Sample 3300021271

Overview

Basic Information
IMG/M Taxon OID	3300021271 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0131209 \| Gp0238794 \| Ga0213897
Sample Name	Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_3
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	18074534
Sequencing Scaffolds	7
Novel Protein Genes	8
Associated Families	8

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	2
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
Name	Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States
Type	Environmental
Taxonomy	Environmental → Terrestrial → Soil → Unclassified → Unclassified → Soil → Switchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States

Alternative Ecosystem Assignments
Environment Ontology (ENVO)	terrestrial biome → land → soil
Earth Microbiome Project Ontology (EMPO)	Free-living → Non-saline → Soil (non-saline)

Location Information
Location	USA: West Virginia
Coordinates	Lat. (^o)	39.458	Long. (^o)	-79.073	Alt. (m)	N/A	Depth (m)	.1
Location on Map

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Family	Category	Number of Sequences	3D Structure?
F002951	Metagenome / Metatranscriptome	518	Y
F015483	Metagenome / Metatranscriptome	254	Y
F021961	Metagenome	216	Y
F032268	Metagenome / Metatranscriptome	180	Y
F053878	Metagenome / Metatranscriptome	140	Y
F062864	Metagenome	130	N
F094088	Metagenome	106	N
F097548	Metagenome / Metatranscriptome	104	N

Family

Category

Number of Sequences

3D Structure?

F002951

Metagenome / Metatranscriptome

518

F015483

Metagenome / Metatranscriptome

254

F021961

Metagenome

216

F032268

Metagenome / Metatranscriptome

180

F053878

Metagenome / Metatranscriptome

140

F062864

Metagenome

130

F094088

Metagenome

106

F097548

Metagenome / Metatranscriptome

104

Scaffold	Taxonomy	Length	IMG/M Link
Ga0213897_100880	Not Available	747	Open in IMG/M
Ga0213897_100908	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium	739	Open in IMG/M
Ga0213897_101068	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	712	Open in IMG/M
Ga0213897_101660	Not Available	639	Open in IMG/M
Ga0213897_102408	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	584	Open in IMG/M
Ga0213897_103118	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium	548	Open in IMG/M
Ga0213897_103751	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	523	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0213897_100880

Not Available

747

Open in IMG/M

Ga0213897_100908

All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → unclassified Gemmatimonadetes → Gemmatimonadetes bacterium

739

Open in IMG/M

Ga0213897_101068

All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium

712

Open in IMG/M

Ga0213897_101660

Not Available

639

Open in IMG/M

Ga0213897_102408

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

584

Open in IMG/M

Ga0213897_103118

All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → unclassified Bacteroidetes → Bacteroidetes bacterium

548

Open in IMG/M

Ga0213897_103751

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria

523

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0213897_100880	Ga0213897_1008801	F021961	LSSLAVLLALPSLASANCYSIYDAKNQLAFQSPIAPVDLSTRISDAMRTRFPGGHLVMVPDDGACREYRTGPTLSPRFDAGNAARTEARPDRTLEASPLLGGTGAGPDLTTREAARSGNVLNVKRP
Ga0213897_100908	Ga0213897_1009081	F032268	MVGLFTTTIGFAALWIRARERATRAESLLEGMRMGGRGDAMSPALDAIAEEVERIGEGQRFITRIMSESAGRVEATRSRGPGSITPH
Ga0213897_101068	Ga0213897_1010682	F053878	RVELLQNAELQRLATLEWATGERREAVAEVRRDLAVSIDALRGERAAVVADLRSIVDVIFLRVAVFLVVAVLLAPLVAHAYARVWPRRWREIGGQRSD
Ga0213897_101660	Ga0213897_1016602	F062864	VRYTYTNPQLERERDAVLRTILDKRGMCTFLARELGISKAAVAQWYSIPEHHVAAISKLLDIPQYQLRGEPSPRAKVDA
Ga0213897_102408	Ga0213897_1024082	F015483	MTDAEIERVIRRAGYDVRWDDVPNHGAAEVYALRDGKRHTRSHPNLLALAEYLGCLERPVKFIEDREALDTVIEKHAKERNAFTVQPGACRVVVFGRNKYVQLVSVGGHESAMYELRTDGLRRTSNGNLPPEVVAA
Ga0213897_103118	Ga0213897_1031181	F094088	AHSQTNSVIGLIGLIAVIVLIIVSWAVLKRRRIKSKTLEKKGMLNSIDWILEQLTLLEKKQIPDKDAVKEYYHQLYQLCRQYFSIEFDINVLYCTTEEWVGILEGVELDKKNKAAFYELVKKADSVRFADRDIAEKQNEEISTARNFVKALHRLKTGSPDKN
Ga0213897_103751	Ga0213897_1037511	F002951	MTPADIDRVFGRGRLRMVTGDHVEVFREHSLPGERRRYTKRFLATAAGDFSEWTEREWRILARLVGHGIKPVPDVVRFDRGAADRAALVQTFDAGVTVDHWATLLPLERDGTTLRNVFEDCAHWWALARHSLI
Ga0213897_104074	Ga0213897_1040741	F097548	MPGYRSLSSNLSGTAAEHAREAELSQRHGDPQSAARLLEEALAASLRSRPEMPGWVCGRLASIYRTLKRYDDEVELLERYRESQTSEEARTRFDARLSKARAIADRKRRPVTGALETVRQVRYRSSQRRRTPPRSQAVSAT

Scaffold ID

Protein ID

Family

Sequence

Ga0213897_100880

Ga0213897_1008801

F021961

LSSLAVLLALPSLASANCYSIYDAKNQLAFQSPIAPVDLSTRISDAMRTRFPGGHLVMVPDDGACREYRTGPTLSPRFDAGNAARTEARPDRTLEASPLLGGTGAGPDLTTREAARSGNVLNVKRP

Ga0213897_100908

Ga0213897_1009081

F032268

MVGLFTTTIGFAALWIRARERATRAESLLEGMRMGGRGDAMSPALDAIAEEVERIGEGQRFITRIMSESAGRVEATRSRGPGSITPH

Ga0213897_101068

Ga0213897_1010682

F053878

RVELLQNAELQRLATLEWATGERREAVAEVRRDLAVSIDALRGERAAVVADLRSIVDVIFLRVAVFLVVAVLLAPLVAHAYARVWPRRWREIGGQRSD

Ga0213897_101660

Ga0213897_1016602

F062864

VRYTYTNPQLERERDAVLRTILDKRGMCTFLARELGISKAAVAQWYSIPEHHVAAISKLLDIPQYQLRGEPSPRAKVDA

Ga0213897_102408

Ga0213897_1024082

F015483

MTDAEIERVIRRAGYDVRWDDVPNHGAAEVYALRDGKRHTRSHPNLLALAEYLGCLERPVKFIEDREALDTVIEKHAKERNAFTVQPGACRVVVFGRNKYVQLVSVGGHESAMYELRTDGLRRTSNGNLPPEVVAA

Ga0213897_103118

Ga0213897_1031181

F094088

AHSQTNSVIGLIGLIAVIVLIIVSWAVLKRRRIKSKTLEKKGMLNSIDWILEQLTLLEKKQIPDKDAVKEYYHQLYQLCRQYFSIEFDINVLYCTTEEWVGILEGVELDKKNKAAFYELVKKADSVRFADRDIAEKQNEEISTARNFVKALHRLKTGSPDKN

Ga0213897_103751

Ga0213897_1037511

F002951

MTPADIDRVFGRGRLRMVTGDHVEVFREHSLPGERRRYTKRFLATAAGDFSEWTEREWRILARLVGHGIKPVPDVVRFDRGAADRAALVQTFDAGVTVDHWATLLPLERDGTTLRNVFEDCAHWWALARHSLI

Ga0213897_104074

Ga0213897_1040741

F097548

MPGYRSLSSNLSGTAAEHAREAELSQRHGDPQSAARLLEEALAASLRSRPEMPGWVCGRLASIYRTLKRYDDEVELLERYRESQTSEEARTRFDARLSKARAIADRKRRPVTGALETVRQVRYRSSQRRRTPPRSQAVSAT

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300021271: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_3

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences