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 Ga0256308_1000004

Scaffold Ga0256308_1000004


Overview

Basic Information
Taxon OID3300024549 Open in IMG/M
Scaffold IDGa0256308_1000004 Open in IMG/M
Source Dataset NameMetatranscriptome of freshwater microbial communities from Columbia River, Oregon, United States - Colum_Atlam_RepC_8d (Metagenome Metatranscriptome)
Source Dataset CategoryMetatranscriptome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)27337
Total Scaffold Genes58 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)5 (8.62%)
Novel Protein Genes4 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)0 (0.00%)
Associated Families4

Taxonomy
Not Available(Source: )

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Aquatic → Freshwater → River → Unclassified → Freshwater → Freshwater Microbial Communities Amended With Dissolved Organic Matter (Dom) From Various Rivers In The United States

Source Dataset Sampling Location
Location NameUSA: Oregon
CoordinatesLat. (o)46.1812Long. (o)-123.1834Alt. (m)Depth (m)5
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F014975Metagenome / Metatranscriptome258Y
F015337Metagenome / Metatranscriptome255Y
F021980Metagenome / Metatranscriptome216Y
F055726Metagenome / Metatranscriptome138Y

Sequences

Protein IDFamilyRBSSequence
Ga0256308_100000434F055726N/AMDWILEDWEYPNDHIYAMEREHDVQVAWQQWEEEEKRKKRLPALIKTVTPILTDETERNSRTVRGAHQKRL
Ga0256308_10000045F014975N/AMEKLFNQFKNMLVVYPKYKGYVCGYNDAHFIIAVETKDDKNFFRKMENPYIMEEYKDVKYRYTFADESQLIKQSNNDKYKKAINKD
Ga0256308_100000453F021980N/AMNKFECSECGTKYSSPETTPPPGIKWSDGHVCTPKPVKS
Ga0256308_100000455F015337N/AMKKTIELEPTEFWHFRKLAFAISLAFGCTISHGVYIVEASIDQLEQLGY
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