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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Sample 3300004184

3300004184: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 1_LOW4



Overview

Basic Information
IMG/M Taxon OID3300004184 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114290 | Gp0111065 | Ga0066401
Sample NameFreshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metagenome 1_LOW4
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size261524419
Sequencing Scaffolds8
Novel Protein Genes9
Associated Families9

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 28-67-81
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → Methylobacter → Methylobacter marinus1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameFreshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension
TypeEnvironmental
TaxonomyEnvironmental → Aquatic → Freshwater → Sediment → Unclassified → Freshwater Sediment → Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension

Alternative Ecosystem Assignments
Environment Ontology (ENVO)freshwater lake biome → freshwater lake → lake sediment
Earth Microbiome Project Ontology (EMPO)Free-living → Non-saline → Sediment (non-saline)

Location Information
LocationUSA: Lake Washington, Seattle, Washington
CoordinatesLat. (o)48.3807Long. (o)-122.1599Alt. (m)N/ADepth (m)N/A
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000982Metagenome / Metatranscriptome814Y
F016989Metagenome243Y
F033105Metagenome / Metatranscriptome178Y
F036304Metagenome / Metatranscriptome170Y
F040165Metagenome162Y
F066900Metagenome126Y
F077414Metagenome117Y
F082950Metagenome / Metatranscriptome113Y
F087391Metagenome / Metatranscriptome110N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0066401_1002826All Organisms → cellular organisms → Bacteria → Proteobacteria2384Open in IMG/M
Ga0066401_1006465All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria1697Open in IMG/M
Ga0066401_1033023All Organisms → cellular organisms → Bacteria → Proteobacteria856Open in IMG/M
Ga0066401_1037567All Organisms → cellular organisms → Bacteria → Proteobacteria810Open in IMG/M
Ga0066401_1077372All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → unclassified Burkholderiales → Burkholderiales bacterium 28-67-8586Open in IMG/M
Ga0066401_1081523All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Methylococcales → Methylococcaceae → Methylobacter → Methylobacter marinus572Open in IMG/M
Ga0066401_1091034All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria544Open in IMG/M
Ga0066401_1099044All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium523Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0066401_1002826Ga0066401_10028264F040165MYAAVLTFCVLAGEAVNLSRGSEVTALTLGNWTLSAALLTALWGYALQRRIGSAGYWRAVFWLVLFANSVMLIPVLLGDRTVAMFTAALTLLIVPAYLAAYLYAYRSPALWSPRALA*
Ga0066401_1006465Ga0066401_10064651F077414CGQLAGWDWQEAARVLDVPPAKFGRLLTLQDALRAAVRNWPGTARSTV*
Ga0066401_1033023Ga0066401_10330231F036304MSDTIIPEEVLALLFPEPASAGNPSSSVTAFVRDPHGGLMLASVVPNRTLLEAALVTGRWNSGTPILDPQTREIIGYELAPLAVA*
Ga0066401_1037567Ga0066401_10375671F087391MKLTKFALLAVAAGCTLASQGVYAQAMEVVTVEAVREIVIGKSPIGAPIKELTIRARVSYADLDLTTATGAATLEKRVRDSATSSCKEIKVDVPVEGWTVDRCIREATEGAMVQVN
Ga0066401_1077372Ga0066401_10773721F066900MIKYQTLPDMLDDSASGDGAIVYLEGEGAEKALKLSELRRR
Ga0066401_1081523Ga0066401_10815231F016989MLTRDKLTIVQWQAVRNTPHHVIIAVSSSGGSAFDEMLERSAGLQGIVDASHSTHPLVSEIGGGTHIMQAQDDVRKWFYTLDEGHRTPDKLQEKALETARHALEALGTHGSAEDLMHYGEFVLSLATRVARAAREGDLMGIGGELVSEKERKFIERLDQLIQERRTR*
Ga0066401_1091034Ga0066401_10910341F033105MEPRRPIREPTYHWPGGPTADDDPTPIESALAALKIGAILAAAITIAFIYLGTYAGIVAGQVESTIIVLAAFVSPSLIAAGRTAW
Ga0066401_1099044Ga0066401_10990441F082950MASMLRSTSASVVAQEQTLMRIAARPCQRLPPHQQVPSAWSSS
Ga0066401_1109096Ga0066401_11090961F000982MPSYRSTSRGRRLLVHHRLRGRAYPTLPYWERLHLMLLEEAEKRGKTPPPAPLVHGLESEPTQADRMERLDEQVAWADRNQLLH
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