3300022368: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Oregon, United States ? S.454 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300022368
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225730 | Ga0210346
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Oregon, United States ? S.454 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 36488240
• Sequencing Scaffolds: 20
• Novel Protein Genes: 21
• Associated Families: 17

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1
Not Available	17
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	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: Oregon
• Coordinates
  • Lat. (^o): 46.178
  • Long. (^o): -123.853
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000237	Metagenome / Metatranscriptome	1498	Y
F000734	Metagenome / Metatranscriptome	915	Y
F001506	Metagenome / Metatranscriptome	681	Y
F002557	Metagenome / Metatranscriptome	548	Y
F004323	Metagenome / Metatranscriptome	443	Y
F006508	Metagenome / Metatranscriptome	371	Y
F009934	Metagenome / Metatranscriptome	311	Y
F014854	Metagenome / Metatranscriptome	259	Y
F017072	Metagenome / Metatranscriptome	243	Y
F020183	Metagenome / Metatranscriptome	225	Y
F025295	Metagenome / Metatranscriptome	202	Y
F041277	Metagenome / Metatranscriptome	160	Y
F060937	Metagenome / Metatranscriptome	132	Y
F077370	Metatranscriptome	117	Y
F078934	Metagenome / Metatranscriptome	116	Y
F082737	Metagenome / Metatranscriptome	113	Y
F088925	Metagenome / Metatranscriptome	109	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210346_100249	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales	3108
Ga0210346_100685	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	2293
Ga0210346_108383	Not Available	845
Ga0210346_109275	Not Available	801
Ga0210346_109387	Not Available	796
Ga0210346_110872	Not Available	734
Ga0210346_111133	Not Available	726
Ga0210346_112110	Not Available	694
Ga0210346_113261	Not Available	662
Ga0210346_113589	Not Available	654
Ga0210346_115982	Not Available	599
Ga0210346_116229	Not Available	595
Ga0210346_117889	Not Available	565
Ga0210346_119036	Not Available	547
Ga0210346_119071	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	546
Ga0210346_119723	Not Available	537
Ga0210346_120289	Not Available	530
Ga0210346_120707	Not Available	525
Ga0210346_122243	Not Available	506
Ga0210346_122434	Not Available	504

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210346_100249	Ga0210346_1002492	F020183	MSLTINAKTFTADKFGVDAVGYIGPAHTLSILDDVQLSRVAPKPTVVFSGVGRTSTKLTRTLTLTGSLTTSGNAIVQINVSVPVGAASADIDALLNDMGSFLSSASYKSHVKGLQISY
Ga0210346_100685	Ga0210346_1006852	F001506	MTKNRKLPTKKKGEILPYPESSKIQSKTFQMKYQKNLSLTAKFILNNFQNKYIYYAIDDILYLLKSKPIERDNLLAILYSPILSLQNNFSVDFFEIWIREVFIDEISKTNKFLKNDSKTLKQSNYITIKFFYKIPVKKKESLWEF
Ga0210346_108383	Ga0210346_1083831	F025295	MVTGLGEAAELLRRREVLIPEKLKFITRKSNLQKLI
Ga0210346_109275	Ga0210346_1092752	F009934	MRPETPLAVENGVGKLAAYRAPNASMGKRAWRTPT
Ga0210346_109387	Ga0210346_1093872	F041277	MRPETPVAVENGVGKPAAHEAPNVGTGKRAWRTPI
Ga0210346_110872	Ga0210346_1108721	F017072	MRMRDLAVGSDEKPLRTESSSPETFRFRMNRSHPEGEQLLLCISTVRAALAESNQIEAAQRKTPKGGQKERGHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKCNLREKRRDPWFRANASSKAMADPGLVVKTRTRDPQACLDLVRKPVAQPPAKAS
Ga0210346_111133	Ga0210346_1111331	F002557	VLMHSSNHYPLGNCDSPGSETNPDYLTQFGAVSHRPSLPSSFFAFTDGARTPPEELVNSASSIACVSTRLRR
Ga0210346_112110	Ga0210346_1121101	F006508	VALANAPSKAVAVQRQVVKTRSNRRRVLTWFASRWRNHQSKRAEKPHSKSSCGDALDGP
Ga0210346_113261	Ga0210346_1132611	F025295	IMVTSPGEAAELLRRREVLIPMKLKFLTRKSDLQKPI
Ga0210346_113589	Ga0210346_1135891	F060937	RGAGNGREIEECTAGIIPGNWGTVGPGWLVQPLRRRIAGFAEVRQNSPAPLAGVAARHNAIEELGGQGR
Ga0210346_113873	Ga0210346_1138731	F000237	PXYYLYLIQLHVMFCHESXDSDSGEATYEDKSGSYISXFYDAFLKEIQDAXYXTIFVFIYFXLHHFNPSTVNYFFFERXNISELDEIRFYGVAPHXYFRPLMGVLVISPTHYEGLMXMGLFFILLTFLPIFYNFYNVNNKHIPTIPMQNSLLQTFAFIIFMMSMFCSASMLPCGRYYYEPEGGYVGNPXVKFSLQYIYLYMAXFIHHLDLIDHYI
Ga0210346_115982	Ga0210346_1159821	F025295	IMVTGPGEAAELLKRREVLIPKKLKHLTRKSNLQKLN
Ga0210346_116229	Ga0210346_1162292	F025295	IKVTGPGEATELLRRREVLIPEKLKFLTRKSNLQKPI
Ga0210346_117889	Ga0210346_1178891	F077370	GKTNDRAIDILVNIFAVNSLGTPFYSFSTSAGSPQLSSNLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNFIGGGTTILQNTPSIFLQASTIPYSTGSVVLQRAIAQSDNSIELDLQTYDPKSYEIFLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNLPDLFLNLGSLATPTFDPSTTS
Ga0210346_119036	Ga0210346_1190361	F082737	MPGLSLSQPSRRTPFRLAPRLRSFSVGASLLSGTPASLPVRSQNLEADFHSPTTTSLLPDRRGGVRIPALLLQLCGTFSDCPVRSDLHPRPVSRTAWGLPRPEPVAAKSCATPACRAKPLLPFRAFPLPDQSTRPRWPTGNLLPVTPDLPSLPTGGRIRNQHQRIIVP
Ga0210346_119071	Ga0210346_1190711	F088925	MGRAGLGDWKEIPMQERKCSKCGSTNVYKNMSNNWHQDGIVLQMIAVDSFHDLFQTEAFLCLDCRHLDIQVLETSTMHGKQKTLIDTVQASNNWRKAXMG
Ga0210346_119723	Ga0210346_1197231	F082737	RFEPVTSGTPDAFRLASRLRSFSVGASLLSGTPASLPVRSRSLEADFHSPTKASLLPDDRGGVRAPALLLPLHDTSPVSPVRSGLHPRPVSRTAWDFNNQNPLLSGPAPLLPASLNRRSPSGLFAPPDQCTRSRWPTENLLSGTPDLPSLPTGGRIRYQHQRIIVPAPLRPFQLAVP
Ga0210346_120289	Ga0210346_1202891	F000734	VVWAGPVKTFRKVGDVKNDTADLWTKGNLRVKRRDPWHRANALPRAAADPALIGEDADKKTQ
Ga0210346_120707	Ga0210346_1207071	F004323	MPLDDLRRLEGMATPAVAIHSPVTRDYPSRALSDVFQAAALR
Ga0210346_122243	Ga0210346_1222431	F014854	ELRWTAVIERKSLVVSRIIPGNWGKVESGWLARPLLDRIARSGGGGRIHQFLWSRSHAVSYAKRNLAARGDKKPLRVGSSSSGRFRAWANRSYPEGKWLLLCIGTGRVTLADSINRLKPPNESHRKVDKRSARTGKITPARQAA
Ga0210346_122434	Ga0210346_1224341	F078934	MTSQSLVLRPQTQPIGQLLRGSPVLSGEGVRLIVRSYFVSSGFTSELVLGMPRADSVPTSKPD