Sample 3300026012

Overview

Basic Information
IMG/M Taxon OID	3300026012 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0111376 \| Gp0116071 \| Ga0208653
Sample Name	Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLB_D1 (SPAdes)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	54411693
Sequencing Scaffolds	9
Novel Protein Genes	9
Associated Families	9

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales → Mycobacteriaceae → Mycobacteroides → Mycobacteroides abscessus → Mycobacteroides abscessus subsp. abscessus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → unclassified Moraxellaceae → Moraxellaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
Not Available	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?
F024580	Metagenome / Metatranscriptome	205	Y
F029283	Metagenome	189	Y
F031074	Metagenome	183	Y
F050465	Metagenome	145	Y
F062893	Metagenome / Metatranscriptome	130	Y
F072360	Metagenome / Metatranscriptome	121	Y
F082105	Metagenome / Metatranscriptome	113	Y
F090594	Metagenome / Metatranscriptome	108	Y
F095691	Metagenome	105	Y

Family

Category

Number of Sequences

3D Structure?

F024580

Metagenome / Metatranscriptome

205

F029283

Metagenome

189

F031074

Metagenome

183

F050465

Metagenome

145

F062893

Metagenome / Metatranscriptome

130

F072360

Metagenome / Metatranscriptome

121

F082105

Metagenome / Metatranscriptome

113

F090594

Metagenome / Metatranscriptome

108

F095691

Metagenome

105

Scaffold	Taxonomy	Length	IMG/M Link
Ga0208653_1000016	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	10884	Open in IMG/M
Ga0208653_1002457	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales → Mycobacteriaceae → Mycobacteroides → Mycobacteroides abscessus → Mycobacteroides abscessus subsp. abscessus	1616	Open in IMG/M
Ga0208653_1005146	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1094	Open in IMG/M
Ga0208653_1011187	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → unclassified Moraxellaceae → Moraxellaceae bacterium	745	Open in IMG/M
Ga0208653_1011418	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	737	Open in IMG/M
Ga0208653_1012772	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	700	Open in IMG/M
Ga0208653_1012807	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	699	Open in IMG/M
Ga0208653_1013153	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	690	Open in IMG/M
Ga0208653_1022353	Not Available	539	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0208653_1000016

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

10884

Open in IMG/M

Ga0208653_1002457

All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales → Mycobacteriaceae → Mycobacteroides → Mycobacteroides abscessus → Mycobacteroides abscessus subsp. abscessus

1616

Open in IMG/M

Ga0208653_1005146

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

1094

Open in IMG/M

Ga0208653_1011187

All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → unclassified Moraxellaceae → Moraxellaceae bacterium

745

Open in IMG/M

Ga0208653_1011418

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

737

Open in IMG/M

Ga0208653_1012772

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

700

Open in IMG/M

Ga0208653_1012807

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

699

Open in IMG/M

Ga0208653_1013153

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

690

Open in IMG/M

Ga0208653_1022353

Not Available

539

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0208653_1000016	Ga0208653_10000167	F072360	LTPGFIFHILLSGMNRNLKILNVFSRKALFIAFILLIGFSFSAVGAPAKGCPGGFGCLNCEAAAHPHMPGMDAEMVNHGCQSAEQNRSCGFEAGSRSDQFDKMATVAQSGTHPYPGIFSAATDEFDQAHLLKGFVAQFQYPDRGQLTPIYLLTLSLLC
Ga0208653_1002457	Ga0208653_10024572	F024580	MKTLFNRNTGIATFAAVVIVGLTGLTLDRGHGGSLPQGVIDVGNLETLAVGGTLYATLPVVEVVGTRDVQLADVATHAEPQG
Ga0208653_1005146	Ga0208653_10051462	F082105	MSIAPMAAPTMHEPPRCAARPNATVQRAVAGTVMRIDSAGSGRANEKK
Ga0208653_1011187	Ga0208653_10111872	F062893	MNSSNPYGYRGALPAVLAALIVGLSGLALDKGHISAAPAGSIEIGTLTPVDVLPQVAALPAVIVSAPRLAMAAGPGRA
Ga0208653_1011418	Ga0208653_10114182	F090594	LAAFLSGTALANPGAIGNETPTAEQAPDKAVAETVNEAGESEPFKVPAGYQPKKRGKRVVYCKKAMESGTRFSQEKCYSEEQLRAMSVERDQDQANFDQTRKVCANPESCAGG
Ga0208653_1012772	Ga0208653_10127721	F050465	MDSYPFMIAEATLLFLAVVLIIESAFRRREVGRQLAENKRIEHQLATYSAELNALNRKLARKSEIADQFPRITKKMTEKFPPDAYPAIAVRSAKNFFTAEKVGYFAPTEDSSDYTLVVGVGFPLDWTGKVRIHSDEGILGMALQKKTTVSRRDLHSSSGRRSSRSSFEDIG
Ga0208653_1012807	Ga0208653_10128072	F095691	MLQHDGSIRIAWQADGFEAILVRARFRPASQRDEFARGVADVALLERNLPDLQAALRACYPGAFDLITDRSLSGPGRVIVSFHPPPGEPNPDPW
Ga0208653_1013153	Ga0208653_10131531	F029283	TPAERRLAESRAALAEMFEPPGEDDFPRSETMRFVMGGKGRIAALGLFTGLLLVKPKLAVGLVRFLPLGKLLPVARILQTLR
Ga0208653_1022353	Ga0208653_10223532	F031074	MATAVKKLDLEIGEMIEVGGRRYEVVSDRVGGLTLEPPIKPMAELDEEWGTSPASTEDFERLTADDPTDGEG

Scaffold ID

Protein ID

Family

Sequence

Ga0208653_1000016

Ga0208653_10000167

F072360

LTPGFIFHILLSGMNRNLKILNVFSRKALFIAFILLIGFSFSAVGAPAKGCPGGFGCLNCEAAAHPHMPGMDAEMVNHGCQSAEQNRSCGFEAGSRSDQFDKMATVAQSGTHPYPGIFSAATDEFDQAHLLKGFVAQFQYPDRGQLTPIYLLTLSLLC

Ga0208653_1002457

Ga0208653_10024572

F024580

MKTLFNRNTGIATFAAVVIVGLTGLTLDRGHGGSLPQGVIDVGNLETLAVGGTLYATLPVVEVVGTRDVQLADVATHAEPQG

Ga0208653_1005146

Ga0208653_10051462

F082105

MSIAPMAAPTMHEPPRCAARPNATVQRAVAGTVMRIDSAGSGRANEKK

Ga0208653_1011187

Ga0208653_10111872

F062893

MNSSNPYGYRGALPAVLAALIVGLSGLALDKGHISAAPAGSIEIGTLTPVDVLPQVAALPAVIVSAPRLAMAAGPGRA

Ga0208653_1011418

Ga0208653_10114182

F090594

LAAFLSGTALANPGAIGNETPTAEQAPDKAVAETVNEAGESEPFKVPAGYQPKKRGKRVVYCKKAMESGTRFSQEKCYSEEQLRAMSVERDQDQANFDQTRKVCANPESCAGG

Ga0208653_1012772

Ga0208653_10127721

F050465

MDSYPFMIAEATLLFLAVVLIIESAFRRREVGRQLAENKRIEHQLATYSAELNALNRKLARKSEIADQFPRITKKMTEKFPPDAYPAIAVRSAKNFFTAEKVGYFAPTEDSSDYTLVVGVGFPLDWTGKVRIHSDEGILGMALQKKTTVSRRDLHSSSGRRSSRSSFEDIG

Ga0208653_1012807

Ga0208653_10128072

F095691

MLQHDGSIRIAWQADGFEAILVRARFRPASQRDEFARGVADVALLERNLPDLQAALRACYPGAFDLITDRSLSGPGRVIVSFHPPPGEPNPDPW

Ga0208653_1013153

Ga0208653_10131531

F029283

TPAERRLAESRAALAEMFEPPGEDDFPRSETMRFVMGGKGRIAALGLFTGLLLVKPKLAVGLVRFLPLGKLLPVARILQTLR

Ga0208653_1022353

Ga0208653_10223532

F031074

MATAVKKLDLEIGEMIEVGGRRYEVVSDRVGGLTLEPPIKPMAELDEEWGTSPASTEDFERLTADDPTDGEG

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300026012: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_CattailNLB_D1 (SPAdes)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences