3300021278: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.302 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021278
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225716 | Ga0210332
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.302 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 34715935
• Sequencing Scaffolds: 15
• Novel Protein Genes: 17
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	10
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Bilateria → Protostomia → Ecdysozoa → Panarthropoda → Arthropoda → Mandibulata → Pancrustacea → Crustacea → Multicrustacea → Hexanauplia → Copepoda → Neocopepoda	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): 46.313
  • Long. (^o): -123.997
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000237	Metagenome / Metatranscriptome	1498	Y
F002557	Metagenome / Metatranscriptome	548	Y
F004323	Metagenome / Metatranscriptome	443	Y
F006508	Metagenome / Metatranscriptome	371	Y
F014031	Metagenome / Metatranscriptome	266	Y
F017072	Metagenome / Metatranscriptome	243	Y
F023281	Metagenome / Metatranscriptome	210	Y
F034200	Metagenome / Metatranscriptome	175	Y
F037756	Metagenome / Metatranscriptome	167	Y
F042355	Metagenome / Metatranscriptome	158	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210332_117227	Not Available	609
Ga0210332_118651	Not Available	690
Ga0210332_120905	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	716
Ga0210332_123224	Not Available	766
Ga0210332_125491	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	761
Ga0210332_131321	Not Available	559
Ga0210332_131606	All Organisms → cellular organisms → Bacteria	840
Ga0210332_136718	Not Available	647
Ga0210332_140134	Not Available	519
Ga0210332_145697	Not Available	619

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210332_117227	Ga0210332_1172271	F060086	NLLLSSGRHGEDRKRQYLYDHETPLLDDLADLLYLALPLLLLFK
Ga0210332_118651	Ga0210332_1186511	F017072	MRMRDLAVGSDEKPLRTESSSPEKFRFRMNRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKRRDPWFRANAPSKAVADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS
Ga0210332_120048	Ga0210332_1200481	F046726	LPPSEQPNFITLGNISEEEKIEIIQRGFQLQKEGRISLKNYYETRDQDSLFQWKGYSIKYESIRRTKLYRHLKP
Ga0210332_120905	Ga0210332_1209051	F075465	AANLESHQGKAYSLILRQCTRLLQDRMKQDADWLTVSTRYNPLSLYRLIEKTVLAQTEDQYPFATVYDQEHAFYLFRQETMTNPQMYEKFNTRVDVGEAIGVTCQHKVLLEFVAQENHTKAFVALGAAEQEAVRVDAQEGYQSYAFLRQSRAQHGHLKQSLQNDFTTGDNHYPKTHQQTLHLLDKFSKTVVPKAVVSEGTAFAQDDGGSDETPFDKEYWKDKKCFNCHKKGHPASHCK
Ga0210332_123224	Ga0210332_1232241	F053305	MLKKSLSIVLTALFVLSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKSLMADPKAVDLKMLKEGDMVSVES
Ga0210332_125491	Ga0210332_1254911	F004323	MPLGDLRRSEGKATPAVAIHSPVTRDYPSRALSNVFQAAALRL
Ga0210332_128393	Ga0210332_1283931	F000237	ISLSATHLSDITLTIVANIFWSLFNNVYKTYYIIFTNKHLNTDQLTRFMILHYFTPXYYLYLVKLHVMFCHESWDTDSGENTYEDKSGSYVSXFYDAFLKEIQDAXYWTIFIFSYFFMHHFDGGTVNYFFFERXNISELDEIRFYGVAPHXYFRPFMGILTISPTHYEGLMXFALXLVLLAFLPVINTFYNPYNRYQSVIPTQNSXLQSAFFMVFMMSLYCASSMLPCGRYYYEPEGGYVGNPXVKFSYQYGYIYLMXTIHHLDALDHXIFNFTQNLKRRYTQNLRVKRTRFWY
Ga0210332_131321	Ga0210332_1313211	F002557	VLMHSSNHYPLGNCDSPGSETNLDYLTQFGTVSNRSSLPRSFFAFTDGARTPPAELVNSASFAKC
Ga0210332_131606	Ga0210332_1316061	F042355	MTSDLKKINKKPNFRRKQNIQEPKLVERLIKISRV
Ga0210332_136718	Ga0210332_1367181	F006508	VAVVNAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSKSSV
Ga0210332_140134	Ga0210332_1401342	F089490	MYRLMKSEKFTLDDAVSGLVSSYRQTEIGHFEKFRAAHHACEVANNDGWSRCYVINESGQEYYGHTWID
Ga0210332_145697	Ga0210332_1456971	F034200	VALGQRTATRGGRPSANGKEAEMKSQTCLYLVRKPA
Ga0210332_150774	Ga0210332_1507741	F045132	VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSNRSSLPSSFFAFTDGARTPPEELVNSASSAKCLSPSLKRGLVNQPDLTFP
Ga0210332_159113	Ga0210332_1591131	F037756	PVPTLGAHLAVAAGFPTLFSTASGVFGLVAGPSSVSRR
Ga0210332_164666	Ga0210332_1646662	F046726	LGKISEQERLEIIQTGFQRQAEGKISLKKYYESTDPDSLFQWKGYSIKYETIRRTKLYQSLKD
Ga0210332_168319	Ga0210332_1683191	F023281	DEYLDANSRSESTKNCEEFFQCPYSIKESFKRNLSGNSL
Ga0210332_174174	Ga0210332_1741741	F014031	MRRHRGRVGLMAVAIMGVLVSGASADIVTERSASVLVFPKVIANGTRDTLIQITNTSNSMVHAHCFYVNAAPTFRDLPPDPVLNPPLWQEIDFDIWLTKQQPTYWRVSTGRQDNYIEGIDDACSFDPRNLD