3300021287: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.380 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021287
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225722 | Ga0210338
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.380 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 43682086
• Sequencing Scaffolds: 20
• Novel Protein Genes: 21
• Associated Families: 19

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	15
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series
• Type: Environmental
• Taxonomy: Environmental → 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

• Location: USA: Washington
• Coordinates
  • Lat. (^o): 46.27
  • Long. (^o): -123.946
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000344	Metagenome / Metatranscriptome	1257	Y
F001346	Metagenome / Metatranscriptome	718	Y
F001506	Metagenome / Metatranscriptome	681	Y
F002557	Metagenome / Metatranscriptome	548	Y
F004925	Metagenome / Metatranscriptome	418	Y
F005632	Metagenome / Metatranscriptome	394	Y
F006508	Metagenome / Metatranscriptome	371	Y
F014031	Metagenome / Metatranscriptome	266	Y
F021307	Metagenome / Metatranscriptome	219	Y
F024806	Metagenome / Metatranscriptome	204	Y
F027192	Metagenome / Metatranscriptome	195	Y
F034947	Metagenome / Metatranscriptome	173	Y
F035541	Metagenome / Metatranscriptome	172	Y
F045132	Metagenome / Metatranscriptome	153	Y
F047147	Metagenome / Metatranscriptome	150	Y
F049453	Metagenome / Metatranscriptome	146	Y
F053305	Metagenome / Metatranscriptome	141	Y
F077370	Metatranscriptome	117	Y
F078934	Metagenome / Metatranscriptome	116	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210338_104499	Not Available	736
Ga0210338_111718	Not Available	628
Ga0210338_120058	Not Available	723
Ga0210338_124547	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	754
Ga0210338_137186	Not Available	778
Ga0210338_141971	Not Available	804
Ga0210338_147844	Not Available	813
Ga0210338_149493	Not Available	692
Ga0210338_154460	Not Available	654
Ga0210338_155179	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Pseudanabaenales → Leptolyngbyaceae → Leptolyngbya	3390
Ga0210338_155987	Not Available	1028
Ga0210338_157556	Not Available	685
Ga0210338_157570	Not Available	671
Ga0210338_164088	All Organisms → cellular organisms → Bacteria	511
Ga0210338_173486	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Ignavibacteriae → Ignavibacteria → unclassified Ignavibacteria → Ignavibacteria bacterium	551
Ga0210338_174347	Not Available	746
Ga0210338_180267	Not Available	796
Ga0210338_184809	Not Available	721
Ga0210338_187285	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	812
Ga0210338_188598	Not Available	678

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210338_104499	Ga0210338_1044991	F077370	NQPRIVNNKQSRNRRNNRKRILKNNSHQLAVPRPMSILGKTNDRAIDILVNIFAVNSLGTPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNFPDLFLNLGSLATPTFDPSTTSGNSVLIGQIHGRMQLSFAGP
Ga0210338_111718	Ga0210338_1117181	F002557	VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSNRSSLPSSFFAFTDGARTPPEELVNSA
Ga0210338_120058	Ga0210338_1200581	F035541	VKRLALIFTLAILASLFIVPAVSAKANTTDLNIIPITDTLEVGTFEWDVTARYNEDFPRGRRVSTRLFGSLYDNFEFGMSWGISRLAGPMELALKYKILDEYEGKWPVSFAVGAEGITGNADRTGMDPTLYGVIGLHDVQLGGWWDWYVGVANNPTGYDDEDNSLFGGFKYWVNDDVQVNVDYSGRNSNEDYTVAGGLNYDWVN
Ga0210338_121543	Ga0210338_1215431	F001506	MIELTHKYKFLNEEEICECRSGKTKKQNLNKRKKRKRNTPRLLAYPPLEEVTLKTFQIKYNKKLSSVAKLILNSFQNKYIYYAMDDILYSFRSNPMERDNLLAILYSPVLSLQNNLSTNFFDIWIHEIHIHEVSKVNRFLKHDFKNVKQLNYITIKLFYKTRVPSKKRDSLW
Ga0210338_124547	Ga0210338_1245471	F001506	MNRILYENRCKCNEEFSITKKRKSPTKSEGKPLQYPKPNEIISKTFQIRYDKKLSTTSKFILNSFQNKYIYYAIDDILYLFELNKTERNNLLAILYSPVLSLQNNFFVNFFDIWIREIYIDEVSKVNKFLNHD
Ga0210338_137186	Ga0210338_1371861	F053305	MLKKSLSIVLTALFVFSFIAVGTVSAAEVKGEVVSVNAETGEMVIKDDAGEMKTLMADPKVVDLKMLKEGDMVSVESDDAGAVQSIKAS
Ga0210338_141971	Ga0210338_1419711	F004925	AAAVERSQQVVSRIRPGDWGKVGSGWLTGLLWITAERPGKGGRIHQFLWQRSRAASNAKKELGDEER
Ga0210338_147844	Ga0210338_1478441	F001346	VSVRTGKDTRPQARPVKTFQPAGDVKNGTAGLRTKGNLRVKRRDPWHRANAPTKSEADPALIGKDADKKSQTCLDLVRKPVAQPPAQAS
Ga0210338_149493	Ga0210338_1494931	F049453	MRPETPLAVENSVGKLAAHAAPNASPGKRAWRTPIP
Ga0210338_154460	Ga0210338_1544601	F006508	VVLANASSQAVADQCRWVKTQKRIHGCVLTWFAGRWRNHQPKRAEKP
Ga0210338_155179	Ga0210338_1551796	F021307	MNRILYENRCKCNKEFAITKKRKSIPRSEGKPLQYPKSNEITSKTFHMKYDKKLSATAKFILNSFQNKYIYYAIDDILYLLKLNQ
Ga0210338_155987	Ga0210338_1559873	F024806	MATNCNFKFTKNTNVTLELPFSDHIEELRQRIFLLFWIILLLTCIAFVEVKSLVKILELPISNV
Ga0210338_157556	Ga0210338_1575562	F005632	LDGFFGAVEVSLWRAVAVQVEHDTEKWNMGIGVGFDFGLRLRAAALDLENMSVGVGWYHK
Ga0210338_157570	Ga0210338_1575701	F006508	VALANALSKAVADQSQVVKTRRRNRRRVLTWFVSRWRNHQPKRAEKPHSKFNAARCWTAL
Ga0210338_164088	Ga0210338_1640882	F014031	MRRHRGRVGLMAATLLGLMVSGASAELTTERSASILVFPKVIANGTRDTIIQITNTSNSMVHAHCFYVNAALTNPQLPPDPVLNPPLWQEIDFDIWLTKQQPTHWVVSRGRAVNPQDPVC
Ga0210338_173486	Ga0210338_1734861	F027192	VLALLLVVGLSTVLAQSEAVTLVTATVESELILTNLDADWGLFSPGQNYTITPGAFKEPPGPGEAAGDQVESAGFEVEGNPNSEVLISLVLPAAFTSEDENGTMPLSNWTYGWNFDDDPSVAFSAAGPVTGSAVSVIIGGGAITGLFLGADVSVPTTAYTGAYIAQIIGSATYTGN
Ga0210338_174347	Ga0210338_1743471	F047147	AIIVAVTEGPVREEQLLHDMCLLGAMTVEITQILTRAGSKYV
Ga0210338_180267	Ga0210338_1802671	F045132	VLMHSSNHYPLGNCDSPGSETNPDYLTQFGTVSHRSSLPSSFFACTDGARTPPEELVNSASSVAYVSTRLHRGRVNQPDPTFPRSPGRILETAADLFSLTVSRLCS
Ga0210338_184809	Ga0210338_1848091	F034947	LLLCISTVRATLADLINRLNPPKENHRKVDKRSGRIGKVTQTRQVA
Ga0210338_187285	Ga0210338_1872852	F000344	MRPIHPHAAESGVGKHTARESESAKACAIGKERVANAHS
Ga0210338_188598	Ga0210338_1885981	F078934	MTSQPSVLRLQAQPIGQLLRGSPVLSGEGETFVVRSYFVSSGFTSELVLGMP