Sample 3300026013

Overview

Basic Information
IMG/M Taxon OID	3300026013 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116069 \| Ga0208534
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Browns_TuleC_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	50441257
Sequencing Scaffolds	17
Novel Protein Genes	19
Associated Families	19

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria	3
Not Available	9
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → Methanosarcinaceae → Methanosarcina → Methanosarcina barkeri	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. FHR47	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria 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 → 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: Browns Island, San Francisco Bay, California
Coordinates	Lat. (^o)	38.04565	Long. (^o)	-121.866287	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F001213	Metagenome / Metatranscriptome	746	Y
F017538	Metagenome / Metatranscriptome	240	Y
F018388	Metagenome / Metatranscriptome	235	Y
F025096	Metagenome / Metatranscriptome	203	Y
F029789	Metagenome	187	Y
F031074	Metagenome	183	Y
F037795	Metagenome	167	Y
F039157	Metagenome / Metatranscriptome	164	Y
F047544	Metagenome / Metatranscriptome	149	Y
F047749	Metagenome	149	Y
F060885	Metagenome / Metatranscriptome	132	Y
F063135	Metagenome / Metatranscriptome	130	Y
F064701	Metagenome / Metatranscriptome	128	Y
F070289	Metagenome / Metatranscriptome	123	N
F078852	Metagenome	116	Y
F086136	Metagenome / Metatranscriptome	111	Y
F090606	Metagenome	108	Y
F092520	Metagenome	107	Y
F095849	Metagenome / Metatranscriptome	105	N

Family

Category

Number of Sequences

3D Structure?

F001213

Metagenome / Metatranscriptome

746

F017538

Metagenome / Metatranscriptome

240

F018388

Metagenome / Metatranscriptome

235

F025096

Metagenome / Metatranscriptome

203

F029789

Metagenome

187

F031074

Metagenome

183

F037795

Metagenome

167

F039157

Metagenome / Metatranscriptome

164

F047544

Metagenome / Metatranscriptome

149

F047749

Metagenome

149

F060885

Metagenome / Metatranscriptome

132

F063135

Metagenome / Metatranscriptome

130

F064701

Metagenome / Metatranscriptome

128

F070289

Metagenome / Metatranscriptome

123

F078852

Metagenome

116

F086136

Metagenome / Metatranscriptome

111

F090606

Metagenome

108

F092520

Metagenome

107

F095849

Metagenome / Metatranscriptome

105

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208534_1001012	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1389	Open in IMG/M
Ga0208534_1001423	All Organisms → cellular organisms → Bacteria	1213	Open in IMG/M
Ga0208534_1002370	Not Available	1020	Open in IMG/M
Ga0208534_1004019	Not Available	859	Open in IMG/M
Ga0208534_1005337	Not Available	783	Open in IMG/M
Ga0208534_1005539	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → Methanosarcinaceae → Methanosarcina → Methanosarcina barkeri	774	Open in IMG/M
Ga0208534_1007028	Not Available	717	Open in IMG/M
Ga0208534_1011364	Not Available	612	Open in IMG/M
Ga0208534_1011658	Not Available	606	Open in IMG/M
Ga0208534_1012513	All Organisms → cellular organisms → Bacteria	592	Open in IMG/M
Ga0208534_1015953	All Organisms → cellular organisms → Bacteria	545	Open in IMG/M
Ga0208534_1018006	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	523	Open in IMG/M
Ga0208534_1018240	Not Available	521	Open in IMG/M
Ga0208534_1018470	Not Available	518	Open in IMG/M
Ga0208534_1018777	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. FHR47	516	Open in IMG/M
Ga0208534_1019036	Not Available	513	Open in IMG/M
Ga0208534_1020391	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	500	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208534_1001012

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

1389

Open in IMG/M

Ga0208534_1001423

All Organisms → cellular organisms → Bacteria

1213

Open in IMG/M

Ga0208534_1002370

Not Available

1020

Open in IMG/M

Ga0208534_1004019

Not Available

859

Open in IMG/M

Ga0208534_1005337

Not Available

783

Open in IMG/M

Ga0208534_1005539

All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanosarcinales → Methanosarcinaceae → Methanosarcina → Methanosarcina barkeri

774

Open in IMG/M

Ga0208534_1007028

Not Available

717

Open in IMG/M

Ga0208534_1011364

Not Available

612

Open in IMG/M

Ga0208534_1011658

Not Available

606

Open in IMG/M

Ga0208534_1012513

All Organisms → cellular organisms → Bacteria

592

Open in IMG/M

Ga0208534_1015953

All Organisms → cellular organisms → Bacteria

545

Open in IMG/M

Ga0208534_1018006

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

523

Open in IMG/M

Ga0208534_1018240

Not Available

521

Open in IMG/M

Ga0208534_1018470

Not Available

518

Open in IMG/M

Ga0208534_1018777

All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. FHR47

516

Open in IMG/M

Ga0208534_1019036

Not Available

513

Open in IMG/M

Ga0208534_1020391

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

500

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208534_1001012	Ga0208534_10010121	F031074	MATAVKKLDLEIGELVEVGGRRYEVVPDRQGGLTLEPPITPVAVLYAERGWELAAREAFEQLTA
Ga0208534_1001423	Ga0208534_10014231	F064701	AMADPLQIGPSAIPSGSVRTLYYSMRHRTQLYLDEGQYRWLRQRAGEAGSIAAVVRQLIDDERARRLDPSADPLLSYLVAEAPGEGREPTSVTSLDRDLYGR
Ga0208534_1002370	Ga0208534_10023702	F078852	MERTELLQLVSHASSLNQISSVMAGIRGWLADHPDDEEMRHAIVELSRLEREHFTYTSR
Ga0208534_1004019	Ga0208534_10040193	F001213	IDGEEVPVRAGTILRFDPETTRVPIAGPDGMTMIAIGARRGSYEPRGPF
Ga0208534_1004655	Ga0208534_10046551	F090606	PVAKEDKVPVAGEDKTPVANEDSQGETGPQAVGSVAKPGLTPDCEKELRRAASLLRFFANRIQVGEDTQAIVADMRQQEKKISAVCE
Ga0208534_1004845	Ga0208534_10048452	F086136	MGRLPRRQFLLVSVAFLARSLAAEAQQAGRVYRIGYL
Ga0208534_1005337	Ga0208534_10053371	F070289	AGPTIVKQFKQLQLPQRLVLTGANVSPQFLQGTCGDVNGAIVNSFLATAWAFLPKTNPVRAQAALLRSILKRPVSNFDGDASGALWAYKAAIERGSATRAGINTALETKLRGLVTPAGRIFLSPRNHQGLQLDSMWVGRIQNCQVRPLFGPAFTKKKK
Ga0208534_1005539	Ga0208534_10055391	F047749	RALHGLYKVGLLGYVQHDRVRGQWRQRFLRPGDATLDPTGALPPASHYLVHPVLTDVIGRLNPAFVQRVNRANLIGYDKPWRDDTAPPEPIATVQHCCVLKADVHGFGGLMRAGTDGPVRRALERAVQRWRPPSATAEAGAGDAVLMVDADPVAIAQAARHLMDDVYHAPGQPRLRIALHYGPVRTRPDPRRHGTEIIGGDAVLCAARVEPVVEPGQIWATEEFREQLSQRPSLWRTTPIPSPSGDGPVNVKKEGNG
Ga0208534_1007028	Ga0208534_10070281	F025096	DNHTKAPLQWVVQAWVKTEAATLYAKSINLEGIIEHVTWNKDGAPSVGDQHLSGDVRTIPFAWMNAKERLLVTEPVRVHFYTLLKEESSAPTPMDHYLGVVTTESIGKGSVITWRVYFDTTGWSPMASIMSSQIKSGLEKGFQSWIDEYGGMLIPVEVKN
Ga0208534_1011364	Ga0208534_10113641	F018388	MIGRTLAVAALVGFATIDVVPLTHAEHIAVSTELLQQASIITPEGITVDPNNKEELKKYDNRHDLSELADSLRKEFGVTTSQLTQLIACTGPVVCKVPSADGKRINIYQGSGSIALQPNILVTVKHAFQDLDTGQLLPIDTCRFHNWKNPNDEIAIIIDDPSQLPPIATSMSKTPQ
Ga0208534_1011658	Ga0208534_10116582	F037795	MVSMMRWEQAIVYAVGALLFIGAATSVFQLYGAALLLGCILMVLSLADGPRGLKLLLRDIKRHVVGP
Ga0208534_1012513	Ga0208534_10125131	F063135	MNAWLTTAKLVPVLGLIPLGAAVQAAFMQREPQRAPLRVSGENTRSPRRSRG
Ga0208534_1015953	Ga0208534_10159531	F060885	TRKTISAAAAVAIVSFGGLVMDQAYLAAAPRGTVEVGELTALDNGATTLAQLPEVVVVAKRDFGTYYATAELPEIVVVAKRVASMVAKEDGGKHAPAPAINAGL
Ga0208534_1018006	Ga0208534_10180061	F095849	MDPLVSIRAKFERFPAAIKGALLLRGADGQPHQIRLEGARATELGGGQPHPVGVEAVVLEASPTQDTFVPFEISTMEMAAGWYALECDVVVDGVPS
Ga0208534_1018240	Ga0208534_10182401	F017538	LTVSLTFVRASRNRDGEWSSDDYDVFEGKQLVGRITLTPQVPEGRPWFWTITARPESSQNKGYAVSPEQAMLELT
Ga0208534_1018470	Ga0208534_10184701	F029789	GGLSMIAAMAVDLDSTAAKVLMVAAAILFVPGAVLTLAFVRRHLGPPR
Ga0208534_1018777	Ga0208534_10187772	F092520	MRRIIQANIDRFKELLKTETNPTKRAMEARLLAEEELKQKHLPAYDKKETKAF
Ga0208534_1019036	Ga0208534_10190361	F047544	VRFNDGVYLAPGKLFRLSSPFPDAPIVSDGSQPDNNNAGAVSFIDETGRMVGVLYMEDKDKTIAAGEDTRHLADWFRDTGFPRFFQANVPDSKVLRDEAGAIDGKPAWIAVAHVPNGAPLGVSVKGSYDIKRNDSWRGIAVVARGKHYYLLQTELRVEKLAAPDWKYDAN
Ga0208534_1020391	Ga0208534_10203911	F039157	KPRKSVEREIEIYRETLKIAKTFTPDDLEDMSLLKKVQEGRAAQGR

Scaffold ID

Protein ID

Family

Sequence

Ga0208534_1001012

Ga0208534_10010121

F031074

MATAVKKLDLEIGELVEVGGRRYEVVPDRQGGLTLEPPITPVAVLYAERGWELAAREAFEQLTA

Ga0208534_1001423

Ga0208534_10014231

F064701

AMADPLQIGPSAIPSGSVRTLYYSMRHRTQLYLDEGQYRWLRQRAGEAGSIAAVVRQLIDDERARRLDPSADPLLSYLVAEAPGEGREPTSVTSLDRDLYGR

Ga0208534_1002370

Ga0208534_10023702

F078852

MERTELLQLVSHASSLNQISSVMAGIRGWLADHPDDEEMRHAIVELSRLEREHFTYTSR

Ga0208534_1004019

Ga0208534_10040193

F001213

IDGEEVPVRAGTILRFDPETTRVPIAGPDGMTMIAIGARRGSYEPRGPF

Ga0208534_1004655

Ga0208534_10046551

F090606

PVAKEDKVPVAGEDKTPVANEDSQGETGPQAVGSVAKPGLTPDCEKELRRAASLLRFFANRIQVGEDTQAIVADMRQQEKKISAVCE

Ga0208534_1004845

Ga0208534_10048452

F086136

MGRLPRRQFLLVSVAFLARSLAAEAQQAGRVYRIGYL

Ga0208534_1005337

Ga0208534_10053371

F070289

AGPTIVKQFKQLQLPQRLVLTGANVSPQFLQGTCGDVNGAIVNSFLATAWAFLPKTNPVRAQAALLRSILKRPVSNFDGDASGALWAYKAAIERGSATRAGINTALETKLRGLVTPAGRIFLSPRNHQGLQLDSMWVGRIQNCQVRPLFGPAFTKKKK

Ga0208534_1005539

Ga0208534_10055391

F047749

RALHGLYKVGLLGYVQHDRVRGQWRQRFLRPGDATLDPTGALPPASHYLVHPVLTDVIGRLNPAFVQRVNRANLIGYDKPWRDDTAPPEPIATVQHCCVLKADVHGFGGLMRAGTDGPVRRALERAVQRWRPPSATAEAGAGDAVLMVDADPVAIAQAARHLMDDVYHAPGQPRLRIALHYGPVRTRPDPRRHGTEIIGGDAVLCAARVEPVVEPGQIWATEEFREQLSQRPSLWRTTPIPSPSGDGPVNVKKEGNG

Ga0208534_1007028

Ga0208534_10070281

F025096

DNHTKAPLQWVVQAWVKTEAATLYAKSINLEGIIEHVTWNKDGAPSVGDQHLSGDVRTIPFAWMNAKERLLVTEPVRVHFYTLLKEESSAPTPMDHYLGVVTTESIGKGSVITWRVYFDTTGWSPMASIMSSQIKSGLEKGFQSWIDEYGGMLIPVEVKN

Ga0208534_1011364

Ga0208534_10113641

F018388

MIGRTLAVAALVGFATIDVVPLTHAEHIAVSTELLQQASIITPEGITVDPNNKEELKKYDNRHDLSELADSLRKEFGVTTSQLTQLIACTGPVVCKVPSADGKRINIYQGSGSIALQPNILVTVKHAFQDLDTGQLLPIDTCRFHNWKNPNDEIAIIIDDPSQLPPIATSMSKTPQ

Ga0208534_1011658

Ga0208534_10116582

F037795

MVSMMRWEQAIVYAVGALLFIGAATSVFQLYGAALLLGCILMVLSLADGPRGLKLLLRDIKRHVVGP

Ga0208534_1012513

Ga0208534_10125131

F063135

MNAWLTTAKLVPVLGLIPLGAAVQAAFMQREPQRAPLRVSGENTRSPRRSRG

Ga0208534_1015953

Ga0208534_10159531

F060885

TRKTISAAAAVAIVSFGGLVMDQAYLAAAPRGTVEVGELTALDNGATTLAQLPEVVVVAKRDFGTYYATAELPEIVVVAKRVASMVAKEDGGKHAPAPAINAGL

Ga0208534_1018006

Ga0208534_10180061

F095849

MDPLVSIRAKFERFPAAIKGALLLRGADGQPHQIRLEGARATELGGGQPHPVGVEAVVLEASPTQDTFVPFEISTMEMAAGWYALECDVVVDGVPS

Ga0208534_1018240

Ga0208534_10182401

F017538

LTVSLTFVRASRNRDGEWSSDDYDVFEGKQLVGRITLTPQVPEGRPWFWTITARPESSQNKGYAVSPEQAMLELT

Ga0208534_1018470

Ga0208534_10184701

F029789

GGLSMIAAMAVDLDSTAAKVLMVAAAILFVPGAVLTLAFVRRHLGPPR

Ga0208534_1018777

Ga0208534_10187772

F092520

MRRIIQANIDRFKELLKTETNPTKRAMEARLLAEEELKQKHLPAYDKKETKAF

Ga0208534_1019036

Ga0208534_10190361

F047544

VRFNDGVYLAPGKLFRLSSPFPDAPIVSDGSQPDNNNAGAVSFIDETGRMVGVLYMEDKDKTIAAGEDTRHLADWFRDTGFPRFFQANVPDSKVLRDEAGAIDGKPAWIAVAHVPNGAPLGVSVKGSYDIKRNDSWRGIAVVARGKHYYLLQTELRVEKLAAPDWKYDAN

Ga0208534_1020391

Ga0208534_10203911

F039157

KPRKSVEREIEIYRETLKIAKTFTPDDLEDMSLLKKVQEGRAAQGR

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026013: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Browns_TuleC_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences