3300004179: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 4_LOW4

Overview

Basic Information

• IMG/M Taxon OID: 3300004179
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114290 | Gp0111068 | Ga0066404
• Sample Name: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 4_LOW4
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 224017928
• Sequencing Scaffolds: 5
• Novel Protein Genes: 5
• Associated Families: 5

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
Not Available	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	2

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Sediment → Unclassified → Freshwater → Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): freshwater lake biome → freshwater lake → lake sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Sediment (non-saline)

Location Information

• Location: USA: Lake Washington, Seattle, Washington
• Coordinates
  • Lat. (^o): 48.3807
  • Long. (^o): -122.1599
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F019851	Metagenome	227	N
F060098	Metagenome / Metatranscriptome	133	Y
F085867	Metagenome	111	Y
F087391	Metagenome / Metatranscriptome	110	N
F105443	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0066404_1005405	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1953
Ga0066404_1020371	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1064
Ga0066404_1033492	Not Available	843
Ga0066404_1060854	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	629
Ga0066404_1063407	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	616

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0066404_1005405	Ga0066404_10054051	F105443	MGGAERQFTLHLITTTKPPVAPARTSGLPIGAWLVLGFALVIGAFTAASVVSLRSTRGATADLERMQQQFEPLSRSVRDLGDGVATFDRSVLAYLRADTRDRHAATVAAAARLSGAASQMLDVDADDAAPPVGPLLQRIADHEAQGFGLLNMQDERRRAIADLESAFAALDRRVRSAGGSGIVV
Ga0066404_1020371	Ga0066404_10203712	F087391	MKLTKFALLAVAAGCTLASQGVYAQAMEVVTVEAVREIVIGKSPIGAPIKELTIRARVSYADLDLTTATGAATLEKRVRDSATSSCKEIKVDVPVEGWTVDRCIREATEGAMVQVNKAVADAKAAKK*
Ga0066404_1033492	Ga0066404_10334921	F085867	MSERKPELPVGTRAPPRDKPGPPERPLTAREVGPRRGANKIGAATDGWDAYNDWLGRVRQPAPPSRQAVISKSLYSIASYKSWADKARGAFDKGK*
Ga0066404_1060854	Ga0066404_10608542	F019851	VKRPDQVCESCWRVSRASPVPVTEIACHHNKVLATWHADTDEWTYQHRVARKRPTQKQSEQLAQMFDQASSATRRRDEP*
Ga0066404_1063407	Ga0066404_10634072	F060098	MDAPTLKRAASAVTMGLGGLLWLAAILFMAQTAQNSEQFSRLHPWILGINIAG