3300006375: 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_Spr_0.19_>0.8_RNA2 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300006375
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114433 | Gp0116185 | Ga0075490
• 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_Spr_0.19_>0.8_RNA2 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 108356578
• Sequencing Scaffolds: 42
• Novel Protein Genes: 45
• Associated Families: 34

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
Not Available	19
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	2
All Organisms → cellular organisms → Eukaryota → Metamonada → Fornicata → Diplomonadida → Hexamitidae → Hexamitinae → Trepomonas → unclassified Trepomonas → Trepomonas sp. PC1	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Eukaryota	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea → Stichotrichia → Sporadotrichida → Halteriidae → Halteria → Halteria grandinella	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 → Predicted Viral	2
All Organisms → cellular organisms → Eukaryota → Sar	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Spirotrichea	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	2
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Atkinsviridae	1
All Organisms → Viruses → environmental samples → uncultured virus	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Collimonas → Collimonas fungivorans	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Atkinsviridae → Helacdivirus → Helacdivirus borborovicinum	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?
F000049	Metagenome / Metatranscriptome	3277	Y
F000203	Metagenome / Metatranscriptome	1619	Y
F000237	Metagenome / Metatranscriptome	1498	Y
F000734	Metagenome / Metatranscriptome	915	Y
F001346	Metagenome / Metatranscriptome	718	Y
F001488	Metagenome / Metatranscriptome	686	Y
F001506	Metagenome / Metatranscriptome	681	Y
F001583	Metagenome / Metatranscriptome	668	Y
F002260	Metagenome / Metatranscriptome	577	Y
F006424	Metagenome / Metatranscriptome	373	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0075490_1002469	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	659
Ga0075490_1006187	Not Available	756
Ga0075490_1006829	Not Available	804
Ga0075490_1014063	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	1414
Ga0075490_1018663	Not Available	681
Ga0075490_1026772	All Organisms → cellular organisms → Eukaryota → Metamonada → Fornicata → Diplomonadida → Hexamitidae → Hexamitinae → Trepomonas → unclassified Trepomonas → Trepomonas sp. PC1	515
Ga0075490_1030493	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	5788
Ga0075490_1042085	Not Available	1110
Ga0075490_1056850	Not Available	644
Ga0075490_1070472	Not Available	766

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0075490_1002469	Ga0075490_10024692	F000734	LHWEGHGVWAGPVKTFRNVGDVKNGTADLWTKGNLRVKRRDPWLGANALSKAVADPELAGEDAEMKT*
Ga0075490_1006187	Ga0075490_10061871	F078768	ELRWLAVINRLSLVVSRIIPGDWGKVESGWLAWPL*
Ga0075490_1006829	Ga0075490_10068293	F014854	LRWTAVIERKSLVVSRIIPGNWGKVESGWLARPLLDRIARFGGGGRIHQFLWSRSHAVSYAKRNLAARGDKKPLRVGSSSSGRFRAWANRSYPEGKWLLLCIGTGRVTLADSINRLKPPNESHRKVDKGSARTGKITQAGQAV*
Ga0075490_1014063	Ga0075490_10140633	F015606	MADMLTTDPFFALTSQIGGVREKVSDSVFENYKLQVAQTNDINNRAMQVALHDASELASIKQEVSNGTLQAMLAAARTDAQIGATASVTQRTIFEQGELTRRLVQDLNTQNLNTALINTNTALTGLGVQYGGLGLAYGGAVSAYQSANSVSAVNALGSALASNGIINTGTLSGTTQTATPTTIR*
Ga0075490_1018663	Ga0075490_10186632	F000734	VAGDIEKNTAGLWTKGNLRDKRRDPWLWANAPSKTAADPELSGPDAK*
Ga0075490_1026772	Ga0075490_10267721	F082866	LNLLLRKASGSGKICVLSQIEPQTPRLVVSFRQYLQVSVLQPYSPQNPKPSGFPRNASEPAFEMVSFKA*
Ga0075490_1030493	Ga0075490_10304934	F020197	MEIDNSQKPFSMGYVLRTTAKHMRKSIDISIRKTFERVPEFANEQEKSQEVFKTLAFLHTMRKQLDDFQAQHSVNFKGE*
Ga0075490_1042085	Ga0075490_10420851	F030134	KKDKIQPVSLRFKLRSCNFLLVEQTNNLSGCNLSEKIIQHRGSN*
Ga0075490_1056850	Ga0075490_10568502	F021791	RSCVDYRIKPHVPPFEQIPANSVKFQPCDCTTQVEYSCVNL*
Ga0075490_1070472	Ga0075490_10704721	F097458	NTLVRLLGIIGLNHTLHRSYKLPPISLSFAFAALIPRRGICALAYTQVIFFSHIIPIDSGYGLVGSPILFDIHTLVV*
Ga0075490_1082094	Ga0075490_10820941	F082866	MHHQLPNRKRTLNLLLRKASGSGKICVLGQIEPQTPRLVVSFRQYFQVSILQSYSPQNPKPYGFPGDANVYVRF*
Ga0075490_1084248	Ga0075490_10842481	F006424	VVGTSWVNSVFIRDDFPELGSDLVTALTGLDVYNFTH
Ga0075490_1187319	Ga0075490_11873191	F023360	MAYVLGGNNNEGDGFTTAISNFALRAMHESMGLVNLTNVVTPTQGNEFLIPNFAPITYQDYNPALTGGSTGFGNANEQNPALAQGSIIATPAVAATAFDVFYAWTTSFQLAATLGAELGESFAEKVDQRVCAGFLSFKATPGNTNYATSADGFVRPTQLGAMELLAAGQTGGTATVGFTSNSVLETVRNVKQAFKVARMPGNPMIVLDS
Ga0075490_1242905	Ga0075490_12429053	F015657	EILDKRYRVVKKLGGGAFGEIYKVEKKKTGEYLAAKVEKAVKM*
Ga0075490_1277772	Ga0075490_12777722	F020793	MKNSKFMTLRPNFIPRGCYKEIRSYQLCVAKSSADACFADKISIMEVCPDHVLELLREKKKWYLRAEMIDNDTYKRAMTVSDFNKHRSVSDLQLKTWDYGKTANMRSDSLWQDDRWLPTKHSHPHRYDNVNFAEQEYMDFFGGTKGTAETEE
Ga0075490_1278813	Ga0075490_12788132	F028939	MKTNRIKNKNYKLFKYNLLKLQVYSNQPHFNVANFSNNILEQIETYLKQVLKIIFEYHVCHFKILFIGFPVVSKMRQMKLVHFTNHNFISEKS*
Ga0075490_1289048	Ga0075490_12890481	F017318	DGINPSVGIFNFSLNDLPNYTEFTGLFDLYKIESIEIEWYPEYTVLSDGGVTSPAVNTQLNTAIDPAGQTPAAVSDILQYRTLHSTGISKTHKRTFVPAYLLDGISPVSAYISTASSSSNLWGIVYGVAPTGTAMEFKSRAKFMLSMAQSR*
Ga0075490_1291711	Ga0075490_12917111	F000237	FTNKHLNVDQLTRLMVLHYFTP*YYLYLVKLHVLFCHES*DSDSGENVYEDKSGSYVS*FYDAFLKEIQDA*Y*TLLIFTYFFFHHANPSTVNYFFFER*NISELDEIRFYGVAPH*YFRPLMGLLVVSPSHYEGLL*MGL*FILLAALPIIYNLYNANNRYLPIIPMQSSLLQTSGFILFMLSMYCTASMLPCGRYYYAPEGGYVGNPCVKFSYQYCYIYMA*ILH
Ga0075490_1305570	Ga0075490_13055701	F002260	QSENYFKEFKVSVPYQRISNATVDDIIFYDPAAERRASALNVNWDTYFHVSSQEWLYKLEFGWWRMYCDTVFGATYYKNNPQGQLISAFNPSQLMKNDQTLKRLDVFGAVMVLYQSLVTDVSNLNDVDMANYKFAQERCETEWAKARELSNFYDLANNAPNGPATKLEENWLADVDYFNGDRRFF*
Ga0075490_1307285	Ga0075490_13072851	F001506	MNRIISKSKYQCKEESSITKKRNQRKKTNSRQESYLSEGDASQTFQIRYDKKLSSIAKLVLNSFQNKYIYYAIDDILYSFKSNPSERDNLLAILYSPVLSLQTISLLTFFDIWIHEIYINEVSKVNKFLNNDSSNFEQRSYITIKFLYKTQVPP
Ga0075490_1307943	Ga0075490_13079431	F000049	MTFWQENYPFIKDVYIMRQTKMIEWMENVEKAISRIMADKVYTSAEFKRERDNFHALCKDLERGEVKKWLKQILEILMAERGKEERTEQISKLDALIKKHEELIPTVLKTQVKVDLYWKCYAYGDELKPHIEFLDGIMLSSTRDIAPSCIENVEELIERQEKSLSQLETKRAVVRDLIVKGKQLLENPDKPKFLDGHVKRIEEGWDETKDKAQARLTLLQNTKAAWE
Ga0075490_1310705	Ga0075490_13107052	F095528	KTSTPKLNVQPSYITLKLPTGNFTTSYGGAKCSGQLVKMKGAFTALDNYVQTAGKTKSYGEAMNDLLNPTLLNRLVPGWDKPIIADTFIAGDSVSFIDGMFTKKYPGKFDVVSVKGKYVYIKVLNKRTGNTENIGFAATELKK*
Ga0075490_1310993	Ga0075490_13109931	F001488	MARLELTLNFPKSFYIKTFNVKSEKKLSPLAKLILQNVQFKHFYYVRDDISYLLKSNPSERDFLLQALYSIVISLQNNLSINFFDMWIYEIYINKVSTHNKFMSQKSQNLEP
Ga0075490_1312056	Ga0075490_13120561	F082737	MPGLSPSHPARRTSLRFAPRLRNFSVGASLLSGTPASLPVRSQNLEADFHSPTTTSLLPDRHGGVRVPALPLQLCDTISVGPVRFDLHPRPVSRTAWGLLQSKPVAFRSCATPACLVESSLPFRVSTLPDQSTRSRWPTGNLLPGTPDLPSLPTGGRIRYQHQRIIVPAPLR
Ga0075490_1313924	Ga0075490_13139242	F010164	SWKALYQKDKIDLVNNKYKLVKTGLSETFSTTENLINNFENKAFITLQQYMIFVTASKILRKFLFLSEAEQSKLIEVTISKLGGVKK*
Ga0075490_1314471	Ga0075490_13144711	F001583	VFYMHVRGVDTLFVLSYTHILKKIYLKNYVTSESDG*LLGGYAFF*FHYIVMLGISLSATHLSDLTLTIIANVF*SLFNFTFKTYYIIFTNKHLNTDQLTRLMVLHYFTP*YYLYLVKLHALFCHES*DSDSGENVYEDKSGSYVS*FYDAFLKEIQDA*Y*TSLVFVYFFMHHFNGGPVNYFFFER*NISEMDEIRFYGVAPH*YFRPLMGLLVVSPSHYEGLM*MGL*FILLA
Ga0075490_1318229	Ga0075490_13182291	F018726	TKSDGYGSERVDTGGNGYTLITQHQKTGKGSRHYIQIIQTVNGVDPYSGLTKKFTASCSFTINRPLYGFTDAAIVALAKALTDYRDDSEVTTARLIQFQS*
Ga0075490_1321803	Ga0075490_13218032	F014988	MAFNLTAITGAAVSGFTAPVYNLTADVAPSQNGKQWAVSSLGGTQANVDVNTVSKPFTLSFFRPAVLKALPAANPSTGVIKSIPVNTYKFITRKGAVPAANQTSQMVRITTTIEVPAGVDTFEPEDLKAALSAHIGGLAQQSSGIGDTVLTGIM*
Ga0075490_1322519	Ga0075490_13225191	F030134	KNNKDKIQPVLQRFKLRSCYFLIVEQTNQKGFFIPSEKKIQHRGSSCIYR*
Ga0075490_1323619	Ga0075490_13236191	F017318	VFNFSLNDLPNYTEFTALFDLYKIERIEVEWTPEYTELTDASLASNAVNVYFNTAIDPAGNTPAAVDDVLQYRTLHSTMITKRHKRDFIPAYLMDGIVPASCYISTASPSSNLWGVVYGIPAAGVAMTFRSRAKFHLSMAQSK*
Ga0075490_1324564	Ga0075490_13245645	F025754	LGFGITGNHERRAKDYTGSWGGEAKFAYLFEGPTPHIKRLENIIKTMHTDMLWKLDDWETEWLDNNWTADQLLNFVKDVILERHLAIKQIR*
Ga0075490_1329677	Ga0075490_13296771	F015606	NFTLKENNMADGMTTDPFFSLLQNVADVKTKVSDSIFENYKLQVAQTNDINNRSMQVALASASALSDLKAAVSKGTLETMLAAGRTDAVIARSAAETQRAVFEQGELTRRLIVDLNTQNLNTALINTNTALSGLNGQYGGLGLAYGGAIAAVQSANSVNALNAVQSAVSGQRLVNTGAMTSTSQTS
Ga0075490_1331541	Ga0075490_13315411	F017318	MLTKSQKKRAVSRRASQNKSPNAIKNPELNQVVKFVRTVEGAFDIITTGLVANVGIFNFSLNDLPSYTEFTALFDLYKIEQIEIEWTPEYTELTDAAPVSNAVNVYFNSAIDPAGNTPASVDDVLQYRSLHSTSITKHHKRTFVPAYLADGILPVSSYISCASPSTNLYGIVYGIPATGVAMTFRSRARFYLSMAQSR*
Ga0075490_1334430	Ga0075490_13344301	F017318	VNRRSSQNKYPVNMRSPTAASPLKFQRTVEGAFDINCDGINPSVGVFNFSLNDLPSYTEFTALFDLYKVERIEIEWLPEYTELSDAGLTSNAINVQFNSAIDPAGNTPSVYTDVLQYRTLHSTGISKRHKRDFIPAYLLDGIVPAACYISTASPSSNLWGVVYGIPATGTAMVFRSRAKFYLSMAQSK*
Ga0075490_1334774	Ga0075490_13347741	F006508	VALANAPSKAVADQCQTVKTRKRNYRCVLTWFASRWRNHQSKRAEKPHSKS
Ga0075490_1335039	Ga0075490_13350391	F001346	VKTFRNAGDIKNGTAGLYTKGNLRVKRRDPWHRANALPKAAADPALSGEDADQKTQTCLDLVRKPV
Ga0075490_1336749	Ga0075490_13367492	F017318	MGIPLLAAPLKFERTVEGLFDIACDGINPSVGLFNFSLSDLPSNSDFTNLFDMYRIDKIECAWYPEYTVLSDSGLVSNAVDVQLNTAIAQISNTPTVVSDVLQYKTCVGTGITQIHKRSFQPSYLMDGICPCSCFLSCNNATANWYGVAYGIAPTGTAMLFKSRAKFFVSFVQSR*
Ga0075490_1339950	Ga0075490_13399501	F103327	SNILSFASSSKIARTLGSKVNDDWKQDQVELAKAVPSHAIILSEVDKKHAGLKYTTINDLFHQEGSLTGNTFRTNFSVVKVEGPTAELVQSYNKTTKKATSAKGTKGGDLIWRVSLLVKDASTASNSNKYRINVNSHEGLGAEFFGKAANLHSEAAALKRVQHQVDNLT
Ga0075490_1341256	Ga0075490_13412561	F044534	MTGIYHQFLWPESCPVSSHTNQELCREARSETALNGVRPTGRFDPCADAVTPEGFGCYCADQNAVAISGGTTPPEGLARSTSGARKEITTAGRERT*
Ga0075490_1347720	Ga0075490_13477201	F070166	YIVQIHRRTKRITLQRFLVSKIAYGKDFSLIELAALFHNQLWLQVKCETDVHFKEKFGVSLEEIAKILKECNFSRGLQPGTISRMKAKVLALEGDFLIPQRNLPNLEAQLRNSITTKWRKQEGVEINKLPPKSFIGKGYRDHGTAPSPEKDGSPSWQEVGSEFSNLEREHTENLLFLLKVIDNEPNISIQEKLQGIRRALEIDTAIKRIN
Ga0075490_1350999	Ga0075490_13509992	F014988	VSFTPASPITGAAVTGLTSPTYTILSDVAPSINGKQYAVSALGGTQTGVDVNTVSKPFTITFFRPQVLRVVPPVNPTTGVIKGIPVNSYKVITRKGAVPAVNQQIQVARITTTIDVPAGVDSYEPEEVRAMISAHFGVCWAQADGIASTVLTGVI*
Ga0075490_1351317	Ga0075490_13513171	F017318	PLVLD*VPKIGVSILLTKNQNSRGAKRRVTRNKTPRQTTMGIPLLAAPLKFERTVEGLFDISCDGINPSVGLFNFSLSDLPSNSDFTTLFDMYKLDKIEVSWFPEYTVLSDSGLVSNAVDVQVNTAIAQISNTPTTVNDVLQYKTCVGTGITKVHRRSFQPSYLMDGICPCSCYLSCNNATANWYGIAYGVAPTGTAMLFKSRAKFYMSFVQSR*
Ga0075490_1352850	Ga0075490_13528502	F000203	LALGAKLAASFPTLFSTASGVSGLVAGPSSAFPPLDFE*
Ga0075490_1356415	Ga0075490_13564151	F073598	MGAGNNLFYQTQGNSENIDIVLKESVPGCEGPGTKGKQPRSLNKVLKKKLSEKTAYQIGTAKRWAWKQPSLRESVIAQ*
Ga0075490_1356939	Ga0075490_13569392	F018726	MLPDPVTIAAASPTPALVFAVIKSDGYGSERVDTGGNGYSLIINHQKGKAVSKHYVQIVQTVDAVDPYTGLTKKQTASCSLTITRPSFGFTDAAIVALAKALTDVRDDSEVTTAKLIQFQS*