3300021268: Metatranscriptome of estuarine water microbial communities from the Columbia River estuary, Oregon, United States ? R9.63.3A (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021268
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225677 | Ga0210294
• Sample Name: Metatranscriptome of estuarine water microbial communities from the Columbia River estuary, Oregon, United States ? R9.63.3A (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 19963883
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	4
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae	1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae → Guillardia → Guillardia theta	1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Cryptomonadales → Hemiselmidaceae → Hemiselmis → Hemiselmis andersenii	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Oligotrichia → Strombidiidae → Strombidium → Strombidium inclinatum	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 → estuarine water
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Oregon
• Coordinates
  • Lat. (^o): 46.249
  • Long. (^o): -123.986
  • Alt. (m): N/A
  • Depth (m): 3

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000344	Metagenome / Metatranscriptome	1257	Y
F001926	Metagenome / Metatranscriptome	616	Y
F011303	Metagenome / Metatranscriptome	292	N
F027881	Metagenome / Metatranscriptome	193	Y
F033054	Metagenome / Metatranscriptome	178	N
F039672	Metagenome / Metatranscriptome	163	N
F067774	Metagenome / Metatranscriptome	125	N
F072520	Metagenome / Metatranscriptome	121	Y
F073633	Metagenome / Metatranscriptome	120	N
F084312	Metagenome / Metatranscriptome	112	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210294_102332	Not Available	1647
Ga0210294_103998	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae	583
Ga0210294_107769	All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae → Guillardia → Guillardia theta	674
Ga0210294_107803	All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Cryptomonadales → Hemiselmidaceae → Hemiselmis → Hemiselmis andersenii	1004
Ga0210294_108936	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	808
Ga0210294_114559	Not Available	1938
Ga0210294_134274	All Organisms → cellular organisms → Eukaryota → Cryptophyceae → Pyrenomonadales → Geminigeraceae	879
Ga0210294_137364	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Oligotrichia → Strombidiidae → Strombidium → Strombidium inclinatum	609
Ga0210294_137682	Not Available	538
Ga0210294_143586	Not Available	666

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210294_102332	Ga0210294_1023323	F067774	MLKLNLKSQDNSLKNLKSSLACYDVSESRFFESNVRKKNDSILLDFGLKHKLRCDDLRINLKLSNPITSKLKDLETPYNDILCDFDAYRKIQSNNELLKLFKEKFNSKSFLKGRLLNGTKRGFSIGVAGVVGFLSMNNTVKINKDKTAILYIDSINMNQGIVSFSQK
Ga0210294_103998	Ga0210294_1039982	F001926	VRHEDIPETNNPKIIFPVLEGDKLMKEVLNGRYNVHPVPPPNSEIKERIRKRYERKRIKIEKLLTL
Ga0210294_107769	Ga0210294_1077691	F033054	VNSMFNLVLQTKDFSANSLKQLMSNNETKFKNFFYQATNNKFVEQFIEPNIQDIEYITNIAKWTIEFFEIISAAQVFGTIYDRLKWKIVDHTFCIWLGAVSKCDYGIHMSFLGLMVAMYSLTMSISMQFLELPPSMIFREIELNAFRLGLWWVTSKNLYYWYNKKISEKYAEGRFRPIDRAEKMALYDQMIGSDTRRTIKMWKWTIRFIVLNLLIRIFEIFTKS
Ga0210294_107803	Ga0210294_1078031	F073633	TMHRRVVMLALAGSAAAFMPGAFVGSTPALAKATSGLRLRSGRTSIKMVDWDWDKKEEEDNYDGPGSERGQINRSDEIGARSKERLENAKKQAMDAGYGSVSGLAAGRSDLKEGDRDPVTGRLILDPLKIPTKDQGAPGTWEEYLKMRKEKEGGTARDVMGNVIDDVKPTYAVQDGTWGPPKEAQKENLDDIFGKKPVSEPVFELDPELERQKAERAADAAKQQDEVEARMAKWMAEAAAKKAAEGGN
Ga0210294_108936	Ga0210294_1089361	F000344	MRPRHPHAAESGVGKHTARESESAKACADGEERVANAHS
Ga0210294_114559	Ga0210294_1145591	F027881	HKFFIMSLTVARSERVRGVLTHASRTEISFNLSGARVSNALRTFRRFM
Ga0210294_134274	Ga0210294_1342741	F011303	NKRCTVEMPGEPKCKKFEDWKKKSEAFLASFKNAKRVIPKGAKPIIVQSKKDEVEVIYPEQCSFTWTAGLADAYPNCTLASGDKSKIFIYNRVLLNAKGECNYFQPVFSSNDFKGADRAEDTDSLLDQIYQEFNAGNARFGDDMKVEFPVVGKMDKAGMFELFAKFGGCQRAMQKGCVPVNMSTGKDEVFEGIVPCVYSFKWSSALNDVFKLELADGADVVLSSYDCLKIKSGKVISFAPHFDPAANIKPAGKSGAA
Ga0210294_137364	Ga0210294_1373641	F039672	VISPKMSPDLTSIRVGQRLPECSAEVVLSTLLFEEIELLEGLQSVDSKDKSVVSSHTKTGHEVLNLDVVEDHSGDVVGVLLSHGLVGVGLNLGGDSVSVSEDGGGDLGAEGSGVVVSLLLGVGDSEREVLGDLVEVTLDGGEELSLWVLLNLSGFGSSRLVSSDVLIGNGVSSHIWESSNVLNGVWVVVVSLDSSSSGDKSA
Ga0210294_137682	Ga0210294_1376821	F084312	ITIGIFTILLTIYLITMNYFLILNDYVHWYFPVVLLVLYIPMIIGSSFFVVFFSKDTQSSRGKLFVSCQFGIISTALACVWILCYYVWIYKSDTVYSGMGDPKDNVYTKQSKKFYLFVVLAETAIICTSYAYFICVTNRYADNMKGKNE
Ga0210294_143586	Ga0210294_1435862	F072520	VTELTDKVVTEDTAPTLTVGDKTYVVADLSNEVKEMLSLHEQAMQMAIGAKRQAVIHDLAVSNIASLIEKKLAETDE