Sample 3300021272

Overview

Basic Information
IMG/M Taxon OID	3300021272 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0131209 \| Gp0238796 \| Ga0213899
Sample Name	Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Shaw_2
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	20412757
Sequencing Scaffolds	16
Novel Protein Genes	16
Associated Families	16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	5
All Organisms → cellular organisms → Bacteria → Proteobacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 8X	1
All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium	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?
F004743	Metagenome / Metatranscriptome	425	Y
F010196	Metagenome / Metatranscriptome	307	Y
F012395	Metagenome / Metatranscriptome	281	Y
F018610	Metagenome	234	Y
F019223	Metagenome / Metatranscriptome	231	Y
F020996	Metagenome / Metatranscriptome	221	Y
F041962	Metagenome	159	Y
F043603	Metagenome	156	Y
F066113	Metagenome / Metatranscriptome	127	Y
F069810	Metagenome / Metatranscriptome	123	Y
F070593	Metagenome / Metatranscriptome	123	Y
F073507	Metagenome / Metatranscriptome	120	Y
F079081	Metagenome / Metatranscriptome	116	Y
F096838	Metagenome	104	N
F103522	Metagenome	101	Y
F104660	Metagenome / Metatranscriptome	100	Y

Family

Category

Number of Sequences

3D Structure?

F004743

Metagenome / Metatranscriptome

425

F010196

Metagenome / Metatranscriptome

307

F012395

Metagenome / Metatranscriptome

281

F018610

Metagenome

234

F019223

Metagenome / Metatranscriptome

231

F020996

Metagenome / Metatranscriptome

221

F041962

Metagenome

159

F043603

Metagenome

156

F066113

Metagenome / Metatranscriptome

127

F069810

Metagenome / Metatranscriptome

123

F070593

Metagenome / Metatranscriptome

123

F073507

Metagenome / Metatranscriptome

120

F079081

Metagenome / Metatranscriptome

116

F096838

Metagenome

104

F103522

Metagenome

101

F104660

Metagenome / Metatranscriptome

100

Scaffold	Taxonomy	Length	IMG/M Link
Ga0213899_100031	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2048	Open in IMG/M
Ga0213899_100135	All Organisms → cellular organisms → Bacteria	1429	Open in IMG/M
Ga0213899_100171	All Organisms → cellular organisms → Bacteria	1349	Open in IMG/M
Ga0213899_100592	All Organisms → cellular organisms → Bacteria	1009	Open in IMG/M
Ga0213899_100674	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	975	Open in IMG/M
Ga0213899_100826	All Organisms → cellular organisms → Bacteria → Proteobacteria	917	Open in IMG/M
Ga0213899_101186	All Organisms → cellular organisms → Bacteria → Proteobacteria	834	Open in IMG/M
Ga0213899_101513	All Organisms → cellular organisms → Bacteria	781	Open in IMG/M
Ga0213899_101580	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	770	Open in IMG/M
Ga0213899_101869	All Organisms → cellular organisms → Bacteria → Proteobacteria	737	Open in IMG/M
Ga0213899_102378	All Organisms → cellular organisms → Bacteria → Proteobacteria	688	Open in IMG/M
Ga0213899_102953	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 8X	645	Open in IMG/M
Ga0213899_104704	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	559	Open in IMG/M
Ga0213899_105309	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	538	Open in IMG/M
Ga0213899_106420	All Organisms → cellular organisms → Bacteria → FCB group → Gemmatimonadetes → Gemmatimonadetes → Gemmatimonadales → unclassified Gemmatimonadales → Gemmatimonadales bacterium	508	Open in IMG/M
Ga0213899_106484	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	506	Open in IMG/M

Scaffold

Taxonomy

Length

IMG/M Link

Ga0213899_100031

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria

2048

Open in IMG/M

Ga0213899_100135

All Organisms → cellular organisms → Bacteria

1429

Open in IMG/M

Ga0213899_100171

All Organisms → cellular organisms → Bacteria

1349

Open in IMG/M

Ga0213899_100592

All Organisms → cellular organisms → Bacteria

1009

Open in IMG/M

Ga0213899_100674

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

975

Open in IMG/M

Ga0213899_100826

All Organisms → cellular organisms → Bacteria → Proteobacteria

917

Open in IMG/M

Ga0213899_101186

All Organisms → cellular organisms → Bacteria → Proteobacteria

834

Open in IMG/M

Ga0213899_101513

All Organisms → cellular organisms → Bacteria

781

Open in IMG/M

Ga0213899_101580

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

770

Open in IMG/M

Ga0213899_101869

All Organisms → cellular organisms → Bacteria → Proteobacteria

737

Open in IMG/M

Ga0213899_102378

All Organisms → cellular organisms → Bacteria → Proteobacteria

688

Open in IMG/M

Ga0213899_102953

All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 8X

645

Open in IMG/M

Ga0213899_104704

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

559

Open in IMG/M

Ga0213899_105309

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

538

Open in IMG/M

Ga0213899_106420

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

508

Open in IMG/M

Ga0213899_106484

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

506

Open in IMG/M

Scaffold ID	Protein ID	Family	Sequence
Ga0213899_100031	Ga0213899_1000312	F019223	LQYTIDADDEFLRVTLSGRDTDQPPSEVCALVLAESRARNRKRILIELDQKFPLSPTSQYHLVTNLPKIGFTAEERIALVHKTPYAQNANHFINLLARNHRVMVRNFTGLEPAKEWLRGNST
Ga0213899_100135	Ga0213899_1001353	F020996	MAIRLISAKRVGDDLAAGRIAAGDQSLYLTASFLIWMIPAYLFLFPAPRTIDPDFFWGIWLVELALLVLICIVGIGFCLRNCRIDPQRNFLVDFSCLNAPISFTTLAIVWGGFHLLAAPWFSWLESPRAYDAVRLLASVAAVFIVFLRIGR
Ga0213899_100171	Ga0213899_1001712	F069810	LRILLLLSVLLALGACQVQEPTARGTVLSVQEAKQALPEDLLKFDDGNLRLPEVAWHVEVQLDDGSQVSTLHTGGRRYAPGERVRLLIDADGALLL
Ga0213899_100592	Ga0213899_1005922	F070593	MEMASLGSWLIMAGWTIGLAILAWWFYMPNPMAKDSKKGKKENKKQP
Ga0213899_100674	Ga0213899_1006742	F010196	VSGLRLLIGVIVMGIAVPITLFLLLDLHAYSALFTIAAVTFLSWGVADLLATILGKPRLQGRSPGKALKEDWERRSK
Ga0213899_100826	Ga0213899_1008262	F103522	MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWFLPTGTDFGFRHVAAVSVLFGLAAAGLFHLWRKPRI
Ga0213899_101186	Ga0213899_1011862	F104660	MRNEFATKFWQRAYESLPAGVRAQYLTQMKAAESWELSLQAIIELASRAKNAVLKLFNTPKTAH
Ga0213899_101513	Ga0213899_1015132	F066113	MAPEFPIRIISDDGRCEVVESPEELMARVDSLDSADPAVWVRDAYDRTVKIRVRGGIVEELDLQR
Ga0213899_101580	Ga0213899_1015802	F018610	MNYQVPMMEVAVVVAIEGVDPEEHFLYLSPYSERREGPETVADYLNGRRRFFPMVVGGVPKMLNRDQILWVRYEKLPTVVDLDSTMVEKLTIIELADGTRIEGMLPIGDRPREYSRISDVLNDATESFVRIDADEDTYFVNKKFIRTVIPR
Ga0213899_101869	Ga0213899_1018691	F073507	MGGGDVRNIMYYGFDKEVMGMISDATAFLHEIKVLPMAQLPKELIDTSWTDEILKKANLKVPLAKIEAQDPSKYPGGKINLPASWRKD
Ga0213899_102378	Ga0213899_1023782	F096838	RAGSPVSMLLLAAGTGCGALGLFIFFTERGVANEIKGFVLLLIAGVLLVGGCVLWELRSIRRGLERRNPE
Ga0213899_102953	Ga0213899_1029531	F041962	MSSNFLAPTSSELERDWGIVLGDDWATDVVGGDYAPIIRRFGLGAAAQREAVLARFGLIPSTAKTARSPGSTVNARSETAA
Ga0213899_104704	Ga0213899_1047042	F043603	MNNIAQTRTTRLETALSASYVLPSMLALNTVALLALDQLGGIPQWVKTAAALFLSF
Ga0213899_105309	Ga0213899_1053091	F079081	MIESFKHLEELAADRDLAEVFLETDEQEHAVPAEQIVEALRKRRAVMRDCVERGRSSDGASMGRLVGSEARLLQ
Ga0213899_106420	Ga0213899_1064201	F004743	MAEPSFLEQIATLNTTLSDVEGRLARGQTAVQELEDFKSALDDVRLRLWGLLSAAGGDDYKGFQERFRIRRATEMSRGLGGDLRTGAVSGRHRELAGLREAANELAQSIEQAQRPAF
Ga0213899_106484	Ga0213899_1064842	F012395	MRFDWVNILATIIFVSIVVTLILAVASYFAYKLREARRPKTAAELRQEGQMKAFFQPYRP

Scaffold ID

Protein ID

Family

Sequence

Ga0213899_100031

Ga0213899_1000312

F019223

LQYTIDADDEFLRVTLSGRDTDQPPSEVCALVLAESRARNRKRILIELDQKFPLSPTSQYHLVTNLPKIGFTAEERIALVHKTPYAQNANHFINLLARNHRVMVRNFTGLEPAKEWLRGNST

Ga0213899_100135

Ga0213899_1001353

F020996

MAIRLISAKRVGDDLAAGRIAAGDQSLYLTASFLIWMIPAYLFLFPAPRTIDPDFFWGIWLVELALLVLICIVGIGFCLRNCRIDPQRNFLVDFSCLNAPISFTTLAIVWGGFHLLAAPWFSWLESPRAYDAVRLLASVAAVFIVFLRIGR

Ga0213899_100171

Ga0213899_1001712

F069810

LRILLLLSVLLALGACQVQEPTARGTVLSVQEAKQALPEDLLKFDDGNLRLPEVAWHVEVQLDDGSQVSTLHTGGRRYAPGERVRLLIDADGALLL

Ga0213899_100592

Ga0213899_1005922

F070593

MEMASLGSWLIMAGWTIGLAILAWWFYMPNPMAKDSKKGKKENKKQP

Ga0213899_100674

Ga0213899_1006742

F010196

VSGLRLLIGVIVMGIAVPITLFLLLDLHAYSALFTIAAVTFLSWGVADLLATILGKPRLQGRSPGKALKEDWERRSK

Ga0213899_100826

Ga0213899_1008262

F103522

MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWFLPTGTDFGFRHVAAVSVLFGLAAAGLFHLWRKPRI

Ga0213899_101186

Ga0213899_1011862

F104660

MRNEFATKFWQRAYESLPAGVRAQYLTQMKAAESWELSLQAIIELASRAKNAVLKLFNTPKTAH

Ga0213899_101513

Ga0213899_1015132

F066113

MAPEFPIRIISDDGRCEVVESPEELMARVDSLDSADPAVWVRDAYDRTVKIRVRGGIVEELDLQR

Ga0213899_101580

Ga0213899_1015802

F018610

MNYQVPMMEVAVVVAIEGVDPEEHFLYLSPYSERREGPETVADYLNGRRRFFPMVVGGVPKMLNRDQILWVRYEKLPTVVDLDSTMVEKLTIIELADGTRIEGMLPIGDRPREYSRISDVLNDATESFVRIDADEDTYFVNKKFIRTVIPR

Ga0213899_101869

Ga0213899_1018691

F073507

MGGGDVRNIMYYGFDKEVMGMISDATAFLHEIKVLPMAQLPKELIDTSWTDEILKKANLKVPLAKIEAQDPSKYPGGKINLPASWRKD

Ga0213899_102378

Ga0213899_1023782

F096838

RAGSPVSMLLLAAGTGCGALGLFIFFTERGVANEIKGFVLLLIAGVLLVGGCVLWELRSIRRGLERRNPE

Ga0213899_102953

Ga0213899_1029531

F041962

MSSNFLAPTSSELERDWGIVLGDDWATDVVGGDYAPIIRRFGLGAAAQREAVLARFGLIPSTAKTARSPGSTVNARSETAA

Ga0213899_104704

Ga0213899_1047042

F043603

MNNIAQTRTTRLETALSASYVLPSMLALNTVALLALDQLGGIPQWVKTAAALFLSF

Ga0213899_105309

Ga0213899_1053091

F079081

MIESFKHLEELAADRDLAEVFLETDEQEHAVPAEQIVEALRKRRAVMRDCVERGRSSDGASMGRLVGSEARLLQ

Ga0213899_106420

Ga0213899_1064201

F004743

MAEPSFLEQIATLNTTLSDVEGRLARGQTAVQELEDFKSALDDVRLRLWGLLSAAGGDDYKGFQERFRIRRATEMSRGLGGDLRTGAVSGRHRELAGLREAANELAQSIEQAQRPAF

Ga0213899_106484

Ga0213899_1064842

F012395

MRFDWVNILATIIFVSIVVTLILAVASYFAYKLREARRPKTAAELRQEGQMKAFFQPYRP

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300021272: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Shaw_2

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences