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 3300025230

3300025230: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Cvi_mMF_r2 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300025230 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0053073 | Gp0101298 | Ga0209563
Sample NameArabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Cvi_mMF_r2 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size126519028
Sequencing Scaffolds16
Novel Protein Genes18
Associated Families15

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Hydrogenophaga → unclassified Hydrogenophaga → Hydrogenophaga sp. T41
All Organisms → cellular organisms → Bacteria → Proteobacteria2
Not Available7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria1

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?
F012876Metagenome / Metatranscriptome276Y
F024826Metagenome / Metatranscriptome204Y
F034241Metagenome / Metatranscriptome175Y
F036775Metagenome / Metatranscriptome169Y
F036776Metagenome / Metatranscriptome169Y
F040130Metagenome / Metatranscriptome162Y
F049682Metagenome / Metatranscriptome146Y
F050419Metagenome / Metatranscriptome145Y
F056275Metagenome / Metatranscriptome137Y
F060114Metagenome / Metatranscriptome133Y
F062899Metagenome / Metatranscriptome130Y
F067349Metagenome / Metatranscriptome125Y
F078153Metagenome / Metatranscriptome116Y
F090602Metagenome / Metatranscriptome108Y
F099381Metagenome / Metatranscriptome103Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0209563_106018All Organisms → cellular organisms → Bacteria2128Open in IMG/M
Ga0209563_108244All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Hydrogenophaga → unclassified Hydrogenophaga → Hydrogenophaga sp. T41655Open in IMG/M
Ga0209563_108929All Organisms → cellular organisms → Bacteria → Proteobacteria1551Open in IMG/M
Ga0209563_110155Not Available1388Open in IMG/M
Ga0209563_110888All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales1306Open in IMG/M
Ga0209563_114146All Organisms → cellular organisms → Bacteria → Proteobacteria1032Open in IMG/M
Ga0209563_117353Not Available865Open in IMG/M
Ga0209563_117739Not Available848Open in IMG/M
Ga0209563_118385All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria821Open in IMG/M
Ga0209563_120435Not Available745Open in IMG/M
Ga0209563_121717Not Available704Open in IMG/M
Ga0209563_122235All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales690Open in IMG/M
Ga0209563_123760Not Available648Open in IMG/M
Ga0209563_123999All Organisms → cellular organisms → Bacteria642Open in IMG/M
Ga0209563_125438Not Available609Open in IMG/M
Ga0209563_127920All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales561Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0209563_106018Ga0209563_1060181F049682MDQREFEAVVDEYGADLQDLVELVETARYEQATAVEISRLLDAREDLLALVARLPALRAVAAPPDMSVPLASLRTRIAHAREALKTSHDSKEILQMVAETGETFATIVAPLQAAGRWPKSRSR
Ga0209563_108244Ga0209563_1082442F012876MTKTTSQAAAIVLSALMTLAVVAGMNGIATKQYAAADALAMAPYGQAHVAVQHVVVIGHRANA
Ga0209563_108929Ga0209563_1089293F067349MQASQWRRMLAPNRLSVLISAALAVATPLLAGAHAWRLVDEEHHWDGGDVLLYWPSLLLDQLPPLAAEAFQRSALPTVLLYFFGYLLMCQLARTLWRSIR
Ga0209563_108998Ga0209563_1089981F099381MSEDFKPGTRPLLRLAGLDAVRAFVSRSDEAHVIWTAVMALMLRLYAEPDAKTRRESGPTDSQIVTALRTVLSENFGSEAADYASWALVRYGCRQKPTMSALHPWEGLMFEWQQRKASAPRISLMLRDGGFEQPIKPASLEAIDGWVTDPVQALGAATDIIEALFGERLVSYDLHDDGTPPAHETLFGGLVASLLPQARLTDLRQNLVRGDSGAVWRVEYSFEGEQRLFDAQANGSTMDVDAVMAAADALFEHLGRPERVYRLAPGRYNNGETGTFVVVNANKFPEVAWRLRLPLLRSPSVSELSPGIPTAAPEPLRVGARPMAPRPVAAAPARPVSA
Ga0209563_110155Ga0209563_1101552F012876MTKTTAQAAAFALSAFMTLATVAGMNGIATKQYAAADSLAMAPYGQTHVAVQHVTIVGHRANA
Ga0209563_110155Ga0209563_1101553F012876MTKTTSQFAALALSAFMTAALVSGMNGLATTQYAAADSLAMAPYGQTHVATQHVTVVGHRTNA
Ga0209563_110888Ga0209563_1108882F078153MGWIVFEALLALGVMLALVWWTFRGRADTAVEEDDADPSQSRH
Ga0209563_114146Ga0209563_1141462F090602MNYSPISPSASRVEWELLPSLLNMLGSRRARSQPAWMDTLLSELDVVEPSGAFEEVLPGLDMREVREPDIFQIFFG
Ga0209563_117353Ga0209563_1173532F056275MDWHCINFTRGRSAETEAADLVLALEDAYGSAGEPPAAEVFLSHRPIGGYAFYLSPEAARMAPSVLQRFHAVTCDPPADLHRCTPMLL
Ga0209563_117739Ga0209563_1177392F034241MSQARPRQYLGALRAALAAAKAENAVRAAAYHVLPNGISCKMDWAGWSDPFYHATARQQALLDVLQDLLDGGETEVPMIALKTALRLEIPESEILRSRDNVGADGESGYFFDDVMHALYMLDAQETEQVFYGLIDRLMQPQSVRTGLLAR
Ga0209563_118385Ga0209563_1183852F040130VKGFLTRTLAILAGIVLGMLVVAGSGPWRELFRKSDSPASAPIQRERAPDTRV
Ga0209563_120435Ga0209563_1204351F036776MNSIVRMLAVYAGLSLLLCGFAQSQWSPLQPNGFGQWVALFLLIFPAAALAEFLGERLLGKRAAVDFEESKSHSDCSWGRIAASVALVTVTVSVVIGAAWWLSHPAASCDDSIGCIR
Ga0209563_121717Ga0209563_1217171F050419MTDARRPSFLRNFGRAAQARRTPDLADMGTAFALDEALDMGDYSTLAPGETPPMRPVVPVAPWRLWLGRKLGA
Ga0209563_122235Ga0209563_1222351F060114MTSPLNDIFEKQRIENARLSGQIVALEMAVKLLFIQHPHPAALGALYSKAIDGLLDITLATRMPEEMRDALDQARDGLLEALRQQPAQGG
Ga0209563_123760Ga0209563_1237602F012876MTKTTAQAAALVLSVLMTLATVAGMNGIATKQYAAADSLAMAPYGLTHVAVQHVTIVGHR
Ga0209563_123999Ga0209563_1239991F062899MNSLAANHTAARPLPLGRELEQHCSFVEDLNWPAARPTPGKKAPRPTDVWVPGPNGQWEGVTPTLQ
Ga0209563_125438Ga0209563_1254382F036775MYDQLDQISAFTEIEDRPGQQQRLCLSDAVFYAGCFGMALLPAALAGVLLYDYIGEPLLFLAAVVVFTWVVVTVALVKIAGPLLRCRAIVAAGGLVSVAMCSLFLLD
Ga0209563_127920Ga0209563_1279202F024826AGKPDSVETSSDDEGGAVETWFYQGGQIELEFEAVPDSKLESITAWSADTTINGVTIIGADLAELPRLAREADIHDLELSDDFAESGQCFQSEQHGLMFWVAKDKVVNLTIFPRFDDSGEEPQWPE
 ⦗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.