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 Ga0209488_10006365

Scaffold Ga0209488_10006365


Overview

Basic Information
Taxon OID3300027903 Open in IMG/M
Scaffold IDGa0209488_10006365 Open in IMG/M
Source Dataset NameVadose zone soil microbial communities from the Eel River Critical Zone Observatory, Northern California, USA - Rivendell_Oct2014_Saprolite_2_DNA_Bulk_2 (SPAdes)
Source Dataset CategoryMetagenome
Source Dataset Use PolicyOpen
Sequencing CenterDOE Joint Genome Institute (JGI)
Sequencing StatusPermanent Draft

Scaffold Components
Scaffold Length (bps)8962
Total Scaffold Genes11 (view)
Total Scaffold Genes with Ribosome Binding Sites (RBS)7 (63.64%)
Novel Protein Genes3 (view)
Novel Protein Genes with Ribosome Binding Sites (RBS)3 (100.00%)
Associated Families3

Taxonomy
All Organisms → cellular organisms → Bacteria → Acidobacteria(Source: UniRef50)

Ecosystem & Geography

Source Dataset Ecosystem
Environmental → Terrestrial → Soil → Unclassified → Unclassified → Vadose Zone Soil → Vadose Zone Soil And Rhizosphere Microbial Communities From The Eel River Critical Zone Observatory, Northern California To Study Diel Carbon Cycling

Source Dataset Sampling Location
Location NameUSA: California, Eel River Critical Zone Observatory
CoordinatesLat. (o)39.7291Long. (o)-123.6419Alt. (m)Depth (m)
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000180Metagenome / Metatranscriptome1730Y
F017689Metagenome / Metatranscriptome239Y
F073846Metagenome / Metatranscriptome120N

Sequences

Protein IDFamilyRBSSequence
Ga0209488_1000636510F000180AGCAGMTITKEHSFVASDYSDRELYTSSRTRERALNSAIVQADINESFEEYLEIFDAFYAADVEASSETRKEPIRGDRVRSLLTNFLVPLHVMAEVGRLSISICQTTIPGDIADETHSAWTLDLVGVSGRTCTVTWRTLRKWRDSLVVYEHHYDEQQNGGPLTSDDLSFDTANVS
Ga0209488_100063653F073846GGAGMHCPLCKAQYGAGYDLCRGCDADLVFTKEQADAEDVVLFLESANLTGVGELADALKEANVPNYSRFAVGKAKAPVIGLFAQAKAAKEQSWQIFVLESDLDRARQVAFAARFAGRYPEPGDRRARLARCLPTKSLTS
Ga0209488_100063655F017689GGAGGMLFATVSRGKNRGMRLRPHRFKDDRYHMQLGKRGLYIPINDSRDIPCCLANGYSLR
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Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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