3300017544: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C Kraft MG (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017544
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191747 | Ga0182735
• Sample Name: Enriched Miracle-Growth compost microbial communities from Emeryville, California, USA - eDNA 5th pass 30_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: 457787885
• Sequencing Scaffolds: 5
• Novel Protein Genes: 6
• Associated Families: 6

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	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?
F012659	Metagenome / Metatranscriptome	278	Y
F013935	Metagenome / Metatranscriptome	267	Y
F016724	Metagenome / Metatranscriptome	245	Y
F027578	Metagenome / Metatranscriptome	194	Y
F031571	Metagenome / Metatranscriptome	182	Y
F036958	Metagenome	169	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0182735_1004649	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	7380
Ga0182735_1032188	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	2012
Ga0182735_1044507	All Organisms → cellular organisms → Bacteria → Proteobacteria	1608
Ga0182735_1071818	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1136
Ga0182735_1211384	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	511

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0182735_1004649	Ga0182735_10046495	F012659	MADEKILEALFEIRNWIRAAAHTPVKASLEAALPDVKSRMAYQMLDGSSSMEQVRVACKMSPNVLLALANLCTSMGLMELNSDKKRVRLFDLLDFGLMDAVASAKSEKKRER
Ga0182735_1006282	Ga0182735_10062821	F016724	MRAKKSVLGLVDSGREVRRPPLVGMQFLHQPSMSAADFIAPRASLQAKDLIS
Ga0182735_1032188	Ga0182735_10321882	F036958	MSVILIFAGFVLVGDTLAVIISYLFERISNSVSLMVFLGLYILVFWVAWKLAVYVTERYIVGEQPVANASPD
Ga0182735_1044507	Ga0182735_10445073	F031571	CAQQVGISTAEMLMHSVVGEDDMGHTQGVRSFVTLNLSALSPFMMGYILQSSGNNFIFAFAVLAVAVVMAAACMIKLAREGY
Ga0182735_1071818	Ga0182735_10718182	F027578	MDRRKFFGMSVAAGGLLAAREQAAAQATGPAYNGAPKLEPQAFHRRQQQFRIGYTTNTRGGWESDPFVGISEGREIGFRYFEIFGASFCATQDGLNAAPRDTQKMKTWPDGYSWKYPTGPRSKREVYYPDRWEALQHRMYEIGAQFVA
Ga0182735_1211384	Ga0182735_12113842	F013935	DAAKLVFERGPLLHQLLGFLRVVPEIGVFGEVIQFGETCSCGIDVKDASSAARLTA