Sample 3300026049

Overview

Basic Information
IMG/M Taxon OID	3300026049 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116109 \| Ga0208781
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	75591354
Sequencing Scaffolds	15
Novel Protein Genes	18
Associated Families	18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	3
Not Available	2
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium algeriense	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Granulosicoccaceae → Granulosicoccus → Granulosicoccus antarcticus	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?
F001489	Metagenome / Metatranscriptome	686	Y
F001884	Metagenome / Metatranscriptome	622	Y
F005815	Metagenome / Metatranscriptome	389	Y
F006527	Metagenome / Metatranscriptome	371	Y
F007702	Metagenome / Metatranscriptome	346	Y
F007779	Metagenome / Metatranscriptome	345	Y
F010115	Metagenome / Metatranscriptome	308	Y
F022487	Metagenome / Metatranscriptome	214	Y
F026912	Metagenome	196	Y
F027172	Metagenome / Metatranscriptome	195	Y
F028324	Metagenome	192	Y
F031133	Metagenome	183	Y
F031547	Metagenome / Metatranscriptome	182	Y
F033171	Metagenome	178	Y
F039208	Metagenome / Metatranscriptome	164	Y
F071763	Metagenome	122	Y
F078557	Metagenome	116	Y
F104362	Metagenome / Metatranscriptome	100	Y

Family

Category

Number of Sequences

3D Structure?

F001489

Metagenome / Metatranscriptome

686

F001884

Metagenome / Metatranscriptome

622

F005815

Metagenome / Metatranscriptome

389

F006527

Metagenome / Metatranscriptome

371

F007702

Metagenome / Metatranscriptome

346

F007779

Metagenome / Metatranscriptome

345

F010115

Metagenome / Metatranscriptome

308

F022487

Metagenome / Metatranscriptome

214

F026912

Metagenome

196

F027172

Metagenome / Metatranscriptome

195

F028324

Metagenome

192

F031133

Metagenome

183

F031547

Metagenome / Metatranscriptome

182

F033171

Metagenome

178

F039208

Metagenome / Metatranscriptome

164

F071763

Metagenome

122

F078557

Metagenome

116

F104362

Metagenome / Metatranscriptome

100

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208781_1001052	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi	2456	Open in IMG/M
Ga0208781_1001441	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	2091	Open in IMG/M
Ga0208781_1003941	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → unclassified Hyphomicrobiaceae → Hyphomicrobiaceae bacterium	1203	Open in IMG/M
Ga0208781_1004004	All Organisms → cellular organisms → Bacteria	1193	Open in IMG/M
Ga0208781_1004437	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1133	Open in IMG/M
Ga0208781_1006182	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	959	Open in IMG/M
Ga0208781_1006378	Not Available	945	Open in IMG/M
Ga0208781_1006745	Not Available	918	Open in IMG/M
Ga0208781_1007960	All Organisms → cellular organisms → Bacteria	851	Open in IMG/M
Ga0208781_1008604	All Organisms → cellular organisms → Bacteria → Acidobacteria	822	Open in IMG/M
Ga0208781_1010612	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	751	Open in IMG/M
Ga0208781_1011089	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	737	Open in IMG/M
Ga0208781_1014538	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium algeriense	659	Open in IMG/M
Ga0208781_1017388	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Granulosicoccaceae → Granulosicoccus → Granulosicoccus antarcticus	614	Open in IMG/M
Ga0208781_1028903	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	503	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208781_1001052

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Methyloceanibacter → Methyloceanibacter caenitepidi

2456

Open in IMG/M

Ga0208781_1001441

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

2091

Open in IMG/M

Ga0208781_1003941

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

1203

Open in IMG/M

Ga0208781_1004004

All Organisms → cellular organisms → Bacteria

1193

Open in IMG/M

Ga0208781_1004437

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

1133

Open in IMG/M

Ga0208781_1006182

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

959

Open in IMG/M

Ga0208781_1006378

Not Available

945

Open in IMG/M

Ga0208781_1006745

Not Available

918

Open in IMG/M

Ga0208781_1007960

All Organisms → cellular organisms → Bacteria

851

Open in IMG/M

Ga0208781_1008604

All Organisms → cellular organisms → Bacteria → Acidobacteria

822

Open in IMG/M

Ga0208781_1010612

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

751

Open in IMG/M

Ga0208781_1011089

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium

737

Open in IMG/M

Ga0208781_1014538

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium algeriense

659

Open in IMG/M

Ga0208781_1017388

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales → Granulosicoccaceae → Granulosicoccus → Granulosicoccus antarcticus

614

Open in IMG/M

Ga0208781_1028903

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

503

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208781_1001052	Ga0208781_10010523	F007779	MFQALLEKHAHHRATHHAYQNAVDDCLAGLFRGFPGGVLPALRQRAGDGGLVRRGEAEGTEPRICAVQVAVLLIRKLIGPLSAQERHDLARAFLRNDASNPTYRGLRFMLCAVERLEISPALVSYLNTEVAGQLRGMSQQAIFGSWVETQIGGAMGRMKQPGLEEGAREADLWQ
Ga0208781_1001441	Ga0208781_10014414	F039208	VARYDDMLAALGAGAAIPGVMGVGPGRTWDAMVAAHAPLLTGDSVTFTALEDGTLVVNEDVPDGSLTPVADQIEEMVAPPYRAATARNEGDMWTAVAESVQIATLAGLEADQVELTIVGGERTLTLGDAVSSSTLPGLDELAEGQGDVAIHAERVDGDLFAVDVFPL
Ga0208781_1003941	Ga0208781_10039412	F033171	LANWTPEEHLAFDIAYALKKVTIPGFRKSLKEEDRFAIGQAVVEHLKLCRWEFSKPFEPIKERP
Ga0208781_1004004	Ga0208781_10040042	F010115	MSQSRGGYVVLQRLRGDDWRVLGDVDRQPGMPARKARAQAVRDVLGREPTRQEVFAVLPRSEWKLAVDH
Ga0208781_1004437	Ga0208781_10044372	F007702	LVEGVPYGFVWCASDYIDSCILSDPSQVWVDPEQQERYREIVTRVRTWDAELPTREGIDAVTEILNRITPRFPTPVLWLVVGVVALLWRRPREWRTIVLLWLAAFLVLLIHAASQGVAPEFALPVYPIFIVAALGALAGDRGPRAQLASTA
Ga0208781_1006182	Ga0208781_10061821	F031133	MHRQTTTFSRRVNRVFTHRADRVAKAVERRGIRATYELHDRLLSNRKSRALFESDRPQLDDVQRRILGDVEANG
Ga0208781_1006378	Ga0208781_10063783	F031547	GTGWWDMKTYTVYRVETNKTERIGKVVDRRRGERNDNALDMLRLAQKIYATSSMDSNIFILRESSIQSIFLSGGR
Ga0208781_1006745	Ga0208781_10067452	F071763	MRKRIAAALLACGALLTFVAPAASFSVVNPKTGECRQILVPGPDTFPGNWEVVSETPAAGPGPWNGHGHANGNTALGPVICP
Ga0208781_1007960	Ga0208781_10079601	F006527	VTAQPHACVRFRRAIERRALWLAEDAARELPNLPLEDALQLVHLYGERGSPKYERAAMRWLERYLTEGSPRLEHF
Ga0208781_1008604	Ga0208781_10086041	F001884	MDTVELWARNGDAVREAIELGDIVHLETSREELTDEFLLFAIESGLLSGWAASFPDPRHESEIGMEVLLASQIAARFAKIYSLRKSGYVLRSAAVLGALGYSPQVLEADEGLSRRGTSDDKLISGDVLRKLLVQMELEVDPESPLELPAAKPSEGVKVRKRQSRRAVKGAVDRVEAEARGQRVAAKLLRWYNEEVAASMVAYAALGEGRRIHILDTTGVQVPLATGTYECSGVVKNDDGRRSRGYKLATLRTLLDH
Ga0208781_1010612	Ga0208781_10106122	F026912	RKEHKPHFSIIDSMIDDSEPLRAEYLRGFHRGIEVQVFGVSDEWIEEHRMLIDYSIGGSGDSYIDTYARGYRHGFDGRTPESPSLSSESLPIASIV
Ga0208781_1011089	Ga0208781_10110892	F078557	MKLVYAVSQGTKPKSPTARHIDNGQGQPLYGGNGREPFLRASEEGEPACKICMDLTLMLASEPGRTHTRQTGGE
Ga0208781_1014538	Ga0208781_10145381	F022487	MPIRRSPNGAHHPRPQPGRDRPEWVVAINRNDWSQSIGTG
Ga0208781_1017388	Ga0208781_10173881	F005815	MTMKVTRLTTYWTLDEAATIIDFLDGLRDALWETYGEKITQMHREDYDNRTQDINQCELGFDDDIPF
Ga0208781_1017560	Ga0208781_10175601	F001489	MAHFEMDCEWRYFLAEHAGTEAGHGWGYIRQANAVYPGRDYARPDPEFEKQYGLTPRTEHHAIMKRDFLSYIFSGNLWPYGHVTAASIQSIEITTPKLLDFEERVVHAEERSHHDAILQKIHDYVWELIDIWGEAPIRKRIGEIERIALNSRPRTI
Ga0208781_1021975	Ga0208781_10219751	F028324	MTHSNLRVEVLGNTIMVAMRGTCFRAKYRKQEAPWLATDEYGPDDPEAAVAFSEFRNLAWTAANDRAQQLGWVRSCDDLHKSTKREPLRAQTHRATIEQNK
Ga0208781_1026585	Ga0208781_10265851	F104362	AGDTAAAISRYRAASDAGNPDASAVARYMLAWVRFQSGDAGGALRELSRPLSDPSFPCGVPSPFEREVVSLSVRAWRESALERLDAYPPVNAGTCGGKVLLAALWEAEEKRGEALRAAEVRDVAARRFPSDANAAALEMETVESLLRVGREREALDRALTLRGKYGPDSAWAR
Ga0208781_1028903	Ga0208781_10289031	F027172	SRLGDIWWHASSHAYPEPVATTEGGEMAEKTILVCDACGRPAAETITIKVSRGNFVKDLCSNHVNELVAGARKPRPGRRKGVVDRGGAASSTKKSSTRTATGKRRGRPPKAKTA

Scaffold ID

Protein ID

Family

Sequence

Ga0208781_1001052

Ga0208781_10010523

F007779

MFQALLEKHAHHRATHHAYQNAVDDCLAGLFRGFPGGVLPALRQRAGDGGLVRRGEAEGTEPRICAVQVAVLLIRKLIGPLSAQERHDLARAFLRNDASNPTYRGLRFMLCAVERLEISPALVSYLNTEVAGQLRGMSQQAIFGSWVETQIGGAMGRMKQPGLEEGAREADLWQ

Ga0208781_1001441

Ga0208781_10014414

F039208

VARYDDMLAALGAGAAIPGVMGVGPGRTWDAMVAAHAPLLTGDSVTFTALEDGTLVVNEDVPDGSLTPVADQIEEMVAPPYRAATARNEGDMWTAVAESVQIATLAGLEADQVELTIVGGERTLTLGDAVSSSTLPGLDELAEGQGDVAIHAERVDGDLFAVDVFPL

Ga0208781_1003941

Ga0208781_10039412

F033171

LANWTPEEHLAFDIAYALKKVTIPGFRKSLKEEDRFAIGQAVVEHLKLCRWEFSKPFEPIKERP

Ga0208781_1004004

Ga0208781_10040042

F010115

MSQSRGGYVVLQRLRGDDWRVLGDVDRQPGMPARKARAQAVRDVLGREPTRQEVFAVLPRSEWKLAVDH

Ga0208781_1004437

Ga0208781_10044372

F007702

LVEGVPYGFVWCASDYIDSCILSDPSQVWVDPEQQERYREIVTRVRTWDAELPTREGIDAVTEILNRITPRFPTPVLWLVVGVVALLWRRPREWRTIVLLWLAAFLVLLIHAASQGVAPEFALPVYPIFIVAALGALAGDRGPRAQLASTA

Ga0208781_1006182

Ga0208781_10061821

F031133

MHRQTTTFSRRVNRVFTHRADRVAKAVERRGIRATYELHDRLLSNRKSRALFESDRPQLDDVQRRILGDVEANG

Ga0208781_1006378

Ga0208781_10063783

F031547

GTGWWDMKTYTVYRVETNKTERIGKVVDRRRGERNDNALDMLRLAQKIYATSSMDSNIFILRESSIQSIFLSGGR

Ga0208781_1006745

Ga0208781_10067452

F071763

MRKRIAAALLACGALLTFVAPAASFSVVNPKTGECRQILVPGPDTFPGNWEVVSETPAAGPGPWNGHGHANGNTALGPVICP

Ga0208781_1007960

Ga0208781_10079601

F006527

VTAQPHACVRFRRAIERRALWLAEDAARELPNLPLEDALQLVHLYGERGSPKYERAAMRWLERYLTEGSPRLEHF

Ga0208781_1008604

Ga0208781_10086041

F001884

MDTVELWARNGDAVREAIELGDIVHLETSREELTDEFLLFAIESGLLSGWAASFPDPRHESEIGMEVLLASQIAARFAKIYSLRKSGYVLRSAAVLGALGYSPQVLEADEGLSRRGTSDDKLISGDVLRKLLVQMELEVDPESPLELPAAKPSEGVKVRKRQSRRAVKGAVDRVEAEARGQRVAAKLLRWYNEEVAASMVAYAALGEGRRIHILDTTGVQVPLATGTYECSGVVKNDDGRRSRGYKLATLRTLLDH

Ga0208781_1010612

Ga0208781_10106122

F026912

RKEHKPHFSIIDSMIDDSEPLRAEYLRGFHRGIEVQVFGVSDEWIEEHRMLIDYSIGGSGDSYIDTYARGYRHGFDGRTPESPSLSSESLPIASIV

Ga0208781_1011089

Ga0208781_10110892

F078557

MKLVYAVSQGTKPKSPTARHIDNGQGQPLYGGNGREPFLRASEEGEPACKICMDLTLMLASEPGRTHTRQTGGE

Ga0208781_1014538

Ga0208781_10145381

F022487

MPIRRSPNGAHHPRPQPGRDRPEWVVAINRNDWSQSIGTG

Ga0208781_1017388

Ga0208781_10173881

F005815

MTMKVTRLTTYWTLDEAATIIDFLDGLRDALWETYGEKITQMHREDYDNRTQDINQCELGFDDDIPF

Ga0208781_1017560

Ga0208781_10175601

F001489

MAHFEMDCEWRYFLAEHAGTEAGHGWGYIRQANAVYPGRDYARPDPEFEKQYGLTPRTEHHAIMKRDFLSYIFSGNLWPYGHVTAASIQSIEITTPKLLDFEERVVHAEERSHHDAILQKIHDYVWELIDIWGEAPIRKRIGEIERIALNSRPRTI

Ga0208781_1021975

Ga0208781_10219751

F028324

MTHSNLRVEVLGNTIMVAMRGTCFRAKYRKQEAPWLATDEYGPDDPEAAVAFSEFRNLAWTAANDRAQQLGWVRSCDDLHKSTKREPLRAQTHRATIEQNK

Ga0208781_1026585

Ga0208781_10265851

F104362

AGDTAAAISRYRAASDAGNPDASAVARYMLAWVRFQSGDAGGALRELSRPLSDPSFPCGVPSPFEREVVSLSVRAWRESALERLDAYPPVNAGTCGGKVLLAALWEAEEKRGEALRAAEVRDVAARRFPSDANAAALEMETVESLLRVGREREALDRALTLRGKYGPDSAWAR

Ga0208781_1028903

Ga0208781_10289031

F027172

SRLGDIWWHASSHAYPEPVATTEGGEMAEKTILVCDACGRPAAETITIKVSRGNFVKDLCSNHVNELVAGARKPRPGRRKGVVDRGGAASSTKKSSTRTATGKRRGRPPKAKTA

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026049: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushOxbow_ThreeSqB_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences