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 Ga0209580_10000004

Scaffold Ga0209580_10000004


Overview

Basic Information
Taxon OID3300027842 Open in IMG/M
Scaffold IDGa0209580_10000004 Open in IMG/M
Source Dataset NameSurface soil microbial communities from Centralia Pennsylvania, which are recovering from an underground coalmine fire - Coalmine Soil_Cen04_05102014_R1 (SPAdes)
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)708731
Total Scaffold Genes684 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)549 (80.26%)
Novel Protein Genes6 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)5 (83.33%)
Associated Families6

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

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Terrestrial → Soil → Unclassified → Unclassified → Surface Soil → Surface Soil Microbial Communities From Centralia Pennsylvania, Which Are Recovering From An Underground Coalmine Fire.

Source Dataset Sampling Location
Location NameUSA: Pennsylvania, Centralia
CoordinatesLat. (o)40.7999Long. (o)-76.3402Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F008713Metagenome / Metatranscriptome329Y
F028235Metagenome / Metatranscriptome192Y
F029844Metagenome / Metatranscriptome187Y
F030838Metagenome / Metatranscriptome184Y
F033207Metagenome / Metatranscriptome178Y
F046529Metagenome / Metatranscriptome151N

Sequences

Protein IDFamilyRBSSequence
Ga0209580_10000004170F030838AGGAGGMSQSFMRDERLILVNPAHGPLLRKVTLWDRLVAIFTDPDLVAVVLFCALGALLTLALIHSLPRWVEVIAPAQQFL
Ga0209580_10000004342F046529N/AMTRFFFDYTAKEQSLLDYGGHEFRSSQAAMEFAQAIAQDLKHSLSGNWLGWTVEVRNASGVRVLSLPVDSPELEAA
Ga0209580_10000004422F029844GAGGMSVLSIDTVRRSAVPAATHWTSDPRNIGQTLELSESRTYDAALETLGAYKLTGNFLVDLEIVLKDLRVLDKITFEIKPKTLLSDTRHVQFRPTDKVHLDRFEEIMRSVKSRIGADPARPWWVRLFQ
Ga0209580_10000004432F028235GGAMKRLWLAGILAAVLPGAACAQGPIPDPWAPNNFVVTPAPGGGSYALGYDSRQWSYWQTQTDPRGNMYGYDAHGNYWTYDRRSNSYRYYGTEPRWQARCYASVADFC
Ga0209580_10000004434F008713GGAMDQIVLYKGFRIRAYEEWSGLWLAETKVPFRPRPGARDHDNTDAEYIATPSGHPTPEAAIDFIKQMIDSPSTR
Ga0209580_10000004659F033207AGGAGMTTNVLADHVMRTVFFSLAAAVVVFVGMLLLTTLHP
 ⦗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.