Sample 3300026065

Overview

Basic Information
IMG/M Taxon OID	3300026065 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116112 \| Ga0208913
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_CattailNLB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	65307270
Sequencing Scaffolds	16
Novel Protein Genes	18
Associated Families	17

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	2
All Organisms → cellular organisms → Bacteria → FCB group	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter	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)	38.224518	Long. (^o)	-122.019257	Alt. (m)	N/A	Depth (m)	0
Location on Map

Zoom:	Powered by OpenStreetMap^©

Family	Category	Number of Sequences	3D Structure?
F000982	Metagenome / Metatranscriptome	814	Y
F002989	Metagenome / Metatranscriptome	515	Y
F023130	Metagenome / Metatranscriptome	211	Y
F031547	Metagenome / Metatranscriptome	182	Y
F031716	Metagenome	182	Y
F031935	Metagenome / Metatranscriptome	181	Y
F041849	Metagenome	159	Y
F043155	Metagenome	157	Y
F046145	Metagenome	151	Y
F053087	Metagenome	141	Y
F054981	Metagenome	139	Y
F056991	Metagenome / Metatranscriptome	137	Y
F072484	Metagenome	121	Y
F085853	Metagenome / Metatranscriptome	111	Y
F091236	Metagenome / Metatranscriptome	107	Y
F095902	Metagenome / Metatranscriptome	105	Y
F104362	Metagenome / Metatranscriptome	100	Y

Family

Category

Number of Sequences

3D Structure?

F000982

Metagenome / Metatranscriptome

814

F002989

Metagenome / Metatranscriptome

515

F023130

Metagenome / Metatranscriptome

211

F031547

Metagenome / Metatranscriptome

182

F031716

Metagenome

182

F031935

Metagenome / Metatranscriptome

181

F041849

Metagenome

159

F043155

Metagenome

157

F046145

Metagenome

151

F053087

Metagenome

141

F054981

Metagenome

139

F056991

Metagenome / Metatranscriptome

137

F072484

Metagenome

121

F085853

Metagenome / Metatranscriptome

111

F091236

Metagenome / Metatranscriptome

107

F095902

Metagenome / Metatranscriptome

105

F104362

Metagenome / Metatranscriptome

100

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208913_1003292	Not Available	1159	Open in IMG/M
Ga0208913_1004170	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1066	Open in IMG/M
Ga0208913_1004895	All Organisms → cellular organisms → Bacteria	1004	Open in IMG/M
Ga0208913_1005236	All Organisms → cellular organisms → Bacteria	980	Open in IMG/M
Ga0208913_1006450	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	907	Open in IMG/M
Ga0208913_1007582	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	855	Open in IMG/M
Ga0208913_1007588	All Organisms → cellular organisms → Bacteria	855	Open in IMG/M
Ga0208913_1009579	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	782	Open in IMG/M
Ga0208913_1010069	All Organisms → cellular organisms → Bacteria	768	Open in IMG/M
Ga0208913_1010916	All Organisms → cellular organisms → Bacteria	744	Open in IMG/M
Ga0208913_1011694	All Organisms → cellular organisms → Bacteria → FCB group	725	Open in IMG/M
Ga0208913_1013460	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium	687	Open in IMG/M
Ga0208913_1015050	Not Available	657	Open in IMG/M
Ga0208913_1018330	Not Available	609	Open in IMG/M
Ga0208913_1023704	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter	550	Open in IMG/M
Ga0208913_1029964	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	501	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208913_1003292

Not Available

1159

Open in IMG/M

Ga0208913_1004170

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

1066

Open in IMG/M

Ga0208913_1004895

All Organisms → cellular organisms → Bacteria

1004

Open in IMG/M

Ga0208913_1005236

All Organisms → cellular organisms → Bacteria

980

Open in IMG/M

Ga0208913_1006450

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

907

Open in IMG/M

Ga0208913_1007582

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium

855

Open in IMG/M

Ga0208913_1007588

All Organisms → cellular organisms → Bacteria

855

Open in IMG/M

Ga0208913_1009579

All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia

782

Open in IMG/M

Ga0208913_1010069

All Organisms → cellular organisms → Bacteria

768

Open in IMG/M

Ga0208913_1010916

All Organisms → cellular organisms → Bacteria

744

Open in IMG/M

Ga0208913_1011694

All Organisms → cellular organisms → Bacteria → FCB group

725

Open in IMG/M

Ga0208913_1013460

All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → unclassified Pirellulales → Pirellulales bacterium

687

Open in IMG/M

Ga0208913_1015050

Not Available

657

Open in IMG/M

Ga0208913_1018330

Not Available

609

Open in IMG/M

Ga0208913_1023704

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter

550

Open in IMG/M

Ga0208913_1029964

All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia

501

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208913_1003292	Ga0208913_10032923	F031547	MKTYTVYRVETNKTERIGKVVDRRRGERNDNALDMLRLAQKIFATSSMDSNIFILRESSIQSIFLSGGG
Ga0208913_1003666	Ga0208913_10036661	F085853	KPLEGYIQALEKEAAGGPVFPLPEGLKPVQESCGSPSDKDPWMECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFAALNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDAFPGLTGMDYVKYILYYLLSAGLFFFGFQRIRDAVKNYGV
Ga0208913_1004170	Ga0208913_10041702	F072484	MRSARVLRENKFRQTYNNRKIGLVFLATLSGVMLFTNVDAANFLFFWKASTDPSVTAYGIYQRTGDSAYELLAEVDAADLDDPDHPDYLVTGLQSGAVYHFAAAAVKASGEESALSNQTCVTDNGQVVECQDKDRNGTVVFINCFINALNR
Ga0208913_1004895	Ga0208913_10048952	F095902	SHNRVTLRPQFSLGIAGGDDGPAAAHTTERSRGFKTEFPSLSCDQVGNLMGFEMPPHILDRIEFGRISRQPFDDEATVGGCHIVFDQQAPVDRGAIPDDQHFPRNMALEMAQKLDDLETFDAASMNLKIEPPEHQTADDRKAFPVEGLVQHRGLPTQRPSARPGGPGAQAAFVDEDDGSSLLAGLFFNAGHSVRCQRRIFFSSRSTARRSGRWQLKPLAPSTRQT
Ga0208913_1005236	Ga0208913_10052362	F046145	MLQVCLNFYWKLFEWITDRYEKTIPDLLECDHMALKPKPFSEAKTGFFIMSRYLRV
Ga0208913_1006450	Ga0208913_10064502	F031716	MSRFTPGPWHVEEEKGSYGVFSNDALLAITLSDDLPDKGAAKANANLMATAPRLLEIIKDIKGHLDNNMIVTGEGLKINDSHLRESIIDAIMRAEGYRL
Ga0208913_1007582	Ga0208913_10075822	F000982	MPVLKLSSRASRLLDHHRLRGRSYPTARYWERLYQMLEEEAEKRGRTPPPPPFTHALDHEPTEQDKIDRLAEQVVWADRNTLLHRVQMFFDAMPP
Ga0208913_1007588	Ga0208913_10075882	F023130	MTRRFWVPATALLLSSIMVMTGSVSHDAMAGIFVLSQSPGASIVEGEGPAKMGPAAEFETHSHRDVSSRYWMRGIVLLLLILLILWLIYRTFTGWKPMISRSVGFLPELQA
Ga0208913_1009579	Ga0208913_10095791	F053087	VGALKLKVWYGLDPGTGRWGNPMRQRWGLGPHQEMSPALEDKLAFTVTATGSYEEAAAVAQKWNSPVDDSTLHALTRRLGTRAEQQTQERLESVASELTAQRAASKLAVFMLDGYLARYRGPGWGKKKTKKKRVEWHEIKTGLFYLQEQAARTEGGRGVLSEKVVICWQ
Ga0208913_1010069	Ga0208913_10100691	F002989	MARFQATEPNGVALQQLEVLVRTAVFQSANQVVAYLLQQAADRIDAAYQPKPGWQRKGRAPLTVDCIFGFFTLERDYYYHPGKQ
Ga0208913_1010916	Ga0208913_10109162	F095902	MAQKLDDLEALDTAGMNLEIEPPEGQAPDDRKAFPVEGLMQHRSFTSWSPSAGPRGTCAQPALVNKDDGSPLLPGLFFNAGHSVRCQRRMAFSSRSTARRSGRWQLKPLAPSKRQT
Ga0208913_1011694	Ga0208913_10116942	F054981	MVLARIVLRLLADLVGLVVPSATPLTRHRIGERLGVRARSVLGGLHHEYVLAPA
Ga0208913_1013460	Ga0208913_10134601	F091236	MRNIKTAIRLIAVQRGLSTSVASGADPVAGREGHPITRSRLARWTAVLALVIALLPGTAPAQEDGTIKISSTFYMDGLYGTVGPDLAEVFANGHEHTWTLTLHGTTQSHSTFSAFGVKRATEIHATSFELEFSGPDAAALNGIVSEHIAGGDVQIYLENSYSSGFGDDFALWSVDVGGPVVSFWTGLLSYASDTLFPSDANGYPVVGPDPFSIWPEGAILRDGRPGND
Ga0208913_1015050	Ga0208913_10150502	F056991	HFIAIAMAWLAIGMWVLPACGDESTAEQQKNYFLKCIDKEIDSYSCKVVHTASRSKNLQTYGRQAALKTAFLSQNKDALLQEMIAQKVSMRPHAVRHFLLNRFNRESHPQTAKLAP
Ga0208913_1018330	Ga0208913_10183301	F031935	MMSDSAKRITAPECLGVPPVGSAHRGRRRAPRWFETLLHFKGFGGGVPLNTETAAVNPR
Ga0208913_1020174	Ga0208913_10201741	F104362	TAAAISRYRAASDAGNPDASAVARYMLAWVRFQSGDAGGALRELSQPLSDPSFPCGVPSPFEREVVSLSVRAWRESGLERLDAYPPVNAGTCGGKVLLAALWEAEEKRGEALRAAEVRDVAARRFPSDANAAALEMETVESLLRVGREREALDRALTLRGKYGPDSAWARSQPAPVGEKTAKELAAMFRTLAGKK
Ga0208913_1023704	Ga0208913_10237041	F041849	MDSLSGLSGTLMGLWLVIVGIAIAFGVLYAIGNSLRHRKRHQNRAYQEGRDG
Ga0208913_1029964	Ga0208913_10299642	F043155	MGYALAKEQQQYVAGLVKTGRFNNQSEAVREAIRRMQAQETEYLTPPPLTPAQVEAIYGKPDQRADAMGRAAFRAVRSAARKGAKP

Scaffold ID

Protein ID

Family

Sequence

Ga0208913_1003292

Ga0208913_10032923

F031547

MKTYTVYRVETNKTERIGKVVDRRRGERNDNALDMLRLAQKIFATSSMDSNIFILRESSIQSIFLSGGG

Ga0208913_1003666

Ga0208913_10036661

F085853

KPLEGYIQALEKEAAGGPVFPLPEGLKPVQESCGSPSDKDPWMECRLRQYMEARAAQYQKILANEIAAPLEKLNIKEFDQWKAELQAGMKKYAERFRSEMTTNPSFWRNFNQKAPIYQSMIEGVHRFWSDHQFEEIGRRMEQAAAASQAEVEQLNQKKEQIQKGKEGLNNALKNIKTRFGKLGLEAEDAILLAPIAFAALFLFAALNLCQNIQLRKSFHRLFQARDPQKVAITDSEIALAMPLWVDPLAPPIQRRLKLAVMMIPAIASVLALAVVFYCWTIPDAFPGLTGMDYVKYILYYLLSAGLFFFGFQRIRDAVKNYGV

Ga0208913_1004170

Ga0208913_10041702

F072484

MRSARVLRENKFRQTYNNRKIGLVFLATLSGVMLFTNVDAANFLFFWKASTDPSVTAYGIYQRTGDSAYELLAEVDAADLDDPDHPDYLVTGLQSGAVYHFAAAAVKASGEESALSNQTCVTDNGQVVECQDKDRNGTVVFINCFINALNR

Ga0208913_1004895

Ga0208913_10048952

F095902

SHNRVTLRPQFSLGIAGGDDGPAAAHTTERSRGFKTEFPSLSCDQVGNLMGFEMPPHILDRIEFGRISRQPFDDEATVGGCHIVFDQQAPVDRGAIPDDQHFPRNMALEMAQKLDDLETFDAASMNLKIEPPEHQTADDRKAFPVEGLVQHRGLPTQRPSARPGGPGAQAAFVDEDDGSSLLAGLFFNAGHSVRCQRRIFFSSRSTARRSGRWQLKPLAPSTRQT

Ga0208913_1005236

Ga0208913_10052362

F046145

MLQVCLNFYWKLFEWITDRYEKTIPDLLECDHMALKPKPFSEAKTGFFIMSRYLRV

Ga0208913_1006450

Ga0208913_10064502

F031716

MSRFTPGPWHVEEEKGSYGVFSNDALLAITLSDDLPDKGAAKANANLMATAPRLLEIIKDIKGHLDNNMIVTGEGLKINDSHLRESIIDAIMRAEGYRL

Ga0208913_1007582

Ga0208913_10075822

F000982

MPVLKLSSRASRLLDHHRLRGRSYPTARYWERLYQMLEEEAEKRGRTPPPPPFTHALDHEPTEQDKIDRLAEQVVWADRNTLLHRVQMFFDAMPP

Ga0208913_1007588

Ga0208913_10075882

F023130

MTRRFWVPATALLLSSIMVMTGSVSHDAMAGIFVLSQSPGASIVEGEGPAKMGPAAEFETHSHRDVSSRYWMRGIVLLLLILLILWLIYRTFTGWKPMISRSVGFLPELQA

Ga0208913_1009579

Ga0208913_10095791

F053087

VGALKLKVWYGLDPGTGRWGNPMRQRWGLGPHQEMSPALEDKLAFTVTATGSYEEAAAVAQKWNSPVDDSTLHALTRRLGTRAEQQTQERLESVASELTAQRAASKLAVFMLDGYLARYRGPGWGKKKTKKKRVEWHEIKTGLFYLQEQAARTEGGRGVLSEKVVICWQ

Ga0208913_1010069

Ga0208913_10100691

F002989

MARFQATEPNGVALQQLEVLVRTAVFQSANQVVAYLLQQAADRIDAAYQPKPGWQRKGRAPLTVDCIFGFFTLERDYYYHPGKQ

Ga0208913_1010916

Ga0208913_10109162

F095902

MAQKLDDLEALDTAGMNLEIEPPEGQAPDDRKAFPVEGLMQHRSFTSWSPSAGPRGTCAQPALVNKDDGSPLLPGLFFNAGHSVRCQRRMAFSSRSTARRSGRWQLKPLAPSKRQT

Ga0208913_1011694

Ga0208913_10116942

F054981

MVLARIVLRLLADLVGLVVPSATPLTRHRIGERLGVRARSVLGGLHHEYVLAPA

Ga0208913_1013460

Ga0208913_10134601

F091236

MRNIKTAIRLIAVQRGLSTSVASGADPVAGREGHPITRSRLARWTAVLALVIALLPGTAPAQEDGTIKISSTFYMDGLYGTVGPDLAEVFANGHEHTWTLTLHGTTQSHSTFSAFGVKRATEIHATSFELEFSGPDAAALNGIVSEHIAGGDVQIYLENSYSSGFGDDFALWSVDVGGPVVSFWTGLLSYASDTLFPSDANGYPVVGPDPFSIWPEGAILRDGRPGND

Ga0208913_1015050

Ga0208913_10150502

F056991

HFIAIAMAWLAIGMWVLPACGDESTAEQQKNYFLKCIDKEIDSYSCKVVHTASRSKNLQTYGRQAALKTAFLSQNKDALLQEMIAQKVSMRPHAVRHFLLNRFNRESHPQTAKLAP

Ga0208913_1018330

Ga0208913_10183301

F031935

MMSDSAKRITAPECLGVPPVGSAHRGRRRAPRWFETLLHFKGFGGGVPLNTETAAVNPR

Ga0208913_1020174

Ga0208913_10201741

F104362

TAAAISRYRAASDAGNPDASAVARYMLAWVRFQSGDAGGALRELSQPLSDPSFPCGVPSPFEREVVSLSVRAWRESGLERLDAYPPVNAGTCGGKVLLAALWEAEEKRGEALRAAEVRDVAARRFPSDANAAALEMETVESLLRVGREREALDRALTLRGKYGPDSAWARSQPAPVGEKTAKELAAMFRTLAGKK

Ga0208913_1023704

Ga0208913_10237041

F041849

MDSLSGLSGTLMGLWLVIVGIAIAFGVLYAIGNSLRHRKRHQNRAYQEGRDG

Ga0208913_1029964

Ga0208913_10299642

F043155

MGYALAKEQQQYVAGLVKTGRFNNQSEAVREAIRRMQAQETEYLTPPPLTPAQVEAIYGKPDQRADAMGRAAFRAVRSAARKGAKP

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026065: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushSE_CattailNLB_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences