3300026056: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026056
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116126 | Ga0208782
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - WestPond_TuleC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 40161979
• Sequencing Scaffolds: 7
• Novel Protein Genes: 7
• Associated Families: 7

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	3
All Organisms → cellular organisms → Bacteria → FCB group	2
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	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: 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?
F018557	Metagenome / Metatranscriptome	234	Y
F034114	Metagenome / Metatranscriptome	175	Y
F052017	Metagenome / Metatranscriptome	143	N
F052687	Metagenome	142	Y
F064862	Metagenome / Metatranscriptome	128	Y
F074658	Metagenome / Metatranscriptome	119	Y
F076224	Metagenome	118	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208782_1000088	Not Available	3256
Ga0208782_1000104	Not Available	3043
Ga0208782_1001439	All Organisms → cellular organisms → Bacteria → FCB group	1094
Ga0208782_1004098	Not Available	774
Ga0208782_1004248	All Organisms → cellular organisms → Archaea	764
Ga0208782_1009955	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → unclassified Syntrophaceae → Syntrophaceae bacterium PtaB.Bin038	573
Ga0208782_1012631	All Organisms → cellular organisms → Bacteria → FCB group	528

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208782_1000088	Ga0208782_10000886	F064862	GSAFEYARGRQALSCGVVAAATGSFFTLQAGADIIVEESAPMVLTTMPIVPDHMYYNDIMEPFDRLRLSVRNPTAGAIIHRAIALLTPV
Ga0208782_1000104	Ga0208782_10001045	F034114	MPMIMVETSVAAGASNPNLYTGSAFEFARARGVVSIGVAQSATGGFCTLQAGADIIAEEFSLPILTRFPIIPDEMYFTDVVEQGDRLVARVRNPTGGALTFRSVVQMSAGG
Ga0208782_1001439	Ga0208782_10014392	F052687	MIRFLTIIIILTALGGGIYYLLSMETVEDVKVTGKLQISQQFGSYVMASQKDDAPYYAVVEGKIKNNLGKPIKNVFIKYMIAGQETSATVFDLAPGQEINFNTSGVATSASNPEYDFVGLYYD
Ga0208782_1004098	Ga0208782_10040981	F074658	LLQPGLFYLRIQKSMREEFNLLIKSCATRTVPAAKTKSIGLQADARVVMVFASPLRQFYRDMTNPAHLSGPRHLDNFIVTNKSCPLTGTMQKRMPTLTLTATH
Ga0208782_1004248	Ga0208782_10042482	F018557	MTELKNGRPIFFPENLVLFGNLALFLWIVLDSVAFMLYNFTTGIVFFILTLILIYGVLHLLGCLRPCYNCIKCTHGMGRLAALYFGRRIFKDYKYNYKLPTAIFFTLYIGGFPAAFALYSTIVDFSAIKAAVFVALLVFTTYGALTWRPRKPKN
Ga0208782_1009955	Ga0208782_10099551	F052017	KDDVERFEGELGKLMVMKKALELALINPAIKDGQKQSYSQALLQCERTLREFRGALIAMRVGLARWAAKERIGQAA
Ga0208782_1012631	Ga0208782_10126311	F076224	KLAEKELKWAEREIRKNEEKIREYTINFKFDSTFINYAGTGSKHSFKVMVDSNICRVDIPDFKLPDQEIPEIAAINPLIEQATNNIHFYAYKIPKIEKSKSEIKIEYYNDDSVYSYVVNYNQLNIDSLVQANSGTDLYNLEKFKPLKPSDDTMLIKYQFNKDYYNRYYSDDEFKQQ