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
Sample 3300021268

3300021268: Metatranscriptome of estuarine water microbial communities from the Columbia River estuary, Oregon, United States ? R9.63.3A (Metagenome Metatranscriptome)



Overview

Basic Information
IMG/M Taxon OID3300021268 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114516 | Gp0225677 | Ga0210294
Sample NameMetatranscriptome of estuarine water microbial communities from the Columbia River estuary, Oregon, United States ? R9.63.3A (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size19963883
Sequencing Scaffolds10
Novel Protein Genes10
Associated Families10

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
Not Available4
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae → Guillardia → Guillardia theta1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Cryptomonadales → Hemiselmidaceae → Hemiselmis → Hemiselmis andersenii1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Oligotrichia → Strombidiidae → Strombidium → Strombidium inclinatum1

Ecosystem and Geography

Ecosystem Assignment (GOLD)
NameEstuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series
TypeEnvironmental
TaxonomyEnvironmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series

Alternative Ecosystem Assignments
Environment Ontology (ENVO)estuarine biome → estuary → estuarine water
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: Oregon
CoordinatesLat. (o)46.249Long. (o)-123.986Alt. (m)N/ADepth (m)3
Location on Map
Zoom:    Powered by OpenStreetMap ©


Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000344Metagenome / Metatranscriptome1257Y
F001926Metagenome / Metatranscriptome616Y
F011303Metagenome / Metatranscriptome292N
F027881Metagenome / Metatranscriptome193Y
F033054Metagenome / Metatranscriptome178N
F039672Metagenome / Metatranscriptome163N
F067774Metagenome / Metatranscriptome125N
F072520Metagenome / Metatranscriptome121Y
F073633Metagenome / Metatranscriptome120N
F084312Metagenome / Metatranscriptome112N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210294_102332Not Available1647Open in IMG/M
Ga0210294_103998All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae583Open in IMG/M
Ga0210294_107769All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae → Guillardia → Guillardia theta674Open in IMG/M
Ga0210294_107803All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Cryptomonadales → Hemiselmidaceae → Hemiselmis → Hemiselmis andersenii1004Open in IMG/M
Ga0210294_108936All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila808Open in IMG/M
Ga0210294_114559Not Available1938Open in IMG/M
Ga0210294_134274All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae879Open in IMG/M
Ga0210294_137364All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Oligotrichia → Strombidiidae → Strombidium → Strombidium inclinatum609Open in IMG/M
Ga0210294_137682Not Available538Open in IMG/M
Ga0210294_143586Not Available666Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210294_102332Ga0210294_1023323F067774MLKLNLKSQDNSLKNLKSSLACYDVSESRFFESNVRKKNDSILLDFGLKHKLRCDDLRINLKLSNPITSKLKDLETPYNDILCDFDAYRKIQSNNELLKLFKEKFNSKSFLKGRLLNGTKRGFSIGVAGVVGFLSMNNTVKINKDKTAILYIDSINMNQGIVSFSQK
Ga0210294_103998Ga0210294_1039982F001926VRHEDIPETNNPKIIFPVLEGDKLMKEVLNGRYNVHPVPPPNSEIKERIRKRYERKRIKIEKLLTL
Ga0210294_107769Ga0210294_1077691F033054VNSMFNLVLQTKDFSANSLKQLMSNNETKFKNFFYQATNNKFVEQFIEPNIQDIEYITNIAKWTIEFFEIISAAQVFGTIYDRLKWKIVDHTFCIWLGAVSKCDYGIHMSFLGLMVAMYSLTMSISMQFLELPPSMIFREIELNAFRLGLWWVTSKNLYYWYNKKISEKYAEGRFRPIDRAEKMALYDQMIGSDTRRTIKMWKWTIRFIVLNLLIRIFEIFTKS
Ga0210294_107803Ga0210294_1078031F073633TMHRRVVMLALAGSAAAFMPGAFVGSTPALAKATSGLRLRSGRTSIKMVDWDWDKKEEEDNYDGPGSERGQINRSDEIGARSKERLENAKKQAMDAGYGSVSGLAAGRSDLKEGDRDPVTGRLILDPLKIPTKDQGAPGTWEEYLKMRKEKEGGTARDVMGNVIDDVKPTYAVQDGTWGPPKEAQKENLDDIFGKKPVSEPVFELDPELERQKAERAADAAKQQDEVEARMAKWMAEAAAKKAAEGGN
Ga0210294_108936Ga0210294_1089361F000344MRPRHPHAAESGVGKHTARESESAKACADGEERVANAHS
Ga0210294_114559Ga0210294_1145591F027881HKFFIMSLTVARSERVRGVLTHASRTEISFNLSGARVSNALRTFRRFM
Ga0210294_134274Ga0210294_1342741F011303NKRCTVEMPGEPKCKKFEDWKKKSEAFLASFKNAKRVIPKGAKPIIVQSKKDEVEVIYPEQCSFTWTAGLADAYPNCTLASGDKSKIFIYNRVLLNAKGECNYFQPVFSSNDFKGADRAEDTDSLLDQIYQEFNAGNARFGDDMKVEFPVVGKMDKAGMFELFAKFGGCQRAMQKGCVPVNMSTGKDEVFEGIVPCVYSFKWSSALNDVFKLELADGADVVLSSYDCLKIKSGKVISFAPHFDPAANIKPAGKSGAA
Ga0210294_137364Ga0210294_1373641F039672VISPKMSPDLTSIRVGQRLPECSAEVVLSTLLFEEIELLEGLQSVDSKDKSVVSSHTKTGHEVLNLDVVEDHSGDVVGVLLSHGLVGVGLNLGGDSVSVSEDGGGDLGAEGSGVVVSLLLGVGDSEREVLGDLVEVTLDGGEELSLWVLLNLSGFGSSRLVSSDVLIGNGVSSHIWESSNVLNGVWVVVVSLDSSSSGDKSA
Ga0210294_137682Ga0210294_1376821F084312ITIGIFTILLTIYLITMNYFLILNDYVHWYFPVVLLVLYIPMIIGSSFFVVFFSKDTQSSRGKLFVSCQFGIISTALACVWILCYYVWIYKSDTVYSGMGDPKDNVYTKQSKKFYLFVVLAETAIICTSYAYFICVTNRYADNMKGKNE
Ga0210294_143586Ga0210294_1435862F072520VTELTDKVVTEDTAPTLTVGDKTYVVADLSNEVKEMLSLHEQAMQMAIGAKRQAVIHDLAVSNIASLIEKKLAETDE
 ⦗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.