3300026030: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_ThreeSqA_D1_rd (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026030
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116073 | Ga0208908
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_ThreeSqA_D1_rd (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 64803763
• Sequencing Scaffolds: 12
• Novel Protein Genes: 12
• Associated Families: 12

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Thermomicrobiales → unclassified Thermomicrobiales → Thermomicrobiales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
Not Available	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	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: Fairfield, San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.197227
  • Long. (^o): -122.010124
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F004591	Metagenome / Metatranscriptome	432	Y
F005672	Metagenome	393	Y
F016021	Metagenome / Metatranscriptome	250	Y
F018371	Metagenome / Metatranscriptome	235	Y
F062893	Metagenome / Metatranscriptome	130	Y
F065699	Metagenome / Metatranscriptome	127	Y
F070315	Metagenome	123	Y
F073725	Metagenome / Metatranscriptome	120	N
F081923	Metagenome / Metatranscriptome	114	N
F084294	Metagenome / Metatranscriptome	112	N
F087396	Metagenome / Metatranscriptome	110	Y
F097616	Metagenome / Metatranscriptome	104	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208908_1003264	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Thermomicrobiales → unclassified Thermomicrobiales → Thermomicrobiales bacterium	1463
Ga0208908_1005069	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1182
Ga0208908_1006737	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium	1034
Ga0208908_1008099	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	946
Ga0208908_1008197	Not Available	941
Ga0208908_1013860	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	741
Ga0208908_1019349	Not Available	635
Ga0208908_1020535	Not Available	617
Ga0208908_1021301	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	607
Ga0208908_1023343	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	582
Ga0208908_1023623	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	579
Ga0208908_1029439	Not Available	522

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208908_1003264	Ga0208908_10032644	F004591	VKNPPILISIIGFFAALAGLAWIVIGLRMLGFDWFGLLGDLQRFEQTGLWGWLAIIVGVLWLAAGLGLWALQPWAWAFAVVVAAIS
Ga0208908_1005069	Ga0208908_10050691	F097616	DSMNGPLLISLLPPEQTWDSPVAISGHTSFVAILLLIGFLLSLLLRHPGH
Ga0208908_1006737	Ga0208908_10067373	F087396	VLDEPTLVNSAVLSYLASVASLIERRTIGREELLHWLRSSMRQRSIGQSPRREYVLRYLHQHPP
Ga0208908_1008099	Ga0208908_10080991	F073725	VCSHLNSVGFGEPVGGRMKNCCVNGLYAELQSRFKTGTVLVVRSTGSSCGFSGDEGFRSLAVAEVKWTESKSVEGGICYATGLKYLMI
Ga0208908_1008197	Ga0208908_10081971	F065699	DRVWRDGDQREHWGRIPILAAVTEQYIGWALALGLVVGGALVWFAVGRLPRSGEEIPDEERAAEAAWISASIDERGGKAPADLVEEVLELHAEYLDRQSQELA
Ga0208908_1013860	Ga0208908_10138601	F081923	KHFFVMAILGAALAVACTMANTGSIQTSAEVTRQFEGLQVNPNYRYWYLNQENNPFGVIGLDREYGFAGGPVWRAVESDSPIFRKVVGLVESFPVASSLTTGYTIFEQQGRPIGVWYSSIGLGVTIDPATKTVSPATTTPWKSPF
Ga0208908_1019349	Ga0208908_10193491	F062893	PYGYRGALPAVLAALIVGLSGLALDKGHISAAPAGSIEIGTLTPVDVLPQVAALPAVIVSAPRLAMAAGPGRA
Ga0208908_1020535	Ga0208908_10205351	F005672	MTQLTHQLEHVSATAADWGLSRPKELGEDERKRPLSAVAIDLNGRLKECCKGAYSPKEAAREMNRHLTLFARYGVPNPKATQL
Ga0208908_1021301	Ga0208908_10213012	F070315	MATDTNGREGSSSGAMAKELDVSPAKVKRALVDLGIEADFVKAGCAYYYPERAEAVRKHLAKT
Ga0208908_1023343	Ga0208908_10233432	F016021	VASTGWTRENVRHALSVLRHGRNPAATVYDSIGADFVVALAPGWLNLGLWEGDGSDPEEAPVAVRRLVRTIAAELPIDGDVLDVGNGLAEQDPLIAEVARTRSLTALNITLSQLI
Ga0208908_1023623	Ga0208908_10236231	F084294	RCEVTSRWTEGLGAATPPNWVKEKGLYYCLVCRRERAMEQAVEKAGGNRVSTADRAKLRSAAVVDFEIARDPDRTEGEIAKAARASIGAVRKARKGRRPE
Ga0208908_1029439	Ga0208908_10294392	F018371	KRLTDMQEMEVHVNGPEGANRLYIYSGMAEVEIRGGLPHPRWSLEVVCFELGRKYDCDHGEEVVNIVATASMAGGRTDGVASFAGWQVFGCAGELDTDSGRVRMNIAAGARDTQAFLEQISFHINVLAKVNE