3300004184: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 1_LOW4

Overview

Basic Information

• IMG/M Taxon OID: 3300004184
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114290 | Gp0111065 | Ga0066401
• Sample Name: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 1_LOW4
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 261524419
• Sequencing Scaffolds: 8
• Novel Protein Genes: 9
• Associated Families: 9

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 28-67-8	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → Methylobacter → Methylobacter marinus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1

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 Sediment → 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?
F000982	Metagenome / Metatranscriptome	814	Y
F016989	Metagenome	243	Y
F033105	Metagenome / Metatranscriptome	178	Y
F036304	Metagenome / Metatranscriptome	170	Y
F040165	Metagenome	162	Y
F066900	Metagenome	126	Y
F077414	Metagenome	117	Y
F082950	Metagenome / Metatranscriptome	113	Y
F087391	Metagenome / Metatranscriptome	110	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0066401_1002826	All Organisms → cellular organisms → Bacteria → Proteobacteria	2384
Ga0066401_1006465	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1697
Ga0066401_1033023	All Organisms → cellular organisms → Bacteria → Proteobacteria	856
Ga0066401_1037567	All Organisms → cellular organisms → Bacteria → Proteobacteria	810
Ga0066401_1077372	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 28-67-8	586
Ga0066401_1081523	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → Methylobacter → Methylobacter marinus	572
Ga0066401_1091034	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	544
Ga0066401_1099044	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	523

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0066401_1002826	Ga0066401_10028264	F040165	MYAAVLTFCVLAGEAVNLSRGSEVTALTLGNWTLSAALLTALWGYALQRRIGSAGYWRAVFWLVLFANSVMLIPVLLGDRTVAMFTAALTLLIVPAYLAAYLYAYRSPALWSPRALA*
Ga0066401_1006465	Ga0066401_10064651	F077414	CGQLAGWDWQEAARVLDVPPAKFGRLLTLQDALRAAVRNWPGTARSTV*
Ga0066401_1033023	Ga0066401_10330231	F036304	MSDTIIPEEVLALLFPEPASAGNPSSSVTAFVRDPHGGLMLASVVPNRTLLEAALVTGRWNSGTPILDPQTREIIGYELAPLAVA*
Ga0066401_1037567	Ga0066401_10375671	F087391	MKLTKFALLAVAAGCTLASQGVYAQAMEVVTVEAVREIVIGKSPIGAPIKELTIRARVSYADLDLTTATGAATLEKRVRDSATSSCKEIKVDVPVEGWTVDRCIREATEGAMVQVN
Ga0066401_1077372	Ga0066401_10773721	F066900	MIKYQTLPDMLDDSASGDGAIVYLEGEGAEKALKLSELRRR
Ga0066401_1081523	Ga0066401_10815231	F016989	MLTRDKLTIVQWQAVRNTPHHVIIAVSSSGGSAFDEMLERSAGLQGIVDASHSTHPLVSEIGGGTHIMQAQDDVRKWFYTLDEGHRTPDKLQEKALETARHALEALGTHGSAEDLMHYGEFVLSLATRVARAAREGDLMGIGGELVSEKERKFIERLDQLIQERRTR*
Ga0066401_1091034	Ga0066401_10910341	F033105	MEPRRPIREPTYHWPGGPTADDDPTPIESALAALKIGAILAAAITIAFIYLGTYAGIVAGQVESTIIVLAAFVSPSLIAAGRTAW
Ga0066401_1099044	Ga0066401_10990441	F082950	MASMLRSTSASVVAQEQTLMRIAARPCQRLPPHQQVPSAWSSS
Ga0066401_1109096	Ga0066401_11090961	F000982	MPSYRSTSRGRRLLVHHRLRGRAYPTLPYWERLHLMLLEEAEKRGKTPPPAPLVHGLESEPTQADRMERLDEQVAWADRNQLLH