3300021844: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.595 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021844
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225745 | Ga0210361
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.595 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 43591454
• Sequencing Scaffolds: 14
• Novel Protein Genes: 15
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
Not Available	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	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?
F000203	Metagenome / Metatranscriptome	1619	Y
F001418	Metagenome / Metatranscriptome	698	Y
F001679	Metagenome / Metatranscriptome	653	Y
F006508	Metagenome / Metatranscriptome	371	Y
F009426	Metagenome / Metatranscriptome	318	Y
F011154	Metagenome / Metatranscriptome	294	Y
F016975	Metagenome / Metatranscriptome	243	Y
F034200	Metagenome / Metatranscriptome	175	Y
F046210	Metagenome / Metatranscriptome	151	N
F047147	Metagenome / Metatranscriptome	150	Y
F061584	Metagenome / Metatranscriptome	131	Y
F075465	Metagenome / Metatranscriptome	119	Y
F077370	Metatranscriptome	117	Y
F089930	Metagenome / Metatranscriptome	108	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210361_106614	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	553
Ga0210361_120200	Not Available	620
Ga0210361_122973	Not Available	653
Ga0210361_141684	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	816
Ga0210361_148459	Not Available	635
Ga0210361_150405	Not Available	888
Ga0210361_169194	Not Available	513
Ga0210361_170530	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	992
Ga0210361_173404	Not Available	517
Ga0210361_176590	Not Available	1228
Ga0210361_177332	Not Available	599
Ga0210361_185152	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	538
Ga0210361_186550	Not Available	776
Ga0210361_189559	Not Available	530

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210361_106614	Ga0210361_1066141	F075465	RGHAYSLILGQCTQLLQDKMKQDADWTTVSTSYDPLTLFRLIEKTVLAQTEDQYPFATVYDQEHAFYSFRQETLTNPQWYEKFNTRIDVAEAIGVTRNHKALLEYVAKDVHKKKFADLGAAIQEAVRVDAEERYRAYVFLRQSGAQHANLRTVLQNDFTTGDDHYPKNRQSALHLLDKFSKTTV
Ga0210361_120200	Ga0210361_1202001	F016975	VSWSGPRAGGATTGSAGLRGLTQQFSDRKALDGPATRPKTPLAVENSV
Ga0210361_122973	Ga0210361_1229731	F077370	NNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNFPDLFLNLGSLATPTFDPSTTSGNSVLIG
Ga0210361_138957	Ga0210361_1389571	F000203	VPALGASGAAGFPTLFSTASGVSGLVAGPSSASPLLDFE
Ga0210361_141684	Ga0210361_1416842	F001679	MSWRQKAMKGVEGCDKLGGTVKQVLIPRYPNYRTMNP
Ga0210361_148459	Ga0210361_1484591	F006508	MANALSKAVADQRQSGQDAEKDHGRVLTWFASRWRNHQPKRAEKPHSK
Ga0210361_150405	Ga0210361_1504051	F061584	ARLAVSPSKVRVIDSASRGLVTEPRWTLMKIGRSTECCERRSCRRIRLPAPTMTSLFPGSLCGLTPPPSPVPLRVRVHPLVNFASPSEHEPFRSCPARCRAWRLPWGFFPHRGINTRSPLSIELPTARTIGPSSAFLTPSTVYSSAYLAGLFHPTTTSGIHLSGVISRYQASPPHRRPVPSCRSSTRSYHRVAPTAPDRADPPTGS
Ga0210361_169194	Ga0210361_1691941	F001418	AEAGFTSSSGGVRAPSVNAKKELGDEVRLETAPSRVK
Ga0210361_170530	Ga0210361_1705302	F001679	VWGMSWRQKAMKGVEGCEKPGVAVKRALIPGFPNYRALNP
Ga0210361_173404	Ga0210361_1734041	F009426	EIDSTAARVNKDLKLPSVMVTSETSETVIVFTTTSPCVISAGAARETLFEGKADYCMNVC
Ga0210361_176590	Ga0210361_1765901	F047147	MAVIEGPVREEQLLHDVCLLGAMTMGTAQILTRVRQAYLNPS
Ga0210361_177332	Ga0210361_1773321	F046210	NIQMKNLKIEAEKGFRRTLFEPELVDPNLEINFVNDAEAALKSCNVNS
Ga0210361_185152	Ga0210361_1851521	F011154	DEKPLRIESSRPGRFRAWANRSYPEGIRLLLCISTGGRLWRSPRGGQPKERRRKAGQSERSNREGHAVWAGPVKTFREVGDVKNDTADLWTKGNLRVKRRDPWHRANALPRAAADPALIGEDADKKTQTCLDLVRKPVAQPPVQAS
Ga0210361_186550	Ga0210361_1865501	F089930	DLFVQAVLTFMLRGGYLSTAIGRNRNVDKTALEPLSLHDILEVRAGCSGFDHTELPTASGKTKKKKDSKGENKQASLFMTIKATPTPLASSRSYIFRFKSRSARNDVMNGLRCILADMQIHEGVSISNLHTEKDAFDEREREEIMVPLSAVHEVINREREAYDRILLMLLQGNEDLKEKEDELLRLRNKLESVVDESKEKDRVQANDSKLIMQLSKKLETLLMDNEDLRDQNDRLNTRLVSVESEKMNLLARQS
Ga0210361_189559	Ga0210361_1895591	F034200	VALGQRTATRGGRPSANGKEAEMKSQTCLYLVRKPASANASRSELRGLTQ