3300026024: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026024
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101405 | Ga0210130
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 121982309
• Sequencing Scaffolds: 10
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	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 → Aquatic → Marine → 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): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: San Francisco Bay, California
• Coordinates
  • Lat. (^o): 38.131752
  • Long. (^o): -122.266335
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F021303	Metagenome / Metatranscriptome	219	Y
F025141	Metagenome / Metatranscriptome	203	Y
F045713	Metagenome / Metatranscriptome	152	Y
F076140	Metagenome	118	Y
F090405	Metagenome / Metatranscriptome	108	Y
F099324	Metagenome / Metatranscriptome	103	Y
F102142	Metagenome / Metatranscriptome	102	Y
F103291	Metagenome	101	Y
F105200	Metagenome / Metatranscriptome	100	Y
F105216	Metagenome / Metatranscriptome	100	Y
F105217	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210130_1000412	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	5607
Ga0210130_1003138	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → unclassified Flavobacteriales → Flavobacteriales bacterium	1669
Ga0210130_1006011	Not Available	1279
Ga0210130_1014514	Not Available	922
Ga0210130_1014718	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	917
Ga0210130_1016686	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → unclassified Desulfobulbaceae → Desulfobulbaceae bacterium	876
Ga0210130_1018144	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → unclassified Nitrosopumilus → Nitrosopumilus sp.	850
Ga0210130_1044719	Not Available	611
Ga0210130_1050517	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	585
Ga0210130_1067685	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	523

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210130_1000412	Ga0210130_10004125	F105217	MASNVNSNNERNSLIDSIQYRLFYAEINLDKIPTFIPLDIFPKDKIASEVAIDGFLFYANSALDLVFVEINKKLELGLPPNQINPENIMLNFNSKKSNDSKMMLEEFQKYFQKPTHEEKIISDKEFNDGLNRYGFDVIGFHAEYEARGQEKYQHFWNRASSRLWEIRNQQDLESYDSLLKNAGKRGKDEPRNYLRIKLADYNRPSVYWDSAHYENPKRYFTNVLSLVKQFIDRILEILKPLYPSDSSLAV
Ga0210130_1003138	Ga0210130_10031382	F103291	MEMFGLSPVVATLTIVSSGVILQNILGWLKSKEGYNVRSALASTIIAFVVGITIIGPQIEAIQNQMLSDLSELTIAASLIASIAGFDVLTKNAFRIANQKINLQNKPV
Ga0210130_1006011	Ga0210130_10060112	F102142	MTNKVTESNETVRDLLKASLVGILAVVITVIPFEQFVAQLAGLSYDEFRGGMPTLYLLPLFLIYAAIGLVLARMKQNLNIGKRGAFLILFAFYYLIVSILPDIEGLIYLPDFTFLSAMTSGLILAGAVVGLIFYLWKQDENPGAKPGEQIKSHFSSRSVLSWIWRFFLVWISFYIVTMILGIVATPFNGSYYEDPMNTLGMVVPSMGTFFAITQFRSLIYILVILPFIIFWNSSKRALFLYLALILIILYPLLGDGLAYFWPA
Ga0210130_1014514	Ga0210130_10145142	F045713	SQAQVMNGRIWEGSCSYLKCADGMIEGRFLFPTPNSPELLGALVGRLAQGVEVIICTEDDDDDD
Ga0210130_1014718	Ga0210130_10147182	F090405	MKAALAFVFAIGLLVPGIAASDPSDCGRLMYQITHYEDMVGRAEALGRDDWAAKTQRHVDLLETRLADRCPAFSARDEQQEAARQMALLLKMAATAAAI
Ga0210130_1016686	Ga0210130_10166861	F099324	VFRKVIFVIMLGWVLVLSGCAATDKGGNIEGEDYRSGSPPRGGYTRTNSHKVLVTEACNIEANNLAGASDFMADDRARRVYFSQCMLRNGYNAAGNYVGIPSK
Ga0210130_1018144	Ga0210130_10181441	F025141	IPYYMIQCDYCPRGFIETANGLAEKTFHELLHEPEVVNK
Ga0210130_1044719	Ga0210130_10447191	F105216	MPTSRSAALFCGLAIAAAACSDEAPKPWKAAEMRKLSEQFGHIAEAYAVVDICLPMIDADQDAKRSVIAKIEIRRYSQLSRINTEAEFANFLAYHRQTGGTDEQAAALDQIYRESYETAARHLTSVDNCAETVSDYANTILQTRVEPVP
Ga0210130_1050517	Ga0210130_10505171	F021303	MTERPISTDVSGLRATVLNHSSEFVELVYRDAPSEYRRLMTQQRFRRELALQNRFNHGKLFAYAEYVVFRKEFQDRFPDASPAACINAFSSLFLKNDISITNLVEFVEGPDHRGQLLLNQPPGPG
Ga0210130_1057791	Ga0210130_10577912	F105200	QPKAFTMDVMRGVRRGQRTRKIILWAFGLVGALFGLSGASMLAGPVSELFSFSLAMPAMQTMQATLFIVGAAAFYLWFMNDDFSLGD
Ga0210130_1067685	Ga0210130_10676852	F076140	MASTAKPVNLFLMTAERMLRCRWDGVSESVEILNAAMDGETVREVERDPANPQKLYAATLTEIHTSEDGGATWQWLPSGGIDHRDIWALAASC