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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Scaffold Ga0307510_10017272

Scaffold Ga0307510_10017272


Overview

Basic Information
Taxon OID3300033180 Open in IMG/M
Scaffold IDGa0307510_10017272 Open in IMG/M
Source Dataset NamePopulus trichocarpa ectomycorrhiza microbial communities from riparian zone in the Pacific Northwest, United States - 12_EM
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)8514
Total Scaffold Genes18 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)13 (72.22%)
Novel Protein Genes6 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)5 (83.33%)
Associated Families6

Taxonomy
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Fungi → Dikarya → Basidiomycota → Agaricomycotina → Agaricomycetes(Source: UniRef50)

Ecosystem & Geography

Source Dataset Ecosystem
Host-Associated → Plants → Roots → Unclassified → Unclassified → Ectomycorrhiza → Soil And Ectomycorrhiza Microbial Communities From Populus Trichocarpa Stands In Riparian Zones In The Pacific Northwest, United States

Source Dataset Sampling Location
Location NameUSA: Oregon
CoordinatesLat. (o)45.654Long. (o)-122.839Alt. (m)Depth (m)
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F016489Metagenome246Y
F016903Metagenome243Y
F029295Metagenome188Y
F044236Metagenome154Y
F059500Metagenome133Y
F075486Metagenome118Y

Sequences

Protein IDFamilyRBSSequence
Ga0307510_1001727210F016489AGGTGGLILYATLDIWETTSKGPYLLGDNLGVMLLGSCKFVPSNQTFDLTGNGEWCGHSLIQDSCALHCASWAAFLASSMDKSCCSRDGMSVFLVGWCTCGV
Ga0307510_1001727211F029295AGGMVEVVNPVLGSSWWTEDMVVGDRERHLRFQGFLYCLVDFQSPLVDPKHGDPRS
Ga0307510_1001727218F016903N/AMTTPSSFGLADLYRTPVQTIVELEDKAMEEGETSDSDSAMEEGQIDNTRQSTLDSMDIGVPRVPSDWLQPGSP
Ga0307510_100172727F059500AGGAGGVSVDFSHLASSAAFDILSYKDFHSRPPVVGCDKLEGFGNSGVSSSFVVMKKGCYSPPKVIVCHDNKCHSVVPVSAVQ
Ga0307510_100172728F044236GGAMDAFEQSMSVIMRMVSYPPDRGNLVMKSIATVSKGQAFSVRVIGNIGG
Ga0307510_100172729F075486GAGGMPVVLLSATEYTKVLFEGLVSMFASSICLRVIGCADVLVNVQDAA
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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