Sample 3300026063

Overview

Basic Information
IMG/M Taxon OID	3300026063 Open in IMG/M
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
Location on Map

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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

Family

Category

Number of Sequences

3D Structure?

F002700

Metagenome / Metatranscriptome

536

F006533

Metagenome / Metatranscriptome

371

F007858

Metagenome / Metatranscriptome

343

F010932

Metagenome / Metatranscriptome

297

F019400

Metagenome

230

F026976

Metagenome

196

F027937

Metagenome

193

F033667

Metagenome / Metatranscriptome

176

F039208

Metagenome / Metatranscriptome

164

F043475

Metagenome / Metatranscriptome

156

F049863

Metagenome / Metatranscriptome

146

F072145

Metagenome

121

F079748

Metagenome

115

F085674

Metagenome / Metatranscriptome

111

F094338

Metagenome

106

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

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208656_1001972

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium

1351

Open in IMG/M

Ga0208656_1002692

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium

1171

Open in IMG/M

Ga0208656_1003292

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium

1069

Open in IMG/M

Ga0208656_1004930

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium

895

Open in IMG/M

Ga0208656_1007816

Not Available

740

Open in IMG/M

Ga0208656_1007880

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia

738

Open in IMG/M

Ga0208656_1008111

All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae

730

Open in IMG/M

Ga0208656_1009498

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → unclassified Hyphomicrobiales → Hyphomicrobiales bacterium

685

Open in IMG/M

Ga0208656_1014857

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium

574

Open in IMG/M

Ga0208656_1015509

All Organisms → cellular organisms → Bacteria

565

Open in IMG/M

Ga0208656_1016022

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria

558

Open in IMG/M

Ga0208656_1020399

All Organisms → cellular organisms → Bacteria

508

Open in IMG/M

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

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

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

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

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences