3300021260: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Shaw_1

Overview

Basic Information

• IMG/M Taxon OID: 3300021260
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0131209 | Gp0238795 | Ga0213898
• Sample Name: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Shaw_1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 17433097
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp.	1
Not Available	5
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin122	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria 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

Associated Families

Family	Category	Number of Sequences	3D Structure?
F015651	Metagenome / Metatranscriptome	253	Y
F020996	Metagenome / Metatranscriptome	221	Y
F025377	Metagenome	202	Y
F042599	Metagenome / Metatranscriptome	158	Y
F064862	Metagenome / Metatranscriptome	128	Y
F069814	Metagenome / Metatranscriptome	123	Y
F082322	Metagenome	113	Y
F099237	Metagenome / Metatranscriptome	103	Y
F103522	Metagenome	101	Y
F104660	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0213898_100208	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1178
Ga0213898_100363	All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp.	1030
Ga0213898_100403	Not Available	1007
Ga0213898_100685	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin122	870
Ga0213898_101328	Not Available	735
Ga0213898_101788	Not Available	676
Ga0213898_102773	Not Available	596
Ga0213898_102844	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	592
Ga0213898_103009	Not Available	582
Ga0213898_104848	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	509

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0213898_100208	Ga0213898_1002082	F082322	VASLASAASIIATSLLVFCSAALGQDARRDSTVELLYVSAADCGFCRRWEAQYLDGQRPLASLDWAEVRFTRVDIGTFRARFSADDAPARLRPGLAKAMAAAGQASLRGTPWFALFVNGEVHSHAFGTTAFESRIQPAMRAALREKARAART
Ga0213898_100363	Ga0213898_1003632	F025377	MRVYWKWVIRSVPSLVLGVLMLLSTVTPRQARSNVEAWLNYFGIEEVPLWLANQYTDTWVFWLAFVGFCAWAIHLYVRTNVRNGKLSIILREGEPWVQVNSGADRSQAARTGGPLYTYRVALVNSDDSTIRNVEVKLI
Ga0213898_100403	Ga0213898_1004032	F103522	MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWLLPTGTDFGFRHVAAVSVLFGLAAAGLFHLRRI
Ga0213898_100685	Ga0213898_1006852	F064862	MPAIQAEVSVAANSTNNNLFNGSAFEYSRGRQLLSLGVTAAATGTLCTIQSGADVILEESATFIKTQFPIVPDEMFYNDIMEMFDRLRVQIRNGTGAAIVARSIALLTPL
Ga0213898_101328	Ga0213898_1013282	F015651	MAPQSSNLTALLTMAPSAFSGGEMPRLPQIKTVAALKEEVTRHFGKMSSQELDALAGWFNRNFFRLER
Ga0213898_101788	Ga0213898_1017881	F020996	AAGDQSLYLTASFLIWMIPAYLFLFPAPRTIDPDFFWGIWLVELALLVLICIVGIGFCLRNCRIDPQRNFLVDFSCLNAPISFTTLAIVWGGFHLLAAPWFSWLESPRAYDAVRLLASVAAVFIVFLRIGRHMNRVSVLRNSSQ
Ga0213898_102773	Ga0213898_1027731	F099237	LDWLLTREVVITLAVLAAIPSVAASLLQVRGKISAARARQLNFAGYVLMGISMAL
Ga0213898_102844	Ga0213898_1028443	F104660	MRNEFATKFWQRAYESLPAGVRAQYLTQMKAAESWELSLQAIIEFVSRTKNAVLKVFNTPKGAH
Ga0213898_103009	Ga0213898_1030091	F042599	IGLNVFMLLWLQTFTPTTRVASRQVDRTPIRVEPPPTVAAPCEPTIAENDGEIAERNAVIARLEEELERTKQTHDADTSAWRAKAAQIERDLSGLQKVAERVMEMDAQHWHEGQLMLAHAMIKKRT
Ga0213898_104848	Ga0213898_1048481	F069814	AMCEHARQEGTSSRNMERRKTPRKEWVISKDDVGRSVLEWKMDPMRAKRMESDPCARTYDFLNRLDHPELAIEDEPKKPTSRRAINPYDHGPGTGARKKKPS