAGSSFADGASGFGGTFGYGAPKALYGKAGIGSTSYDGLDGSSFDFGVGAGYQIPLETTRTAELCPVANLSIGSGPNDIAGSGVDLSSRTFSFGASVGVLVNKSSKVQILPNAAFQFANTRNTVDDGTTSLSGSESYGLLTLGTGFVFH
Ga0208143_104620	Ga0208143_1046201	F019545	AAAEVQASNVLTDAPAKVIVDKWSVDQAIDWEDKKIKEIYDTLRG
Ga0208143_105130	Ga0208143_1051301	F082782	RCLRLSTVQGNYRFILDEAIEQDITYAYDGRTVLAVSETVSRDLWGITVDCAVEDGKRKLIFRKATQGEPFDAIREQPDAVPPAWRASEHERLLAEIAEIGRQIASLRGGSKSALREQLSVLEAAKQEKWDAIRALWAGDGGWHKRNGMVPASTAD
Ga0208143_105711	Ga0208143_1057112	F026848	RRAARAIRPATDRMIRASIGVLLLSLALAGRLAAQTDRWQVTLDGDKYVWDIQLVRLDGDSLVVKQSDSLVRVPVEHINEIRLIRKVEVDLGAGAAGTMNALTGGGDEIYDLSALDLPERLRKVEKILEVHPVGP