3300026039: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleB_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026039
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116083 | Ga0208288
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - MayberryNE_TuleB_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 77031072
• Sequencing Scaffolds: 7
• Novel Protein Genes: 7
• Associated Families: 7

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
Not Available	5
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanothrix sp.	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Wetlands → Unclassified → Natural And Restored Wetlands → Natural And Restored Wetland Microbial Communities From The San Francisco Bay, California, Usa, That Impact Long-Term Carbon Sequestration

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → wetland area → soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Antioch, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.052509
  • Long. (^o): -121.76873
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F040697	Metagenome / Metatranscriptome	161	Y
F050777	Metagenome / Metatranscriptome	145	N
F057298	Metagenome	136	Y
F069503	Metagenome	124	Y
F069913	Metagenome / Metatranscriptome	123	Y
F090409	Metagenome	108	Y
F104554	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208288_1000815	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	2405
Ga0208288_1009375	Not Available	911
Ga0208288_1016802	All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Methanomicrobia → Methanotrichales → Methanotrichaceae → Methanothrix → unclassified Methanothrix → Methanothrix sp.	709
Ga0208288_1017565	Not Available	696
Ga0208288_1017662	Not Available	694
Ga0208288_1023313	Not Available	615
Ga0208288_1024482	Not Available	602

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208288_1000815	Ga0208288_10008152	F069913	MTIEEYNLLEQEFSTSETDIKTFLLTKGVSLHKYYYWKRKSRDLQEASSQSEGQFLPINVLCGGSIKPGKRGKNLKQPFISQGEIEIELRTPSGAELRIRGMMDSLMVSTIIASSGGRRN
Ga0208288_1009375	Ga0208288_10093752	F069503	MDATRLRFTLRPLFKGAYTQIRLQGPVATVPQPREVRRLMALLWLWHGRPLDVVLCADVTSTGACWLEIWEDVLGRVPGHHLDMRYLQLPKTLVHGARP
Ga0208288_1016802	Ga0208288_10168022	F040697	MRLTENLEECEIIDDILREAAEGYGDLTAAALVHKVDVKYLQTRVVELRDLRAAWIS
Ga0208288_1017565	Ga0208288_10175651	F057298	KNTSYKVQVDVDTDAIRNAYQIEEGAYVTTSSGVYTVWNGEWRKLYPQGGSESSLGWARYDDSTYTSSNKLALSDGVEVVLPNDADTIYRSHTGIDYYSDGKVLADFENDTYLMTIVFKYSAPNANQTYLEMHFEGGNGTPYDRIRDTVTFAKGNDVAHDYHGIFQYYADENFVNSGSEWKITSIGGGSFIWDIIFFIQKVQNYG
Ga0208288_1017662	Ga0208288_10176621	F050777	MEDDIIYEKAVEIQNPGRLYFAIKAMRKSPVKISFDMGDLNLTSGAVSSLVSIEGKLPEEVQAMQWFVPLEDLKILQDLIPQDTYYWENRALDLEWQCDLFVDSTIEEKTPLESLEQEDEHRDQLLVANRDYRELQMALDDCSAHIPQVLFSIYPDRLNFAVNCSEHDEIVGTMIQLRSQKDK
Ga0208288_1023313	Ga0208288_10233131	F090409	LAKGRSNGGGRMRKEFAGTLLTSFGMMGTVHFNLEMPGSIIGDTNQFLEEAKGKRVLVTVETQEVAA
Ga0208288_1024482	Ga0208288_10244822	F104554	MSTFPEIESELNRKRVVAEMDALRLEEEAVKGKTLLDKNLALLGNLMVSAGEKLRRRYRSSQEANSVKLVNKVV