3300020591: Enriched Organic Plus compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C Kraft OP (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300020591
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191748 | Ga0180223
• Sample Name: Enriched Organic Plus compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C Kraft OP (version 2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 343503552
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	3
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
Not Available	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?
F013535	Metagenome / Metatranscriptome	270	Y
F021809	Metagenome / Metatranscriptome	217	Y
F030808	Metagenome / Metatranscriptome	184	Y
F037437	Metagenome / Metatranscriptome	168	Y
F037930	Metagenome / Metatranscriptome	167	Y
F040613	Metagenome / Metatranscriptome	161	Y
F064866	Metagenome / Metatranscriptome	128	Y
F080249	Metagenome / Metatranscriptome	115	Y
F084466	Metagenome / Metatranscriptome	112	Y
F099198	Metagenome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0180223_1000326	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Chitinophagia → Chitinophagales → Chitinophagaceae	69610
Ga0180223_1001428	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	18511
Ga0180223_1004966	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	5971
Ga0180223_1008165	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	4016
Ga0180223_1010554	All Organisms → cellular organisms → Bacteria → Proteobacteria	3326
Ga0180223_1013079	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	2831
Ga0180223_1013740	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	2727
Ga0180223_1101945	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	635
Ga0180223_1134548	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	510
Ga0180223_1136061	Not Available	505

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0180223_1000326	Ga0180223_100032643	F064866	MKAPYLCCLLPVSILLYPLLSSAQPEENDSLAKYSYPIFAVTGKQQFTGTAFFYHSGDTTYLVSNYHAIKGMSPLKKAITFNSDTLYLKYSAKDSGGSKILPIDVSDAAIGETEIFSMVDRIDLLKIPLELPDGADIHFINDLIDPAYLNAVPEEVVVFGFPTGPGNIPPFYSQQQKLAGKVNQQGVADYDASLKVNFPGSSDSARAILSGTARYYYFIKPYAAQGYSGAPVFGKFRTADGQIVYRFTGVVFAGQPMTRQTWAIKGSVALQYLMGEL
Ga0180223_1001428	Ga0180223_10014289	F080249	MADDKQNRGSPDRNLISFKQRYEFNYAVKQLQKQVSDTTRQEAKDALTAAAKANSPSEGREKIMRAARKILRD
Ga0180223_1004966	Ga0180223_10049661	F030808	MLNLNLSAFQSQEFIVGIAVAAILVSALAASSMFRNIALALAAGGVVLLYLQGGVPALLATSAMVEKEIRSLPDFSNGLIVGLAVSAVFMLGMQKRSA
Ga0180223_1008165	Ga0180223_10081655	F084466	MTARTAAFALVFWAAASAEAFAIASVNVYGLRAPEEISGFTLNDSTNFEKVKPGDGYGLDYSQSGWKLDVFIYDLKRAAIPDDAKSAIVRAEFERARADAYLAQPRGIYAQVYLRRNF
Ga0180223_1010554	Ga0180223_10105541	F037437	MTLWKCPLALVLLTGLAWPAVAANVSILGKWQIVEATPAPWSDPKDQPALAAEGKRLLKTEVTFAPGSVVSKFKPFNCKSKVLYEVNSIEVDALFQGNLPEPNPTAAAARLGFPRGDIPGVDVRCLKALYTFHFRDPDTAMINLNRVIYTFKRQ
Ga0180223_1013079	Ga0180223_10130792	F021809	VIRLPRPLRGAALACVLTLLPGAALAQQNDCTREAAAIRKAETQLPRLDVAPPNDQQIVCITLETNILFARRLAAHVSQCPRSPLARDAQAWQRIGSQYTAQFGERRCKPAIRGYRG
Ga0180223_1013740	Ga0180223_10137402	F099198	MADAITALVGAVIMIGYMVLVAGKLAALPLWICTVIGLALMLWAFWGDDWKPLLVRDKK
Ga0180223_1101945	Ga0180223_11019451	F013535	MPFDLLLLYTYRLMAAIVAIMMIWVLFRERDWRSQFFAMLVFVPFALRAAGVK
Ga0180223_1134548	Ga0180223_11345481	F037930	VTTTTKPRLTAQQAQIERTYRNVITLFLAGRLGNFSHQRHVHVANILWHLPYGRELMHLGLQVMAYRNFVPDKYSPEITDREWAKLDGTLPDPAVFADVPGGADGRA
Ga0180223_1136061	Ga0180223_11360611	F040613	LVLERGPLLHQALGAFLIIPKFGVFGELVQLRQPGLRLVEVKDASSAVRPTA