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 Ga0063356_100013008

Scaffold Ga0063356_100013008


Overview

Basic Information
Taxon OID3300004463 Open in IMG/M
Scaffold IDGa0063356_100013008 Open in IMG/M
Source Dataset NameCombined assembly of Arabidopsis thaliana microbial communities
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)7580
Total Scaffold Genes12 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)9 (75.00%)
Novel Protein Genes4 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)4 (100.00%)
Associated Families4

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

Ecosystem & Geography

Source Dataset Ecosystem
Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling

Source Dataset Sampling Location
Location NameUSA: Walnut Creek, California
CoordinatesLat. (o)37.931388Long. (o)-122.021761Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F016640Metagenome / Metatranscriptome245Y
F021438Metagenome / Metatranscriptome219Y
F046231Metagenome / Metatranscriptome151Y
F064480Metagenome / Metatranscriptome128Y

Sequences

Protein IDFamilyRBSSequence
Ga0063356_10001300810F064480AGGAGMSSTTDHVPEGPDTTAAALPEARGAERTRYAPPETEASFEEIER*
Ga0063356_10001300812F016640GGAGMSSLLIVVVVLACASWMAWSRWQYWRPLTASIPAEDRSPKTRAFEAFLHGNTCLTAGHFADATTAFEQAWTLDPKRPYVADRLAEVARRQHAASTWAPVAAAG*
Ga0063356_1000130087F021438AGGAGMTFVKTPTQLRLTQDLLERADALIEIMAADPEVRALGMPTRTAVLRLAIARGLRNLEGQYQPPGAASMPRSTTTPSEATPPAHEGTFSQVSAARNGSGGSAPAPQGPR*
Ga0063356_1000130088F046231AGGAMNPGRWPPSLVMDVRVLVTHPDSVTRMEREMGHPPRIIRGPDLCYLFQARDAERLPGLVDRWESYVIAAQVLQIPPMGGHHPATATPPP*
 ⦗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.