3300022365: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.186 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300022365
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225706 | Ga0210322
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.186 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 22451694
• Sequencing Scaffolds: 6
• Novel Protein Genes: 7
• Associated Families: 7

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Nitzschia → Nitzschia inconspicua	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	2
Not Available	3

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?
F008361	Metagenome / Metatranscriptome	334	Y
F030134	Metagenome / Metatranscriptome	186	Y
F037756	Metagenome / Metatranscriptome	167	Y
F038776	Metagenome / Metatranscriptome	165	Y
F042051	Metagenome / Metatranscriptome	159	Y
F047147	Metagenome / Metatranscriptome	150	Y
F075465	Metagenome / Metatranscriptome	119	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210322_100373	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Bacillariales → Bacillariaceae → Nitzschia → Nitzschia inconspicua	2121
Ga0210322_102608	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	982
Ga0210322_103793	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	842
Ga0210322_105390	Not Available	722
Ga0210322_108082	Not Available	605
Ga0210322_108383	Not Available	597

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210322_100373	Ga0210322_1003731	F008361	EATKDLEKATLAVEMAETSKSRLDASVELKKATARVEAINYLS
Ga0210322_102608	Ga0210322_1026082	F042051	MTTVFGEVSWNDDVYPGGGGGNKNSKDLFMRLDEGSNEMRLVTQPFQYLVHKYKKEGDSGWGQKVSCSAIHGSCPLCASGDKPKPRWLLGVISRKTNTYKILDISYAVFSQIRKLARNTQRWGDPTKYDIDIVVDKQGGPTGYYSVQPISKEPLSASDQQIKDTVDFDDLKRRVSPLTPENVQKRIDKINGVETGGK
Ga0210322_103793	Ga0210322_1037931	F038776	VHSVYMGDMMSKFEINYSELETAIVKKAYRLEDVKDRIERVAFDVVRFKDDDEGANLWQIQSADDGDYIVAIYQQEPEEKVASDWSVQVSKVASALLVSYKGDPIVRIAAANIGIPPTELPQAEKYLPKKLAENKKLVKALLNELEESAKKEVLNKYPELV
Ga0210322_105390	Ga0210322_1053901	F037756	ALFPVPTFGAHLAAAAGFPTPFSAANGVSGLVAGPSNLLQG
Ga0210322_108082	Ga0210322_1080821	F047147	QPLSVIIVAVTEGLVREEQLLHDMCLLSATTVDITQTLTRAGQSF
Ga0210322_108383	Ga0210322_1083831	F030134	PSVLKYLKIKAKDKIQPVSQRFKLRSCTVLIVEQTNPLSTYNQGGTIIQHRGSNHVFR
Ga0210322_110693	Ga0210322_1106931	F075465	KTQYSNESRTYRERVSKLETHRGQVYSLILGQCTQLLHDKLKQAAKWTKVSTSYNPLTLFRLIEKTVLAQTEDQYPFATVYDQEHALYSFRQELMTNAQWYEKFNTRVDVGEAIGVTRQHKVLLEFVAQETHNQAFTALGAVEQAAVRDDAEERYRSYVFLKQSGGQHGHLKQTLQNDF