3300021304: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.300 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021304
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225715 | Ga0210331
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.300 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 75029987
• Sequencing Scaffolds: 17
• Novel Protein Genes: 17
• Associated Families: 12

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar	2
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	1
Not Available	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → Acinetobacter → Acinetobacter towneri → Acinetobacter towneri DSM 14962 = CIP 107472	1
All Organisms → cellular organisms → Eukaryota	2
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata	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): 46.302
  • Long. (^o): -123.036
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001506	Metagenome / Metatranscriptome	681	Y
F001679	Metagenome / Metatranscriptome	653	Y
F004023	Metagenome / Metatranscriptome	456	Y
F017072	Metagenome / Metatranscriptome	243	Y
F021307	Metagenome / Metatranscriptome	219	Y
F025295	Metagenome / Metatranscriptome	202	Y
F034767	Metagenome / Metatranscriptome	174	Y
F042356	Metagenome / Metatranscriptome	158	Y
F058634	Metagenome / Metatranscriptome	134	Y
F060086	Metagenome / Metatranscriptome	133	Y
F085004	Metagenome / Metatranscriptome	111	Y
F098745	Metagenome / Metatranscriptome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210331_1007405	All Organisms → cellular organisms → Eukaryota → Sar	1004
Ga0210331_1015001	All Organisms → cellular organisms → Eukaryota → Sar	2633
Ga0210331_1028059	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	732
Ga0210331_1031313	Not Available	520
Ga0210331_1035026	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	10728
Ga0210331_1042749	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	768
Ga0210331_1050698	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → Acinetobacter → Acinetobacter towneri → Acinetobacter towneri DSM 14962 = CIP 107472	606
Ga0210331_1072014	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1940
Ga0210331_1079718	Not Available	3645
Ga0210331_1095809	Not Available	650
Ga0210331_1104079	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	4591
Ga0210331_1109082	All Organisms → cellular organisms → Eukaryota	1355
Ga0210331_1109498	All Organisms → cellular organisms → Eukaryota	1674
Ga0210331_1109965	Not Available	810
Ga0210331_1130400	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	626
Ga0210331_1157779	Not Available	504
Ga0210331_1158125	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata	1313

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210331_1007405	Ga0210331_10074051	F021307	MNRILYENRCKCNEEFSITKKRKSPTKSEGKPLQYPKPNEIISKTFQIRYDKKLSTTSKFILNSFQNKYIYYAIDDILYL
Ga0210331_1015001	Ga0210331_10150011	F098745	MKKLFAKDQKNRQIVKKLELKNFILKQISANSNFSRTTQWNALSKLSSLTKKRSK
Ga0210331_1028059	Ga0210331_10280592	F001506	MNRILYENRCRCNEEFSLTKKRQSTTRSEGKPLQYPNYTESTSKTFQIKYDKKLSSLAKAILNSFQKKYIYYAIDDILYFLKGNSIEQENLLAILYSPILSLHNNFSINFFDIWIGAVYIEEISKVNKFLTKDSQTFTQFSYITIKLFYKTG
Ga0210331_1031313	Ga0210331_10313131	F042356	VHQHGASDSGGFDQPFETAQRNPLKDGQKERMTRESHDGSAGRVKNFRAPAMLKTAPLACEQKAT
Ga0210331_1035026	Ga0210331_103502615	F001506	MNQILYERRCRCNEEVSITKKLSSNKRSEGKPIPYPDPELNEITSKIFQIRYDRKLSTIAKFILNSFENKYIYYAIDDILYLLKSNPIERDNLLTLIYSPVLSLQNNFSVNFFDIWIQEIYINEVSKVNKFIVNDSNNLEQFSEITIKLFYTTRLPIKKKDSLW
Ga0210331_1042749	Ga0210331_10427491	F058634	MSLTRLAGSALLSCAAFAVALTGCSSEQSEAGIGNVDMAVTLATPPSGPNEQIDTVDVSFYCEGIDPVLGVPRPPQSSPETFTINTSTSQGPEPKNTIGLFEKQGLPAGPCHFDFSAVSNSGNTECTGKLTLVVATNATTSGEVVLACIHTPRYGGVRPDGTFNQCAEYRQILVSPTTQAIGNPIDVATQVYDPDGDPVTVAVQAAGACGNVM
Ga0210331_1050698	Ga0210331_10506982	F001679	VWGMSWRQKAMKGVEGCDKPGEAVKRALIPGSLNHRMMNT
Ga0210331_1072014	Ga0210331_10720145	F021307	MNRILYESRCRCNEEFLITKKRSLSNRSEGKPLQYPKPNEITSKTFQIKYEKELSSIAKFVLNSFQNKYIYYAIDDILYLLKSNPIER
Ga0210331_1079718	Ga0210331_10797182	F085004	MGLKNMTLSAGVTLTPSGGTNQVFADDGITIQNGVHLIVPADTDYETRRQATAKYRPPAYNANDGSYGKDKKSISYAVPIVLASGKVVFNTIRVEREVHPELSASDAAEMLKIGAQLLDHSDTSAFWSTGSLS
Ga0210331_1095809	Ga0210331_10958091	F060086	DPFELDSNLLLSSGRHGEDRKRQYLYDHETPLLDDLADLLYLALPLLLLFK
Ga0210331_1104079	Ga0210331_11040792	F001506	MTKNRKLPTKKKGEILPYPESSEIQSKTFQMKYQKNLSLTAKFILNNFQNKYIYYAIDDILYLLKSKPIERDNLLAILYSPILSLQNNFSVDFFEIWIREVFIDEISKTNKFLKNDSKTLKQSNYITIKFFYKIPVKKKESLWEF
Ga0210331_1109082	Ga0210331_11090821	F021307	MNRILYEKRCKCNEEFSIIKKRKPKTRSEGKPLEYPQSSEITSKTFQIKYHKNLSTTAKCILNSFHNKYIYYAIDDILYLLKSKPMERDNLLAVIYS
Ga0210331_1109498	Ga0210331_11094982	F034767	MFGSKIGKCTLDILRGINATVWGGVEGADKVGKIVKTGLSGADVVIGTSHALEDLGCNDYVCGSLDIIGSVSSAVGLVLGNIPSTKSLTVITGSVTVGCRSVRYYCKRYGTFWGCTVAAGEGIKK
Ga0210331_1109965	Ga0210331_11099651	F025295	IVVTNSGEDTELLQRSKVLIPEKPTFKTRKSNKRKQI
Ga0210331_1130400	Ga0210331_11304002	F058634	MSRTRLASSFVLTCAALAVALPGCSSDQTQGADGVGNVGMEVTLATPPAGPNEQIDTVDVSFYCDGVDPVLGVPRPPQSSPEEFTINTATSQGPEPKNTIGLFEKQGLPAGNCYFSFAAASNTGNTQCTGELTVAVV
Ga0210331_1157779	Ga0210331_11577791	F017072	MRMRDLAVGSDEKPLRTESSSPEKFRFRMNRSHPEGEQLLLCISTVRKTLAGTNKIESAQRKTPKGGQKEQTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKGNLREKR
Ga0210331_1158125	Ga0210331_11581253	F004023	MFQLVVFLGLILCCTHLSEITLTIAANIMHTFFLFYGKFYWWLFTDKQLNCDTVIRLAYAHYVSAFFLTYLAVIHAFDMHFDWKTESVFDGIDSEMIWWDEALSSELTNVLIAMLLVCIACYFMYPDPEALSYELFAWGDIGLISDIRFYGVAPH