3300020593: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 37_C Kraft MG (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300020593
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191741 | Ga0180221
• Sample Name: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 37_C Kraft MG (version 2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 275411377
• Sequencing Scaffolds: 13
• Novel Protein Genes: 15
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Rhodanobacteraceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
Not Available	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Unclassified → Compost → Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → anthropogenic environment → compost
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: USA: Emeryville, California
• Coordinates
  • Lat. (^o): 37.83
  • Long. (^o): -122.29
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000116	Metagenome	2132	Y
F001736	Metagenome / Metatranscriptome	644	Y
F001784	Metagenome / Metatranscriptome	635	Y
F005784	Metagenome / Metatranscriptome	390	Y
F011022	Metagenome / Metatranscriptome	296	Y
F011188	Metagenome / Metatranscriptome	294	Y
F021823	Metagenome / Metatranscriptome	217	Y
F031088	Metagenome / Metatranscriptome	183	Y
F065880	Metagenome / Metatranscriptome	127	Y
F072653	Metagenome	121	Y
F076629	Metagenome / Metatranscriptome	118	Y
F081712	Metagenome	114	Y
F090842	Metagenome / Metatranscriptome	108	Y
F094455	Metagenome / Metatranscriptome	106	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0180221_1001145	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → Rhodanobacteraceae	18897
Ga0180221_1005774	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	5737
Ga0180221_1007705	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	4571
Ga0180221_1009848	All Organisms → cellular organisms → Bacteria	3743
Ga0180221_1011004	All Organisms → cellular organisms → Bacteria	3420
Ga0180221_1011994	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	3182
Ga0180221_1015972	All Organisms → cellular organisms → Bacteria → Proteobacteria	2505
Ga0180221_1018679	Not Available	2191
Ga0180221_1021732	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1917
Ga0180221_1026296	All Organisms → cellular organisms → Bacteria → Proteobacteria	1633
Ga0180221_1037909	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1174
Ga0180221_1071372	Not Available	669
Ga0180221_1091091	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	536

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0180221_1001145	Ga0180221_100114512	F072653	MNIRMQLVRAGAALAIIGGIAAAATLSPPATDLDCPFAKAVKPQRILLLDPIQRHPIWIDARRDSDDPQLQSTADAKHPLSHGVVTS
Ga0180221_1002373	Ga0180221_10023733	F000116	MSAPVRPIGLPPLSQHLRELASRRDAWLVIARNLIPVVGIWFFGWSAALSVFNYWFDGLSALAAIVAALVPRALRESQPDTVDPVTRLVLGVFVWAFLVGIVGLPYWIVLIPLHDLLLGDELWHRIATSPSLWVAFGMMASLHLRKALAVGYGALPENELKQRVRWDVYLLMLRGMAMFAMAAHGLAFILVPLMALLLSYFEIWPERVLGAVFGDPSKLYLHDPGGAPTRRRTKRK
Ga0180221_1005774	Ga0180221_10057746	F094455	MYNVTEFPIDRLSDRELRIREWEVVMSGGYGSSEHKRLQSEIRRRTVNLYAAAQPYTTH
Ga0180221_1007705	Ga0180221_10077055	F001736	MPDHGDRTPRSTYLREFFERAQRSAEAERDALAVVRAFNARSSSRRPVWFWPKIAAALVAKHPWLVVVCESCNLVVDLDLRVKPRDSEASIRVALREVRCPRCNGHGRPRIVALSKTPTC
Ga0180221_1009848	Ga0180221_10098483	F065880	MKGELPMDREAVQVKLTDGDWQPAVYQDGQFFDLYGLPLDYRKITSWRPAGGSPNGSAAADRRSARL
Ga0180221_1011004	Ga0180221_10110043	F090842	MLKRFFGSSEEPLIPVCPDHHVEMRLRGKMGKPTRFTDQSSSEYTLIYFCPVEGCNNTATRERQRLQIPAPGVAPERPIFARPNDRQ
Ga0180221_1011994	Ga0180221_10119943	F031088	MKLNVLAIALAATAFSAFGANAQTVIEERRDPAVVIEHDRPASSVTVEKREGLIGEKKTITKETTGSAGCDSKTVHREGIGGSTTVKKTNCD
Ga0180221_1015972	Ga0180221_10159723	F021823	MVMLNFVRRLLMHYGIYRRYPLSRLPALKNAWRMAR
Ga0180221_1018679	Ga0180221_10186792	F076629	VIRTLVVGALLALATAGPVSAYSLVSLAPQERETMLSTCGRLGGNDRALCRQVVDDHHVIANYKRSCLEAMTLLLQGSTWAKVKSLPATLTCREGLAQAGYPVKDIMRKLTGAQ
Ga0180221_1021732	Ga0180221_10217321	F005784	AVERRSEPMICQGARLLHIDGRNLQFDGDAVSAEDGCEIHITNSHIIAGGVGVTARAANVHIKNSVIEGKSGSVSASDGANVYTQSSTFRGLSRRLDTASFHDLGGTVWN
Ga0180221_1026296	Ga0180221_10262963	F001784	MGEVIHATFGTEREWKQTRDKTVDGLLTIGTLFGDDEELMRAKADCVYHILRQIVEGIPTVQITTRLPENLSEEQLAILTESIRQAALKGIEVAMTHSVQVLMSSIYDLCTSKLKDARY
Ga0180221_1037909	Ga0180221_10379092	F011188	VDTYNIYMDELPAGEEIDGEEIIEVEFRVVPGSSDDNDPESNAVIAGLDLVDLINLRDALQQEIDNYALTALEASASQIADIEVGGL
Ga0180221_1071372	Ga0180221_10713722	F011022	MPHPMVKEARAALEEAQSQLDAALSAWDASVSELWRTSIALTQAQKRVTHAHELLREALDAAGLEASSSPND
Ga0180221_1091091	Ga0180221_10910912	F001736	TPRSTYLREFVERAKRGAEAERDALAVVRAFNARSSSGRPVWFWPKIAAALVAKHPWLVVVCESCDLVVDLDLRVKPRDPEASIRVALRDVRCPRCNGHGRPRIIALSKIPSR
Ga0180221_1098155	Ga0180221_10981551	F081712	MSAVLLAVFDDYDAADRVRSALVRDGFPTDRVDLTASREPG