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 Ga0055539_1000154

Scaffold Ga0055539_1000154


Overview

Basic Information
Taxon OID3300003752 Open in IMG/M
Scaffold IDGa0055539_1000154 Open in IMG/M
Source Dataset NameArabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Cvi_mCL_r2
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)66426
Total Scaffold Genes71 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)47 (66.20%)
Novel Protein Genes2 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)2 (100.00%)
Associated Families2

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

Ecosystem & Geography

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

Source Dataset Sampling Location
Location NameUSA: North Carolina
CoordinatesLat. (o)35.6667Long. (o)-78.5097Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F049748Metagenome / Metatranscriptome146Y
F077376Metagenome / Metatranscriptome117Y

Sequences

Protein IDFamilyRBSSequence
Ga0055539_100015458F077376GGAMTTYVLSLTGDEEKAANATHWATFRKAKLLSVSRNPRDRASARLAGRDSIVITGQGPIDPPDARHASLTRHPQALAALLVRTLDIQDGAGVVLADFDSDEFAADVVAEIAALGREVTCSGRAANFAFSAVV*
Ga0055539_100015467F049748GAGGMDIKQDPNAIPNFNSGGRLGEPQRNEPEQTQSSVELDPTAGGDGAASEAAEHESLGGEMVQPTGGIGGTGGADGRLDPTKTGPGAVDGLVGAP*
 ⦗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.