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
Scaffold Ga0307512_10000293

Scaffold Ga0307512_10000293


Overview

Basic Information
Taxon OID3300030522 Open in IMG/M
Scaffold IDGa0307512_10000293 Open in IMG/M
Source Dataset NamePopulus trichocarpa ectomycorrhiza microbial communities from riparian zone in the Pacific Northwest, United States - 14_EM
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)72107
Total Scaffold Genes87 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)54 (62.07%)
Novel Protein Genes5 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)2 (40.00%)
Associated Families5

Taxonomy
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Fungi → Dikarya → Ascomycota → saccharomyceta → Pezizomycotina → Pezizomycetes → Pezizales → Pyronemataceae(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)45.6996Long. (o)-121.669Alt. (m)Depth (m)
Location on Map
Zoom:    Powered by OpenStreetMap ©

Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F004778Metagenome423Y
F004891Metagenome / Metatranscriptome419Y
F008227Metagenome336Y
F010438Metagenome303Y
F026456Metagenome197Y

Sequences

Protein IDFamilyRBSSequence
Ga0307512_1000029321F004891GGTGGMIAQASGLGMGVGRFSRPLRGVGVLAMVDAKQDATRHIESVSQVPPGAGGLQLFVPGIAVGVFIDRRCVVDGVAVTD
Ga0307512_1000029322F010438N/AMVSGSRSIHRFGHSDMTRLDFATDTLMELYLWNRLLCMSGSNLEMVSYATRRVEKALAEAPHWQIIEKYWNTAMQQNNIWSIACEARTKEILKEVC
Ga0307512_1000029346F008227N/AMDTQPPPPGESRSYTGRSVGATSNTDILGTQRERRHKLVLHDAAYAATKPMTEDAHLNIVRKTGSSKNKKQHAVGCEYIHIEANGGQLTV
Ga0307512_1000029351F004778N/AVLSRFELTDSRLLGITTDNVSSNYSMTRELQSTLEASGIEWPALRNHIPCMAHVIHLALGAFMSSLGVKGHTKSWEAHERDQQFGDNESIDIGNSQRLRKEGNARIDKVSAMRPGLAKIIEKVHIS
Ga0307512_1000029358F026456GGAMVTLHHVITDYNDMFDHMDGIMRALVKKKTQWKEDLYFTVNFAQQKFSKYYTEVTPTTGVHFNLAHILDPFQKLLSFRKSDKAMHINPENVTSYTTQYQAAFLKYVEN
 ⦗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.