NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
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Sample 3300021260

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



Overview

Basic Information
IMG/M Taxon OID3300021260 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0131209 | Gp0238795 | Ga0213898
Sample NameSwitchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Shaw_1
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size17433097
Sequencing Scaffolds10
Novel Protein Genes10
Associated Families10

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria2
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp.1
Not Available5
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin1221
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameSwitchgrass-Associated Microbial Communities From Reclaimed Mine Lands Soil In West Virginia, United States
TypeEnvironmental
TaxonomyEnvironmental → 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
LocationUSA: West Virginia
CoordinatesLat. (o)39.458Long. (o)-79.073Alt. (m)N/ADepth (m).1
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F015651Metagenome / Metatranscriptome253Y
F020996Metagenome / Metatranscriptome221Y
F025377Metagenome202Y
F042599Metagenome / Metatranscriptome158Y
F064862Metagenome / Metatranscriptome128Y
F069814Metagenome / Metatranscriptome123Y
F082322Metagenome113Y
F099237Metagenome / Metatranscriptome103Y
F103522Metagenome101Y
F104660Metagenome / Metatranscriptome100Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0213898_100208All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria1178Open in IMG/M
Ga0213898_100363All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp.1030Open in IMG/M
Ga0213898_100403Not Available1007Open in IMG/M
Ga0213898_100685All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium ADurb.Bin122870Open in IMG/M
Ga0213898_101328Not Available735Open in IMG/M
Ga0213898_101788Not Available676Open in IMG/M
Ga0213898_102773Not Available596Open in IMG/M
Ga0213898_102844All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria592Open in IMG/M
Ga0213898_103009Not Available582Open in IMG/M
Ga0213898_104848All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium509Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0213898_100208Ga0213898_1002082F082322VASLASAASIIATSLLVFCSAALGQDARRDSTVELLYVSAADCGFCRRWEAQYLDGQRPLASLDWAEVRFTRVDIGTFRARFSADDAPARLRPGLAKAMAAAGQASLRGTPWFALFVNGEVHSHAFGTTAFESRIQPAMRAALREKARAART
Ga0213898_100363Ga0213898_1003632F025377MRVYWKWVIRSVPSLVLGVLMLLSTVTPRQARSNVEAWLNYFGIEEVPLWLANQYTDTWVFWLAFVGFCAWAIHLYVRTNVRNGKLSIILREGEPWVQVNSGADRSQAARTGGPLYTYRVALVNSDDSTIRNVEVKLI
Ga0213898_100403Ga0213898_1004032F103522MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWLLPTGTDFGFRHVAAVSVLFGLAAAGLFHLRRI
Ga0213898_100685Ga0213898_1006852F064862MPAIQAEVSVAANSTNNNLFNGSAFEYSRGRQLLSLGVTAAATGTLCTIQSGADVILEESATFIKTQFPIVPDEMFYNDIMEMFDRLRVQIRNGTGAAIVARSIALLTPL
Ga0213898_101328Ga0213898_1013282F015651MAPQSSNLTALLTMAPSAFSGGEMPRLPQIKTVAALKEEVTRHFGKMSSQELDALAGWFNRNFFRLER
Ga0213898_101788Ga0213898_1017881F020996AAGDQSLYLTASFLIWMIPAYLFLFPAPRTIDPDFFWGIWLVELALLVLICIVGIGFCLRNCRIDPQRNFLVDFSCLNAPISFTTLAIVWGGFHLLAAPWFSWLESPRAYDAVRLLASVAAVFIVFLRIGRHMNRVSVLRNSSQ
Ga0213898_102773Ga0213898_1027731F099237LDWLLTREVVITLAVLAAIPSVAASLLQVRGKISAARARQLNFAGYVLMGISMAL
Ga0213898_102844Ga0213898_1028443F104660MRNEFATKFWQRAYESLPAGVRAQYLTQMKAAESWELSLQAIIEFVSRTKNAVLKVFNTPKGAH
Ga0213898_103009Ga0213898_1030091F042599IGLNVFMLLWLQTFTPTTRVASRQVDRTPIRVEPPPTVAAPCEPTIAENDGEIAERNAVIARLEEELERTKQTHDADTSAWRAKAAQIERDLSGLQKVAERVMEMDAQHWHEGQLMLAHAMIKKRT
Ga0213898_104848Ga0213898_1048481F069814AMCEHARQEGTSSRNMERRKTPRKEWVISKDDVGRSVLEWKMDPMRAKRMESDPCARTYDFLNRLDHPELAIEDEPKKPTSRRAINPYDHGPGTGARKKKPS
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