3300022373: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.180 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300022373
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225703 | Ga0210319
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.180 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 68319276
• Sequencing Scaffolds: 16
• Novel Protein Genes: 18
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1
All Organisms → cellular organisms → Eukaryota → Metamonada → Fornicata → Diplomonadida → Hexamitidae	1
Not Available	6
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Corethrophycidae → Corethrales → Corethraceae → Corethron → Corethron hystrix	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Stichotrichia → Urostylida → Pseudourostylidae → Pseudourostyla → Pseudourostyla cristata	2
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Phaeodactylaceae → Phaeodactylum → Phaeodactylum tricornutum	1
All Organisms → cellular organisms → Eukaryota → Sar	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): 46.27
  • Long. (^o): -123.946
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000344	Metagenome / Metatranscriptome	1257	Y
F000734	Metagenome / Metatranscriptome	915	Y
F001583	Metagenome / Metatranscriptome	668	Y
F004323	Metagenome / Metatranscriptome	443	Y
F008361	Metagenome / Metatranscriptome	334	Y
F012678	Metagenome / Metatranscriptome	278	Y
F021307	Metagenome / Metatranscriptome	219	Y
F027191	Metagenome / Metatranscriptome	195	Y
F038934	Metagenome / Metatranscriptome	164	Y
F042669	Metagenome / Metatranscriptome	157	Y
F045132	Metagenome / Metatranscriptome	153	Y
F054544	Metagenome / Metatranscriptome	139	Y
F064269	Metagenome / Metatranscriptome	128	Y
F082737	Metagenome / Metatranscriptome	113	Y
F082866	Metagenome / Metatranscriptome	113	Y
F104152	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210319_1001423	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1626
Ga0210319_1001446	All Organisms → cellular organisms → Eukaryota → Metamonada → Fornicata → Diplomonadida → Hexamitidae	1616
Ga0210319_1003748	Not Available	1139
Ga0210319_1005146	All Organisms → cellular organisms → Bacteria	1018
Ga0210319_1009844	Not Available	794
Ga0210319_1009974	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	791
Ga0210319_1012094	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Corethrophycidae → Corethrales → Corethraceae → Corethron → Corethron hystrix	736
Ga0210319_1019374	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Stichotrichia → Urostylida → Pseudourostylidae → Pseudourostyla → Pseudourostyla cristata	619
Ga0210319_1020549	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Stichotrichia → Urostylida → Pseudourostylidae → Pseudourostyla → Pseudourostyla cristata	605
Ga0210319_1022072	Not Available	590
Ga0210319_1024954	Not Available	564
Ga0210319_1029836	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	530
Ga0210319_1030467	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Phaeodactylaceae → Phaeodactylum → Phaeodactylum tricornutum	526
Ga0210319_1030908	All Organisms → cellular organisms → Eukaryota → Sar	523
Ga0210319_1035181	Not Available	500
Ga0210319_1035226	Not Available	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210319_1001423	Ga0210319_10014234	F021307	MNRILYESRCRCKEEISITPKRKLSARSEGKPLQYPNEMMSKTFQIRYDKKLSSLAKFILNSFKNKYIYYAIDDILYLLKSNPVER
Ga0210319_1001446	Ga0210319_10014462	F082866	MHHQLPNRKRSLSLLLRKASGSGKICVLGQIEPQTPRLVVSLRQYLQVSDLHPYFPQSLKPFGFLGAVSTCAHCLDGSV
Ga0210319_1003748	Ga0210319_10037482	F008361	VELSEARKELEKATLAVENAETSKSRLDASVELKKATARLEAINYLS
Ga0210319_1005146	Ga0210319_10051461	F012678	MLNQHSLEEIADIHNLLCDIKQEYEKGIKPILVKKSPNLFKNPHTVPKLKKIEII
Ga0210319_1009844	Ga0210319_10098441	F045132	VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSHRSSLPSSFFACTDGARTPPEELVNSASSVAYVSTRLHRGRVNQPDPTFPRSPGRILETAADSFS
Ga0210319_1009974	Ga0210319_10099741	F004323	MPLDDLRRLEGRATPAVAIHSPVTRDYPSRALSDVFQAA
Ga0210319_1009974	Ga0210319_10099742	F000344	MRPIHPHAAESGVGKHTARESESAKACAIGKERVAN
Ga0210319_1012094	Ga0210319_10120941	F008361	LSEATKDLEKATLAVEMAETSKSRLDASVELKKATARVEAINYLS
Ga0210319_1019374	Ga0210319_10193741	F001583	SDLTLTIIANIYXSLFNNIYKTYYVVFTNKHLNTDQMTRIMMFHYFTPXYYLYLIQLHVLFCHESXDSDSGENTYEDKSISYISXFYDAFLKEIQDAXYXTIFVFVYFXLHHFDAHTINYFFFERXNISELDEIRFYGVAPHXYFRPLMGVLVITPTHYEGLMXLGLFFILLTFLPIVYNFYNTFNKHIPTIPMQNSVLQTFFFIF
Ga0210319_1020549	Ga0210319_10205491	F001583	ISLSATHLSDLTLTIIANIYXSLFDNIYKTYYVIFTNKHLNTDQMTRLMMFHYFTPXYYLYLIQLHVMFCHESXDSDSGEATYEDKSGSYISXFYDAFLKEIQDAXYXTMFVFIYFXLHHFNPSTVNYFFFERXNISELDEIRFYGVAPHXYFRPLMGLLVISPTHYEGLMXMGLFFILLTCMPILYNFYNSYFKHIPTIP
Ga0210319_1022072	Ga0210319_10220721	F000734	VVWAGPVKTFRKVGDVKNDTADLWTKGNLRVKRRDPWHRANALPRAAADPALIGEDADKK
Ga0210319_1024954	Ga0210319_10249541	F082737	LGCSSLPNLHARFEPVTSGTPDAFRLASRLRSFSVGASLLSGTPASLPVRSRSLEADFHSPTKASLLPDDRGGVRAPALLLPLHDTSPVSPVRSGLHPRPVSRTAWDFNNQNPLLSGPAPLLPASLNRRSPSGLFAPPDQCTRSRWPTENLLSGTPDLPSLPTGGRIRYQHQRIIVPAPLRPFQLAVP
Ga0210319_1029836	Ga0210319_10298361	F042669	GAFCGEKVLLVCQVDDFALGCGQESTAKSVYATIGTKLTLHNEAEAPFEYLSLVDSFDGYDVLQTRDYIKLSAESYIRRLLKAHGWENPSPRESSNKPKPPLHESDVANLFNLAAGPVENTPEHKALETEHGFGYRSVLGEILFAYVLCRPDIGYAVTTLAKFSTAPNALHYKSLK
Ga0210319_1030467	Ga0210319_10304671	F038934	WDGIWTFEKILTHQKVKSGDKNHRGSGTNCLVLWSTGEQTWEPLYNRTGKSGLWIDDPVTVAIYARDNGLLDEPGWKLPGLKKMAKTQKKLLRLANKAKLHSFRNKPIYMYGFQVPRNHIEAMELDRMNGNSMWRDAEITELNQIDEYKLFIDKGIGFNPGSDFKTIRVHLVYAV
Ga0210319_1030908	Ga0210319_10309081	F027191	KVVRFLISPKIKKMKIEVNKIMNPAFLLGTAFNIAYWHRKYHSGTICKGVSNAQASNALSGCEREETPK
Ga0210319_1034835	Ga0210319_10348351	F064269	VLRLITFLPLSVLMFMIPVLLAVCMVFACVPKILYLIFGIDTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTQEQRFQRLSKRKALDRMFFMFLLMNHGRVSAKSARRGLIRLRPATKSG
Ga0210319_1035181	Ga0210319_10351811	F104152	MERSIGLLQKISLIEIISTVVLLAIVVVVDLLESSMLLIQLHFNLFAGAHLPLMEY
Ga0210319_1035226	Ga0210319_10352261	F054544	PHLDPMRITQVNDNGTVKLVKVADNNGGVVSQTWNIRNIEPRMA