NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
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Sample 3300021270

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 OID3300021270 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114516 | Gp0225744 | Ga0210360
Sample NameMetatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.593 (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size34262212
Sequencing Scaffolds13
Novel Protein Genes13
Associated Families11

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
Not Available9
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Halamphora → Halamphora calidilacuna1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameEstuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series
TypeEnvironmental
TaxonomyEnvironmental → 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
LocationUSA: Washington
CoordinatesLat. (o)46.313Long. (o)-123.997Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000344Metagenome / Metatranscriptome1257Y
F001024Metagenome / Metatranscriptome803Y
F001506Metagenome / Metatranscriptome681Y
F006508Metagenome / Metatranscriptome371Y
F017072Metagenome / Metatranscriptome243Y
F025295Metagenome / Metatranscriptome202Y
F030135Metagenome / Metatranscriptome186Y
F036102Metagenome / Metatranscriptome170Y
F037756Metagenome / Metatranscriptome167Y
F046726Metagenome / Metatranscriptome151Y
F059360Metagenome / Metatranscriptome134Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210360_100687Not Available627Open in IMG/M
Ga0210360_104205All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila816Open in IMG/M
Ga0210360_108816Not Available761Open in IMG/M
Ga0210360_116012All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria2665Open in IMG/M
Ga0210360_116281Not Available730Open in IMG/M
Ga0210360_116300Not Available627Open in IMG/M
Ga0210360_121146All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales762Open in IMG/M
Ga0210360_139582Not Available592Open in IMG/M
Ga0210360_145605Not Available681Open in IMG/M
Ga0210360_148087All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Halamphora → Halamphora calidilacuna2124Open in IMG/M
Ga0210360_168645Not Available750Open in IMG/M
Ga0210360_168898Not Available812Open in IMG/M
Ga0210360_170070Not Available760Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210360_100687Ga0210360_1006871F006508VALANAPSEAVADQCQAVKTQERIHGCVLTWFASRWRNHQPKRAEKPH
Ga0210360_104205Ga0210360_1042052F000344MRPIHPHAAESGVGKHTARESESAKACAIGKERVANAHSH
Ga0210360_108816Ga0210360_1088161F025295VTGPGKVAELLRRREVLIPEKLKSFNRKVNLQKPI
Ga0210360_116012Ga0210360_1160125F001506MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTRLSTTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVTVKKQASLW
Ga0210360_116281Ga0210360_1162811F017072MRMRDLAVGSDEKPLRTESSSPEKFRFRMNRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKRRDPWFWANAPSKAVADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS
Ga0210360_116300Ga0210360_1163002F006508VAVANAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSKF
Ga0210360_121146Ga0210360_1211461F046726NFITLGRIPEQERIEIIQRGFQLQAEGKISLKKYYEGTETDSLFQLKGYRIKYEAIRKNKFYQSLKA
Ga0210360_139582Ga0210360_1395821F001024MRPKIPLAVENSVGESAAITRRLMPARERESGELP
Ga0210360_145605Ga0210360_1456052F036102MDTKEMQELFRATAEATPEGQAAFRAFAAAITTPILQKIELESIMRGMFNVERLAPGAQAVYPVAEDFEIPVWVLPGLGYMAQNFIEGIGEEVYVPTFAINASADWKITYARDSRVDIAQRAAARVAK
Ga0210360_148087Ga0210360_1480872F059360MTLFKEVLVPANTRASSRVIREGQALSGMTGRKESVDRNVS
Ga0210360_168645Ga0210360_1686452F030135REEFAKLSSTSDIWHSTFIGCQLPDAIPPGTEDFDLVAGPLD
Ga0210360_168898Ga0210360_1688982F000344MRPKSAHAALSGVGEHPARESESAKWCAEGKERVANAHP
Ga0210360_170070Ga0210360_1700701F037756QALFPVPTFGAHLAVAAGFPTPFSAANGVSGLVAGPSNLLQG
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