3300026031: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_ThreeSqA_D2_rd (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026031
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116074 | Ga0208909
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - Joice_ThreeSqA_D2_rd (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 82394504
• Sequencing Scaffolds: 11
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
Not Available	5
All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	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?
F011594	Metagenome	289	Y
F017668	Metagenome	239	Y
F023130	Metagenome / Metatranscriptome	211	Y
F024001	Metagenome / Metatranscriptome	208	Y
F026037	Metagenome / Metatranscriptome	199	Y
F035352	Metagenome / Metatranscriptome	172	Y
F069475	Metagenome / Metatranscriptome	124	Y
F073725	Metagenome / Metatranscriptome	120	N
F077315	Metagenome / Metatranscriptome	117	Y
F085674	Metagenome / Metatranscriptome	111	Y
F089490	Metagenome / Metatranscriptome	109	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208909_1000401	All Organisms → cellular organisms → Bacteria → Proteobacteria	7811
Ga0208909_1002821	All Organisms → cellular organisms → Bacteria → Proteobacteria	2240
Ga0208909_1004025	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1789
Ga0208909_1007192	Not Available	1244
Ga0208909_1007618	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	1201
Ga0208909_1010507	All Organisms → cellular organisms → Archaea → TACK group → Candidatus Bathyarchaeota → unclassified Candidatus Bathyarchaeota → Candidatus Bathyarchaeota archaeon	986
Ga0208909_1012299	Not Available	898
Ga0208909_1027517	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	580
Ga0208909_1027945	Not Available	575
Ga0208909_1030628	Not Available	548
Ga0208909_1034024	Not Available	520

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208909_1000401	Ga0208909_10004013	F011594	LLKQREGGGGGGMTFGELENLILLADRMIVSCAPRKADYGRGYQSGIKYQFYNPQTESLPDHYLIAEMARSNGCRNVHAYARGYHDGCKGLKPEYSD
Ga0208909_1002821	Ga0208909_10028213	F023130	MTRRFRVPATAFLLSSIMAMTGSVSQDAMAGIVLMSQVPGASIVQGEGPAKTRSAENVAPHPQRGVSARNWTRGIVLLLIILLILWLIYRTFTGWKPMIS
Ga0208909_1004025	Ga0208909_10040251	F077315	MVIRKASTLYLSRFACCQVWALLLLLGLLIPSQAAEALKPDTLPQAQATLERLEKQFATAQTVTAQELKTLRKEIATVRSSAQDCVQRAEPKIEILDSELAILQPAKPKDTQAKTAEETQPAEQPEAPVSPAIARQLQDLQSRKASLE
Ga0208909_1007192	Ga0208909_10071922	F085674	MPGEVMLVGIATIAIAIAGFTAITSALEPPGGSWSPAMRLRQRSIVSTSFNVGLESFAPLIAFAWLEELHSALVVASLVVAIYTTSVVLFRGRQFVRAGGMHTGVAGLTLFALGPTATLLFWANAIVFASLAIFALALLVQLLVAMISFYSLVSAASS
Ga0208909_1007618	Ga0208909_10076182	F035352	MPNYSKKPILSANDEEYTLLIEVSEEFWKQKNDRTLREKFGSPAEIVIRNHLLRRTLNLSMNPKIVLQGSKIKNALLLLKKDVDPNQENYTFNDVRMIMEIKNNSVGGKILENGKREDPNKVLRFRFNELEAKTKVRNFGVIVLSETLLPPKTPYKYRFKENAIGKENCKVFTLVARELYPRGGLYIKSNLTEMLQKGQMKKTGEFQ
Ga0208909_1010507	Ga0208909_10105072	F017668	MKMNKGRLYEELIPIEQLTYKGYNTSELANARIKQILDEVKKEMPPFTEKWVNTEYDNPDWKATCEAMNERTIAREKWFIKWFGEQK
Ga0208909_1012299	Ga0208909_10122993	F026037	VKPEKGARGMEEKDKVLQLLNAEMKVERQLERLEDVQTLTEIIRYYRQKRARSSEIALAIVKFVKEG
Ga0208909_1027517	Ga0208909_10275172	F073725	MEKRAARRHRIDSSIVCSHLNSVGFGEPVDGRMKNCCVNGLYAELQSRFRTGTVLVVRSTGSSCGFSGDEGFRSLAVAEVKWTESKSVEGGI
Ga0208909_1027945	Ga0208909_10279451	F089490	MTDDPDRASNSSDNDLSVYRLMKSEKFTLDHLTSGLVSFYRQTQVKRFGRLRAALGACEVSNNGGGSRHYLLNEFGQEYYGGTWID
Ga0208909_1030628	Ga0208909_10306282	F069475	AIAARPLIAALRDDQKQMALGLAQEMGLGPVLAALN
Ga0208909_1034024	Ga0208909_10340241	F024001	YRWWKKPSKGSRKNKFANLGVEAPGRQGAKTKEYLDIPSFCNMAGRDTSAPKM