3300021270: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.593 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021270
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225744 | Ga0210360
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.593 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 34262212
• Sequencing Scaffolds: 13
• Novel Protein Genes: 13
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	9
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Halamphora → Halamphora calidilacuna	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?
F000344	Metagenome / Metatranscriptome	1257	Y
F001024	Metagenome / Metatranscriptome	803	Y
F001506	Metagenome / Metatranscriptome	681	Y
F006508	Metagenome / Metatranscriptome	371	Y
F017072	Metagenome / Metatranscriptome	243	Y
F025295	Metagenome / Metatranscriptome	202	Y
F030135	Metagenome / Metatranscriptome	186	Y
F036102	Metagenome / Metatranscriptome	170	Y
F037756	Metagenome / Metatranscriptome	167	Y
F046726	Metagenome / Metatranscriptome	151	Y
F059360	Metagenome / Metatranscriptome	134	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210360_100687	Not Available	627
Ga0210360_104205	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	816
Ga0210360_108816	Not Available	761
Ga0210360_116012	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	2665
Ga0210360_116281	Not Available	730
Ga0210360_116300	Not Available	627
Ga0210360_121146	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales	762
Ga0210360_139582	Not Available	592
Ga0210360_145605	Not Available	681
Ga0210360_148087	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Halamphora → Halamphora calidilacuna	2124
Ga0210360_168645	Not Available	750
Ga0210360_168898	Not Available	812
Ga0210360_170070	Not Available	760

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210360_100687	Ga0210360_1006871	F006508	VALANAPSEAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPH
Ga0210360_104205	Ga0210360_1042052	F000344	MRPIHPHAAESGVGKHTARESESAKACAIGKERVANAHSH
Ga0210360_108816	Ga0210360_1088161	F025295	VTGPGKVAELLRRREVLIPEKLKSFNRKVNLQKPI
Ga0210360_116012	Ga0210360_1160125	F001506	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTRLSTTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVTVKKQASLW
Ga0210360_116281	Ga0210360_1162811	F017072	MRMRDLAVGSDEKPLRTESSSPEKFRFRMNRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKRRDPWFWANAPSKAVADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS
Ga0210360_116300	Ga0210360_1163002	F006508	VAVANAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSKF
Ga0210360_121146	Ga0210360_1211461	F046726	NFITLGRIPEQERIEIIQRGFQLQAEGKISLKKYYEGTETDSLFQLKGYRIKYEAIRKNKFYQSLKA
Ga0210360_139582	Ga0210360_1395821	F001024	MRPKIPLAVENSVGESAAITRRLMPARERESGELP
Ga0210360_145605	Ga0210360_1456052	F036102	MDTKEMQELFRATAEATPEGQAAFRAFAAAITTPILQKIELESIMRGMFNVERLAPGAQAVYPVAEDFEIPVWVLPGLGYMAQNFIEGIGEEVYVPTFAINASADWKITYARDSRVDIAQRAAARVAK
Ga0210360_148087	Ga0210360_1480872	F059360	MTLFKEVLVPANTRASSRVIREGQALSGMTGRKESVDRNVS
Ga0210360_168645	Ga0210360_1686452	F030135	REEFAKLSSTSDIWHSTFIGCQLPDAIPPGTEDFDLVAGPLD
Ga0210360_168898	Ga0210360_1688982	F000344	MRPKSAHAALSGVGEHPARESESAKWCAEGKERVANAHP
Ga0210360_170070	Ga0210360_1700701	F037756	QALFPVPTFGAHLAVAAGFPTPFSAANGVSGLVAGPSNLLQG