3300022370: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.182 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300022370
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225704 | Ga0210320
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.182 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 57539366
• Sequencing Scaffolds: 11
• Novel Protein Genes: 14
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	2
Not Available	7
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	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): 46.302
  • Long. (^o): -123.036
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000203	Metagenome / Metatranscriptome	1619	Y
F001506	Metagenome / Metatranscriptome	681	Y
F006508	Metagenome / Metatranscriptome	371	Y
F008361	Metagenome / Metatranscriptome	334	Y
F011154	Metagenome / Metatranscriptome	294	Y
F021307	Metagenome / Metatranscriptome	219	Y
F026908	Metagenome / Metatranscriptome	196	Y
F027192	Metagenome / Metatranscriptome	195	Y
F034767	Metagenome / Metatranscriptome	174	Y
F037756	Metagenome / Metatranscriptome	167	Y
F053305	Metagenome / Metatranscriptome	141	Y
F069754	Metagenome / Metatranscriptome	123	Y
F069879	Metagenome / Metatranscriptome	123	Y
F077370	Metatranscriptome	117	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210320_1005261	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	989
Ga0210320_1007163	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	879
Ga0210320_1010042	Not Available	768
Ga0210320_1010046	Not Available	768
Ga0210320_1012000	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	716
Ga0210320_1012669	Not Available	702
Ga0210320_1012852	Not Available	698
Ga0210320_1015846	Not Available	641
Ga0210320_1016379	Not Available	632
Ga0210320_1017234	Not Available	619
Ga0210320_1023780	All Organisms → cellular organisms → Eukaryota → Sar	545

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210320_1005261	Ga0210320_10052611	F034767	MFGSKIGKCTLDILRGINATVWGGVEGADKVGKIVKTGLSGADVVIGTSHALEDLGCNDYVCGSLDIIGSVSSAVGLVLGNIPSTKSLTVITGSVTVGCRSVRYYCKRYGTFWGCTVAAGEGIKKRVKFIINK
Ga0210320_1007163	Ga0210320_10071631	F001506	MKRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSTTAKCLLNNFQNKYIYYAIDDILYSMKAKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDLTTLKEFNYITIKFFYKIRVPVKKQESLW
Ga0210320_1009087	Ga0210320_10090871	F000203	AGVRHTLFPMPTLGATWAAGFPTLFSVAKRVSGLVAGPSSTFRSLNY
Ga0210320_1010042	Ga0210320_10100421	F008361	IIDVELNEATQELEKATLAVEEAETSKDRLDASVELKKATARLEAMNYLS
Ga0210320_1010046	Ga0210320_10100461	F037756	VGVRQALFPVPTFGAHLAAAAGFPTPFSAANGVSGLVAGPSNLLQG
Ga0210320_1012000	Ga0210320_10120001	F027192	MKRFMFVLALLLVVGLSTVLAQSEAVTLVTATVESELILTNLDADWGLFSPGQNYTITPGAFKEPPGPGEAAGDQVESAGFEVEGNPNSEVLISLVLPAAFTSEDENGTMPLSNWTYGWNFDDDPSVAFSAAGPVTGSAVSVIIGGGAITGLFLGADVSVPTTAYTGGYIAQIIGSATYTGN
Ga0210320_1012669	Ga0210320_10126691	F077370	QPRIVNNKQSRNRRNNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNFPDLFLNLGSLATPTFDPSTTSGNSVLIGQI
Ga0210320_1012852	Ga0210320_10128522	F026908	LIWFAGRWRNHQSKRAEKPHSKSSSGDALDGPATRPKTPLAVVNGVGKPAAARKGVRLMSARERELGELPSP
Ga0210320_1015846	Ga0210320_10158461	F069754	SDWTQQDVTETSWYWGRVEFTETRGIAHWHFLAKIPHTLLTELLGRMIHNGRVVRNELKRGNIIESKREQAWEMIEMGLLASRYVALFSQSLSMASFYMEDVGIDGHDDKKVIKLETLRDEFVKNYKQGNINLNTHPIMRRFDDPECNDNVYHEMASVAAISCVHNCMPLSCGGNPLDGAGCRFDMPKKTLKHTVCAVMQVNANQNETRVLLR
Ga0210320_1016379	Ga0210320_10163791	F053305	MLKKSLSIVLTALFVFSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKTLMADPKVVDLKMLKEGDMVNVES
Ga0210320_1017234	Ga0210320_10172341	F006508	VALANAPSEAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPHSKFSAVRRWTAL
Ga0210320_1021984	Ga0210320_10219842	F069879	GTTEMGVFLRHSDHGSLAGIRFGVPLTPAKELPPWRFRPRLPDLYTYEQRTTVFTEVNVIRSDIGRLLTTNHEIERVYWNRDRLYPAYIRQHVDTLKQVVRRWIDDVP
Ga0210320_1023780	Ga0210320_10237801	F021307	MNRILYENRCRCNEEFSLTKKRQSTTRSEGKPLQYPKSNEVLSQTFQIKYDKQLSATAKVILNSFQNKYIYYAID
Ga0210320_1028165	Ga0210320_10281651	F011154	MRSDEKPLRIESSRPGRFRAWVNRSYPEGIRLLLCISTGGRLWRSPRGGQPKERRRKAGQSERSNREGHAVWAGPVKTFREVGDVKNDTADLWTKGNLRVKRR