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 3300001228

3300001228: Switchgrass rhizosphere microbial communities from Knoxville, Tennessee, USA - 12_joined



Overview

Basic Information
IMG/M Taxon OID3300001228 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0087863 | Gp0055704 | Ga0012561
Sample NameSwitchgrass rhizosphere microbial communities from Knoxville, Tennessee, USA - 12_joined
Sequencing StatusPermanent Draft
Sequencing CenterUniversity of Tennessee
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size19207606
Sequencing Scaffolds19
Novel Protein Genes20
Associated Families20

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Brevundimonas → unclassified Brevundimonas → Brevundimonas sp. BAL31
Not Available6
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium1
All Organisms → cellular organisms → Bacteria → Proteobacteria2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium1
All Organisms → cellular organisms → Bacteria → FCB group → Fibrobacteres → Fibrobacteria → Fibrobacterales → Fibrobacteraceae → Fibrobacter → Fibrobacter succinogenes1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameSwitchgrass Rhizosphere Microbial Communities From Knoxville, Tennessee, Usa
TypeHost-Associated
TaxonomyHost-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Switchgrass Rhizosphere → Switchgrass Rhizosphere Microbial Communities From Knoxville, Tennessee, Usa

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

Location Information
LocationEast Tennessee Research and Education Center, Knoxville, Tennessee, USA
CoordinatesLat. (o)35.9606Long. (o)-83.9208Alt. (m)N/ADepth (m)N/A
Location on Map
Zoom:    Powered by OpenStreetMap ©


Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F001181Metagenome / Metatranscriptome756Y
F001186Metagenome / Metatranscriptome754Y
F003794Metagenome / Metatranscriptome468Y
F005543Metagenome / Metatranscriptome397Y
F008109Metagenome / Metatranscriptome339Y
F010936Metagenome / Metatranscriptome297Y
F012389Metagenome / Metatranscriptome281N
F017389Metagenome / Metatranscriptome241Y
F020336Metagenome224Y
F031915Metagenome / Metatranscriptome181Y
F038297Metagenome / Metatranscriptome166Y
F038368Metagenome / Metatranscriptome166N
F042788Metagenome / Metatranscriptome157N
F053475Metagenome / Metatranscriptome141N
F064981Metagenome128Y
F074524Metagenome119Y
F085355Metagenome / Metatranscriptome111Y
F091754Metagenome107Y
F092669Metagenome / Metatranscriptome107N
F097459Metagenome / Metatranscriptome104N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
SwM_102805All Organisms → cellular organisms → Bacteria574Open in IMG/M
SwM_105728All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium534Open in IMG/M
SwM_105954All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Brevundimonas → unclassified Brevundimonas → Brevundimonas sp. BAL3623Open in IMG/M
SwM_110045All Organisms → cellular organisms → Bacteria518Open in IMG/M
SwM_114063Not Available502Open in IMG/M
SwM_116876All Organisms → cellular organisms → Bacteria598Open in IMG/M
SwM_125266All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium589Open in IMG/M
SwM_127559Not Available889Open in IMG/M
SwM_128468All Organisms → cellular organisms → Bacteria → Proteobacteria589Open in IMG/M
SwM_135023All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium522Open in IMG/M
SwM_135654All Organisms → cellular organisms → Bacteria529Open in IMG/M
SwM_140699Not Available553Open in IMG/M
SwM_140705All Organisms → cellular organisms → Bacteria → Proteobacteria637Open in IMG/M
SwM_141856All Organisms → cellular organisms → Bacteria635Open in IMG/M
SwM_142188Not Available562Open in IMG/M
SwM_142255Not Available554Open in IMG/M
SwM_142869Not Available519Open in IMG/M
SwM_143378All Organisms → cellular organisms → Bacteria → FCB group → Fibrobacteres → Fibrobacteria → Fibrobacterales → Fibrobacteraceae → Fibrobacter → Fibrobacter succinogenes539Open in IMG/M
SwM_144712All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales524Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
SwM_102805SwM_1028051F031915MKFMFTIYHDGKVLAAMADNERQALVDSAIEYAEELQTERSLRRLECSAA
SwM_102805SwM_1028052F010936ERALVLARNRRTALWYEPRILATLADAKLAAGDRSGARALLSEARELVDRGRGWRLGAFDVALAWVRLLASEPASDRTAIESALESVDALTAELGSDRYRRIAELERARLAT*
SwM_105728SwM_1057282F053475LGIGSDSGITLLTGFFIGTALTWFSTIELLCHLGEKQGRQIMLRVMQSLCVLCIAAGVVQLARAANLLGI*
SwM_105954SwM_1059541F012389SALGAGFEMLTSRLLGIFVVVSALVSSGAEFAVARDAPANDFSSLLEWKNQIAADIEHNKRYLPGVRTRGKIGVVYFDLNINRAGWVLPGTRIVTVDRELGSAALLLLQQSQPFPAPDHVGLRDTTFRILVPIRFNEIPPQDAAGLADLERRKLLECDEADREELEYQRRRAAYRNAEPPTTVNRMPVWVSRGEAAGGRASMAGRGT
SwM_110045SwM_1100452F091754MRIGLAYNQKPDTDPTPDRASKTADVYAEWDEPSTIDAVEQALG
SwM_114063SwM_1140631F038368ATRLRAEALEPELNAAILEIGKEDFLLDNCDLQSLFSESLNRYYSDEVVLWLGTELANGKQAAFQRLADVLGPVHTVLEMGVGCVDVFRVVSSFQDSQGDLISEWEAVLGGPYSTGAAIRWRTVRVWKQRVVIAERIEGLASVGDHFAAKGAERPRGC*
SwM_116876SwM_1168761F020336LRVAAVEALRLAATPAALGTLEGLSDDGDREVREAASRGVAELKRKTRR*
SwM_125266SwM_1252662F074524RVIVLINKVETLSDRTPARETAEQLLSSSAIESVVLASARRDKPVLELCTR*
SwM_127559SwM_1275592F042788MNMRPLIAGCVVAEILLNATSLVGQTLDIKPPTTGPEFRPDHDQRREEKSSVARPGLNEPHFISPFSVKTDARQLGIAGWTSTNPNVPPGHSLSGDGAGSLGFGVAAEWGARPRSERPLIR*
SwM_128468SwM_1284682F005543MVMKAAEDGRRYDAAHVLDSAMDRSVFVERPMSPQLVIIGSILRQDPAQV
SwM_135023SwM_1350231F038297MGQAAKPTRHNRTITVDFHDETTYLALLDTPHAFVEFVLAFLLALSAFSSSTKPAAV
SwM_135654SwM_1356542F064981TKKAKDFAASTDLKEAMIKAGVLDTPTIYFLESID*
SwM_140699SwM_1406991F092669LYNRNMKDGANVMLRVDRIGSDGAVTGTYRRRVVGDVLSGGRSVFDVPVADVGTYRVSVEAVDWVKECR*
SwM_140705SwM_1407051F003794MSLPDDDDTKHNVVRLGTETLFAIAEQLRRMYDADLRTKPSEELERLMRRIERGE
SwM_141856SwM_1418561F001186MASQYSLPTRLRDYIAFLLPWAHGHQLKAIGDFVAAIIEQQTACQAQLARYFGKHEAAVKRLSRLLHNERLDPRQLADAVLLQALHQLPTHGKVRLAIDWTIEADQHLLVVSLVVGRRAVPMYWRAYDASV*
SwM_142188SwM_1421881F001181MHALVVRVTIHNADRTREVLNSQVVPQVSGAPGFKTGYWTWATGGGGLNGLSMVVFDSEENARGAGDRVSAIAADAPDDVTLDGVEVREVVASA*
SwM_142255SwM_1422552F008109GLDRLLAGPGFLGAGTFPEISFRSELLVWVPAGWRAVGRLQVKDTEHDLACQLDLHYGETRPDGSRRVIIVSSWVIDARWVTSQRVPGLGRRIVMTCSSSLEPDM*
SwM_142869SwM_1428692F097459DNMSHKGRNRDPGRIPREPAVTHKKSTALMEAQLESLKRNSGSELIKAGDKRLEPRAGATLKTKFETRPLRGRRHRSDRS*
SwM_143378SwM_1433781F017389TNDLGADWLDRLELMMVVEDQFAGVEITGADVDRIKVVGDLIRHIETVDKERRRQGAAPVVRKLFGPGLAHTVKLTKQQKGCEEAALFFLRLAGDAMRNLIGWCPETRQPIDLQLYVDDATLARIWSNVLRFRCPHCGTKHETEVQRLASKPFSLEPPQTKRTRHQKAAPLFARAS*
SwM_144712SwM_1447121F085355MDSLKAALTSVKDLLDWLPDLVVALLILAIAVLFALALHRW
 ⦗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.