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_10000004

Scaffold Ga0307510_10000004


Overview

Basic Information
Taxon OID3300033180 Open in IMG/M
Scaffold IDGa0307510_10000004 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)654130
Total Scaffold Genes560 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)420 (75.00%)
Novel Protein Genes5 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)4 (80.00%)
Associated Families5

Taxonomy
All Organisms → cellular organisms → Bacteria → Proteobacteria(Source: IMG/M)

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?
F004592Metagenome / Metatranscriptome432Y
F022707Metagenome213Y
F047518Metagenome149Y
F048505Metagenome / Metatranscriptome148Y
F087742Metagenome / Metatranscriptome110Y

Sequences

Protein IDFamilyRBSSequence
Ga0307510_10000004181F087742AGTAGMDHEAIYRLRNAVTTARQAAEQARLDNCDVGDIDVALEAVDDELAKPTPNKNTVSLYLNSVARSLIAAPSARDARDQIDSALRKSGLPATWEQ
Ga0307510_10000004445F004592AGGMSATEELRAEWLGTQFWDRLDRLEELHQRVHTEHRIVRRNLQRVTPQEADELRIAWRRYCEVITELEKTTAEFETFRTFER
Ga0307510_10000004446F022707GAGMRLLSRRALDELAELQDAMQELADHRGAALRIFITSRNTTTPVAQREFWLEFSWIDQEYRAAVVKLAQFCSRYGDSVRGKYELLQRRARKLE
Ga0307510_10000004505F047518N/AMDEARRIVRFRGGVSCRRDDSPFGLTLIGRTIDRSDEIATLAFLGTAPPGLPEALEDATVEEIAAGQYRIWSGRREWLIPARSVHLHREVSATFYRAIAPRLVPWNKKLFWRIVLSMAASRVGKSLLLTLRRR
Ga0307510_10000004523F048505AGGAGMNALNAALKAGACGLGALAITAVMSWSFVQSTSTAPGVVPVAQMAKLTIQQRHVWFGQSQPAVLVD
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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