NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
x
This website uses cookies to improve user experience. By using NMPFamDB you consent to all cookies in accordance with our privacy policy. OK
Scaffold Ga0209588_1000188

Scaffold Ga0209588_1000188


Overview

Basic Information
Taxon OID3300027671 Open in IMG/M
Scaffold IDGa0209588_1000188 Open in IMG/M
Source Dataset NameVadose zone soil microbial communities from the Eel River Critical Zone Observatory, Northern California, USA - Rivendell_Oct2014_Saprolite_2_DNA_Rhizosphere_1 (SPAdes)
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)17343
Total Scaffold Genes18 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)15 (83.33%)
Novel Protein Genes2 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)2 (100.00%)
Associated Families2

Taxonomy
All Organisms → cellular organisms → Archaea(Source: UniRef50)

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Terrestrial → Soil → Unclassified → Unclassified → Vadose Zone Soil → Vadose Zone Soil And Rhizosphere Microbial Communities From The Eel River Critical Zone Observatory, Northern California To Study Diel Carbon Cycling

Source Dataset Sampling Location
Location NameUSA: California, Eel River Critical Zone Observatory
CoordinatesLat. (o)39.7291Long. (o)-123.6419Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F007216Metagenome / Metatranscriptome355Y
F088676Metagenome / Metatranscriptome109Y

Sequences

Protein IDFamilyRBSSequence
Ga0209588_100018815F088676AGGVIVTVLNVGPQDAKFDGLVLRLILVGLLTLVFRLIGPATAGAHFNESPALPELPVPPLPENVMLSGFVDHRAFGAVLKAKPTAA
Ga0209588_10001882F007216GGALLPIFLPYGWEMALITGSVLFFLMSVTQLYSSGWGRFSPGQLVPDTIVKAGHRYLILHDSGKRATSFLSSTLKGLIDSGARVVISASSNGWLVGNLSVHESHFSEWKENGRVVVSESGGGHILPHEGFSDRLSFGPTSTVFVNELGQDNLAGVVSSPGSGTEEKHQQRAELFLLESSKAPRPQLTEFLRRNSGMELLNLSESTDPFSSLVDLDHQRIRGSIILLEYETSSDYEGVVDKFLAEGISNAELCVLFTTKSSKLYRAIKGKRMIKIIAASSLISVPDELPDGEMQIPDKELGLVAAVLSDFIDNSKNSGASFVFDSITELIRGERWEQVYSGIKQLIDLLSVPNATALFLANINTMEPKFLGALHGAFALQLRLDNQGLKAVKVPVN
 ⦗Top⦘



Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
© Pavlopoulos Lab, Bioinformatics & Integrative Biology | B.S.R.C. "Alexander Fleming" | Privacy Notice
Make sure JavaScript is enabled in your browser settings to achieve functionality.