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
Sample 3300025303

3300025303: Arabidopsis rhizosphere microbial communities from North Carolina, USA - plate scrape MF_Cvi_mMS_r2 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300025303 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0053073 | Gp0101313 | Ga0209051
Sample NameArabidopsis rhizosphere microbial communities from North Carolina, USA - plate scrape MF_Cvi_mMS_r2 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size421927747
Sequencing Scaffolds7
Novel Protein Genes7
Associated Families5

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Azohydromonas1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium1
Not Available1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameArabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations
TypeHost-Associated
TaxonomyHost-Associated → Plants → Roots → Endophytes → Unclassified → Arabidopsis Root → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations

Alternative Ecosystem Assignments
Environment Ontology (ENVO)Unclassified
Earth Microbiome Project Ontology (EMPO)Host-associated → Plant → Plant rhizosphere

Location Information
LocationUSA: North Carolina
CoordinatesLat. (o)35.6667Long. (o)-78.5097Alt. (m)N/ADepth (m)N/A
Location on Map
Zoom:    Powered by OpenStreetMap ©


Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F026918Metagenome / Metatranscriptome196N
F027546Metagenome / Metatranscriptome194Y
F033107Metagenome / Metatranscriptome178Y
F044538Metagenome / Metatranscriptome154Y
F073010Metagenome / Metatranscriptome120Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0209051_1001844All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales16718Open in IMG/M
Ga0209051_1004716All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales8276Open in IMG/M
Ga0209051_1006732All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales6414Open in IMG/M
Ga0209051_1008803All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Azohydromonas5292Open in IMG/M
Ga0209051_1008989All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium5203Open in IMG/M
Ga0209051_1016835All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales3285Open in IMG/M
Ga0209051_1100411Not Available780Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0209051_1001844Ga0209051_10018443F044538MRLIARFVVLMVAVFGVSLAFAWAWDRSDTPPATTPVRGS
Ga0209051_1004716Ga0209051_10047166F073010MNGWLLRPRVLAVLACATFACILLYQLPWSPAASAHFTARTGQLPFDERPAGYTLSGALRDFQRLGPEGLQDYRAYRVLDLLFPWLLCALVAGVMLRLEAARATMWPWLAALADSAENVALWAMFLTRDDLSPRLVPVASFLTQLKFCLYAAMLLMLLAVGVRYVLRERRRARMAG
Ga0209051_1006732Ga0209051_10067326F027546MKTAGETDPAPVQPLGDRVQAPKPVRPEWQPLAHAPCIEVNRQGQLRTNLPLPK
Ga0209051_1008803Ga0209051_10088036F033107MKTLSALALLGLGFVALSRVANVHKGRNHGRPAAKPEEVQTWEGEGGGLPTGGPGPGVKVSTPVSDPDLAHGTTH
Ga0209051_1008989Ga0209051_10089893F026918MDSKQLFIEHLAGELQAMEVGRVPMNPLRYRVHAKMLKKALGDLPAPLVMSRPGGAHPQVLHEMANRFFEDTGHLPRPDAAAHKARSLLERTLAQCRAPRPL
Ga0209051_1016835Ga0209051_10168352F044538MRLIARFVVLMVAVFGLSIAFAWAWDRSDAPKTAQHA
Ga0209051_1100411Ga0209051_11004112F027546MKTAGEPDPAPFQPLGDRVQAPKPARPEWQPLAHAPSIEVNRQGQLRTNLP
 ⦗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.