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 Ga0209646_1000069

Scaffold Ga0209646_1000069


Overview

Basic Information
Taxon OID3300025246 Open in IMG/M
Scaffold IDGa0209646_1000069 Open in IMG/M
Source Dataset NameArabidopsis root microbial communities from the University of North Carolina, USA - plate scrape CL_Col_mTSA (SPAdes)
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)230340
Total Scaffold Genes217 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)161 (74.19%)
Novel Protein Genes3 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)3 (100.00%)
Associated Families3

Taxonomy
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales(Source: IMG/M)

Ecosystem & Geography

Source Dataset Ecosystem
Host-Associated → Plants → Roots → Epiphytes → Unclassified → Arabidopsis Root → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations

Source Dataset Sampling Location
Location NameUniversity of North Carolina, USA
CoordinatesLat. (o)35.9082Long. (o)-79.0499Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F024826Metagenome / Metatranscriptome204Y
F040712Metagenome161Y
F052031Metagenome / Metatranscriptome143Y

Sequences

Protein IDFamilyRBSSequence
Ga0209646_1000069170F052031GGAGMTIDLPATHPAATEHHEEIVQFVFRSAASPGLLAHARALLGAAPKELAESFEQAVRSAGLAS
Ga0209646_100006970F024826GAGMADATPYFGIAPFVLGMTRELARAAAGKPDSVETTSDDEGAAVETWFYDGGEIELEFDPAPEAKLESITAWSDKTTVNGVAIIGCELGDLQRLAKQADIHDLELTDDFADSGQCWQSEQHGLMFWAAKGKVVNMTIFPRFDDSGEEPQWPE
Ga0209646_100006979F040712GGCGGMAGRPAAGENGALLIRLPASMSLRCFIVRRCLHASLEAVGLRAVNLPLVVDARRHVHPPVPLDAGYLVVDRRAFARITFPRADGREAATMQTVGFASLSGVLRAICAERIGLAGRAAIPGPRRALELRREGRWSEVLEASERVEAPMRARLDAWLRSWRFATWRFALQAFKRL
 ⦗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.