3300026060: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleA_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026060
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116124 | Ga0208295
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleA_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 42540038
• 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
All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon ADurb.BinA087	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	1
Not Available	3

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: Twitchell Island, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.107521
  • Long. (^o): -121.649681
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F028541	Metagenome / Metatranscriptome	191	Y
F032323	Metagenome	180	Y
F053838	Metagenome / Metatranscriptome	140	Y
F056356	Metagenome	137	Y
F063193	Metagenome / Metatranscriptome	130	N
F077462	Metagenome / Metatranscriptome	117	Y
F105433	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208295_1002027	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1015
Ga0208295_1002954	All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon ADurb.BinA087	895
Ga0208295_1003485	All Organisms → cellular organisms → Bacteria	849
Ga0208295_1004339	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	792
Ga0208295_1006925	Not Available	676
Ga0208295_1007406	Not Available	661
Ga0208295_1008831	Not Available	622

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208295_1002027	Ga0208295_10020272	F056356	MKKITPGLIILILALLASCGRDLEQAKRYSDIKSETDSLITQAKLIINEQKAMTDSLTEIRDDIYKNKSQKYKLSELDKEVTKNAEIKTNIETVRKHLESIKKFAENGERATKRLLYFKRKYITYATEIQVHDENIMIQEITDGLSAKKYLSKYLPKEKK
Ga0208295_1002954	Ga0208295_10029542	F105433	MPENTSSTRIEEASDSLNTGKFYILLLFVSLIGVIGALMMIAFIFLQDILTAILWKDIPVDSLTPVFNPGILVICLAGGLGAGVI
Ga0208295_1003485	Ga0208295_10034852	F028541	MDERDRRKLIEKLKTSKKSEERDQILWYLAGQDKTTRGKPSKPEPVAAGAPSASPTQDRMQIRLPVGRLGGVGSITALLFVVYGMIAIIPAVMKILQGETDGEEIRQIITGG
Ga0208295_1004339	Ga0208295_10043392	F077462	VKQRLSVGVTALLFLFACAGFACADVSKELKKISEEREKSVGYAKIAKVTFKKQQKKLTQAMLYYTDAKSIGNPMIQHLQTSLTSRSMKESQVREMLSDDVKRLVQVNEKFRAFIESGETSNRALPGLAAVAGMAGPITDACVNLWKEYKDADKKKVDNMVQVLDGYKWEDWDKL
Ga0208295_1006925	Ga0208295_10069251	F053838	NDTTHGKTLMRRDFWPFVVPLVADHLCASAKTAGRADFLLGMERNLPAAPAGDVGELVHLAH
Ga0208295_1007406	Ga0208295_10074061	F063193	MKKNLLLGFLILFVLSTTAFAGLSDPKKENEKPAVSRENKLSDEEIGRMNRRAEIDNISNSNLLNNEKSSSPKDLKTTNQIIVESGHHRHGGYYMYGGGLLLVIILVIILV
Ga0208295_1008831	Ga0208295_10088312	F032323	MSYFVFRMKNDSELKSRVLYAILSQNPSYTVKEYKEEPDPADNNYHIISVTAFEKGPYRLIRKILAEFIKNNEITCLNGPSSDLLQ