3300021263: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.433 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021263
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225727 | Ga0210343
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.433 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 32080367
• Sequencing Scaffolds: 18
• Novel Protein Genes: 19
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	5
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	2
All Organisms → cellular organisms → Eukaryota → Sar	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales	1
All Organisms → cellular organisms → Eukaryota	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Aphanothecaceae	1
All Organisms → cellular organisms → Bacteria	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?
F001506	Metagenome / Metatranscriptome	681	Y
F004323	Metagenome / Metatranscriptome	443	Y
F006508	Metagenome / Metatranscriptome	371	Y
F012678	Metagenome / Metatranscriptome	278	Y
F014031	Metagenome / Metatranscriptome	266	Y
F021307	Metagenome / Metatranscriptome	219	Y
F034767	Metagenome / Metatranscriptome	174	Y
F042356	Metagenome / Metatranscriptome	158	Y
F046726	Metagenome / Metatranscriptome	151	Y
F061006	Metagenome / Metatranscriptome	132	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210343_100647	Not Available	699
Ga0210343_109245	Not Available	742
Ga0210343_115100	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	917
Ga0210343_119265	Not Available	659
Ga0210343_128323	All Organisms → cellular organisms → Eukaryota → Sar	512
Ga0210343_128416	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	726
Ga0210343_137405	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	2710
Ga0210343_141564	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya	3782
Ga0210343_142205	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales	2257
Ga0210343_143083	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1618
Ga0210343_143810	Not Available	544
Ga0210343_148538	Not Available	505
Ga0210343_151423	All Organisms → cellular organisms → Eukaryota	2847
Ga0210343_152080	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	5811
Ga0210343_159588	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Aphanothecaceae	589
Ga0210343_161927	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1829
Ga0210343_162535	All Organisms → cellular organisms → Bacteria	730
Ga0210343_167890	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1850

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210343_100647	Ga0210343_1006471	F006508	VALANAPSEAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPHSKSSAVRRWTAL
Ga0210343_109245	Ga0210343_1092452	F046726	LGKISEQEKLEIIQTGFQLNEEGKISLKKYYERVSEANSLFQSKGYYIKYGTKLYKNLND
Ga0210343_115100	Ga0210343_1151001	F001506	MNRILYDNRCRCNEEFSVTKKRKSTTRSEGKPLQYPKANEMTSQTFQIKYEKKLSSTAKAIFNSFHNKYIYYAIDDILYSLKGNLIERDSLLAILYSTILSLQNNFSVNFFDIWIREVYIQEISKMNPFLNQDSQTLTQFSYITIKLFYKTRVPVKKQESLW
Ga0210343_119265	Ga0210343_1192651	F006508	VAVANAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSK
Ga0210343_119265	Ga0210343_1192652	F042356	VHQHGASDSGGFDQPFETAQRKPLKDGQKERMTRESHDGSAGRVKNFRAPAMLKTAPLACEQKAT
Ga0210343_128323	Ga0210343_1283232	F021307	MNRILYENRCKCNEEFSITKKRKSNTRSEGKPLQYPKPSEIMSKTFQIKYHETLSPTAKFILNSFQNKYIYYAIDDILYSL
Ga0210343_128416	Ga0210343_1284162	F021307	MNRILYESRCRCKEEISITPKRKLSARSEGKPLQYPNEMMSKTFQIRYDKKLSSLAKFILNSFKNKYIYYAIDDILDSLKLNLLERDNILAILYS
Ga0210343_137405	Ga0210343_1374055	F001506	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLLKAKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIRDVYIDEISKTNRFLKNDSTTFKEFNYITIKFFYKTRVPVKKQESLW
Ga0210343_141564	Ga0210343_1415641	F001506	MNRILYENRCRCNEEFSLTKKRQSTTRSEGKPLQYPNYTESTSKTFQIKYDKKLSSLAKAILNSFQKKYIYYAIDDILYFLKGNSIEQENLLAILYSPILSLHNNFSINFFDIWIGEVYIEEISKVNKFLTKDSQTFTQFSYITIKLFYKTGVPIKKKESLW
Ga0210343_142205	Ga0210343_1422052	F046726	LSKISEEDKIEIIQTGFRLNQEGKISLKKCSESTAEYSLFQLKGYSIKYKSIRRTKLYQNLKE
Ga0210343_143083	Ga0210343_1430831	F001506	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQKSLSTTAKCILNSFQNKYIYYAIDDILYLLKSKPSDRDNLLAVLYSPILSLQNNFSVNFFDIWVREVYIDEISKTNKFLKNDSTTLKQFNYITIKFFYKTRVPVKKQESFW
Ga0210343_143810	Ga0210343_1438101	F061006	KRIDQMLPKKAGQSPEDRANDIDNTLTWLRNRGVDEPQFGPEEPFKKAQSLPMPDSRTPEQKATDLDNVLNWVRNPKENDTPQTEPFKRMDQLLPKKPGQTPEDRAKDIDNALTWVRNRGVDQPESEPTSPFEKLNSLPIDRRTPEQKAKDVEDILNWKRNPKENDSPKTEPFKKIDQLL
Ga0210343_148538	Ga0210343_1485381	F004323	MPLGDLRRSEGKATPAVAIHSPVTRDYPSRALSNVFQAAALRLF
Ga0210343_151423	Ga0210343_1514232	F034767	MFGSKIGKCTLDILRGINATVWGGVEGADKVGKIVKTGLSGADVVIGTSHALEDLGCNDYVCGSLDIIGSVSSAVGLVLGNIPSTKSLTVITGSVTVGCRSVRYYCKRYGTFWGCTVAAGEGIKKSVKFIINK
Ga0210343_152080	Ga0210343_1520804	F001506	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSIEITSKTFQMKYQKSLSTTAKCILNSFQNKYIYYAIDDILYSLKSKPIERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVPVKKQASLW
Ga0210343_159588	Ga0210343_1595883	F012678	MLNQHSLEEIGDIHNLLEDIKKEYEEGLKPILIKNSPERFKNPHTVPKLKKIQINRCLGL
Ga0210343_161927	Ga0210343_1619273	F001506	MNRILYENRCRCNEEFSITKKRKTTTRSEGKPLQYPKSNEVLSQTFQIKYDKQLSATAKVILNSFQNKYIYYAIDDILYLLKGNPIERDNLLAILYSPVLSLQNNFSINFFDIWIREVYIEKMSKVNKFLTNDSQTLEQFSYITIKLFYKTRVPVKKQESLW
Ga0210343_162535	Ga0210343_1625351	F014031	MRRHRGRVGLMAVAIMGVLVSGASADIVTERSASVLVFPKVIANGTRDTLIQITNTSNSMVHAHCFYVNAAPTFRDLPPDPVLNPPLWQEIDFDIWLTKQQPTYWRVSTGRQDNYIEGIDDACSFDPRNLDCPNAGFDPGAVPPVVDDFVGELKCVETDQVGAPISGNHLKGEATVITYD
Ga0210343_167890	Ga0210343_1678901	F021307	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQKNLSTTAKCILNSFQNKYIYYAIDDILYLLKSKPSERENLLAVLYSPILSLQNNFSVNFFDIW