Sample 3300026027

Overview

Basic Information
IMG/M Taxon OID	3300026027 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116081 \| Ga0208910
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleA_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	41002437
Sequencing Scaffolds	17
Novel Protein Genes	17
Associated Families	17

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 → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Atribacterota → unclassified Atribacterota → Candidatus Atribacteria bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → unclassified Nitrospiraceae → Nitrospiraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria	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

Zoom:	Powered by OpenStreetMap^©

Family	Category	Number of Sequences	3D Structure?
F001819	Metagenome / Metatranscriptome	630	Y
F007838	Metagenome / Metatranscriptome	344	Y
F010394	Metagenome / Metatranscriptome	304	Y
F020200	Metagenome	225	Y
F032323	Metagenome	180	Y
F042958	Metagenome	157	N
F043160	Metagenome / Metatranscriptome	157	N
F052021	Metagenome / Metatranscriptome	143	Y
F067249	Metagenome	126	Y
F069913	Metagenome / Metatranscriptome	123	Y
F080208	Metagenome / Metatranscriptome	115	Y
F087388	Metagenome	110	Y
F087857	Metagenome / Metatranscriptome	110	N
F098592	Metagenome	103	Y
F098776	Metagenome / Metatranscriptome	103	Y
F103514	Metagenome	101	N
F103518	Metagenome	101	N

Family

Category

Number of Sequences

3D Structure?

F001819

Metagenome / Metatranscriptome

630

F007838

Metagenome / Metatranscriptome

344

F010394

Metagenome / Metatranscriptome

304

F020200

Metagenome

225

F032323

Metagenome

180

F042958

Metagenome

157

F043160

Metagenome / Metatranscriptome

157

F052021

Metagenome / Metatranscriptome

143

F067249

Metagenome

126

F069913

Metagenome / Metatranscriptome

123

F080208

Metagenome / Metatranscriptome

115

F087388

Metagenome

110

F087857

Metagenome / Metatranscriptome

110

F098592

Metagenome

103

F098776

Metagenome / Metatranscriptome

103

F103514

Metagenome

101

F103518

Metagenome

101

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208910_1000062	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Bacteroidia → Bacteroidales	2620	Open in IMG/M
Ga0208910_1000132	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica	2061	Open in IMG/M
Ga0208910_1001431	Not Available	1123	Open in IMG/M
Ga0208910_1002636	Not Available	921	Open in IMG/M
Ga0208910_1003070	Not Available	876	Open in IMG/M
Ga0208910_1003842	Not Available	813	Open in IMG/M
Ga0208910_1004463	All Organisms → cellular organisms → Bacteria → Atribacterota → unclassified Atribacterota → Candidatus Atribacteria bacterium	774	Open in IMG/M
Ga0208910_1005031	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	741	Open in IMG/M
Ga0208910_1005665	Not Available	713	Open in IMG/M
Ga0208910_1006904	All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → unclassified Nitrospiraceae → Nitrospiraceae bacterium	666	Open in IMG/M
Ga0208910_1007418	Not Available	650	Open in IMG/M
Ga0208910_1007722	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	641	Open in IMG/M
Ga0208910_1008068	Not Available	631	Open in IMG/M
Ga0208910_1010413	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	577	Open in IMG/M
Ga0208910_1012726	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	538	Open in IMG/M
Ga0208910_1013305	All Organisms → cellular organisms → Bacteria	530	Open in IMG/M
Ga0208910_1015447	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	502	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208910_1000062

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

2620

Open in IMG/M

Ga0208910_1000132

All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanomicrobiales → Methanoregulaceae → Methanoregula → Methanoregula formicica

2061

Open in IMG/M

Ga0208910_1001431

Not Available

1123

Open in IMG/M

Ga0208910_1002636

Not Available

921

Open in IMG/M

Ga0208910_1003070

Not Available

876

Open in IMG/M

Ga0208910_1003842

Not Available

813

Open in IMG/M

Ga0208910_1004463

All Organisms → cellular organisms → Bacteria → Atribacterota → unclassified Atribacterota → Candidatus Atribacteria bacterium

774

Open in IMG/M

Ga0208910_1005031

All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon

741

Open in IMG/M

Ga0208910_1005665

Not Available

713

Open in IMG/M

Ga0208910_1006904

All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → unclassified Nitrospiraceae → Nitrospiraceae bacterium

666

Open in IMG/M

Ga0208910_1007418

Not Available

650

Open in IMG/M

Ga0208910_1007722

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

641

Open in IMG/M

Ga0208910_1008068

Not Available

631

Open in IMG/M

Ga0208910_1010413

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

577

Open in IMG/M

Ga0208910_1012726

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

538

Open in IMG/M

Ga0208910_1013305

All Organisms → cellular organisms → Bacteria

530

Open in IMG/M

Ga0208910_1015447

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

502

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208910_1000062	Ga0208910_10000623	F069913	SETDIKTFLLTKGVSLHKYYYWKRKSRDLQEASSQSEGQFLPISVLCGGSIKPGKRGKNLKQPFISQGEIEIELRTPSGAELRIRGMMDSLMVSTIIASSGGRRNV
Ga0208910_1000132	Ga0208910_10001322	F032323	MSYLVLRLKNDTSLKSRLLTSILHVNPSYSVKEYREEPDPVDNNYCIISLTSYEKSPYCPIRRILSEFVKNNEIEYLNESSADQFT
Ga0208910_1001431	Ga0208910_10014312	F052021	MKKNKQIELDCSKNCKSVQACEAKGRSRDECENRYNDCVSR
Ga0208910_1002636	Ga0208910_10026361	F010394	MSETRKPVRPAHGDARRWQTEFDELELRMDALRQAFTEAIRSFEMTEETVERIHARFDDLGEQVHAMHCTYPFGGWPGQEDCRFEPPVPYESEARRAQD
Ga0208910_1003070	Ga0208910_10030701	F087388	DRGEPLEGAISMTLGDGGLDEEVLVELQVAGLRDAVIHEAFHELLEWHANFGGLAEFLEIDEAIHRTAERIGHDFDQDLPDHPGEGSSSRLVH
Ga0208910_1003842	Ga0208910_10038422	F103518	MICAEATGIQTTRKGGPCVMKAKSMRKPILLEPEKVETAEITISNHDFARLLRKQEEVERYLEEIKRATASIEKILAGKAPKRSYEIRYVADIDDYYM
Ga0208910_1004463	Ga0208910_10044631	F043160	MAKKNFDNLTKNSHLGGGLSNLIPEMNEKHESKKNKVASNDVPKTFLMLLEDYEYLQTYSRYMAFHNNSKYPLKRSLSDAIKLLKEAHPEIR
Ga0208910_1005031	Ga0208910_10050311	F067249	NLNLSAIPKVTIQGSRIENNLLLLKIGVDPNQKTYPSNQVKMVIEVKSSGVGAKNLPNGKLIDPNKGLRTKFNELQATTNVRNYAVIVLSETLLPPGGPYKWRFKEEAIRKENCKVFTLVARELYPAGGLFVKSNIEEMLQKEQMKKTGEFEQLIKYLRCL
Ga0208910_1005665	Ga0208910_10056651	F042958	MRKGILVTKKGTREGYFPIFIDDREFVQSVLAEAMEQWKQRETQDAVHDGMEFFEIANAIGKERTKSHQFIGAESIPERELEAGFNQASYIFAVDFKEGKVRKVK
Ga0208910_1006904	Ga0208910_10069043	F020200	NLISGWNEEREFQEKTSNDRYHRGLSKGFSECVKDLSEAVASMRLKGLCGKVPEYEGSINDKQRLDILDDLLKLGDEDSNQG
Ga0208910_1007418	Ga0208910_10074181	F103514	MREDIRIKRIAFNLKQHMKFIEIEVPGDEILRSVAADSPEFENRVKQKVIDYIKAL
Ga0208910_1007722	Ga0208910_10077221	F098776	MSIKYFDFTTPQFFLFRNQSKHLSIPQYHILILAWCALVILYGEPGLSPTPKHSET
Ga0208910_1008068	Ga0208910_10080682	F007838	SDRLREYAKLTEQVKTQKESLQVIRDATEKLRKINRKVANYHNLELAIAQVSDSYTRVLGSLKAINEHNCFKPSEYHMLSESMMGLLSQTSYSITTLTVVLTDNFSEMSDGERLLNMNQAIKELRENIGVINSAIIEVEILDNQRMQLRTLNYINSVFK
Ga0208910_1010413	Ga0208910_10104131	F087857	MKRNLIVVPLLVIAFVAFQIVPPAQAEPITLTIMAIAGIATVMTAASADMAVHGVAITQANSPKEMPAEVYAKDRSADSANNHDS
Ga0208910_1012726	Ga0208910_10127262	F098592	MDFGNIRRWVAGIVLVMAAVGLGLLPVAAAEKESKALLSWVTAIDLDECEPYQIRDKIMALHPQYGTIVVAEREIRALDVVADGKLIKTEFLTMDGKPESPSALSVGQYVWVKGVLHPDGFVAAFVVQQIAKPQEEKFIYKPNV
Ga0208910_1013305	Ga0208910_10133051	F001819	NKAEVVVESANFYATNFELGAIPPLFIHQLSRSRWRIDAEVFQTITTDCHLKHPAVHQSTALVVLTMIRLLAYALSLVFYQRQICSHARGSCDSFHEFAKRLAYGFVALSFNTS
Ga0208910_1015447	Ga0208910_10154472	F080208	MQAEEFINVINECEVLRDDIDDIRGRVPLTRTEGNKLNQAVSCVDKAKSILSGLFPAIQSLSEDVREELQGELGETD

Scaffold ID

Protein ID

Family

Sequence

Ga0208910_1000062

Ga0208910_10000623

F069913

SETDIKTFLLTKGVSLHKYYYWKRKSRDLQEASSQSEGQFLPISVLCGGSIKPGKRGKNLKQPFISQGEIEIELRTPSGAELRIRGMMDSLMVSTIIASSGGRRNV

Ga0208910_1000132

Ga0208910_10001322

F032323

MSYLVLRLKNDTSLKSRLLTSILHVNPSYSVKEYREEPDPVDNNYCIISLTSYEKSPYCPIRRILSEFVKNNEIEYLNESSADQFT

Ga0208910_1001431

Ga0208910_10014312

F052021

MKKNKQIELDCSKNCKSVQACEAKGRSRDECENRYNDCVSR

Ga0208910_1002636

Ga0208910_10026361

F010394

MSETRKPVRPAHGDARRWQTEFDELELRMDALRQAFTEAIRSFEMTEETVERIHARFDDLGEQVHAMHCTYPFGGWPGQEDCRFEPPVPYESEARRAQD

Ga0208910_1003070

Ga0208910_10030701

F087388

DRGEPLEGAISMTLGDGGLDEEVLVELQVAGLRDAVIHEAFHELLEWHANFGGLAEFLEIDEAIHRTAERIGHDFDQDLPDHPGEGSSSRLVH

Ga0208910_1003842

Ga0208910_10038422

F103518

MICAEATGIQTTRKGGPCVMKAKSMRKPILLEPEKVETAEITISNHDFARLLRKQEEVERYLEEIKRATASIEKILAGKAPKRSYEIRYVADIDDYYM

Ga0208910_1004463

Ga0208910_10044631

F043160

MAKKNFDNLTKNSHLGGGLSNLIPEMNEKHESKKNKVASNDVPKTFLMLLEDYEYLQTYSRYMAFHNNSKYPLKRSLSDAIKLLKEAHPEIR

Ga0208910_1005031

Ga0208910_10050311

F067249

NLNLSAIPKVTIQGSRIENNLLLLKIGVDPNQKTYPSNQVKMVIEVKSSGVGAKNLPNGKLIDPNKGLRTKFNELQATTNVRNYAVIVLSETLLPPGGPYKWRFKEEAIRKENCKVFTLVARELYPAGGLFVKSNIEEMLQKEQMKKTGEFEQLIKYLRCL

Ga0208910_1005665

Ga0208910_10056651

F042958

MRKGILVTKKGTREGYFPIFIDDREFVQSVLAEAMEQWKQRETQDAVHDGMEFFEIANAIGKERTKSHQFIGAESIPERELEAGFNQASYIFAVDFKEGKVRKVK

Ga0208910_1006904

Ga0208910_10069043

F020200

NLISGWNEEREFQEKTSNDRYHRGLSKGFSECVKDLSEAVASMRLKGLCGKVPEYEGSINDKQRLDILDDLLKLGDEDSNQG

Ga0208910_1007418

Ga0208910_10074181

F103514

MREDIRIKRIAFNLKQHMKFIEIEVPGDEILRSVAADSPEFENRVKQKVIDYIKAL

Ga0208910_1007722

Ga0208910_10077221

F098776

MSIKYFDFTTPQFFLFRNQSKHLSIPQYHILILAWCALVILYGEPGLSPTPKHSET

Ga0208910_1008068

Ga0208910_10080682

F007838

SDRLREYAKLTEQVKTQKESLQVIRDATEKLRKINRKVANYHNLELAIAQVSDSYTRVLGSLKAINEHNCFKPSEYHMLSESMMGLLSQTSYSITTLTVVLTDNFSEMSDGERLLNMNQAIKELRENIGVINSAIIEVEILDNQRMQLRTLNYINSVFK

Ga0208910_1010413

Ga0208910_10104131

F087857

MKRNLIVVPLLVIAFVAFQIVPPAQAEPITLTIMAIAGIATVMTAASADMAVHGVAITQANSPKEMPAEVYAKDRSADSANNHDS

Ga0208910_1012726

Ga0208910_10127262

F098592

MDFGNIRRWVAGIVLVMAAVGLGLLPVAAAEKESKALLSWVTAIDLDECEPYQIRDKIMALHPQYGTIVVAEREIRALDVVADGKLIKTEFLTMDGKPESPSALSVGQYVWVKGVLHPDGFVAAFVVQQIAKPQEEKFIYKPNV

Ga0208910_1013305

Ga0208910_10133051

F001819

NKAEVVVESANFYATNFELGAIPPLFIHQLSRSRWRIDAEVFQTITTDCHLKHPAVHQSTALVVLTMIRLLAYALSLVFYQRQICSHARGSCDSFHEFAKRLAYGFVALSFNTS

Ga0208910_1015447

Ga0208910_10154472

F080208

MQAEEFINVINECEVLRDDIDDIRGRVPLTRTEGNKLNQAVSCVDKAKSILSGLFPAIQSLSEDVREELQGELGETD

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026027: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleA_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences