3300026063: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026063
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116110 | Ga0208656
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 47595921
• Sequencing Scaffolds: 12
• Novel Protein Genes: 15
• Associated Families: 15

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	2
Not Available	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	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 → 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 biome → wetland area → soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Fairfield, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.198971
  • Long. (^o): -122.026955
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F002700	Metagenome / Metatranscriptome	536	Y
F006533	Metagenome / Metatranscriptome	371	Y
F007858	Metagenome / Metatranscriptome	343	Y
F010932	Metagenome / Metatranscriptome	297	Y
F019400	Metagenome	230	Y
F026976	Metagenome	196	Y
F027937	Metagenome	193	Y
F033667	Metagenome / Metatranscriptome	176	Y
F039208	Metagenome / Metatranscriptome	164	Y
F043475	Metagenome / Metatranscriptome	156	Y
F049863	Metagenome / Metatranscriptome	146	Y
F072145	Metagenome	121	Y
F079748	Metagenome	115	Y
F085674	Metagenome / Metatranscriptome	111	Y
F094338	Metagenome	106	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208656_1001972	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1351
Ga0208656_1002692	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium	1171
Ga0208656_1003292	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1069
Ga0208656_1004930	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	895
Ga0208656_1007816	Not Available	740
Ga0208656_1007880	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	738
Ga0208656_1008111	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae	730
Ga0208656_1009498	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium	685
Ga0208656_1014857	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	574
Ga0208656_1015509	All Organisms → cellular organisms → Bacteria	565
Ga0208656_1016022	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	558
Ga0208656_1020399	All Organisms → cellular organisms → Bacteria	508

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208656_1001293	Ga0208656_10012932	F033667	MILLVTSNQRRAECGAALEEAIGERVEVCDAVRKAALLAQRHEYTAVLLDDPMVEAEGDALEPLLAGMGMAVPVYVNLAVSNAQRVAREMRLAQRRHRESRLIAARAAESQLRSELRDAVTGILLSTELAMRTPEIPPDAVEKLNSVCQLATTIRARLDSVP
Ga0208656_1001972	Ga0208656_10019722	F039208	DDMLAALGAGAAIPGVMGVGPGRTWDAMVAAHAPLLTGDSVTFTALEDGTLVVNEDVPDGSLTPVADQIEEMVAPPYRAATARNEGDMWTAVAESVQIATLAGLEADQVELTIVGGERTLTLGDAVSSSTLPGLDELAEGQGDVAIHAERVDGDLFAVDVFPL
Ga0208656_1002478	Ga0208656_10024782	F002700	MILLHDAESEKSMAIVFFDTEEDYQTGHATLEAMPRPDTPGQRTSVAKYEVASRMTL
Ga0208656_1002692	Ga0208656_10026921	F006533	MMSSSSISYGESVLSHLEKVQELSAEVQADIAKRVGTYLTIARAAKNEAILQQIASSAAQEQAKAIGKGVHTMDPRWAGPALAEAWCYATMSLSKGYLD
Ga0208656_1003292	Ga0208656_10032922	F007858	REALVALKASTVSAEWELAPGAIDLRSTLDQIDADRPHVMVAFGDHVELVGIVRERFPSMRIVTDRDTPGATVVATSLDEVRGLVLGLPRPGGPVGA
Ga0208656_1004930	Ga0208656_10049302	F010932	FDAVETSYGMKVVSRKPGPTADTEYVDEKSFALPSILQIGDTEFTHFKQPREALRAGSHNAHFMFVTPDDDNSFRLFTVNHYTGSDPEFFEKLAPSRRVEAKSQKKSYDRRKFSPFRGNVRTEDMACQATQPLLDERAEQLATSDRGVILIRKIILDAVRSVQKGQIPKGIPSRGEARGMVQIDSFTGIRTKGGS
Ga0208656_1007816	Ga0208656_10078161	F085674	MLVGIATIAIAIAGFTAITSALEPPGGSWSPAMRLRQRAIVSTSFNVGLESFAPLIALAWLEDLRSALVVASLAVAIYTTAVVLFRARQFIRAGGLHTGMAGLTLFALGPIATLLFWSNAIVFASLAIFALALLVQLLVAIISFYSLVSAASS
Ga0208656_1007880	Ga0208656_10078803	F043475	MADVDAARRELEAALGPEAVLSDPLARRLYARDASMVEGGCALVALP
Ga0208656_1008111	Ga0208656_10081112	F079748	MNTKYLLIVATITVMLVGATALSTTDSAFAGKKKYEKSQAASQANACGNGKLPLNVFCQNLLSQI
Ga0208656_1009498	Ga0208656_10094982	F027937	MLETYRDKEAPPQSRTPALKPRLRSWTGRVWRSSSTAFQLMLKLDASLAMSEIENTDVRETLAPFAADLASFPLYLDYTDENHLPVSWAVGAFYVERGKNAFMRFYDFLESISAHVLVTLLPAAGAQSDLILSVIPYSLETNR
Ga0208656_1011157	Ga0208656_10111572	F072145	MADHRDRILPRFRYGVIHPRANEGVQRGPGYQLYRLVPLEIME
Ga0208656_1014857	Ga0208656_10148571	F094338	IVLVDLLDLPLEYARFGQVVPISLLKTRRQSLLKFVEGLIEGIYVFKTNRELVLSVLKQSGIESPQYGYERVAAALRERPFPEPLGVQAVLDSVKTTKSKVTIAKDVIDASLVEEINNSGYIAKLYGK
Ga0208656_1015509	Ga0208656_10155091	F026976	TFDIRDLQGGLVTRVSHLQDHREQVRAMIRATLQSMDIIMKNEAEVVAYLQKDFGLEPKIAADTYRILKRVVNADGDIEDAVFKSIIEKIRQESNIAAEVPPERLADLSILHEIKKR
Ga0208656_1016022	Ga0208656_10160221	F019400	MPNDPTACREQARRCAELAAFAATAEEREHFLSLEKALTRFAAELESASEFCGTMDEIDLKEPYSPEAA
Ga0208656_1020399	Ga0208656_10203992	F049863	ATAEEQAAVNQFDAAGRSLLNVIGRLADVLVVMRQ