3300004568: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metatranscriptome 10_HOW4 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300004568
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114290 | Gp0111160 | Ga0066496
• Sample Name: Freshwater sediment methanotrophic microbial communities from Lake Washington under simulated oxygen tension - Sediment Metatranscriptome 10_HOW4 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 18031158
• Sequencing Scaffolds: 11
• Novel Protein Genes: 11
• Associated Families: 8

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	6
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	2
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → cellular organisms → Eukaryota → Haptista → Haptophyta → Prymnesiophyceae → Coccolithales → Coccolithaceae → Coccolithus → Coccolithus braarudii	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Sediment → Unclassified → Freshwater Sediment → Freshwater Sediment Methanotrophic Microbial Communities From Lake Washington Under Simulated Oxygen Tension

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): freshwater lake biome → freshwater lake → lake sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Sediment (non-saline)

Location Information

• Location: USA: Lake Washington, Seattle, Washington
• Coordinates
  • Lat. (^o): 48.3807
  • Long. (^o): -122.1599
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001633	Metagenome / Metatranscriptome	660	Y
F001904	Metagenome / Metatranscriptome	619	Y
F014145	Metagenome / Metatranscriptome	265	Y
F024800	Metagenome / Metatranscriptome	204	Y
F037503	Metagenome / Metatranscriptome	168	Y
F053640	Metagenome / Metatranscriptome	141	Y
F082737	Metagenome / Metatranscriptome	113	Y
F094695	Metagenome / Metatranscriptome	105	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0066496_102822	Not Available	524
Ga0066496_104290	Not Available	544
Ga0066496_107504	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	548
Ga0066496_107914	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	767
Ga0066496_109999	All Organisms → cellular organisms → Bacteria	1222
Ga0066496_112443	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	788
Ga0066496_113260	Not Available	563
Ga0066496_134478	Not Available	914
Ga0066496_141440	All Organisms → cellular organisms → Eukaryota → Haptista → Haptophyta → Prymnesiophyceae → Coccolithales → Coccolithaceae → Coccolithus → Coccolithus braarudii	1087
Ga0066496_144209	Not Available	713
Ga0066496_145631	Not Available	529

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0066496_102822	Ga0066496_1028221	F053640	GIIPGDRGKVGGSWCRHPLPKAKAGERHISPVPLAGVVSGQFTHESGTERQGAIRNRVEPSQAHGRFRPVCRRSYPRGFWLLLRRPERSHGSRRANPAKRPHSQHEGGAQGSRDGGERADLAKSVKPPQWGGVKNHVTPLQKRKQP*
Ga0066496_104290	Ga0066496_1042901	F082737	SK*PSLQLAPQPACQV*ACHIQHAGRCPRLAPRPRCFSVGASMLGGPPASLPVRSQNLETDFHSPTKTNLLPDRRGGVRVPALPLQLCGTLAVSPVRSDLHPRPVSRTAWDFYDQNPLLPDPAPLLPASLNRRSPLGFFAPPDQSARSRWPTGNLLSATPDLPSLPTGGRIRYQHQRIIV
Ga0066496_107504	Ga0066496_1075041	F001633	TRLGALAFAGGVLPDATLRGMRMSRSHGGTVLTVAGRDLSSEASAPGSEIPCREDHAGRGADTPAIFIVSRPHPYHGDGTGFWPVVGPALRV*
Ga0066496_107914	Ga0066496_1079141	F001633	VGVRHALFPDGTRLGALAFAGGVLPDATLRGMRMFRSHGGTVLTVTGRDLSSEASAPGSATPCRERHARRGADTPAIFIVSRRHRYHGDGTSFWLAVGPALRV*
Ga0066496_109999	Ga0066496_1099991	F037503	LSVIEVELLIGLGGFTAYQILTNSEYYNIYSGVSPWVLRSVGERERTQTNS*
Ga0066496_112443	Ga0066496_1124432	F001633	PGGTRLGALAFAGGVLPDATLRGMRMFRSHGGTVLTVTGRDLLSEASSPGSDAPCRERRAGRGADTPAIFIVSRLHPYHGDGTSFWPAVGPALRV*
Ga0066496_113260	Ga0066496_1132602	F001633	RHALFPGGTRLGALAFAGCVLPDATLRGMRMFRSHGGTVLTVAGRDLLSEASSPSSVAPAGSGTPDVVRTRLQSYFASARYHGDGASLWLAVGPALRV*
Ga0066496_134478	Ga0066496_1344781	F094695	VMPSCSPLQRCQLLDGGISVCSVRDPCFRETWDDVQRFSDESIGSSWVQPSTVRRSPFPVASFRDSLSAVVRRFSRPRHSSLRLTCLLEALPPINRPRMRTREHLSYGFVPYSAQQKQASVSPGASNLRHCPSSGFLTLSTSCSACNPDQFVSPGLRSWGSTKSVYSPPSFDEGRVRRAWVSSPKLSPFP*
Ga0066496_141440	Ga0066496_1414401	F001904	MRTSFILCLLAALAFAAMVSAETDFMAAVAEVEGDCHPECRWQCDDPVCPAVCHPVCERPKCQIHCEETECAKCKIHCDKPQCNVRCPKDLCEKKDCPKCETVCSPANCRTQCEAPNAVCTPMCEATKCDWKCKKPITCPKPKCELVCERPACDTRARKTGTKGGCCSCAVQANLAATIRAANSLMEESSEVSAMMPSFMEVMHSIKASSQEGKGMCCKCAA*
Ga0066496_144209	Ga0066496_1442091	F024800	VARGQRTAKSGGRPRADGRDAETELRTCLNLVRRPVAQPSAQAGQEASLEIQRARAVGRPCYEAERTPLAVENSVGKPAA
Ga0066496_145631	Ga0066496_1456311	F014145	DFQPGSLPACTAWSTANKSAGRFASPLPVGRFLQPPDQCFLARRLPPLARNRSLVTAFRSPTTAAASRRPPFRGQSSQPATSLPSKFASVPVRPFGSTTASRFAPVAAVSLPLARCTSTTRFSLPRLRSPLPSGTFTSLGIKAFNRVCRLPVHLTNPPDFLSLPAARPDESWGCGS