3300021276: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.491 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021276
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225738 | Ga0210354
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.491 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 57834377
• Sequencing Scaffolds: 15
• Novel Protein Genes: 18
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	6
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	4
All Organisms → cellular organisms → Eukaryota → Sar	1
All Organisms → cellular organisms → Eukaryota	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?
F001506	Metagenome / Metatranscriptome	681	Y
F002996	Metagenome / Metatranscriptome	514	Y
F010686	Metagenome / Metatranscriptome	300	Y
F012678	Metagenome / Metatranscriptome	278	Y
F013050	Metagenome / Metatranscriptome	275	Y
F021307	Metagenome / Metatranscriptome	219	Y
F023254	Metagenome / Metatranscriptome	210	Y
F025295	Metagenome / Metatranscriptome	202	Y
F030135	Metagenome / Metatranscriptome	186	Y
F038934	Metagenome / Metatranscriptome	164	Y
F060086	Metagenome / Metatranscriptome	133	Y
F062310	Metagenome / Metatranscriptome	130	Y
F064269	Metagenome / Metatranscriptome	128	Y
F065810	Metagenome / Metatranscriptome	127	Y
F067805	Metagenome / Metatranscriptome	125	Y
F077370	Metatranscriptome	117	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210354_1007883	Not Available	800
Ga0210354_1010393	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	641
Ga0210354_1018790	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	661
Ga0210354_1018909	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	16742
Ga0210354_1024195	All Organisms → cellular organisms → Eukaryota → Sar	1616
Ga0210354_1027607	Not Available	657
Ga0210354_1034838	Not Available	616
Ga0210354_1066519	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	2276
Ga0210354_1068786	Not Available	720
Ga0210354_1077392	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1591
Ga0210354_1095812	Not Available	807
Ga0210354_1118066	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	804
Ga0210354_1122347	Not Available	501
Ga0210354_1124424	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1304
Ga0210354_1125065	All Organisms → cellular organisms → Eukaryota	715

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210354_1007883	Ga0210354_10078832	F013050	MSKGKQPRTRFKVPKLFLSEIKKVFIKVDKKIGLEAAIIL
Ga0210354_1010393	Ga0210354_10103932	F001506	MNRILYDNRCRCNEEFSVTKKRKSTTRSEGKPLQYPKANEMTSQTFQIKYEKKLSSTAKAIFNSFHNKYIYYAIDDILYSLKGNLIERDSLLAILYSTILSLQNNFSVNFFDIWIREVYIQEISKMNPFLNQDSQTLTQFSYITIKLFYKT
Ga0210354_1018790	Ga0210354_10187902	F010686	VHHCGQTHKGVWGMSWRQLAMKGVEGCEKPGGAVKRALIPGSLNYRTLNT
Ga0210354_1018909	Ga0210354_10189096	F001506	MNRILYENRCKCNKEFAITKKRKSIPRSEGKPLQYPKSNEITSKTFHMKYDKKLSATAKFILNSFQNKYIYYAIDDILYLLKLNQIERDNLLAILYSPVLSLHNNFSVNFFDIWIREVSIDEISKVNKFLNKDSQPSEQFSYITIKLFYKTKVPVKKQESLW
Ga0210354_1024195	Ga0210354_10241951	F067805	MGKPKSKKDEDITLSKKDQKKVAKLESQIPYHEGRGNQEEVDKIKEQIGAIWTKAREAAY
Ga0210354_1027607	Ga0210354_10276071	F062310	WTNLFKGRISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDHQGRANKLKDVAFREMTHLYTFEEAVPEDIRWLFQTPLEECLHWPLFRQRAWITNWEHIIKKEYATQMETG
Ga0210354_1034838	Ga0210354_10348381	F002996	ASESHNDVSTSLKVKTKTIRVLLDTGSSGDLLFMQKGKIDIPIVKRAVPQSWNTSNGTFQTKKVGDIELSFLDYSSSKRVRVTPDIVEYSGNAPPMYDLILGKQSLHDLGVILDFKEKTITIDEILLPMRNIARLQLEPSVSRALRLNTCQAQEPVSTRTATKRVVEILDAKYKKAHLPAIIRENCSHLKPSEREKLLSVLLKF
Ga0210354_1051298	Ga0210354_10512981	F064269	VLRLITFLPLSVLMFMIPVLLAVCMVFACVPEVLYLLFGIDTKRSTSRKLKSFIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTKEQRLQRPSKRKALDRMFFMFLLMNHGRVSAKSARRTSYRGRPELSEIPQAIPQDLSAEMLAPWDNIPQGWSQ
Ga0210354_1066519	Ga0210354_10665193	F012678	MLNQHSLEEIADIHNLLGDIKKEYNEGVKPILIKNSPKLFKNPHTVPKLKKFRLIEDLA
Ga0210354_1068786	Ga0210354_10687862	F030135	PKDRVELATLSTNTGIWHSTFVGCQFPDAILPGEEAIDLVAGPLNQLPDQVIE
Ga0210354_1077392	Ga0210354_10773924	F021307	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSIEITSKTFQMKYQKSLSTTAKCILNSFQNKYIYYAIDDILYSLKSKPIERDNLLAVLYS
Ga0210354_1084956	Ga0210354_10849561	F038934	ADHLKHRKPGEENPLEEPLKFGKKALRTLNPTEDNLKPKEMIGRTFFMPPTADGSRHRAKIMEAIRDMKDEAHKDPAYIKFKCLVNNSFKEVVAYNDLVDHIETDTTWDGVWTFEKILSHKKVRAGDKDHRGSGTNCLVLWSTGEQTWEPLYDRSGKTGLWIDDPVTVAIYARDNGLLDEPGWKLPGLKKMAKTQKKLIRMANKAKLHSFRSKPIYMYGFQVPRNHAEALELDRVNGN
Ga0210354_1095812	Ga0210354_10958122	F025295	IMVTGPGKVAELLRRREVLIPEKLKSFNRKVNLQKPI
Ga0210354_1115059	Ga0210354_11150591	F077370	TPFYSFAVSAGSPQVSANLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNYIGGGTTILQNTPSIFLQASTIPYNVGTVSLQRAIAQSDNSIEIDLQTYDPKSYDILLPPHIVSNNRVNNQTFAFGSQTWISTRLNNVQNFPDLFLNLGSLATPTFDPSTTSGNSVLI
Ga0210354_1118066	Ga0210354_11180661	F065810	KYIYYAMDDILYSFRSNPMERDNLLAILYSPVLSLQNNLSTNFFDIWIHEIHIHEVSKVNRFLKHDFKNVKQLNYITIKLFYKTRVPSKKRDSLW
Ga0210354_1122347	Ga0210354_11223471	F023254	NCMKRVYISDFKKDRKGTKGRRSCNTICSTERATRRKYRGAYITAIDDEEIVTLNQAKEKLKELRNKSVDTFTMILAREPRPSKSMMRRAYDKLELPEFDLDENLGEDYFASDGNLESNSSVTASGETNAFGTDYVPPIGTKIYKDFGTKGFFAGTVTSGPRTRTE
Ga0210354_1124424	Ga0210354_11244243	F021307	MNRILYENRCRSNEDFSITKKRKSTTRSEGKPLQYPKSNEVLSQTFQIKYDKQLSATAKVILNSFQNKYIYYA
Ga0210354_1125065	Ga0210354_11250651	F060086	DPFELDSNLLLSSGRQGEDRKRQYFLYDHETPLLVDLADLLYYFGIAF