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 3300028528

3300028528: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.376 (Metagenome Metatranscriptome)



Overview

Basic Information
IMG/M Taxon OID3300028528 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114516 | Gp0225720 | Ga0210336
Sample NameMetatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.376 (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size96167125
Sequencing Scaffolds12
Novel Protein Genes14
Associated Families14

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
Not Available7
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium1
All Organisms → cellular organisms → Bacteria1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Electrothrix → Candidatus Electrothrix marina1
All Organisms → cellular organisms → Eukaryota1

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 → sediment
Earth Microbiome Project Ontology (EMPO)Free-living → Saline → Water (saline)

Location Information
LocationUSA: Washington
CoordinatesLat. (o)46.302Long. (o)-123.036Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F009271Metagenome / Metatranscriptome320Y
F011154Metagenome / Metatranscriptome294Y
F027700Metagenome / Metatranscriptome193Y
F036294Metagenome / Metatranscriptome170Y
F053305Metagenome / Metatranscriptome141Y
F056298Metagenome / Metatranscriptome137Y
F059103Metagenome / Metatranscriptome134Y
F060937Metagenome / Metatranscriptome132Y
F076890Metagenome / Metatranscriptome117N
F087396Metagenome / Metatranscriptome110Y
F092076Metagenome / Metatranscriptome107Y
F098390Metagenome / Metatranscriptome103Y
F105215Metagenome / Metatranscriptome100Y
F105482Metagenome / Metatranscriptome100Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210336_1004245Not Available953Open in IMG/M
Ga0210336_1005227Not Available895Open in IMG/M
Ga0210336_1007870Not Available795Open in IMG/M
Ga0210336_1014132Not Available670Open in IMG/M
Ga0210336_1015764All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria650Open in IMG/M
Ga0210336_1022170Not Available590Open in IMG/M
Ga0210336_1024586All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium574Open in IMG/M
Ga0210336_1025420All Organisms → cellular organisms → Bacteria568Open in IMG/M
Ga0210336_1026203All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Electrothrix → Candidatus Electrothrix marina563Open in IMG/M
Ga0210336_1032911All Organisms → cellular organisms → Eukaryota528Open in IMG/M
Ga0210336_1038642Not Available505Open in IMG/M
Ga0210336_1040058Not Available500Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210336_1004245Ga0210336_10042451F105215MYIKTDPRNSEGSSRTLLFHQDPDIRLDAALQLGGDTNRIADQRLALEALTTALEDPCSTVQEAVLQSLMRMSVKNG
Ga0210336_1005227Ga0210336_10052271F009271MIRPMTSNVSALSGIVANGHQAIHFVSSAPSKIPYGGFSPVRLQTRLTPRPPSRTAPRPLIGRHCSYLHSRRFIRSGSCDQAAPRTSDQNRESSGPWLPGRLCCPARSSLTMATSAPLSAPERLMDYSVRLRVQPANRRGSPIYSASPFTPFRRPYSGGPGECAQQCLPRRFCLRRICTGSATTGPTIPDRVGRVTKLQRSLYATACECRLPCSGQDVYDRACVGRVTPIPHVGYHWMVHCHLPSPVFHRLDWQPYGLRADSRGSTQIRRLRTKEGGVTSGRS
Ga0210336_1007870Ga0210336_10078701F060937NRGAGSGRKIEECTAGIIPGDWGTAGPGWLVPPLGSRIARFEERRQYSPAPLAGIATRHNAIEELGGEER
Ga0210336_1014132Ga0210336_10141321F098390MYHGKVTSGPNETQDKDGKNLCNRWQVVYDDGDVEEMTASEIDAWKMPPKEVRAATKKVRATGPSGDHIEELRDNVPKPIKDASAPTHRRRTTKRQQQSAEAARMHFLESNPYLPMDSLSMYEAATCRIHLNDNDPYDELLQNVDEVETLLQDPEVITAIYKLLDPDSDLEDLKLRALQSEAITPEEQALPRFSRRALQKLPTWDLWHKNEIEQL
Ga0210336_1015764Ga0210336_10157641F092076DKLQEIIFTQASGTPTTVTMMDHIQNVMNDPDFDAKYNSIIVLEEHTHIAGVPTEKIETIRRVLDGYAQQRTGRNWAVVAPNERLEAFVKLNLELISPVIFNIRIFRSEEDALNWIKRRQPPLC
Ga0210336_1022170Ga0210336_10221702F053305MLKKSVSMALMALFVFSFIAVATVSADETQKITGTVMSVNVETGEVIVKDDAGEMKSLMADPKAEGAVDLKMLKEGDPVSVESDSNGVIKSLKAGE
Ga0210336_1024586Ga0210336_10245862F059103MSAPDPRDFVLRFAPLDARTAAWMLDFCGHLQQEIWRAYGDEIEALWAATDPEQPIYGPLQPPTPSRKRR
Ga0210336_1025420Ga0210336_10254201F105482MDLIHPNSRDEVVRAIRDANSTNKRVLVIGGRRHIDKGNETEVDAEM
Ga0210336_1026203Ga0210336_10262031F036294MDRGSSDEAKVGVKLIAEEDAVTYLRVKLSESDKDVGAEGWN
Ga0210336_1032911Ga0210336_10329111F027700YTKSALPPMPLSDSTKEMSLEQADKAGISMIEDHPLNSPSHELKLHQLSARQERLLWHQRLGHCGDEQLSKAHEYCDGVPKISSKAKSVVDECHVCIAANMKARERGDGITRTATISGQGLSIDFSFAGQHSKNALNPERMRINDYMGLNGETCYLLLYDHATERLSGVCKQSKA
Ga0210336_1033888Ga0210336_10338882F076890MIGTRSVAAMLVAMSALGTSACSTLEVDDYCRYSETRSIRTADPESLALVLGVQAGRTRQTPFVVIRSLSESRPGASVTLHTTPAAHPMPMGLDESRCARVDWSTYTLAVDPDEWNAFWQDDRNSPFEIGIAFLEDF
Ga0210336_1038642Ga0210336_10386422F087396SPSVEKPQTMDESPSVEKPQTMDESPSVDTSPALLEHLTLNLDGFVLDERAVVQSRILPYVRMVASVLERRTISREELIAALLRSMRQRSMARAPRREYVLRYLNQHPP
Ga0210336_1039502Ga0210336_10395021F056298MRARDRGDGDTRTATIAGQGLSIDFSFAGQTSKNSTDPDRMRINDYMGLHGETCYLLVYDHATEQLEGVCKQSKAPPVAWLRRWLRKNVDKDVKNRYVFMDQGGELYKSKAIRDLFEKEFDYDIRVTGTAAHHQNGLVERANQTVDKAIRALLIGAGPEVKFWPYVF
Ga0210336_1040058Ga0210336_10400581F011154MRSDEKPLRIESSRPGRFRAWVNRSYPEGIRLLLCISTGGRLWRPPEGGLPNERRRKAGQSERPNREGHAASAGPVKTFQAVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDADQKTQTCLDLVRKPVAQPPAQAS
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