Sample 3300026017

Overview

Basic Information
IMG/M Taxon OID	3300026017 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116072 \| Ga0208001
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLC_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	62502161
Sequencing Scaffolds	14
Novel Protein Genes	14
Associated Families	14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Desulfuromonadaceae → Desulfuromonas → Desulfuromonas soudanensis	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.	1
All Organisms → cellular organisms → Archaea → Asgard group → Candidatus Heimdallarchaeota → Candidatus Heimdallarchaeota archaeon	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans	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)	38.197102	Long. (^o)	-122.010033	Alt. (m)	N/A	Depth (m)	0
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F007886	Metagenome / Metatranscriptome	343	Y
F009467	Metagenome	317	Y
F011594	Metagenome	289	Y
F015265	Metagenome / Metatranscriptome	256	Y
F020201	Metagenome / Metatranscriptome	225	Y
F023539	Metagenome / Metatranscriptome	209	Y
F025141	Metagenome / Metatranscriptome	203	Y
F029273	Metagenome / Metatranscriptome	189	Y
F050465	Metagenome	145	Y
F069800	Metagenome	123	Y
F090594	Metagenome / Metatranscriptome	108	Y
F100441	Metagenome	102	Y
F105202	Metagenome	100	Y
F105956	Metagenome / Metatranscriptome	100	N

Family

Category

Number of Sequences

3D Structure?

F007886

Metagenome / Metatranscriptome

343

F009467

Metagenome

317

F011594

Metagenome

289

F015265

Metagenome / Metatranscriptome

256

F020201

Metagenome / Metatranscriptome

225

F023539

Metagenome / Metatranscriptome

209

F025141

Metagenome / Metatranscriptome

203

F029273

Metagenome / Metatranscriptome

189

F050465

Metagenome

145

F069800

Metagenome

123

F090594

Metagenome / Metatranscriptome

108

F100441

Metagenome

102

F105202

Metagenome

100

F105956

Metagenome / Metatranscriptome

100

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208001_1000048	All Organisms → cellular organisms → Bacteria → Proteobacteria	19325	Open in IMG/M
Ga0208001_1000944	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	3407	Open in IMG/M
Ga0208001_1002808	Not Available	1843	Open in IMG/M
Ga0208001_1003051	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Desulfuromonadaceae → Desulfuromonas → Desulfuromonas soudanensis	1763	Open in IMG/M
Ga0208001_1003854	All Organisms → cellular organisms → Bacteria	1539	Open in IMG/M
Ga0208001_1004110	All Organisms → cellular organisms → Bacteria → Proteobacteria	1485	Open in IMG/M
Ga0208001_1004895	All Organisms → cellular organisms → Bacteria → Nitrospirae	1340	Open in IMG/M
Ga0208001_1008046	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	996	Open in IMG/M
Ga0208001_1012818	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.	757	Open in IMG/M
Ga0208001_1015304	Not Available	685	Open in IMG/M
Ga0208001_1016497	Not Available	656	Open in IMG/M
Ga0208001_1017995	All Organisms → cellular organisms → Bacteria → Nitrospirae	627	Open in IMG/M
Ga0208001_1025802	All Organisms → cellular organisms → Archaea → Asgard group → Candidatus Heimdallarchaeota → Candidatus Heimdallarchaeota archaeon	515	Open in IMG/M
Ga0208001_1026735	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans	505	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208001_1000048

All Organisms → cellular organisms → Bacteria → Proteobacteria

19325

Open in IMG/M

Ga0208001_1000944

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium

3407

Open in IMG/M

Ga0208001_1002808

Not Available

1843

Open in IMG/M

Ga0208001_1003051

All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfuromonadales → Desulfuromonadaceae → Desulfuromonas → Desulfuromonas soudanensis

1763

Open in IMG/M

Ga0208001_1003854

All Organisms → cellular organisms → Bacteria

1539

Open in IMG/M

Ga0208001_1004110

All Organisms → cellular organisms → Bacteria → Proteobacteria

1485

Open in IMG/M

Ga0208001_1004895

All Organisms → cellular organisms → Bacteria → Nitrospirae

1340

Open in IMG/M

Ga0208001_1008046

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

996

Open in IMG/M

Ga0208001_1012818

All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.

757

Open in IMG/M

Ga0208001_1015304

Not Available

685

Open in IMG/M

Ga0208001_1016497

Not Available

656

Open in IMG/M

Ga0208001_1017995

All Organisms → cellular organisms → Bacteria → Nitrospirae

627

Open in IMG/M

Ga0208001_1025802

All Organisms → cellular organisms → Archaea → Asgard group → Candidatus Heimdallarchaeota → Candidatus Heimdallarchaeota archaeon

515

Open in IMG/M

Ga0208001_1026735

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Nevskiales → Steroidobacteraceae → Steroidobacter → Steroidobacter denitrificans

505

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208001_1000048	Ga0208001_100004812	F105202	MPKNSYRLKTPLFCVFWALVIGCAHTPEPGPADVYVPSISALKPEEYSGEVDKYNKIIQSDLHLDVQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELNILKRQSLAFRGSRQDIQSANLKLQKRIGQLQKKVRNLERSNAKLNKTIEMLSTLDSRLEEKRINFIKTDSIEEK
Ga0208001_1000944	Ga0208001_10009442	F090594	LIRGGRTETNQGSRLMRSMMLAVLAAFLSGTALANPGAIGNETPTAEQAPDKAVAETVNEAGESEPFKVPAGYQPKKRGKRVVYCKKAMESGTRFSQEKCYSEEQLRAMSVERDQDQANFDQTRKVCANPESCAGG
Ga0208001_1002808	Ga0208001_10028082	F020201	MRIVSRTARSVREQEREKSTRKREAAGTLATAFPRCEQVRIHLQFVAKDGPAPAARTHALYASAQAYFEFACPHGDCDGSIDLNSVALPLLRSSGTQAEGTVHCPGTRADGGNARPPCNQRVDYWIAARYQSLARAAG
Ga0208001_1003051	Ga0208001_10030511	F011594	ELENLILLADRMIVSCAPRKADYGRGYQSGIKYQFYNPQTESLPDHYLIAEMARSNGCRNVHAYARGYHDGCKGLKPEYSD
Ga0208001_1003854	Ga0208001_10038543	F009467	MKLVHEAVIERSEIFETLRASFFKAFKEKNLRTGVYLFQELTQLSHGITVGWNSEDIVHEALDELLSDILAGKIAFRKFP
Ga0208001_1004110	Ga0208001_10041102	F023539	MIHRALLGSALALPLSISAALAGDTMEKGTEIACTEVKYSSEFLTKYPDAPAACLEARDHDGKRYAKFNARVFLNSADRTTVELLNVKGDRISTFSFKPSPEAGVNIDGKKVKFTDLKKGETISFWVSEDRLTASELPGSSEESWAVLPPE
Ga0208001_1004895	Ga0208001_10048952	F007886	VVVAVVEVLGVVLVGVLAGVDAAAEAGVEGAVDVVCSDVFGTGSFFSPVVGAGASLPGDGFSLSE
Ga0208001_1008046	Ga0208001_10080461	F050465	MDSYPFMIAEATLLFLAVVLIIESAFRRREVGRQLAQNRLRQQQLAKLSAELKDLNRKLARKSDIAEQIPRITKKLTEKFPPDAYPAIAVRSVKEFFQAGKVGYFAPVEGSSDYTLLIGVGFPQDWAGKVRIHSDEGILGMALQKNMVVSRMDQQSSSGRRSSRSSLEDMGITPEFVAPVVGVPG
Ga0208001_1012818	Ga0208001_10128181	F025141	VPYNMIQCEYCPRGFIETANGLAEKTFHELLHEPEVVNK
Ga0208001_1015304	Ga0208001_10153043	F015265	HITKNPTLIEKNAIVNLNNVGLPVFLYPINAIIPMASPTKNPIRFNIFSNKNSNDA
Ga0208001_1016497	Ga0208001_10164971	F100441	WAGPPMQYVESTSNTTPFYASALQCTPHYQDWSTVGLLHVTGSAIVPSSIYDVENVAASCMGAEAGCTAVSEPLEVATTRWGDVEQPYNPPNPTAQPDVGDISALVNKFRSAAGAPIKARALLAGDDAFGNINLSPDLSFNHISACVDAFRGKPYPYTIQSCP
Ga0208001_1017995	Ga0208001_10179952	F105956	MKKIEEPTLAEKLPIYMVAWSLPPAFVVLAVVVLALDSFSESGVAVLKGEYMFLLVVGGTLLNLWLYAVRQFKLKREFSPLHIIASIIFAIAYACFYYGVDTTIVVAIC
Ga0208001_1025802	Ga0208001_10258021	F029273	QFKRGRIMDIDPITKELLESLLQEVPKRTSRTIVSRNTKIKRATGQLSAIAARDKNDPLYKRMVFYREKYYKYRAMIHKKYSPRVRSKARR
Ga0208001_1026735	Ga0208001_10267351	F069800	RCPSFALLSLDYMAGQCAAHGGTLKARQPSEAWSLDVDGDASAEVLVDLVGNFDCEGAPGAFACGSTGCPFLLYKKRDDTWAEIGAINADDGPGIEVLPAPEGTFATLRGGCLGQQPCSELTHYEWKGQAYERTWINFKGHPVDVAPGGLMMLTQDTAVRDAPDAKK

Scaffold ID

Protein ID

Family

Sequence

Ga0208001_1000048

Ga0208001_100004812

F105202

MPKNSYRLKTPLFCVFWALVIGCAHTPEPGPADVYVPSISALKPEEYSGEVDKYNKIIQSDLHLDVQQRAHLYLASLYFSPMNPKRDYGLALEHLETYALFDPDFANAVDPRLLLAAIIEIERFSALAEAQTKEIQALSQELNILKRQSLAFRGSRQDIQSANLKLQKRIGQLQKKVRNLERSNAKLNKTIEMLSTLDSRLEEKRINFIKTDSIEEK

Ga0208001_1000944

Ga0208001_10009442

F090594

LIRGGRTETNQGSRLMRSMMLAVLAAFLSGTALANPGAIGNETPTAEQAPDKAVAETVNEAGESEPFKVPAGYQPKKRGKRVVYCKKAMESGTRFSQEKCYSEEQLRAMSVERDQDQANFDQTRKVCANPESCAGG

Ga0208001_1002808

Ga0208001_10028082

F020201

MRIVSRTARSVREQEREKSTRKREAAGTLATAFPRCEQVRIHLQFVAKDGPAPAARTHALYASAQAYFEFACPHGDCDGSIDLNSVALPLLRSSGTQAEGTVHCPGTRADGGNARPPCNQRVDYWIAARYQSLARAAG

Ga0208001_1003051

Ga0208001_10030511

F011594

ELENLILLADRMIVSCAPRKADYGRGYQSGIKYQFYNPQTESLPDHYLIAEMARSNGCRNVHAYARGYHDGCKGLKPEYSD

Ga0208001_1003854

Ga0208001_10038543

F009467

MKLVHEAVIERSEIFETLRASFFKAFKEKNLRTGVYLFQELTQLSHGITVGWNSEDIVHEALDELLSDILAGKIAFRKFP

Ga0208001_1004110

Ga0208001_10041102

F023539

MIHRALLGSALALPLSISAALAGDTMEKGTEIACTEVKYSSEFLTKYPDAPAACLEARDHDGKRYAKFNARVFLNSADRTTVELLNVKGDRISTFSFKPSPEAGVNIDGKKVKFTDLKKGETISFWVSEDRLTASELPGSSEESWAVLPPE

Ga0208001_1004895

Ga0208001_10048952

F007886

VVVAVVEVLGVVLVGVLAGVDAAAEAGVEGAVDVVCSDVFGTGSFFSPVVGAGASLPGDGFSLSE

Ga0208001_1008046

Ga0208001_10080461

F050465

MDSYPFMIAEATLLFLAVVLIIESAFRRREVGRQLAQNRLRQQQLAKLSAELKDLNRKLARKSDIAEQIPRITKKLTEKFPPDAYPAIAVRSVKEFFQAGKVGYFAPVEGSSDYTLLIGVGFPQDWAGKVRIHSDEGILGMALQKNMVVSRMDQQSSSGRRSSRSSLEDMGITPEFVAPVVGVPG

Ga0208001_1012818

Ga0208001_10128181

F025141

VPYNMIQCEYCPRGFIETANGLAEKTFHELLHEPEVVNK

Ga0208001_1015304

Ga0208001_10153043

F015265

HITKNPTLIEKNAIVNLNNVGLPVFLYPINAIIPMASPTKNPIRFNIFSNKNSNDA

Ga0208001_1016497

Ga0208001_10164971

F100441

WAGPPMQYVESTSNTTPFYASALQCTPHYQDWSTVGLLHVTGSAIVPSSIYDVENVAASCMGAEAGCTAVSEPLEVATTRWGDVEQPYNPPNPTAQPDVGDISALVNKFRSAAGAPIKARALLAGDDAFGNINLSPDLSFNHISACVDAFRGKPYPYTIQSCP

Ga0208001_1017995

Ga0208001_10179952

F105956

MKKIEEPTLAEKLPIYMVAWSLPPAFVVLAVVVLALDSFSESGVAVLKGEYMFLLVVGGTLLNLWLYAVRQFKLKREFSPLHIIASIIFAIAYACFYYGVDTTIVVAIC

Ga0208001_1025802

Ga0208001_10258021

F029273

QFKRGRIMDIDPITKELLESLLQEVPKRTSRTIVSRNTKIKRATGQLSAIAARDKNDPLYKRMVFYREKYYKYRAMIHKKYSPRVRSKARR

Ga0208001_1026735

Ga0208001_10267351

F069800

RCPSFALLSLDYMAGQCAAHGGTLKARQPSEAWSLDVDGDASAEVLVDLVGNFDCEGAPGAFACGSTGCPFLLYKKRDDTWAEIGAINADDGPGIEVLPAPEGTFATLRGGCLGQQPCSELTHYEWKGQAYERTWINFKGHPVDVAPGGLMMLTQDTAVRDAPDAKK

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026017: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLC_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences