3300021264: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_1

Overview

Basic Information

• IMG/M Taxon OID: 3300021264
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0131209 | Gp0238792 | Ga0213895
• Sample Name: Switchgrass-associated microbial communities from reclaimed mine lands soil in West Virginia, United States ? Hamp_Cave_1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 22028185
• Sequencing Scaffolds: 16
• Novel Protein Genes: 16
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Rhodocyclales → Rhodocyclaceae → Aromatoleum → Aromatoleum aromaticum → Aromatoleum aromaticum EbN1	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. SCGC AG-212-E16	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Myxococcaceae → unclassified Myxococcaceae → Myxococcaceae bacterium	1
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	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?
F012081	Metagenome / Metatranscriptome	284	Y
F013740	Metagenome / Metatranscriptome	268	Y
F021258	Metagenome / Metatranscriptome	219	Y
F030799	Metagenome	184	Y
F032460	Metagenome / Metatranscriptome	180	Y
F038633	Metagenome / Metatranscriptome	165	Y
F040166	Metagenome / Metatranscriptome	162	Y
F042599	Metagenome / Metatranscriptome	158	Y
F044764	Metagenome / Metatranscriptome	154	Y
F062538	Metagenome / Metatranscriptome	130	Y
F069810	Metagenome / Metatranscriptome	123	Y
F077001	Metagenome	117	Y
F081517	Metagenome	114	N
F085328	Metagenome	111	Y
F092317	Metagenome	107	Y
F103522	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0213895_100040	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Rhodocyclales → Rhodocyclaceae → Aromatoleum → Aromatoleum aromaticum → Aromatoleum aromaticum EbN1	2114
Ga0213895_100454	All Organisms → cellular organisms → Bacteria	1234
Ga0213895_100609	All Organisms → cellular organisms → Bacteria → Proteobacteria	1135
Ga0213895_100804	All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. SCGC AG-212-E16	1049
Ga0213895_100828	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales	1039
Ga0213895_100836	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Myxococcaceae → unclassified Myxococcaceae → Myxococcaceae bacterium	1037
Ga0213895_101360	Not Available	894
Ga0213895_101495	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	866
Ga0213895_101835	Not Available	812
Ga0213895_102926	Not Available	694
Ga0213895_103284	Not Available	668
Ga0213895_104014	Not Available	622
Ga0213895_104875	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	581
Ga0213895_105700	Not Available	547
Ga0213895_106069	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	535
Ga0213895_106150	Not Available	532

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0213895_100040	Ga0213895_1000402	F021258	MKVKLSFPRLLDRVDLRPQVIGAQEIVGDPQPAGRIAF
Ga0213895_100454	Ga0213895_1004542	F081517	MHPILIADVPSMDARYWAALAGWSLAFTRTMEEARATLAAQRCAAVVIGVYFDDSQMFDLVRAIRADDFQNEVPIVCVRGTPSYTAVSTSTLETALRVLAADAFVDLLHFAQEQSGDAALRATVQRYLKG
Ga0213895_100609	Ga0213895_1006091	F012081	MSNMRGIRFWKNWGLVSRLMLAVGIAIITGGGVQTALLVAEGAAEHSARLKRELNETLTFMAPLIADQALVGEYAVIS
Ga0213895_100804	Ga0213895_1008041	F044764	MFSAWDFNSWFFSVGTVLFMLGFLTGFSALASVLMSRMWGDACDDAATVRLCRRTKEVPIRHVP
Ga0213895_100828	Ga0213895_1008281	F013740	VRFSLLALIAALPGCAAPSLAPESSVAVVWNRVEEPHAVCESLSGRKNFFNVLGCSHWSAPAAEGGARVCSIYAPAPRSERDLQRFATLGHELMHCFDGNWHDRWGRMNPSTQSAAAGGS
Ga0213895_100836	Ga0213895_1008362	F077001	MKKFWLAALLSACSTPQWEKAGAAPDDVALDLKQCEAAAPLAPRAAPGPRSKPGSNVIDFDSASERSFERMRKDDEHIAACMRAKGYSR
Ga0213895_101360	Ga0213895_1013601	F092317	PQVPYWAMPLWLSIPIVAALWVSSWISGLDLTTGDRAETYIMWGVTAIASALLLRRLVRA
Ga0213895_101495	Ga0213895_1014952	F062538	MRYDFTYIQALQSRARRERSEAIYEMLIAPLVALFTRRPARKELQHAPRPHFAR
Ga0213895_101835	Ga0213895_1018352	F103522	MLRSLTVFSIAGTLHFLLSVLGLAFILPAAFETQGGAGFWAAPGKSMLVWMSNVLLAPLWLLPTGTDFGFRHVAAVSVLFGLAAAGLFHL
Ga0213895_102926	Ga0213895_1029261	F040166	MSLHRLVCLAAALLSGCSMHSNWYLMDSGYSINPVDGDAQAYAVEVHVNQLKQLGGDVNSAEARLFIAERLKWHGVCPAGWQPLPCVQDGSCVQRTRRSVTVPGRCVTP
Ga0213895_103284	Ga0213895_1032842	F038633	QLMADQVGKGLESMVTRKLLTATAVGLSVGLLAQHATGAETPTVQKAPVAEEFTVDAELFRNEIADYVRELNRQMRTTLNEELRRELAPKVVASNELRTRS
Ga0213895_104014	Ga0213895_1040141	F032460	MAVHVVFGPPLEAPMRSEEAKPLQVAAQAAAKWCMQKLDMKEGGFGKNHEHSESERAALHVAHSIAACEVARLQSIVDGR
Ga0213895_104875	Ga0213895_1048751	F085328	VTTYSIEPNLFSEPKTMNDPLPASPDPAVHKAQLARMLLAAARSHIHAVPERAADCTAIYTLADPRDVRCPRYVGQTRDPRRRFAQHLHTARLWLPDSTPWWVRSPKYRPLYDWIRALYRDGGRLPFMWVAEWAEPGTDALAAERAAIMRLLAQRAELLNVEARLLGAQLPLL
Ga0213895_105700	Ga0213895_1057001	F069810	DWRRRPAPLSEVLERAGIGLALRILLLLSVLLALGACQVQDPTARGTVLSVQEAKQALPEDLLKFDDGNLRLPEVAWHVEVQLDDGSQVSTLHTGGRRYAPGERVRLLIDADGALLL
Ga0213895_106069	Ga0213895_1060692	F030799	SGYPENDYICVHTDADPLDDTVVLATIERVTDRTKGKVKRVKTLLARVRMSIDAALGLATSYAEWKQVPVVYADSPPRHTL
Ga0213895_106150	Ga0213895_1061501	F042599	MHPLSRPVRFIIGLCVVIIGLNVFMLWWLQKLTPTTVPQVEHTPIRVEPPPAVAPCEPIVAGNEGEIAERDTMIARLEAEVERMKRAHDDDRSAWRTKAEQIEKDLMMLEKAAERVLRMDAQHWHEG