3300021308: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.462 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021308
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225734 | Ga0210350
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.462 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 100794428
• Sequencing Scaffolds: 18
• Novel Protein Genes: 20
• Associated Families: 13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	3
All Organisms → cellular organisms → Eukaryota	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	4
Not Available	6
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Porifera → Demospongiae → Heteroscleromorpha → Haplosclerida → Niphatidae → Amphimedon → Amphimedon queenslandica	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea	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
F006424	Metagenome / Metatranscriptome	373	Y
F008512	Metagenome / Metatranscriptome	332	Y
F012917	Metagenome / Metatranscriptome	276	Y
F021307	Metagenome / Metatranscriptome	219	Y
F024806	Metagenome / Metatranscriptome	204	Y
F034946	Metagenome / Metatranscriptome	173	Y
F042669	Metagenome / Metatranscriptome	157	Y
F046120	Metagenome / Metatranscriptome	151	Y
F046726	Metagenome / Metatranscriptome	151	Y
F062310	Metagenome / Metatranscriptome	130	Y
F064269	Metagenome / Metatranscriptome	128	Y
F075465	Metagenome / Metatranscriptome	119	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210350_1003547	All Organisms → cellular organisms → Bacteria	769
Ga0210350_1009173	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	554
Ga0210350_1013249	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	871
Ga0210350_1030152	All Organisms → cellular organisms → Eukaryota	1053
Ga0210350_1030241	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	646
Ga0210350_1043414	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	2166
Ga0210350_1046611	Not Available	546
Ga0210350_1048073	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	807
Ga0210350_1052097	Not Available	1475
Ga0210350_1068536	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	6024
Ga0210350_1068976	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Metazoa → Porifera → Demospongiae → Heteroscleromorpha → Haplosclerida → Niphatidae → Amphimedon → Amphimedon queenslandica	597
Ga0210350_1099222	Not Available	529
Ga0210350_1124318	Not Available	1418
Ga0210350_1138192	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea	573
Ga0210350_1139333	Not Available	594
Ga0210350_1152087	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1925
Ga0210350_1160617	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1778
Ga0210350_1167483	Not Available	1725

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210350_1003547	Ga0210350_10035471	F012917	IDKILNGMILFKFLRFPLNDCGYYEKYSSFSEVNQVWDRKRHLKRKRWSQE
Ga0210350_1008074	Ga0210350_10080741	F064269	VLRLITFLPSSVLMFMIPVLLAVCMVFACVPKVLYLIFGIDTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTQEQRCQRPSKRKALDRMFFMFLLMNHGRVSAKSARRGLIRLRPATKFEIPQAIPQDLSAEMLAPWDNIPQGW
Ga0210350_1009173	Ga0210350_10091731	F021307	MNRILYESRCRCKEEISITPKRKLSARSEGKPLQYPNEMMSKTFQIRYDKKLSSLARFILNSFRNKYIYYAIDDILYLMKSNP
Ga0210350_1013249	Ga0210350_10132491	F001506	MNRILYENRCKCNEEFSITKPRTSTTKSEGKPLQYPKPNEIISKTFQIRYDKKLSTTSKFILNSFQNKYIYYAIDDILYLFELNKTERNNLLAILYSPVLSLQNNFFVNFFDIWIREIYIDEVSKVNKFLNHDSQTSEQFSYIIIKFFYKTRVPVKKQESLW
Ga0210350_1022835	Ga0210350_10228351	F075465	KTLNISEWRTYRERSANLLKHRGQAYSLILGQCTQLLQDKMKQDADWTTVSTSYDPLTLFRLIEKTVLAQTEDQYPFATVYDQEHAFYSFRQETLTNPQWYEKFNTRIDVAEAIGVTRNHKALLEYVAKDVHKKKFADLGAAIQEAVRVDAEERYRAYVFLRQSGAQHANLRTVLQNDFTTGDDHYPKNRQSALHLLDKFSKTTVSKATTQSEGTAFAQGGGRGRGAGRGQQKTFDKEYWKDKECYKCHKLGHPASHCKQK
Ga0210350_1030152	Ga0210350_10301521	F006424	VVGSGGVNSVFVRDDFPKFGSDLVSALSGLDVNDFSHFF
Ga0210350_1030241	Ga0210350_10302412	F021307	MNRILYENRCRCNEEFSITKKRKTTTRSEGKPLQYPKSNEVLSQTFQIKYDKQLSATAKVILNSFQNKYIYYAIDDILYLLKGNPIERDNLLAILYSPVLSLQNNFSINFFDIWIREV
Ga0210350_1043414	Ga0210350_10434141	F021307	MNQILYENRCRCNEEFSITKKHKSSTRSEGKPLQYPKPNETISQTFQIKYEKKLSSTAKAILNSFQNKYIYYAIDDILYLLKADPIELNSLLALLYSPILSLQNNFSINFFDIWIREVYI
Ga0210350_1046611	Ga0210350_10466112	F062310	NLAAAQEAIGWTNLFKGWISKQWIERQRHHIGDKATTKNNALNWATTVIDYFFTQWFKVWDQRNLDRHGNDYQGHANKLKDVAFREMTHLYTFEETVPEDIRWLFQTPLEECLHWPLLRQRAWITNWEHIIKKEYATQMETG
Ga0210350_1048073	Ga0210350_10480731	F075465	MLQDKMKQDADWNTVSTSYDPLQLYRLIEKTILAQTEDQYPFATVYDQELGLYSFRQEIMTNAQWYERFNTKVDVANAIGVTRQHKVLLEWVSQETHNQAFDTLTPQQKETVRADAEERYLAYAFLRQRGKQHATLRVDLQNDFTTGDNRYPRDRQQTLH
Ga0210350_1052097	Ga0210350_10520971	F024806	MVTNSNFNFTNNTNVTLELPFSEHIEELRQRIFLLFWIILLLTCIAFIEVKSLVKILELP
Ga0210350_1068536	Ga0210350_106853611	F001506	MNRILYESRCRCKEEISITPRRKLSARSEGKPLQYPNEMMSKTFQIRYQKKLSSLARFILNSFRNKYIYYAIDDILYLMKSNPIERENLLALLYSPVLSLHNNLCINFFDIWIHEIYINETFKVNKFLENESQNLEQFTDITIKFLYKTRIPVKKLDSLW
Ga0210350_1068976	Ga0210350_10689761	F042669	EKVLLVRQVDDFALGCHQESTAKSVYATIGTKLTLHNEAEAPFEYLGLVDSFDGYDVLQTRDYIKLSAESYIRRLLKAHGWENPSPRESSNKPKPPLHESDVANLFNLAAGPVENTPEHKALETEHGFGYRSVLGEILFAYVLCRPDIGYAVTTLAKFSTAPNALHYKSLKHLAIYLRQTQDWGIMYWRDEPVASLPE
Ga0210350_1099222	Ga0210350_10992221	F008512	LLLCISTVRTALADLNQIKTAQRKTPKGGQKERTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIRGNLREKRRDPWPRANAPSKAV
Ga0210350_1124318	Ga0210350_11243182	F046726	LGKISEAEKIEIIKLGFQFQAKGKISLKKYYESTDRNSLFQFKGYSVKYESIRRNKLYKNLND
Ga0210350_1138192	Ga0210350_11381921	F034946	AINFYSSNFPEYYWQKGHYNLGNKIVHSDLYKTLNPIRARFDYKPNDYSQMPYFLGHVPQFSWVYGNLDYSFNKYHRHYQAHDDWYPDRKGKTLGHKNGGNCESVMKSSKYMTLIPNFIPRGCYKEIRKYQMCAASKDQEACLNDKISIMEVCPDHVLDGLKEKKKWYLRAEVIDNQTYRRAMQVGNYNK
Ga0210350_1139333	Ga0210350_11393331	F046120	IDDEEIVTLDQAKEKLKELQGKKVDTFTMILAREPRPSKSMTRRAYDELELPDFDLDENLGEDYFETEGDLEGNSSMTNSHETNAFGTDYVPKIGTKIYKDFGTKGFFAGTITSGPHTRTKDGDDVTTWKVQYADGDREDMTASEIAYWKALTEEVHTSTTKAKSKKPKKTIATKPSGDRSEELEDAIPTLGRDASA
Ga0210350_1152087	Ga0210350_11520875	F021307	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTSLSPTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVNFFDIWI
Ga0210350_1160617	Ga0210350_11606171	F021307	MNRILYKNRCRCNEEISITKKRNSRNRSEGKPLQYPKPNEITSKTFQITYEKKLSPIAKLVLNSFHNKYIYYAIDDILYSFQSNPHERD
Ga0210350_1167483	Ga0210350_11674831	F046726	LYNLSSNQNKAQNGSNLVTLSPISQQERVEIIKKGFQLQAEGKISLKKYYESTDQYSLFQLRGYSIKYES