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 3300021297

3300021297: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.669 (Metagenome Metatranscriptome)



Overview

Basic Information
IMG/M Taxon OID3300021297 Open in IMG/M
GOLD Reference
(Study | Sequencing Project | Analysis Project)		Gs0114516 | Gp0225753 | Ga0210369
Sample NameMetatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.669 (Metagenome Metatranscriptome)
Sequencing StatusPermanent Draft
Sequencing CenterDOE Joint Genome Institute (JGI)
Published?N
Use PolicyOpen

Dataset Contents
Total Genome Size44968496
Sequencing Scaffolds22
Novel Protein Genes24
Associated Families18

Dataset Phylogeny
Taxonomy GroupsNumber of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar2
Not Available11
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta5
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris1
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Cnidaria → Anthozoa → Hexacorallia → Scleractinia1
All Organisms → cellular organisms → Bacteria1

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)46.313Long. (o)-123.997Alt. (m)N/ADepth (m)0
Location on Map
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Associated Families

FamilyCategoryNumber of Sequences3D Structure?
F000203Metagenome / Metatranscriptome1619Y
F001105Metagenome / Metatranscriptome776Y
F001506Metagenome / Metatranscriptome681Y
F006508Metagenome / Metatranscriptome371Y
F012678Metagenome / Metatranscriptome278Y
F012874Metagenome / Metatranscriptome276Y
F021307Metagenome / Metatranscriptome219Y
F034767Metagenome / Metatranscriptome174Y
F037756Metagenome / Metatranscriptome167Y
F045132Metagenome / Metatranscriptome153Y
F046726Metagenome / Metatranscriptome151Y
F053305Metagenome / Metatranscriptome141Y
F059979Metagenome / Metatranscriptome133Y
F061147Metagenome / Metatranscriptome132Y
F065810Metagenome / Metatranscriptome127Y
F075465Metagenome / Metatranscriptome119Y
F077370Metatranscriptome117Y
F087250Metagenome / Metatranscriptome110Y

Associated Scaffolds

ScaffoldTaxonomyLengthIMG/M Link
Ga0210369_1007560All Organisms → cellular organisms → Eukaryota → Sar601Open in IMG/M
Ga0210369_1013717Not Available548Open in IMG/M
Ga0210369_1022064Not Available889Open in IMG/M
Ga0210369_1024223All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta915Open in IMG/M
Ga0210369_1027106Not Available1009Open in IMG/M
Ga0210369_1034014Not Available511Open in IMG/M
Ga0210369_1037246Not Available594Open in IMG/M
Ga0210369_1040730All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta967Open in IMG/M
Ga0210369_1041440All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta679Open in IMG/M
Ga0210369_1047042Not Available539Open in IMG/M
Ga0210369_1048526All Organisms → cellular organisms → Eukaryota → Sar578Open in IMG/M
Ga0210369_1048853All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta939Open in IMG/M
Ga0210369_1049074All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta586Open in IMG/M
Ga0210369_1055278Not Available610Open in IMG/M
Ga0210369_1056761Not Available800Open in IMG/M
Ga0210369_1056965Not Available556Open in IMG/M
Ga0210369_1062238All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria522Open in IMG/M
Ga0210369_1063773Not Available734Open in IMG/M
Ga0210369_1069270All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris643Open in IMG/M
Ga0210369_1074815All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Eumetazoa → Cnidaria → Anthozoa → Hexacorallia → Scleractinia1180Open in IMG/M
Ga0210369_1076258Not Available800Open in IMG/M
Ga0210369_1089757All Organisms → cellular organisms → Bacteria534Open in IMG/M

Sequences

Scaffold IDProtein IDFamilySequence
Ga0210369_1007560Ga0210369_10075601F012678MLNQHSLEEIAEIHNLLGDIKKEYEKGIKPILIKNSPKLFKNPHTVPKLKKIQINRGLRLAAQNTNVLKKNIEEFEKIT
Ga0210369_1013717Ga0210369_10137172F053305MLKKSVSMALMALFVFSFIAVATVSADETQKITGTVMSVNVETGEMIVKDDAGEMKSLMTDPKAGVDLKMLKEGDPVSVESDSDGVIKSIAVSK
Ga0210369_1022064Ga0210369_10220642F046726LGKIPEQEKIEIIKTGFQLQNQGKISLKKYYESTDSDSLFQYNNGYNIKYQTIRKTTLYQNLKE
Ga0210369_1024223Ga0210369_10242231F001506MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQIKYQKNLSTTAKCILNSFQNKYIYYAIDDILYLLKSKPSERENLLAVLYSPILSLQNNFSVNFFDIWIGEVYIDEISKNNKFLKNDLTTLKQFNYITIKFFYKTRVPVKKQESFW
Ga0210369_1027106Ga0210369_10271061F046726KIEIIKTGFQRQSEGTISLRKYYESTDPNSLFQLKGYSIKYESIRKNKLYQQLKA
Ga0210369_1034014Ga0210369_10340141F077370RNRRNNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSRQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRA
Ga0210369_1037246Ga0210369_10372461F012874MPAKAGIQNSLKTLDCRIRGNDAKGRFKTFYENIKIPLAIGFIQR
Ga0210369_1040730Ga0210369_10407301F001506IKTRSEGKPLQYPKSIEITSKTFQMKYQKSLSTTAKCILNSFQNKYIYYAIDDILYSLKSKPIERDNLLAVLYSPILSLQNNFSVNFFDIWIREVYIDEISKNNKFLKNDSTTLKQFNYITIKFFYKTRVPVKKQASLW
Ga0210369_1041440Ga0210369_10414401F034767KGVNATIWGGVQEADKVGKIVKTGISGADVVIGTSHALEDFGCNDYVCGSLDVIGSVSSAVGLVLGNIPSTKPLTLITGSVTIGCRSVRYYCKNYGTFWGCTVAAGQGIKESVKFIINK
Ga0210369_1047042Ga0210369_10470422F006508VALANAPSKAVAVQCQTVKTRKRNRRRVLTWFASRWRNHQPKRAEK
Ga0210369_1048526Ga0210369_10485262F021307MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLL
Ga0210369_1048853Ga0210369_10488531F001506GKPLQYPKANEMTSQTFQIKYEKKLSSTAKAIFNSFHNKYIYYAIDDILYSLKGNLIERDSLLAILYSTILSLQNNFSVNFFDIWIREVYIQEISKMNPFLNQDSQTLTQFSYITIKLFYKTRVPAKKQESLW
Ga0210369_1049074Ga0210369_10490742F065810MKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLLKAKPVERDNLLAVLYSPILSLQNNFSVNFFDIWIRDVYIDEISKTNRFLKNDSTTFKEFNYITIKFFYKTRVPVKKQESLW
Ga0210369_1055278Ga0210369_10552781F053305MLKKSLSLVLVALFALSFIAVATLSADETQKITGTVMSVNAETGEVILKDDAGEMKTLMADPKAEGAVDIKMLKEGDSVDVESDSNGVIKSLKAGE
Ga0210369_1056761Ga0210369_10567611F053305MLKKSLSIVLTALFVLSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKSLMADPKAVDLKMLKEGDMVSVESDDAGAVQSIKASE
Ga0210369_1056965Ga0210369_10569651F046726KIEIIKTGFQLQAEGKISLKKYYQSTDPDSLFQWKGYSIKYETIRRTKLYQSLKD
Ga0210369_1062238Ga0210369_10622381F059979MKSFLLVLAQLSLVTLVYAFAYRAGYRSAQSKAISVVKKFADPVTCLLDSLKDTIDELVKDEDENG
Ga0210369_1063773Ga0210369_10637731F000203MGVRHSLFPVPTLGASGAAGFPTLFSTASGVSGLVAGPSSASPLLDFE
Ga0210369_1063773Ga0210369_10637732F045132VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSNRSSLPSSFFAFTDGARTPPEELVNSASFAKCVSTSLKRGLVNQPDL
Ga0210369_1069270Ga0210369_10692701F075465LRQCTRLLQDRMKQDADWLTVSTRYNPLSLYRLIEKTVLAQTEDQYPFATVYDQEHAFYSFRQELMTNAMWYEKFNTRVDVGEAIGITRQHTVLLEFVAQEVHTKAFTALTAAEQQVIRLDAEERYQSYVFLRQSGAQHSHLKQSLQNDFTTGDNHYPKNRQQTLHLLDKFSKTVAPKVAPIQSEGTAFAQGSGDQKQPFDKKFWKDKECFKCH
Ga0210369_1072259Ga0210369_10722592F087250SKTGLQGAAAEAGFTSSSGGVRAPSVNAKKELGDEER
Ga0210369_1074815Ga0210369_10748151F001105MSTTQQSKITKTITDAAVITGLVAGIGWVGRKVLREDFTKDPSANAMNYAKMTAAVAGAVALKGYLEDQKILPM
Ga0210369_1076258Ga0210369_10762581F037756QALFPVPTFGAHLAAAAGFPTPFSAANGVSGLVAGPSNLLQG
Ga0210369_1089757Ga0210369_10897572F061147MNSRTRTTTTPSHSLAALLEQIGLHALAGEVDDFVARATKQRW
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Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"
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