3300026042: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqB_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026042
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116107 | Ga0208538
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqB_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 38900910
• Sequencing Scaffolds: 6
• Novel Protein Genes: 6
• Associated Families: 6

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2

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: Fairfield, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.209766
  • Long. (^o): -122.033424
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F007558	Metagenome / Metatranscriptome	349	Y
F014394	Metagenome / Metatranscriptome	263	Y
F024001	Metagenome / Metatranscriptome	208	Y
F034114	Metagenome / Metatranscriptome	175	Y
F073725	Metagenome / Metatranscriptome	120	N
F081923	Metagenome / Metatranscriptome	114	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208538_1000020	Not Available	3056
Ga0208538_1002358	All Organisms → cellular organisms → Bacteria	860
Ga0208538_1003239	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	778
Ga0208538_1003651	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	751
Ga0208538_1007167	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	605
Ga0208538_1011454	All Organisms → cellular organisms → Bacteria	518

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208538_1000020	Ga0208538_10000204	F034114	VPVIMRETSVAAGAVNENLLAGSAFEFARQNSLVSIGINQSATGGFATINSGADVVAEEFAPPINTVYPIIPDGMYFSDVAAAGDRLVIRYRNPTGGALTVRVVCQVTPL
Ga0208538_1002358	Ga0208538_10023582	F073725	MEKRATRRYRISTSIVCSYLNSVDFGKPVDGRMRNCCVNGLYAELGTHYKAGTVLVVRTTGSSCGYSNEKGFRLLAVAEVKWSRPRSIEGGACYATGLKYLML
Ga0208538_1003239	Ga0208538_10032391	F014394	MRAGSRFLATLFAAVVWIYAGMSVASRPVAQEAITPSVLDVAASCAAAVMD
Ga0208538_1003651	Ga0208538_10036511	F007558	MQTIAEIKMLLLEILESAFQSGDVNATQQMGVNMTNAVKREGVVIIQNQNVEVYARIMPLMVKTLKLCDAVESSWRGQATIELEPQQKQLPPPADDDDPDPIEACCSWLYDNHIQWQDMQDLMKARYLAYVIGRFKTKTEAAKWLGVGSTYLCKLSKTTLHAVSQN
Ga0208538_1007167	Ga0208538_10071671	F081923	MKRLIVNISSAIRPVMHRKHFFVMAILGAALAVACTMANTGSIQTSAEVTRQFEGLQVNPNYRYWYLNQENNPFGVIGLDREYGFAGGPVWRAVESDSPIFRKVVGLVESFPVASSLTTGYTIFEQQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208538_1011454	Ga0208538_10114541	F024001	AKGSRKNKLAILGVEAPGRQGAKTQEYLDIPSFCNAAGRDALASKMLSYF