Sample 3300026038

Overview

Basic Information
IMG/M Taxon OID	3300026038 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116085 \| Ga0208536
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleC_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	54284679
Sequencing Scaffolds	15
Novel Protein Genes	16
Associated Families	16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → unclassified Actinobacteria → Actinobacteria bacterium ADurb.BinA094	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	2
Not Available	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	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: Antioch, San Francisco Bay, California
Coordinates	Lat. (^o)	38.052509	Long. (^o)	-121.76873	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F014212	Metagenome	265	Y
F014394	Metagenome / Metatranscriptome	263	Y
F019675	Metagenome	228	Y
F031716	Metagenome	182	Y
F036769	Metagenome / Metatranscriptome	169	Y
F049730	Metagenome / Metatranscriptome	146	Y
F064643	Metagenome / Metatranscriptome	128	Y
F065906	Metagenome	127	Y
F069913	Metagenome / Metatranscriptome	123	Y
F072484	Metagenome	121	Y
F081921	Metagenome / Metatranscriptome	114	Y
F082883	Metagenome / Metatranscriptome	113	Y
F086617	Metagenome	110	Y
F088154	Metagenome	109	Y
F090576	Metagenome	108	N
F103518	Metagenome	101	N

Family

Category

Number of Sequences

3D Structure?

F014212

Metagenome

265

F014394

Metagenome / Metatranscriptome

263

F019675

Metagenome

228

F031716

Metagenome

182

F036769

Metagenome / Metatranscriptome

169

F049730

Metagenome / Metatranscriptome

146

F064643

Metagenome / Metatranscriptome

128

F065906

Metagenome

127

F069913

Metagenome / Metatranscriptome

123

F072484

Metagenome

121

F081921

Metagenome / Metatranscriptome

114

F082883

Metagenome / Metatranscriptome

113

F086617

Metagenome

110

F088154

Metagenome

109

F090576

Metagenome

108

F103518

Metagenome

101

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208536_1000218	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	2577	Open in IMG/M
Ga0208536_1000295	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → unclassified Actinobacteria → Actinobacteria bacterium ADurb.BinA094	2379	Open in IMG/M
Ga0208536_1001428	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1433	Open in IMG/M
Ga0208536_1003369	All Organisms → cellular organisms → Bacteria	1065	Open in IMG/M
Ga0208536_1005315	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	897	Open in IMG/M
Ga0208536_1006482	Not Available	829	Open in IMG/M
Ga0208536_1006517	Not Available	828	Open in IMG/M
Ga0208536_1008231	Not Available	757	Open in IMG/M
Ga0208536_1008798	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	739	Open in IMG/M
Ga0208536_1010243	All Organisms → cellular organisms → Bacteria	695	Open in IMG/M
Ga0208536_1013811	Not Available	619	Open in IMG/M
Ga0208536_1014575	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	606	Open in IMG/M
Ga0208536_1023179	All Organisms → cellular organisms → Bacteria	504	Open in IMG/M
Ga0208536_1023245	Not Available	504	Open in IMG/M
Ga0208536_1023463	Not Available	502	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208536_1000218

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales

2577

Open in IMG/M

Ga0208536_1000295

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → unclassified Actinobacteria → Actinobacteria bacterium ADurb.BinA094

2379

Open in IMG/M

Ga0208536_1001428

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

1433

Open in IMG/M

Ga0208536_1003369

All Organisms → cellular organisms → Bacteria

1065

Open in IMG/M

Ga0208536_1005315

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038

897

Open in IMG/M

Ga0208536_1006482

Not Available

829

Open in IMG/M

Ga0208536_1006517

Not Available

828

Open in IMG/M

Ga0208536_1008231

Not Available

757

739

All Organisms → cellular organisms → Bacteria

695

Open in IMG/M

Ga0208536_1013811

Not Available

619

Open in IMG/M

Ga0208536_1014575

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

606

Open in IMG/M

Ga0208536_1023179

All Organisms → cellular organisms → Bacteria

504

Open in IMG/M

Ga0208536_1023245

Not Available

504

Open in IMG/M

Ga0208536_1023463

Not Available

502

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208536_1000218	Ga0208536_10002183	F069913	LFRLNNFVLKLKAMTIEEYNLLEQEFSTSETDIKTFLLTKGVSLHKYYYWKRKSRDLQEASSQSEGQFLPINVLCGGSIKPGKRGKNLKQPFISQGEIEIELRTPSGAELRIRGMMDSLMVSTIIASSGGRRNV
Ga0208536_1000295	Ga0208536_10002954	F088154	MSWWVYGTVWFIIWVVCLWLVWRMVDRKDLNRAGWIILTIFFPIIGLIVVAILPAKRRQTPPETLP
Ga0208536_1001428	Ga0208536_10014281	F086617	MPTIHASVDVDAPLEFAELEWSEFLLESLLSGYARGLIDEEPLLDEDDMEAGDVRFTTEGDRLVKVDVRLDYRPRSVGGAATETARAQATLERDLDRYRRFVIGRCERLGCRQD
Ga0208536_1003369	Ga0208536_10033691	F103518	MKAKSMRKPILLEPEKVETAEITISNHDFARLLRKQEEVERYLEEIKRATASIEKILAGKAPKRSYEIRYVADIDDYYM
Ga0208536_1004218	Ga0208536_10042182	F082883	MAGRPSHFAAPLLLAVITGLIVYVSLYPFRFELDGPTLREALQALSWQRAGRGDMLNNLL
Ga0208536_1005315	Ga0208536_10053151	F036769	DPADVQAAAPQDVMAGTWVLTFEDGRVGWANLVSDDYAKTSFSSKGKVEVPGFKQVDITSGVIPEFYKVGQVILYNAQATQKPFHFVRFVIEGNQFMTGYVATFDNKQYKFKARKR
Ga0208536_1006482	Ga0208536_10064821	F065906	MTMSEPLPLTPDEDVVFREFIRLDVEPNHIPPELFVGFLERLAKEVDIPLQRVRVATQGLIDKGKFDAVDAGNEERIHHEREIIRDLLLHDPEIRDLLK
Ga0208536_1006517	Ga0208536_10065172	F031716	MSRFTPGPWLVNEENGSYGVFSNDALLAVTLSDDLKDKNAAKANAHLMASAPLLLEVIKQIKEHLDNNMIVTEEGLKINDSHLRDSIIDAILRAEGYRL
Ga0208536_1008231	Ga0208536_10082312	F014212	MKIRLILAFLIISVSASAQLIHVEGSKALGINYAYVKNGFNVSSRITFYKSGNLAYRASLDYERVSFDLSKASVVYANPELMYTFYTLGDKVFFNVNGGILTGAEFISNSILDRKKSQFFIGENIGVCTEYFISNKIMLNLDLDQRFFQMSKVGKASFIIKLGINYNFY
Ga0208536_1008798	Ga0208536_10087981	F049730	MLKETALSRRQMRDKRKPSMLILGSFEKLKQDLIPALFRIAGDREIGHIDIRSSPETVNLKQLTGYTLIFVAFEIYRDNESFFRMLPESIRDRITILSRPADFPSVAPEIQCSCYCSDLKALLPREEAQLFEHHTKSAKPR
Ga0208536_1010243	Ga0208536_10102432	F019675	MNRTKQIILVLTAVLGVLLVVRGAWDGVWPVSLQLVAGVLLLVYAGLRLWTLR
Ga0208536_1013811	Ga0208536_10138111	F081921	MNTLPQSEQQEIHLQERAGETLADDSLPATQVIEEQSNDAEQNNAPRFIP
Ga0208536_1014575	Ga0208536_10145752	F072484	MKRRNVGLLFLATLSALMSTTDLNAADFLYFWKASTDPSVAAYGIYQRTEDSSYAKIDEVSVQDLDNPATPSYILTGLADGTTYWFAVTSISASGSESNHSNQTCITVNGSIVECTDTNEDGATVFISCFITAAGR
Ga0208536_1023179	Ga0208536_10231792	F014394	QVMGRLRGRDMRAGSRLLAVIVASAVWIYAGMSVASRPLAQQAITPTVLDVAASCALAAI
Ga0208536_1023245	Ga0208536_10232451	F064643	IIDRIAKLTTDCDAFTNDLRYYMVKEIVNGNKTKFSPLMMNQDVVKMAVK
Ga0208536_1023463	Ga0208536_10234631	F090576	MSNEGGGCGGNLFTNLVPARQADYLAMLAQEARLLEFSLEGEDPDSVRIGDRLQRALESALDADGPDEVRGARDELEEVLNGARDAGLRLSAHLTEVDVDGVLGTMKMRVLSTVLAPPAQAMNA

Scaffold ID

Protein ID

Family

Sequence

Ga0208536_1000218

Ga0208536_10002183

F069913

LFRLNNFVLKLKAMTIEEYNLLEQEFSTSETDIKTFLLTKGVSLHKYYYWKRKSRDLQEASSQSEGQFLPINVLCGGSIKPGKRGKNLKQPFISQGEIEIELRTPSGAELRIRGMMDSLMVSTIIASSGGRRNV

Ga0208536_1000295

Ga0208536_10002954

F088154

MSWWVYGTVWFIIWVVCLWLVWRMVDRKDLNRAGWIILTIFFPIIGLIVVAILPAKRRQTPPETLP

Ga0208536_1001428

Ga0208536_10014281

F086617

MPTIHASVDVDAPLEFAELEWSEFLLESLLSGYARGLIDEEPLLDEDDMEAGDVRFTTEGDRLVKVDVRLDYRPRSVGGAATETARAQATLERDLDRYRRFVIGRCERLGCRQD

Ga0208536_1003369

Ga0208536_10033691

F103518

MKAKSMRKPILLEPEKVETAEITISNHDFARLLRKQEEVERYLEEIKRATASIEKILAGKAPKRSYEIRYVADIDDYYM

Ga0208536_1004218

Ga0208536_10042182

F082883

MAGRPSHFAAPLLLAVITGLIVYVSLYPFRFELDGPTLREALQALSWQRAGRGDMLNNLL

Ga0208536_1005315

Ga0208536_10053151

F036769

DPADVQAAAPQDVMAGTWVLTFEDGRVGWANLVSDDYAKTSFSSKGKVEVPGFKQVDITSGVIPEFYKVGQVILYNAQATQKPFHFVRFVIEGNQFMTGYVATFDNKQYKFKARKR

Ga0208536_1006482

Ga0208536_10064821

F065906

MTMSEPLPLTPDEDVVFREFIRLDVEPNHIPPELFVGFLERLAKEVDIPLQRVRVATQGLIDKGKFDAVDAGNEERIHHEREIIRDLLLHDPEIRDLLK

Ga0208536_1006517

Ga0208536_10065172

F031716

MSRFTPGPWLVNEENGSYGVFSNDALLAVTLSDDLKDKNAAKANAHLMASAPLLLEVIKQIKEHLDNNMIVTEEGLKINDSHLRDSIIDAILRAEGYRL

Ga0208536_1008231

Ga0208536_10082312

F014212

MKIRLILAFLIISVSASAQLIHVEGSKALGINYAYVKNGFNVSSRITFYKSGNLAYRASLDYERVSFDLSKASVVYANPELMYTFYTLGDKVFFNVNGGILTGAEFISNSILDRKKSQFFIGENIGVCTEYFISNKIMLNLDLDQRFFQMSKVGKASFIIKLGINYNFY

Ga0208536_1008798

Ga0208536_10087981

F049730

MLKETALSRRQMRDKRKPSMLILGSFEKLKQDLIPALFRIAGDREIGHIDIRSSPETVNLKQLTGYTLIFVAFEIYRDNESFFRMLPESIRDRITILSRPADFPSVAPEIQCSCYCSDLKALLPREEAQLFEHHTKSAKPR

Ga0208536_1010243

Ga0208536_10102432

F019675

MNRTKQIILVLTAVLGVLLVVRGAWDGVWPVSLQLVAGVLLLVYAGLRLWTLR

Ga0208536_1013811

Ga0208536_10138111

F081921

MNTLPQSEQQEIHLQERAGETLADDSLPATQVIEEQSNDAEQNNAPRFIP

Ga0208536_1014575

Ga0208536_10145752

F072484

MKRRNVGLLFLATLSALMSTTDLNAADFLYFWKASTDPSVAAYGIYQRTEDSSYAKIDEVSVQDLDNPATPSYILTGLADGTTYWFAVTSISASGSESNHSNQTCITVNGSIVECTDTNEDGATVFISCFITAAGR

Ga0208536_1023179

Ga0208536_10231792

F014394

QVMGRLRGRDMRAGSRLLAVIVASAVWIYAGMSVASRPLAQQAITPTVLDVAASCALAAI

Ga0208536_1023245

Ga0208536_10232451

F064643

IIDRIAKLTTDCDAFTNDLRYYMVKEIVNGNKTKFSPLMMNQDVVKMAVK

Ga0208536_1023463

Ga0208536_10234631

F090576

MSNEGGGCGGNLFTNLVPARQADYLAMLAQEARLLEFSLEGEDPDSVRIGDRLQRALESALDADGPDEVRGARDELEEVLNGARDAGLRLSAHLTEVDVDGVLGTMKMRVLSTVLAPPAQAMNA

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026038: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleC_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences