3300021848: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.667 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021848
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225752 | Ga0210368
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.667 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 31700259
• Sequencing Scaffolds: 11
• Novel Protein Genes: 15
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Amphiprora → Amphiprora paludosa	1
Not Available	6
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Fragilariophyceae → Fragilariophycidae → Rhabdonematales → Grammatophoraceae → Grammatophora → Grammatophora oceanica	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?
F007629	Metagenome / Metatranscriptome	347	Y
F022655	Metagenome / Metatranscriptome	213	N
F024006	Metagenome / Metatranscriptome	207	Y
F033314	Metagenome / Metatranscriptome	177	Y
F038082	Metagenome / Metatranscriptome	166	Y
F042669	Metagenome / Metatranscriptome	157	Y
F044534	Metagenome / Metatranscriptome	154	Y
F045132	Metagenome / Metatranscriptome	153	Y
F046120	Metagenome / Metatranscriptome	151	Y
F046726	Metagenome / Metatranscriptome	151	Y
F054544	Metagenome / Metatranscriptome	139	Y
F056298	Metagenome / Metatranscriptome	137	Y
F094641	Metagenome / Metatranscriptome	105	Y
F106082	Metagenome / Metatranscriptome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210368_109781	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Amphipleuraceae → Amphiprora → Amphiprora paludosa	652
Ga0210368_119052	Not Available	740
Ga0210368_132169	Not Available	882
Ga0210368_133377	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	826
Ga0210368_136425	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	550
Ga0210368_154768	Not Available	679
Ga0210368_161254	Not Available	812
Ga0210368_165630	Not Available	532
Ga0210368_166083	All Organisms → Viruses → Predicted Viral	1575
Ga0210368_167051	Not Available	554
Ga0210368_168363	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Fragilariophyceae → Fragilariophycidae → Rhabdonematales → Grammatophoraceae → Grammatophora → Grammatophora oceanica	504

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210368_109781	Ga0210368_1097812	F033314	MSAGTVDFVVGVDKKLWIGSGLFKNCKSFFGAKGAVFGSECFDHTDWIALPEDAAGYSAALISWGWVGVIELGCEMFGVGVRFLALID
Ga0210368_112943	Ga0210368_1129431	F024006	ISSGQVIIVIRRYWWHSSLGTGCITSCGYVLQPNIQEREFGRYAPTLEDLDPAKIRNWYMDMVRVAHDFGIFLPAYEDYRPEETFSTIECGDTRTARLPSFCRSQIPRWQAIIHHHLKRDKVIPSSHPQFNEIRHNPNGYEALMLLLAPYHPAFTDNGILIQAHPRQGR
Ga0210368_119052	Ga0210368_1190521	F054544	LDPMRITHVYDNGTVRLVKVANNGGAVSQTWNIRNIEPRKA
Ga0210368_125779	Ga0210368_1257791	F038082	KAFAYIMHDYCTDGLKTRLVALPDFTTSIQDDPLALLKAIKTCVHENAVTQYPPVTIQQHWSRLLQLKQSSDEDPPTYAKRFEQQLETVKGYVGNTFTDGFAEHMPDYKANAYKHDSGKITALLATHVTDDAARQALATDLHDLFSHYKPKETQAQLDLKAQVRSEFEAYLFLRSASKAK
Ga0210368_132169	Ga0210368_1321692	F046726	LGKISEEEKIEIIQRGFQLQAEGKISLKKYYESTDSNSLFQSKGYSIKYESIRRTKLYQKLKEIFT
Ga0210368_133377	Ga0210368_1333771	F042669	VGFKNTTHEKNIYTGTFCGEKVLLVRQVDDFALGCRQESTAKSVYATIGAKLTLHNEAEAPFEYLGLVDSFDGYDVLQTRDYIKLSAESYIRRLLKAHGWENPSPRESSNKPKPPLHESDVANLFNLAAGPVENTPEHKALEAEHGFGYRSVLGEILFAYVLCRPDIGFAVTTLAKFSTAANAL
Ga0210368_136425	Ga0210368_1364251	F044534	VAFPSERRKSPRGIYHQFLWPESCPVSSHTNQELSGEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP
Ga0210368_142072	Ga0210368_1420721	F007629	VGAKWLGQKAHPHRRRFTKPNQGSNVKQKDVAELVSKLDAKYNVKVTAQGKGQKNDHVLIEGSDNGSISPVIQAGNQGSRPENTVRPKGKDTNPRTEQSKGIKK
Ga0210368_143943	Ga0210368_1439431	F056298	VCLAANMKSRNRGDGETRTATKPGQGLSLDFSFAGQHSKNATDPKKMRINDYMGIHGETCYLLLYDHATERLDGVCRQLKAPPLAWLKRWLKKNVKDEVKDRYVYMDQGEELYRSKAIRDLFEKEFGYKIRVTGAGAHHQNGLVERGNQTMDKAIRAMLIGAGLP
Ga0210368_154768	Ga0210368_1547681	F045132	VLMHSSNHYPLGNCDSPESETNPGYLTQFRAASNRPWLPSSFFAFTGRARTPPEELVNTASAAKCVSTSPLRGLINQPDLTFP
Ga0210368_161254	Ga0210368_1612543	F046726	LSKISEEDKIEIIQTGFRLNQEGKITLKKCSESTAEYSLFQLKGYSIKYKSIRR
Ga0210368_165630	Ga0210368_1656301	F022655	MTMKTMMTNEEAAKQLFGHLVDTCESCKQKLGVWTENPFDADVRNEHNMMFLCKECFHELQMDV
Ga0210368_166083	Ga0210368_1660832	F106082	MGSIRNNDGEVVVGRGAELTNLQEQFIERIREEGINAQGKVAKELNYTSYYRDKNNPGTAFYLALRDVVRLSEERIEVAKGSNLDMLVKMRDEAFINGDTKVALETIKIINDMQGYKAPVKVQQTKIDVKATIDLTKSPDENEQLYIDVDYED
Ga0210368_167051	Ga0210368_1670511	F046120	ELRNKNVDTFTMILAREPRPSKSMTRRAYDELELPEFDLDENLGEDYFASDGNLEGDSSMTASGETNAFGTDYAPPIGTKISKDFGTKGFFTGIVTSGPHIRDKDGDDVTVWKVQYEDGDREDMTASEIAHWKMPTEEVHTSQTKAKSKKPKQTMATKPSGDRSEELEDAIPKPGRDASAPTHV
Ga0210368_168363	Ga0210368_1683631	F094641	LMQALHIAKVIMEMRNGASEHGVSFSQNCICQKGVKKFGERGRKAAGKELDQLHQRNCYTPIDVSAMTPEEKAQAMEALMFPQEKKDGTVKGRMVYNGKPTREWLSREDSASPTAALESIFLTSIIDAKEERDVMSADVPNAFIQTPMPDDNKKVIMKITGVLVHLM