NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters
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Sample 3300025272

3300025272: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mCL_r2 (SPAdes)



Overview

Basic Information
IMG/M Taxon OID3300025272 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0053073 | Gp0101302 | Ga0209455
Sample NameArabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mCL_r2 (SPAdes)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size201830048
Sequencing Scaffolds13
Novel Protein Genes13
Associated Families13

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Bordetella → unclassified Bordetella → Bordetella sp. FB-81
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae1
All Organisms → cellular organisms → Bacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Aeromonadales → Aeromonadaceae → Aeromonas1
Not Available5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → unclassified Methylovirgula → Methylovirgula sp. 4M-Z181

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
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F023377Metagenome / Metatranscriptome210Y
F027546Metagenome / Metatranscriptome194Y
F031516Metagenome / Metatranscriptome182Y
F035339Metagenome / Metatranscriptome172Y
F040711Metagenome / Metatranscriptome161Y
F044585Metagenome / Metatranscriptome154Y
F052031Metagenome / Metatranscriptome143Y
F055847Metagenome / Metatranscriptome138Y
F070251Metagenome123Y
F080227Metagenome / Metatranscriptome115Y
F080539Metagenome / Metatranscriptome115Y
F080973Metagenome114Y
F095729Metagenome105Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0209455_1003683All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria5310Open in IMG/M
Ga0209455_1004631All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Bordetella → unclassified Bordetella → Bordetella sp. FB-84441Open in IMG/M
Ga0209455_1019431All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae1373Open in IMG/M
Ga0209455_1019456All Organisms → cellular organisms → Bacteria1371Open in IMG/M
Ga0209455_1021638All Organisms → cellular organisms → Bacteria → Proteobacteria1243Open in IMG/M
Ga0209455_1028704All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Aeromonadales → Aeromonadaceae → Aeromonas969Open in IMG/M
Ga0209455_1030542All Organisms → cellular organisms → Bacteria → Proteobacteria917Open in IMG/M
Ga0209455_1033850Not Available836Open in IMG/M
Ga0209455_1035075Not Available811Open in IMG/M
Ga0209455_1038916Not Available738Open in IMG/M
Ga0209455_1045627Not Available640Open in IMG/M
Ga0209455_1048550Not Available606Open in IMG/M
Ga0209455_1059853All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → unclassified Methylovirgula → Methylovirgula sp. 4M-Z18502Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0209455_1003683Ga0209455_10036835F080973MVLAAATISMAYPTQGDVREMIAGAIGELTGTPAAEVDLGNSRVLVLTDTRSGYNWSYPDAMVKARFRPFVHRAVSMVRQQYPILR
Ga0209455_1004631Ga0209455_10046312F070251MSAPGRPKRSFPPWGEGAQRQGGAMSAPGRPKRSFPLGGKARSAKGAI
Ga0209455_1019431Ga0209455_10194312F055847MNRRYAYRDYAILVSAHPAAGARGWRPEICVIAPDDRWEFVPTHHSLVANDPQYCLEIGRLCAESAIQSMDPAREKAAYAGLLH
Ga0209455_1019456Ga0209455_10194561F040711MHRGHSRSGALDLPDPSLLVEQALMSSDSSRDRLAAALGDDAKNVLMERGYSLGFVGVHGQVRLVQFRLSKKGFALDAAADDSDFATMLDEFTTLVTRLLMERWGGIALRAAFDAEGELVERLYETGTLDRCDEMDPVSPAKKLVKDGEQVDARELLVRASARLVEN
Ga0209455_1021638Ga0209455_10216381F027546MKVAGETEPERWRPLGERVAHTPPAKPEWQPLPHAPCIEVNRQGQL
Ga0209455_1028704Ga0209455_10287041F080227SGAFAADDGCRTNANGVQTCDVATGHESSRAAVVAEIHAKADTSTGCRTVANGVQVCDLPTGRERTREAVVADLHGGAGYAIEGCRTVANGVQKCDVPTPFAARRETTTAAAR
Ga0209455_1030542Ga0209455_10305422F052031MTIDPPATHPAATEHHEEMVQFVFRSAASSGLLEHARALLGAAPRELAESFEQAVRSAGLAS
Ga0209455_1033850Ga0209455_10338501F035339ADRLASAPLTLRQLRADRVVLWCWLPLGGFAMFAVVAGWRHLAGEPPPWLYTTLDVLWIAVTFTLIARRSTARCPRCNHRWLRAFPWMSLGKVECGVCGHEMPEG
Ga0209455_1035075Ga0209455_10350751F095729MKLSFRQFALVSTLLATAAFPLLSHAQDVRREDRVLHFLDSGHIDANKDGMVSKKEFMDAMSKTWDMHMDDAKKAEPMMQKDKMTLQQ
Ga0209455_1038916Ga0209455_10389161F044585MTPAEIDHQALTALRLLPDEPERAMRVWDDAFARATAAGLDRTLLRLRIVKMHHQARFGDRHALGPKMLAATVEARAHGWRTESLLVDLLEVFLATLSANHADGMGDVEAIRAEAEAHLDPIELSWMELMAGHFRGYMLGWALEPERTYRALNRLIACPDSPPGLVANVQMNIGHSHLLVGNVDLA
Ga0209455_1045627Ga0209455_10456271F031516MNDIRNPSDVDMLHFDTAQMAAITQAHFFSRVAEFIRDQTTVPAYRQAALDTALRTSLWAPHWSTLRDATEHDAALFMCFLLACATLGVDATRAAEAVRQTSDPETSMKLFLSERGLLRFSAF
Ga0209455_1048550Ga0209455_10485502F023377MTHRPVRLPRAFRMAMAATFALAAVGVQAMTVSYQCTGRRVLTAELTPRQGQLHFEGHDWTVRRVPDGHEARYVNKKDAVSVVTRERTMTFTHGDETLQCFLYSDALPGDAPQQKAN
Ga0209455_1059853Ga0209455_10598531F080539LEGFDIRITGVYTKPRPFGFDFDCKRPRDLLVLARSKAVLNEDKDDTLEGAVSAEQTHGTGFRQIGTGPRLHLEIAMDRKCNVHIDSHGYVVGPGQYDWNRALEHGYWDLLSDKAPGLFGAFGKQGQVGPMIRPMQGVDGRMRWVIGLTGHW
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