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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Scaffold Ga0102820_1003180

Scaffold Ga0102820_1003180


Overview

Basic Information
Taxon OID3300007554 Open in IMG/M
Scaffold IDGa0102820_1003180 Open in IMG/M
Source Dataset NameEstuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.709
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)4628
Total Scaffold Genes14 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)10 (71.43%)
Novel Protein Genes3 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)2 (66.67%)
Associated Families3

Taxonomy
Not Available(Source: )

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series

Source Dataset Sampling Location
Location NameColumbia River Estuary, USA
CoordinatesLat. (o)46.2Long. (o)-123.94Alt. (m)Depth (m)
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F001942Metagenome / Metatranscriptome613Y
F013088Metagenome / Metatranscriptome274Y
F018155Metagenome / Metatranscriptome236Y

Sequences

Protein IDFamilyRBSSequence
Ga0102820_10031803F018155GGAGMGQNSKAVSKRREELEQEKLDKSIKMYYFQKGAGEHYREIQYQSGRVVRTDFND*
Ga0102820_10031804F013088AGGAGMDEKTKKALWISEDLHKEIKIFAIKNNMNIETASQMVLKLGMCSYKAEKKNGSK*
Ga0102820_10031808F001942N/AMPRKTSDQHQNNSRLGALGESLVQTFLLEYADFCFPTQEKHPADLMVEFGSAKYTVQVKSRRATKEKKFVFAAENSRSQSETYRQYTCDILAFVFFDDEQKRIMFKPNTSSQNYFTFDKKAITETMELDSLQETLATLSSVPVLNPII*

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