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 3300021313

3300021313: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.304 (Metagenome Metatranscriptome)



Overview

Basic Information
IMG/M Taxon OID3300021313 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114516 | Gp0225717 | Ga0210333
Sample NameMetatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.304 (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size190066344
Sequencing Scaffolds21
Novel Protein Genes23
Associated Families20

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta2
Not Available9
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium2
All Organisms → cellular organisms → Eukaryota2
All Organisms → cellular organisms → Bacteria2
All Organisms → cellular organisms → Bacteria → Terrabacteria group1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales1

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)46.27Long. (o)-123.946Alt. (m)N/ADepth (m)0
Location on Map
Zoom:    Powered by OpenStreetMap ©


Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F001314Metagenome / Metatranscriptome725Y
F001346Metagenome / Metatranscriptome718Y
F001506Metagenome / Metatranscriptome681Y
F001679Metagenome / Metatranscriptome653Y
F007629Metagenome / Metatranscriptome347Y
F012678Metagenome / Metatranscriptome278Y
F013273Metagenome / Metatranscriptome272Y
F017072Metagenome / Metatranscriptome243Y
F036102Metagenome / Metatranscriptome170Y
F038934Metagenome / Metatranscriptome164Y
F048318Metagenome / Metatranscriptome148Y
F054544Metagenome / Metatranscriptome139Y
F057770Metagenome / Metatranscriptome136Y
F061584Metagenome / Metatranscriptome131Y
F062310Metagenome / Metatranscriptome130Y
F064269Metagenome / Metatranscriptome128Y
F070130Metagenome / Metatranscriptome123Y
F087396Metagenome / Metatranscriptome110Y
F095415Metagenome / Metatranscriptome105N
F105059Metagenome / Metatranscriptome100N

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210333_1006476All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta759Open in IMG/M
Ga0210333_1060178Not Available504Open in IMG/M
Ga0210333_1084522All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium655Open in IMG/M
Ga0210333_1088820All Organisms → cellular organisms → Eukaryota1111Open in IMG/M
Ga0210333_1115247Not Available539Open in IMG/M
Ga0210333_1127438Not Available507Open in IMG/M
Ga0210333_1139550Not Available943Open in IMG/M
Ga0210333_1152764Not Available891Open in IMG/M
Ga0210333_1174412All Organisms → cellular organisms → Bacteria561Open in IMG/M
Ga0210333_1178660All Organisms → cellular organisms → Bacteria → Terrabacteria group731Open in IMG/M
Ga0210333_1209161Not Available650Open in IMG/M
Ga0210333_1211046All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium970Open in IMG/M
Ga0210333_1217201All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta656Open in IMG/M
Ga0210333_1257642All Organisms → cellular organisms → Bacteria4077Open in IMG/M
Ga0210333_1263876All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium552Open in IMG/M
Ga0210333_1285728Not Available661Open in IMG/M
Ga0210333_1301686Not Available596Open in IMG/M
Ga0210333_1342878All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Streptomycetales → Streptomycetaceae → Streptomyces701Open in IMG/M
Ga0210333_1346283All Organisms → cellular organisms → Eukaryota508Open in IMG/M
Ga0210333_1347800All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales567Open in IMG/M
Ga0210333_1371446Not Available550Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210333_1006476Ga0210333_10064762F001506MNRILYENRCRCNEEFSLTKKRQSTTRSEGKPLQYPNYTESTSKTFQIKYDKKLSSLAKAILNSFQKKYIYYAIDDILYFLKGNSIEQENLLAILYSQILSLHNNFSINFFDIWIGEVYIEEISKVNKFLTKDSQTF
Ga0210333_1060178Ga0210333_10601782F007629MAPEAAGKEGSNVETKDVAEMVSKLDAKYNVKVTAQGKGQKNDHVLIEGSDNGSISPVIQAGNQGSRPENTVRPKGKDTNPRTEQSKGIKK
Ga0210333_1084522Ga0210333_10845221F070130MTQVRPLPDSSASQPDFFAGWWEIVFHTRDGEQTDVTGIIEHVDAAGNFAVFSGGERIGAGCHVDFTLDPDGFTNVQEAPDPHEQTARELAIYRFSGDVLEVCKASEHGGRPTSFGSPRGSGWTHVAIRRISDDDPRVRAQR
Ga0210333_1088820Ga0210333_10888201F062310KFMSGLRKKLNSLDTELGLMEMVLAGIKSALIRQPFSVPQDLRNLAAAQEAIGWTNLFKGRISKQWIEQQRHYIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGRANKLKDVAFREMTHLYTFEEAIPEDIRWLFQTPLEECLHWPLFRQRAWITNWEHIIKKEHAAQMETG
Ga0210333_1115247Ga0210333_11152471F017072MNRSHPEGEQLLLCISTVRAALAESNQIEAAQRKTPKGGQKERGHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKCNLREKRRDPWFRANASSKAMADPGLVVKTRTRDPQACLDLVRKPVAQPPAKAS
Ga0210333_1127438Ga0210333_11274381F095415LVRTIRMNGRNQMKGEMIRWLDAHPHASALDLVKHFCGTIWMGGGTEDGRYKEGQNFNP
Ga0210333_1139550Ga0210333_11395501F012678MLNQHSLEEIADIYNLLGDIKKEYEEGIKPILIKNSPKLFKNPHTVPKLKKFKLIVDLD
Ga0210333_1152764Ga0210333_11527641F061584PSKVRVIDSASRGLVTEPRWTLMKIGRSTECCERRSCRRIRLPAPTMTSLFPGSLCGLTPPPSPVPLRVRVHPLVNFASPSEHEPFRSCPARCRAWRLPWGFFPHRGINTRSPLSIELPTARTIGPSSAFLTPSTVYSSAYLAGLFHPTTTSGIHLSGVISRYQASPPHRRPVPSCRSSTRSYHRVAPTAPDRADPPTGS
Ga0210333_1174412Ga0210333_11744121F087396LDGFVLDESTLFNSRILPYVRMVASVLERRTISREELIAALLRSMRQRSMARAPRREYVLRYLNQHPP
Ga0210333_1178660Ga0210333_11786602F001314MWILFQVPCPTTDGQSAKDLYDKRVTGITEAMQASAEQHGCQFHRAWHASDGSAFYAIAKWESREGASAFFEEWQIEDEPGEIAVIPEGDVGLVPQP
Ga0210333_1209161Ga0210333_12091611F001346VVWAGPVKTFRKVGDVKNDTADLWTKGNLRVKRRDPWPRANALPQAAADPELSGQDADRKTQTCLDPVRKPVAQPPAQAS
Ga0210333_1211046Ga0210333_12110462F070130VYVRQMPDTPASQPDFFVGWWEIVFRSRDDEQTDVTGILEHVDAAGNFTVFRDGERIGAGRHVDFRVDPDGFTNVQEVPGEHTQTGRELAVYRFSGDVLEVCKASEHAGRPTSFASPRGSGWTHVAIRRISDDDPRVRTQR
Ga0210333_1217201Ga0210333_12172011F001506NRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSIEITSKTFQMKYQKSLSTTAKCILNSFQNKYIYYAIDDILYSLKSKPIERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVPVKKQASLW
Ga0210333_1257642Ga0210333_12576427F012678MLNQHSLEEIAEIHNLLGDIKKEYKEGIKPILIKNSPKLFKNPHSVPKLKKYKSIGVLGLQLKIQIF
Ga0210333_1263876Ga0210333_12638761F048318MATVENVRLDITASTTKPGHSKIAYSYELHPSEMDCAWQREYTVSVDFWGEDLIDDDLLAWGKDEHTVKFDDSGPCEPKKVERVFEVETKILDEDLFGDDEVYLIVEASSGLGSDEAGEDPVVGRSNTVIGDF
Ga0210333_1285728Ga0210333_12857281F013273MSSRKTSKELQEEIDALTDQLAATLRLEIADLTRQAEEGEIQYQALLRRMIGRRILITKKNDPLFGMEAIITGPRGQSKKPMYWWFQTTTGLKQYKARTSFNLLPDDQQE
Ga0210333_1301686Ga0210333_13016861F057770CYYTPDIPNFILSPNSFKALLGKHYNGYKLECDDDKKNFRFSLNHKMRKSGSVLLRGTTRGGLCYTRPAIPPMPTTEGTAEMSLDMADKAAISMVEDHPKNSYRHEMKLHALSAKAERLLWHQRLAHCGDEQLCRAHMFSDGIPEITRGKDSALDSCPVCLAANMRSRNRGNGETRTATEPGQGLSLDVLFAGQHSKN
Ga0210333_1306890Ga0210333_13068904F105059MKISVEYWDYTCGDGCCYDWGYDVFVDGEKIGQINDTPEELADLLNEYFNTKEK
Ga0210333_1342878Ga0210333_13428782F001679VWGMSWRQKAMKGVEGCDKPGEAVKRALIPGFPNDRTLNT
Ga0210333_1346283Ga0210333_13462831F054544VTHVYDNGTVRLEKVANNNGGAVSETWNIRNIEPRKA
Ga0210333_1347800Ga0210333_13478001F038934AYNDIVDHIEKDCSWVRVWTLEKIITHKKVKPKDKDYRGSSTNCLVLWSSGEQTWEPLYNRNGKQGLWIDDPVTVAIYARDNGLLDEKGWKLPGLKKMAKTQKKLIRLANKAKLQSFRSKPIFMYGFQVPRNHVEAMELDRINGNTMWKDAETTELGQIDEHESFIDKGIGYKPGSEHKKIRVHMVYA
Ga0210333_1348349Ga0210333_13483491F064269MFMIPVLLAVCMVFACVPKVLYLIFGIDTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTQEQRCQRPSKRKALDRMFFMFLLMNHGRVSAKSARRGLIRLRPATKSEIPQAIPQDLSAEMLAPWDNIPQGWSQRLLNGSELKQFDPDNVIPVSETIDPNTGAINPASWLIQSAPRLPEFQ
Ga0210333_1371446Ga0210333_13714461F036102MDTKEMQELFRATAEATPEGQAAFRAFAAAITTPILQKIELESIMRGMFNVERLAPGAQAVYPVAEDFEIPVWVLPGLGY
 ⦗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.