3300006364: Aqueous microbial communities from the Delaware River and Bay under freshwater to marine salinity gradient to study organic matter cycling in a time-series - DEBay_Fall_0.3_>0.8_RNA1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300006364
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114433 | Gp0116177 | Ga0075482
• Sample Name: Aqueous microbial communities from the Delaware River and Bay under freshwater to marine salinity gradient to study organic matter cycling in a time-series - DEBay_Fall_0.3_>0.8_RNA1 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 49645227
• Sequencing Scaffolds: 17
• Novel Protein Genes: 23
• Associated Families: 20

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	12
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales	1
All Organisms → Viruses → unclassified viruses → unclassified DNA viruses → unclassified ssDNA viruses → Circovirus-like genome RW-C	1
All Organisms → Viruses → environmental samples → uncultured virus	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Choreotrichia → Tintinnida → Xystonellidae → Favella → Favella ehrenbergii	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Aqueous Microbial Communities From The Delaware River/Bay And Chesapeake Bay Under Freshwater To Marine Salinity Gradient To Study Organic Matter Cycling In A Time-Series
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Coastal → Unclassified → Aqueous → Aqueous Microbial Communities From The Delaware River/Bay And Chesapeake Bay Under Freshwater To Marine Salinity Gradient To Study Organic Matter Cycling In A Time-Series

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): marine biome → river → sea water
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Delaware
• Coordinates
  • Lat. (^o): 39.283
  • Long. (^o): -75.3633
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000048	Metagenome / Metatranscriptome	3365	Y
F000073	Metagenome / Metatranscriptome	2639	Y
F000080	Metagenome / Metatranscriptome	2485	Y
F001346	Metagenome / Metatranscriptome	718	Y
F001679	Metagenome / Metatranscriptome	653	Y
F001758	Metagenome / Metatranscriptome	640	Y
F006508	Metagenome / Metatranscriptome	371	Y
F007695	Metagenome / Metatranscriptome	346	Y
F008512	Metagenome / Metatranscriptome	332	Y
F017318	Metagenome / Metatranscriptome	241	Y
F020094	Metagenome / Metatranscriptome	226	Y
F024800	Metagenome / Metatranscriptome	204	Y
F025295	Metagenome / Metatranscriptome	202	Y
F026580	Metagenome / Metatranscriptome	197	Y
F037756	Metagenome / Metatranscriptome	167	Y
F042356	Metagenome / Metatranscriptome	158	Y
F044534	Metagenome / Metatranscriptome	154	Y
F067804	Metagenome / Metatranscriptome	125	N
F078768	Metagenome / Metatranscriptome	116	Y
F099393	Metagenome / Metatranscriptome	103	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0075482_1000233	Not Available	686
Ga0075482_1000747	Not Available	760
Ga0075482_1008230	Not Available	755
Ga0075482_1022101	Not Available	657
Ga0075482_1032660	All Organisms → cellular organisms → Bacteria	908
Ga0075482_1132496	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales	526
Ga0075482_1140322	All Organisms → Viruses → unclassified viruses → unclassified DNA viruses → unclassified ssDNA viruses → Circovirus-like genome RW-C	617
Ga0075482_1145659	All Organisms → Viruses → environmental samples → uncultured virus	1136
Ga0075482_1149296	Not Available	742
Ga0075482_1149519	Not Available	719
Ga0075482_1153972	Not Available	602
Ga0075482_1156266	Not Available	618
Ga0075482_1159771	Not Available	632
Ga0075482_1162315	Not Available	594
Ga0075482_1165547	Not Available	628
Ga0075482_1165909	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Choreotrichia → Tintinnida → Xystonellidae → Favella → Favella ehrenbergii	512
Ga0075482_1167564	Not Available	766

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0075482_1000233	Ga0075482_10002332	F001758	RLGQAGWLSPSQAGSKGAGAEAGFTSSSGGVRALSVHAKKGLNG*
Ga0075482_1000747	Ga0075482_10007471	F007695	VKRRDPWFEANALPKAVAVLGLSGQDAEISHRSVLIWFAGRWRNHQSKRAEKPHSKSSGGNALDGPATRPETPLAVENSVGKLAAPEAPNA
Ga0075482_1004385	Ga0075482_10043851	F000080	MTFWQENYPFIKDVYIMRQTKMIEWMENVEKAISRIMADKVYTSAEFKRERDNFHALCKDLERGEVKKWLKQILEILMAERGKEERTEQINKLDGLIKKHEELIPTVLKTQVKVDLYWKCYAYGDELKPHIEFLDGIMLSSTRDIAPSCIENVEELIERQEKSLSQLETKRAIVRELISKGKQLLENPDKPKFLDGHVQRIEEGWDETKDKAQARLQLLQNTKAAWEGYAEGLEQIAVEFEKAEEEMKKVKKRFNLQAAFEDLERRQTIFNICKSTIENMFGSIQHNYDVMTMTLPEDKKDFVKKEVKAVQEKLEVVGRFEEKVKKIEDFCASLNDFDKTIRVIDGWMKDADSQLNTIKNKSDQMTPEDRVSYTMELQEDVAAKVQMIKKAIATESELLPQGDKVPQDAQDYKDELKRIEDFVTDLHKRVMKECDNFSEDVKYW
Ga0075482_1008230	Ga0075482_10082302	F078768	LRWLAVINRLSLVVSRIIPGDWGKVESGWLAWPL*
Ga0075482_1022101	Ga0075482_10221011	F044534	HQFLWPESCPVSSHTNQELCGKARLETASSRVRPTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPEGLARRTREARNGAATAGRERIWQSS*
Ga0075482_1032660	Ga0075482_10326602	F001679	MSWHQKAKKGVEVCEKPGVVDKRTLIPGFPNQRALNS*
Ga0075482_1125984	Ga0075482_11259841	F000048	KELQDRYEKVKAVSDEWVKKVDTLVKEWKLLDSTVSELNSWVAQDRGAEGEAMFSLEKMESTLGELKNIFKEKEKLVENL*
Ga0075482_1132496	Ga0075482_11324961	F020094	VLLFVCINLHNVKVKINYFISYLYFSFFNRQKLISHVIHINLSLTNTLINVNTIKGNPRLFYSAGMCNLQKSQKTRQPKAILTILRILLTKTKFFKSKPVAIHFNNLFFNQQSYILKKLKKKVFTKLIASYRCYSHNG
Ga0075482_1140322	Ga0075482_11403221	F017318	MKFQRTVQAAYDITTNGIAANVGLINFSLSDLPSSSDFTNLFDLYKIERLDIAWTPEYTELTDASALSNAVNVYFHTAIDPAGIVPAAVDDILQYRTLHSTPITKMHKRDFVPAILLDGIIPASCYISTGSPNSNLFGIVYGIPATGVAMTFRSVA
Ga0075482_1145659	Ga0075482_11456591	F017318	VEDAYNIICDGINPSVGSFNFSLNDLPSYTEFTGLFDLYRIDEIEIEWYPEYTVLSDGGVTSPAVNVQLNTAIDPAGNTPILVTDVLQYRSLHATGISKPHKRRFVPSYLLDGISPAKCYISCASPSSNLWGIVYGVPPTGTAMTIRSRARFFLSLAQSR*
Ga0075482_1149296	Ga0075482_11492961	F099393	QRERETLMLVERGMPMRQIFPHGESQAPDSACGQVTGSGPMVGRVKKVVLFSVCLPALLIALGAGESLNLAYGQSESNAAASSAVRATASGVSDQTFSTRERSEPTVTGAAMHVALFVPRH*
Ga0075482_1149519	Ga0075482_11495191	F024800	VARGQRIARSDGRPRANGGDAETKSRACLHQVRRPVAQPPVQAGLEASLEFQRARAAGRPCYEAERTPLAVENSVGKPAA
Ga0075482_1149519	Ga0075482_11495192	F001758	GLEDSQATGERLGQAGWLNPSEAVSQGAGEEAGFTGSSGGVRALPATRKTEPRGEER*
Ga0075482_1151041	Ga0075482_11510412	F000073	MEEHNNLRTICDDGKGKLQWEREIPHDALDNLQNLANSDFHKNLGTIIHDIYLTAHKMFSDMPQGDHKKRAKYRFASKTLMRILPDNLKNEVEGLIAKNTMTLDLYEILGQCTWGQRSL*
Ga0075482_1153972	Ga0075482_11539721	F026580	VRGDEKPLRVESNVSQAGFEPGRIAVTQRVFGCYCASARTDNSGGLREGVSQRKDAERRDKVSVRSGKDTWSRQDP*
Ga0075482_1153972	Ga0075482_11539722	F001346	VKTFREAGDSKNAVAGLWMKGNLRDKRRDPWHRANAPPKAVADPALSGGDVKMQSQTCLRLVREPVAQPPVQAS*
Ga0075482_1156266	Ga0075482_11562661	F008512	VRTALAGAIKIETAQRKTPKGGQKERTHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKSSLREKRRDPWFGANASSKAMADPEPVVKTRK*
Ga0075482_1159771	Ga0075482_11597712	F006508	VALANASSKAVADQCQVVKTRSRNRRRVLTWFASRWRNHQPKRAEKPHSK
Ga0075482_1162315	Ga0075482_11623151	F025295	MVTGPGEAAELLRRREALIPEKLKFITRKSNLQKPI*
Ga0075482_1165547	Ga0075482_11655472	F042356	LSETQLPRGYLVATVHQHGASDSGGFDQPFETAQRKPLKDGQKERMTRESHDGSAGRVKNFRAPAMLKTAPLACEQKAT*
Ga0075482_1165547	Ga0075482_11655473	F006508	VAVVNAPLKAVADQSQVVKTRRPNRRRVLTWFASRWRNHQPKRAEKPHSKFN
Ga0075482_1165909	Ga0075482_11659091	F067804	ADNAHDDVKIAGLVQGFFVGAFDFHGMTDVAHCVSDANPVEQHFENAMRGFWNGSYQEVTKGVDQLGLAVSDIGDMLDHCGKIDHHDYEQIQRMAESFLHPKQVLLEAAESLIVNGVNIFEDTREGLHDYRLGKWVDAGEHFGQAAAMLLYGKTQMVDHEELFFDFDNHW
Ga0075482_1167564	Ga0075482_11675642	F037756	LFPVPTFGAHLAVAAGFPTPFPAANGVSGLVAGPSNLLRG*