3300028528: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.376 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300028528
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225720 | Ga0210336
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.376 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 96167125
• Sequencing Scaffolds: 12
• Novel Protein Genes: 14
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	8
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Electrothrix → Candidatus Electrothrix marina	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): estuarine biome → estuary → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Washington
• Coordinates
  • Lat. (^o): 46.302
  • Long. (^o): -123.036
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F009271	Metagenome / Metatranscriptome	320	Y
F011154	Metagenome / Metatranscriptome	294	Y
F027700	Metagenome / Metatranscriptome	193	Y
F036294	Metagenome / Metatranscriptome	170	Y
F053305	Metagenome / Metatranscriptome	141	Y
F056298	Metagenome / Metatranscriptome	137	Y
F059103	Metagenome / Metatranscriptome	134	Y
F060937	Metagenome / Metatranscriptome	132	Y
F076890	Metagenome / Metatranscriptome	117	N
F087396	Metagenome / Metatranscriptome	110	Y
F092076	Metagenome / Metatranscriptome	107	Y
F098390	Metagenome / Metatranscriptome	103	Y
F105215	Metagenome / Metatranscriptome	100	Y
F105482	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210336_1004245	Not Available	953
Ga0210336_1005227	Not Available	895
Ga0210336_1007870	Not Available	795
Ga0210336_1014132	Not Available	670
Ga0210336_1015764	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	650
Ga0210336_1022170	Not Available	590
Ga0210336_1024586	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	574
Ga0210336_1025420	All Organisms → cellular organisms → Bacteria	568
Ga0210336_1026203	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Electrothrix → Candidatus Electrothrix marina	563
Ga0210336_1032911	Not Available	528
Ga0210336_1038642	Not Available	505
Ga0210336_1040058	Not Available	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210336_1004245	Ga0210336_10042451	F105215	MYIKTDPRNSEGSSRTLLFHQDPDIRLDAALQLGGDTNRIADQRLALEALTTALEDPCSTVQEAVLQSLMRMSVKNG
Ga0210336_1005227	Ga0210336_10052271	F009271	MIRPMTSNVSALSGIVANGHQAIHFVSSAPSKIPYGGFSPVRLQTRLTPRPPSRTAPRPLIGRHCSYLHSRRFIRSGSCDQAAPRTSDQNRESSGPWLPGRLCCPARSSLTMATSAPLSAPERLMDYSVRLRVQPANRRGSPIYSASPFTPFRRPYSGGPGECAQQCLPRRFCLRRICTGSATTGPTIPDRVGRVTKLQRSLYATACECRLPCSGQDVYDRACVGRVTPIPHVGYHWMVHCHLPSPVFHRLDWQPYGLRADSRGSTQIRRLRTKEGGVTSGRS
Ga0210336_1007870	Ga0210336_10078701	F060937	NRGAGSGRKIEECTAGIIPGDWGTAGPGWLVPPLGSRIARFEERRQYSPAPLAGIATRHNAIEELGGEER
Ga0210336_1014132	Ga0210336_10141321	F098390	MYHGKVTSGPNETQDKDGKNLCNRWQVVYDDGDVEEMTASEIDAWKMPPKEVRAATKKVRATGPSGDHIEELRDNVPKPIKDASAPTHRRRTTKRQQQSAEAARMHFLESNPYLPMDSLSMYEAATCRIHLNDNDPYDELLQNVDEVETLLQDPEVITAIYKLLDPDSDLEDLKLRALQSEAITPEEQALPRFSRRALQKLPTWDLWHKNEIEQL
Ga0210336_1015764	Ga0210336_10157641	F092076	DKLQEIIFTQASGTPTTVTMMDHIQNVMNDPDFDAKYNSIIVLEEHTHIAGVPTEKIETIRRVLDGYAQQRTGRNWAVVAPNERLEAFVKLNLELISPVIFNIRIFRSEEDALNWIKRRQPPLC
Ga0210336_1022170	Ga0210336_10221702	F053305	MLKKSVSMALMALFVFSFIAVATVSADETQKITGTVMSVNVETGEVIVKDDAGEMKSLMADPKAEGAVDLKMLKEGDPVSVESDSNGVIKSLKAGE
Ga0210336_1024586	Ga0210336_10245862	F059103	MSAPDPRDFVLRFAPLDARTAAWMLDFCGHLQQEIWRAYGDEIEALWAATDPEQPIYGPLQPPTPSRKRR
Ga0210336_1025420	Ga0210336_10254201	F105482	MDLIHPNSRDEVVRAIRDANSTNKRVLVIGGRRHIDKGNETEVDAEM
Ga0210336_1026203	Ga0210336_10262031	F036294	MDRGSSDEAKVGVKLIAEEDAVTYLRVKLSESDKDVGAEGWN
Ga0210336_1032911	Ga0210336_10329111	F027700	YTKSALPPMPLSDSTKEMSLEQADKAGISMIEDHPLNSPSHELKLHQLSARQERLLWHQRLGHCGDEQLSKAHEYCDGVPKISSKAKSVVDECHVCIAANMKARERGDGITRTATISGQGLSIDFSFAGQHSKNALNPERMRINDYMGLNGETCYLLLYDHATERLSGVCKQSKA
Ga0210336_1033888	Ga0210336_10338882	F076890	MIGTRSVAAMLVAMSALGTSACSTLEVDDYCRYSETRSIRTADPESLALVLGVQAGRTRQTPFVVIRSLSESRPGASVTLHTTPAAHPMPMGLDESRCARVDWSTYTLAVDPDEWNAFWQDDRNSPFEIGIAFLEDF
Ga0210336_1038642	Ga0210336_10386422	F087396	SPSVEKPQTMDESPSVEKPQTMDESPSVDTSPALLEHLTLNLDGFVLDERAVVQSRILPYVRMVASVLERRTISREELIAALLRSMRQRSMARAPRREYVLRYLNQHPP
Ga0210336_1039502	Ga0210336_10395021	F056298	MRARDRGDGDTRTATIAGQGLSIDFSFAGQTSKNSTDPDRMRINDYMGLHGETCYLLVYDHATEQLEGVCKQSKAPPVAWLRRWLRKNVDKDVKNRYVFMDQGGELYKSKAIRDLFEKEFDYDIRVTGTAAHHQNGLVERANQTVDKAIRALLIGAGPEVKFWPYVF
Ga0210336_1040058	Ga0210336_10400581	F011154	MRSDEKPLRIESSRPGRFRAWVNRSYPEGIRLLLCISTGGRLWRPPEGGLPNERRRKAGQSERPNREGHAASAGPVKTFQAVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS