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 Ga0102873_1005049

Scaffold Ga0102873_1005049


Overview

Basic Information
Taxon OID3300007545 Open in IMG/M
Scaffold IDGa0102873_1005049 Open in IMG/M
Source Dataset NameEstuarine microbial communities from the Columbia River estuary - metaG 1547B-3
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)4116
Total Scaffold Genes12 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)10 (83.33%)
Novel Protein Genes4 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)4 (100.00%)
Associated Families4

Taxonomy
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Nitrosomonadales → Methylophilaceae → unclassified Methylophilaceae → Methylophilaceae bacterium(Source: UniRef50)

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)46.2314Long. (o)-123.8828Alt. (m)Depth (m)
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000473Metagenome / Metatranscriptome1097Y
F000671Metagenome / Metatranscriptome945Y
F016396Metagenome / Metatranscriptome247Y
F073544Metagenome / Metatranscriptome120Y

Sequences

Protein IDFamilyRBSSequence
Ga0102873_100504910F000473AGGMEFINKDKDHFKHGINLWNGEPNKPVFYTKEMSSKIRELKKPVPDLMLDIVQYPEFLAVRLYEDNFIQYEGIKKEQVIDYVGKVKKLIESYGVRCELEGVPSARILRSN*
Ga0102873_10050494F016396GGAMRKSERLRLLEMQVVRLEMMVELYTQTLSNLLESQGLSAPTQLDAGKWYKAKLDQLDKE*
Ga0102873_10050498F000671GAGGMEKILCYCCNKTKNKLNLKKSTLIPINLFMCESCISSKFEPRWVIILAGRQLGSDSVKEFIIKKRYCGADIAASELLV*
Ga0102873_10050499F073544AGGVREYYEVINIVFIHELRLWGTCDSLGLYASKIKYQKDGIEYEEMLDNEEFTVMEEIVIEHQEEDN*
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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