3300026050: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqA_D1 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026050
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0111376 | Gp0116106 | Ga0208293
• Sample Name: Natural and restored wetland microbial communities from the San Francisco Bay, California, USA, that impact long-term carbon sequestration - RushMan_ThreeSqA_D1 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 48306687
• Sequencing Scaffolds: 15
• Novel Protein Genes: 16
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	3
Not Available	5

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): 38.209766
  • Long. (^o): -122.033424
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001489	Metagenome / Metatranscriptome	686	Y
F005988	Metagenome / Metatranscriptome	384	N
F009539	Metagenome / Metatranscriptome	316	Y
F011513	Metagenome / Metatranscriptome	290	Y
F018543	Metagenome / Metatranscriptome	234	Y
F025366	Metagenome / Metatranscriptome	202	Y
F027322	Metagenome / Metatranscriptome	195	Y
F029547	Metagenome / Metatranscriptome	188	Y
F036220	Metagenome / Metatranscriptome	170	Y
F046228	Metagenome / Metatranscriptome	151	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0208293_1000150	All Organisms → cellular organisms → Bacteria → Proteobacteria	2032
Ga0208293_1000679	All Organisms → cellular organisms → Bacteria	1489
Ga0208293_1002531	All Organisms → cellular organisms → Bacteria	1037
Ga0208293_1003683	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	921
Ga0208293_1005163	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	819
Ga0208293_1006608	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	747
Ga0208293_1007476	Not Available	717
Ga0208293_1007884	All Organisms → cellular organisms → Bacteria	702
Ga0208293_1013783	Not Available	569
Ga0208293_1014148	Not Available	563

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0208293_1000150	Ga0208293_10001502	F086537	MSEDGGGEQLAQWLKEAGRRTQAAKAPPATADSDESYNSPASLHHYLEELAGRKLESHAEVLRYLREVAGAQPEGLRAQERRRMVREVSLLVLLAISYLHFYYWEVQLQIAALQSVGVFIPAPPARPHKISS
Ga0208293_1000679	Ga0208293_10006792	F009539	VRRSGGSLSVLLFALAVLAAIVGISFALGYILGKLLL
Ga0208293_1002531	Ga0208293_10025311	F025366	GLALLMLASTVTPREAGSNVEAWFIYFGMERVPPWATDKSIDTWVFWMAFVGAAVWGARLYTRSNIVEGKLSVLIREDEPWVQLDPGLDRWQAAQSGGSWYRYRIALVNSGDSTLRNVQVKLASLEKKPQNFHAIGSHLQLRLDRAGIMNFDLYPTKDPQWRDAMFVDVFSFCGGPRGCSFLRVTSLPEEANPYIPVDRYDVKIVATSESGEMAIADVAFIPHPGQMPDFRLRNMQSFPG
Ga0208293_1003683	Ga0208293_10036832	F027322	VKRPAGITVLAIIFAAAGLSYMMLGFQMTTAVTFGPLPSGQGTWIWGWLIVLTGLAFWAGGLAAWRLAPWGWMLGHVLAILGIIEAVFALLGTGNLSYALASTAFPFIVLWYLNRPSVKKAFGLVEE
Ga0208293_1005163	Ga0208293_10051631	F047144	RLVASGVANVPRELDPADPLAGLDGNPQTGWKRDLLAALVERALTALVR
Ga0208293_1006608	Ga0208293_10066081	F069221	FGGWAVIRFIRRYHVRGIWRSPTPQESSTYIRLLLIVLLLDIGSKALFFRWDRPEKVEILPNFGLHSVFHVTDFETFHVYLLLYFVYCFLLGPLFFRFANRALDRLWLGSAPFALGGALALSLERLFFGGVHNSFYFAGPLMWICPPCASPSFSSYAWTPADLFVHAAILPFIILLLSYFPPARPSVAEINGR
Ga0208293_1007476	Ga0208293_10074763	F011513	ISRSDAAHNASVSSIDAARVHDFRIMVAHGFRSLPIKQL
Ga0208293_1007624	Ga0208293_10076241	F084199	MSTTSSSRRKPRTTASSRFGLVLVAAAALAACGGRPRETFVTYFNGDHGVSLRHPAGWRTDQAEQEGVWYRYFLAPPAGPQNRSPVSVTLLAGPAAGSLDEYAERYLAGHNVVAATPEERQGVTGKSWVFAASDGATRYRLLLFAKDDKVVGLYAQGDAAGFEQQAKALDEVWSSLTFERPERYPRREWGAQKTSLG
Ga0208293_1007884	Ga0208293_10078841	F001489	AHFEMDCEWRYFLAEHAGTEAGHGWGYIRQANAVYPGRDYARPDPEFEKQYGLTPRTEHHAIMKRDFLSYIFSGNLWPYGHVTAASIQSIEITTPKLLDFEERVVHAEERSHHDAILQKIHDYVWELIDIWGEAPIRKRIGEIERIALNSRPRTIFDPPRREFLRKYFKVPLENVRRFPAWREYLYLNVLGFPPEPVYIGNWPAEIPQPKIGA
Ga0208293_1013783	Ga0208293_10137831	F018543	MILENMWIEPSNQGAAANRRPALQSDGSDNLSATLAADGAFPAAVAELDR
Ga0208293_1014148	Ga0208293_10141481	F091998	DVAPATHGALRCAPCSGARSTLPRRWRYGMHPQAVGSQIVALGRVELRIGEALRLEMVKTDTESDDMVHLQYYVSTESGGWALWLSCPRNDVAALEAPLQALTPPSVG
Ga0208293_1014333	Ga0208293_10143331	F005988	GTQALMESANMRIRTYNMQDEQFAFHRALRSEEVRIQFRGDALDLSEFENVEVSPGEITIIPLGISHSVISIPPEDEDFLRLNFYSKVRWRVPIDPTRHYFDSKFEISTTVHKQAEWREKLAAGR
Ga0208293_1014533	Ga0208293_10145332	F036220	VNLGRRRRVVVETPSVVLRLSEASIERLEADEPETAAALHRWLASTLAVRLTAADRAYSASMD
Ga0208293_1014918	Ga0208293_10149181	F046228	MKRLRSVLSPMVTTAGILALSGAVLAQSPSESHRAASARAHEIMSSAPCPLPKVTKEKITEDEGRDLAQAFADKNMSGFRVVRPLSYGGGYTTMCYQTVNAAPARPLVLYSVEYSMDLKNPAGETRNLCVDQYGTVSEFCSDFGFAGATGPAGPMGPS
Ga0208293_1015698	Ga0208293_10156981	F070315	IRQEESMAKDASGREGFSTGAMAKELEVSPATVKRALTELQIEPDFVKAGCAYYYVERTSAVKKAIKV
Ga0208293_1016072	Ga0208293_10160722	F029547	YKELDIRGAYGATHRQYRITMDYLDRKQELLAAVVTHRWPLEQIAEAFETIRSGSGLKMVIVP