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 Ga0209953_1000004

Scaffold Ga0209953_1000004


Overview

Basic Information
Taxon OID3300026097 Open in IMG/M
Scaffold IDGa0209953_1000004 Open in IMG/M
Source Dataset NameSalt pond water microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2_restored_H2O_MG (SPAdes)
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)179647
Total Scaffold Genes281 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)207 (73.67%)
Novel Protein Genes4 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)3 (75.00%)
Associated Families4

Taxonomy
Not Available(Source: )

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Aquatic → Non-Marine Saline And Alkaline → Saline → Unclassified → Pond Water → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.

Source Dataset Sampling Location
Location NameSouth San Francisco, USA
CoordinatesLat. (o)37.4958Long. (o)-122.1331Alt. (m)Depth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F019234Metagenome / Metatranscriptome231Y
F055541Metagenome / Metatranscriptome138Y
F058743Metagenome / Metatranscriptome134Y
F075969Metagenome / Metatranscriptome118Y

Sequences

Protein IDFamilyRBSSequence
Ga0209953_1000004122F075969GGAGMIDRQSKDGGLTKEQLQEYLDKGGTITKCPPGERTENLEFKRSFYGSKKKKADE
Ga0209953_1000004151F019234AGGMSKKLRRPQAPKRRNFEAKAVRDPQGPFRPQVIKNKIKKKPKYNKIDWDD
Ga0209953_1000004212F058743N/AMIEYEYYDWTSLINASARERMAQDIHSLVEQGKYWKNSPPYQTDVNVFGLPGEDWNNLKMSFIWSAFAYMKQERQIKTIKSWGYKTNVDTQEDRNTYWHQHIRQDSLVLSGVYYLHIPEGTDLETSGTEFALMGPESDGHFYAPAKLGQWIIFPGKSWHRPGILEKKEWRYIVAADMEL
Ga0209953_100000480F055541AGGAGMIRWYDYPAALLAADIMLTMAFTIPYVGFVAAYALYEFGWEAYCQWRLKQENE
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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