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 Ga0228711_1029036

Scaffold Ga0228711_1029036


Overview

Basic Information
Taxon OID3300022739 Open in IMG/M
Scaffold IDGa0228711_1029036 Open in IMG/M
Source Dataset NameRoot nodule microbial communities from Medicago polymorpha collected in Santa Monica, California, United States - brown nodules
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)3100
Total Scaffold Genes5 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)3 (60.00%)
Novel Protein Genes4 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)3 (75.00%)
Associated Families3

Taxonomy
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fabales → Fabaceae → Papilionoideae → 50 kb inversion clade → NPAAA clade → Hologalegina → IRL clade → Trifolieae(Source: UniRef50)

Ecosystem & Geography

Source Dataset Ecosystem
Host-Associated → Plants → Roots → Nodule → Unclassified → Root Nodules → Root Nodule Microbial Communities Of Legume Samples Collected From Usa, Mexico And Botswana

Source Dataset Sampling Location
Location NameUSA: California
CoordinatesLat. (o)34.0136Long. (o)-118.4673Alt. (m)Depth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F002299Metagenome573Y
F003802Metagenome467Y
F021933Metagenome216Y

Sequences

Protein IDFamilyRBSSequence
Ga0228711_10290361F003802N/AVSTAIDLEFIPYQAQRLLKNWTLRLPWIFQFIGSEVYNIVDKTFPLPLLLMEGYVWFRGRSLLFHGINGSRLRPILDRSGGSAAAGRLMLLLVYDCF
Ga0228711_10290362F002299AGGVTSSRDRSLALSGRLAVSVATAKRLPSAKDSLLTPDARTSKAFSDGHMLLNTDSYGISTTPRSNNPSLDVSF
Ga0228711_10290363F021933GAGGMVSRPELAIPRNKWNLTPTHFGQERRVRRSGKDDAAFGFRLPLSHHQPQKDTSKERLFDRGVVLIPYESVLRSMCPSEKALEVRASGVRSESFALGKRFAVAKLTPTLLPRAKLRPRLLVTSGCLFRHPRSKSAPARIS
Ga0228711_10290365F002299AGGVTSSRGRSLALGDRLAVSLATPQRLPRAKDSLLTPDARTSKAFSDGHMLLTIDSYGISMTPRSNNTSMDVSFWD

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