3300026352: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026352
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0101408 | Ga0210107
• Sample Name: Wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - White_ThreeSqC_D2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 142362338
• Sequencing Scaffolds: 21
• Novel Protein Genes: 22
• Associated Families: 21

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	8
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	2
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium RIFCSPLOWO2_02_FULL_53_8	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Peregrinibacteria → Candidatus Peribacteria → Candidatus Peribacterales → Candidatus Peribacteraceae → unclassified Candidatus Peribacteraceae → Candidatus Peribacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylocystaceae → Methylosinus → unclassified Methylosinus → Methylosinus sp. C49	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales 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?
F009170	Metagenome / Metatranscriptome	322	Y
F009304	Metagenome	320	Y
F026445	Metagenome / Metatranscriptome	198	Y
F029294	Metagenome	189	Y
F034771	Metagenome / Metatranscriptome	174	Y
F036294	Metagenome / Metatranscriptome	170	Y
F037736	Metagenome / Metatranscriptome	167	Y
F048676	Metagenome / Metatranscriptome	148	Y
F055469	Metagenome / Metatranscriptome	138	Y
F056621	Metagenome	137	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210107_1008458	Not Available	1495
Ga0210107_1009562	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1411
Ga0210107_1020298	Not Available	989
Ga0210107_1021761	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	958
Ga0210107_1022612	All Organisms → cellular organisms → Bacteria	942
Ga0210107_1022627	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium RIFCSPLOWO2_02_FULL_53_8	941
Ga0210107_1023676	All Organisms → cellular organisms → Bacteria	922
Ga0210107_1024678	Not Available	905
Ga0210107_1028247	Not Available	849
Ga0210107_1029148	Not Available	837

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210107_1008458	Ga0210107_10084581	F037736	VPYRVQLDGLQILWLLANPLWTHGIGESRSKTITGWLLMGAADANHIWWLNTNPFTGLLLHLNSYRILHLPCGLLNMLCFLLLCHRQRNDNY
Ga0210107_1009562	Ga0210107_10095621	F026445	VNIDQAKPKRQKRTITLHLGNTLAEYEATYLTEAGLKALIREVEIADSLNWGCLATEHEAGCPRQLHFTHHDSYTRWAKHFNGGQSRVVIPRVRCLDCGAVFSVQPSFIIRYKRYETDAVEKLMTLLFITEDSYRMAGISQSLALDKQQAGTWVALETQQAHAIQPMALWRLVQWLGQLSPAQLNLALGVEPPQTIIEDEKHATECGQKSYIPLVYAPKEALIWWVDYLHGVSEAELTASLERFKAISDRLADITGATVDGWEAAQNALRATFEGITLVECHFHALLKLGQHLATYKRQREQAGQPLSEVEETNIRAAFWRVLKATTPDQYQQALDQLPEAFDQAPLASRKQSLVEKQALFQAWTSDDRLVAVTTALDQCLKFLNRKLDNMQTFHSHQSGLATVNAWAITRNCWRFLKGAKRAGLSP
Ga0210107_1020298	Ga0210107_10202982	F029294	MTQETGETRDAIIEADNKMLQDILNANSSRTEKYWIVLFAKPSKRSVDGKPTLIKHMKAYPKRPSSQVGMLIGEVDNKKGSVEWEINMPQAPMDFNALGALGAKASRDVVTETTTIPQAYITK
Ga0210107_1021761	Ga0210107_10217611	F056621	LNDKERFALAERIQKWIQEQNPYLRLIKRRDEIEKKLKEKNENRKS
Ga0210107_1022612	Ga0210107_10226122	F078289	PKMRELGVSQEVIQYFISNQTSSVSSEDVIKMKQSGLKNDDIMSAIKSDLYRPEQKSTSMKEAELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNMTKQYTNESQRTQYPTEGATFPKPDNYGYDPLNGRFLLLVKPQNQ
Ga0210107_1022627	Ga0210107_10226271	F055469	MLKRTVVILAAAAFFWGTVPTQTAQARDDIWDLMNPSWWADKMFDNDDDWRHYRHYAYNPYWGGPYAQRPRVIVIQ
Ga0210107_1023676	Ga0210107_10236761	F009304	MSPRRTIAVARKEFLHIRRDPRSLGMALASIQSRREFLRPAVQAVLDAIRVIVNQKDKTVPVLMKQLALSQDEAGYVYDALRSGWALDGRPTAEAIKLDAELSQRSLGLKELPRPGQTYDFSLLDEIVAGKR
Ga0210107_1024678	Ga0210107_10246781	F105216	AAACSDEAPKPWKAAEMRKLSEQFGHIAEAYAVVDICLPMIDADQDAKRSVIAKIEIRRYSQLSRINTEAEFANFLAYHRQTGGTDEQAAALDQIYRESYETAARHLTSVDNCAETVSDYANTILQTRVEPVP
Ga0210107_1028247	Ga0210107_10282471	F073570	MNESINQIVGILNTTFHQMYQNRVPVGSLTDAQVDNKKTSHKYTIENDLIVYEKYDRHGKLISRVPWSPKPVAEKA
Ga0210107_1029148	Ga0210107_10291481	F078289	MLIIVVFPLYGFNSLVRHEDIPKMRELGISQEVIQYIISNQTSSVSSEDVIKMKQSGLNNNDIMSAIKSDLYRPEQKSTSMKEVELIAKLKESGMSDEAVLQFIQTVKSTRRVDSDGNVTKQYTNESQRTQYPTTGATFPKLDNYGYDPSNGRFLFFIKPQNQE
Ga0210107_1030915	Ga0210107_10309152	F076109	MGVLFNILFVIAVIATIICLCVFLGSLFNLFKKNEMLDIEDV
Ga0210107_1032724	Ga0210107_10327241	F070131	MMGKMLTKIGIIGVFAFCFLLQVDLAGGDNRAYGQNKQKSNVPMEIELHFSSTPMLNEYTVLNVEIRALKDAPNTLIEIKIPSDGFELISGSTQHHEDLSSGSTTLYQLGVLPVALGQYKIAASAISGETDYIFGKREELYVNIGEGFSELSTSSFIPEIADNRSRAVKIGNLSEPPTRVLPDHKPVEGQEVSYLAAPGPGQIEVRGYWFYQDKSGINRPLRDAMVEIWDADLSGDTLLDTTYTNN
Ga0210107_1034077	Ga0210107_10340771	F048676	YSHLCGTASDAIDAVKLESPQGFKLLKFKITEYLKNIIIVTISKI
Ga0210107_1037299	Ga0210107_10372992	F036294	VTVTDRGSSEEAIVGVKPVADEDAVTYPRVKLSESDREVGAEGRHM
Ga0210107_1038421	Ga0210107_10384212	F090795	SGKVTRGSANIAWMPSEFSYVRLEYSHAKADAGVHPTDDRLTLQMSTRIGHHPAHAY
Ga0210107_1042945	Ga0210107_10429451	F099323	LATPTDVQLKNNQHPMNKILGFWRKFKAFLGHRLILELAIIGSFIAFTINPGSLGDIMRICGAFFLFNVLFGNYRIGDVTEGHLVVLGIFLIMLLINAFMPDEMIHRRSFRYFLALPGMMLAIHCLSKRTKPDSKNLVLYCSIAVLALTIQFVAYHTVERVVNSGGLESYGLSGNMHHFGSFAGLILPVLFYFSTQIKGWLRLLCVAGVIAAFYLLWESSSRIAWFAFFSSIL
Ga0210107_1048517	Ga0210107_10485171	F034771	MPRTRPQKLATLDVADEVARRVPGYKGYQDLAQCRDDDRRFRSSIAEYLNSEAHRLERIESHQLGDDYTDLLEEVDTGARKLEYLADSIAMPTTPKGELPSDQAVDELGGLDARIVDELEPLHRVVHELEKAYTHDERFEMNLSELRGITERIADFIEQRNVALAK
Ga0210107_1049637	Ga0210107_10496372	F062568	MPGDCITPAEISDLAQKDTQRLVGSIAKALAANAPFMNVIGGGVFPSGVSDEIKSTVQMQAAPGDSLAVPTFECDTDVCGTVGLQDLTDAVNFTTRLETKRGFGPRICVKKGYAAFRGSYMAAEDSLKKLIVQY
Ga0210107_1068360	Ga0210107_10683602	F059979	MKSFFLILAQLSLVTLVYVFAYRAGYRSAQSKAVSVVKKFADPVACLLDSLSETIDESIS
Ga0210107_1069673	Ga0210107_10696731	F099818	MGLERRGRVIVTGLGPTGHAGRSPLVQWKAAAFVRWQEPDDARVSSPDVRPAKAGM
Ga0210107_1074131	Ga0210107_10741311	F103291	VILQNFLGWLKSKEDYDIKNALASTIIAFIVGITIIGPQIEAIQDQMLSELSELTIFASLIASIAGFDVLTKNVFKIANSKIHLQNKPI
Ga0210107_1085883	Ga0210107_10858831	F009170	QTERRLLELGQPIPALGRQAQQVLEQANELTTGQRERLTGELTTALHAQEQIRHQSQRLTQGKKLRQCKIVNAYDPTIAPILKGKSNCPTQFGRKPGIMAEPATGFLFAALVPAGNPSDVSYVVPLLDKVQGAIQRVTTTPKRQVHSVAGDLGINDATLRHTLHARGILTV