Sample 3300006372

3300006372: 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_RNA1 (Metagenome Metatranscriptome)

Overview

Basic Information
IMG/M Taxon OID	3300006372 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0114433 \| Gp0116184 \| Ga0075489
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_RNA1 (Metagenome Metatranscriptome)
Sequencing Status	Permanent Draft
Sequencing Center	DOE Joint Genome Institute (JGI)
Published?	N
Use Policy	Open

Dataset Contents
Total Genome Size	91899957
Sequencing Scaffolds	33
Novel Protein Genes	38
Associated Families	29

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	15
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	2
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	4
All Organisms → cellular organisms → Eukaryota	2
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Mediophyceae → Biddulphiophycidae → Eupodiscales → Odontellaceae → Pseudictyota → Pseudictyota dubia	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Collimonas → Collimonas fungivorans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	1
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Hymenostomatida → Tetrahymenina → Tetrahymenidae → Tetrahymena → Tetrahymena thermophila	1
All Organisms → Viruses → environmental samples → uncultured virus	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas alcaligenes	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
Location on Map

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Associated Families

Family	Category	Number of Sequences	3D Structure?
F000075	Metagenome / Metatranscriptome	2622	Y
F000237	Metagenome / Metatranscriptome	1498	Y
F000734	Metagenome / Metatranscriptome	915	Y
F001418	Metagenome / Metatranscriptome	698	Y
F002557	Metagenome / Metatranscriptome	548	Y
F004323	Metagenome / Metatranscriptome	443	Y
F006508	Metagenome / Metatranscriptome	371	Y
F009465	Metagenome / Metatranscriptome	317	Y
F014854	Metagenome / Metatranscriptome	259	Y
F015606	Metagenome / Metatranscriptome	253	Y
F017318	Metagenome / Metatranscriptome	241	Y
F018726	Metagenome / Metatranscriptome	233	Y
F020183	Metagenome / Metatranscriptome	225	Y
F020197	Metagenome / Metatranscriptome	225	Y
F020793	Metagenome / Metatranscriptome	222	Y
F021791	Metagenome / Metatranscriptome	217	Y
F022658	Metagenome / Metatranscriptome	213	Y
F023360	Metagenome / Metatranscriptome	210	Y
F024119	Metagenome / Metatranscriptome	207	Y
F025295	Metagenome / Metatranscriptome	202	Y
F039655	Metagenome / Metatranscriptome	163	Y
F044534	Metagenome / Metatranscriptome	154	Y
F054064	Metagenome / Metatranscriptome	140	Y
F059360	Metagenome / Metatranscriptome	134	Y
F070166	Metatranscriptome	123	N
F080128	Metagenome / Metatranscriptome	115	Y
F082737	Metagenome / Metatranscriptome	113	Y
F092248	Metagenome / Metatranscriptome	107	Y
F093948	Metagenome / Metatranscriptome	106	Y

Associated Scaffolds

Scaffold	Taxonomy	Length	IMG/M Link
Ga0075489_1001325	Not Available	887	Open in IMG/M
Ga0075489_1001645	Not Available	639	Open in IMG/M
Ga0075489_1002672	Not Available	627	Open in IMG/M
Ga0075489_1004965	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	3194	Open in IMG/M
Ga0075489_1013858	Not Available	699	Open in IMG/M
Ga0075489_1014018	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	1619	Open in IMG/M
Ga0075489_1016005	Not Available	929	Open in IMG/M
Ga0075489_1046515	All Organisms → cellular organisms → Eukaryota	668	Open in IMG/M
Ga0075489_1046917	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	832	Open in IMG/M
Ga0075489_1053662	Not Available	609	Open in IMG/M
Ga0075489_1167758	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	507	Open in IMG/M
Ga0075489_1196823	Not Available	588	Open in IMG/M
Ga0075489_1198101	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	665	Open in IMG/M
Ga0075489_1201042	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Mediophyceae → Biddulphiophycidae → Eupodiscales → Odontellaceae → Pseudictyota → Pseudictyota dubia	578	Open in IMG/M
Ga0075489_1241103	Not Available	532	Open in IMG/M
Ga0075489_1250353	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1427	Open in IMG/M
Ga0075489_1251191	All Organisms → Viruses → Predicted Viral	1070	Open in IMG/M
Ga0075489_1268891	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Oxalobacteraceae → Collimonas → Collimonas fungivorans	548	Open in IMG/M
Ga0075489_1283500	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	1191	Open in IMG/M
Ga0075489_1285266	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	538	Open in IMG/M
Ga0075489_1285269	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea → Hymenostomatida → Tetrahymenina → Tetrahymenidae → Tetrahymena → Tetrahymena thermophila	610	Open in IMG/M
Ga0075489_1285986	Not Available	622	Open in IMG/M
Ga0075489_1293889	Not Available	861	Open in IMG/M
Ga0075489_1293946	All Organisms → Viruses → environmental samples → uncultured virus	951	Open in IMG/M
Ga0075489_1294876	All Organisms → cellular organisms → Eukaryota	913	Open in IMG/M
Ga0075489_1298141	Not Available	501	Open in IMG/M
Ga0075489_1298187	Not Available	631	Open in IMG/M
Ga0075489_1300042	Not Available	558	Open in IMG/M
Ga0075489_1301573	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	727	Open in IMG/M
Ga0075489_1302396	All Organisms → Viruses → environmental samples → uncultured virus	1153	Open in IMG/M
Ga0075489_1303292	Not Available	876	Open in IMG/M
Ga0075489_1303887	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas aeruginosa group → Pseudomonas alcaligenes	507	Open in IMG/M
Ga0075489_1305408	Not Available	869	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0075489_1001325	Ga0075489_10013251	F017318	QQSRAAKRRVSRNKTPRQTTMGIPLLAAPLKFERTVEGLFDISCDGINPSVGLFNFSLSDLPSNSDFTTLFDMYKIDKIEVSWFPEYTVLSDSGLVSNAVDVQVNTAIAQISNTPTTVNDVLQYKTCVGTGITKVHRRSFQPSYLMDGICPCSCYLSCNNATANWYGIAYGVAPTGTAMLFKSRAKFYMSFVQSR*
Ga0075489_1001645	Ga0075489_10016451	F001418	AQARWEEAEFTSSSGGLRGPSVHAKKELGGEGRLETVPSRIK*
Ga0075489_1002672	Ga0075489_10026722	F002557	MIISGRQSHLSVLMHSSNHYPLGNCDSPKSETNLGYLTQFEAVSHRSSLPSSFFAFTDSARTLPEELVNPA
Ga0075489_1004965	Ga0075489_10049653	F018726	MLADPVTIAAASPTPSLVLSVTKSDGYGSERVDTGGNGYTVITQHAKTGKGSRHYVQIVQRVNAVDPYSGLTKSQVASCSFTINRPSFGFTDAAIVALAKALSDYRDDSEVTTARLIQFQS*
Ga0075489_1013858	Ga0075489_10138582	F080128	VALANAPSKAVADQSQTVKTRKRSHGSVLTWFAGRWRNHQPKRAEKPHSKFNVARRWTALLRGRRLRLPWRIASGS
Ga0075489_1014018	Ga0075489_10140181	F023360	MAYILGGDSGEGFGFEKAIANFSLRAVHESTGLVNMTTVVTPTQGNVFEIPLFAPITYQDYNPSGSGGDISGNASEQNPALLQSSITASPAVAGTSFDIFYGWTTSFNLAATLGSELGESFAEKVDQRVAGAFAAFKATPGNTNYATSADGFTRPSALGAMELLVEGATPTGATAGFTATSVLELIRLVKQNFKAARIPGNP
Ga0075489_1016005	Ga0075489_10160052	F059360	MTLFKEVLVPANLVPAAAVIREGQALSEITGRKESVDCNISYMLKFKA*
Ga0075489_1046515	Ga0075489_10465152	F092248	LLRLLLPLSDKVYETSRKWFKPIRSPDSSPHHSKSVGATGGVYKGQGRIQHRLMTCAYKEFLVQDL*
Ga0075489_1046917	Ga0075489_10469172	F018726	MLPDPVTIAAASPTPALVFAVIKSDGYGSERVDTGGNGYSLIINHQKGKAVSKHYVQIVQTVNAVDPYTGLTKKQTASCSLTITRPSFGFTDAAIVALAKALTDVRDDSEVTTAKLIQFQS*
Ga0075489_1053662	Ga0075489_10536621	F025295	DHGNWPGKATELLRRREVLIPEKLKFTTRKRNLQKPI*
Ga0075489_1167758	Ga0075489_11677581	F009465	VNLGNDLTKFRVSIAQIEKSANVNYAYPVGVTELQPGAEWKVDFGALTKAKRAKCGKAD*
Ga0075489_1196823	Ga0075489_11968232	F017318	NPSVGLFNFSLSDLPSNSDFTNLFDMYRIDKIECAWYPEYTVLSDSGLVSNAVDVQLNTAIAQISNTPTVVSDVLQYKTCVGTGITQIHKRSFQPSYLMDGICPCSCFLSCNNATANWYGVAYGVAPTGTAMLFKSRAKFFVSFVQSR*
Ga0075489_1198101	Ga0075489_11981012	F022658	NAQGKIVSAFNPSQLVKTDQTLIRLDCFKAIAIFYESLVTDVSNINEVDKVNYDHSIARYLTEYEKATQLSNFYDLFQDGFISKLEENYQADVDFFQGDRRYF*
Ga0075489_1201042	Ga0075489_12010421	F039655	INNTCTVSAPGGFAPGKSVTIELAGTTTKRLLAGVFKYQVYEDYVPSFVASGNIQYFTCTIKGCNTAEPIALSLGSQSAVPTGYTGIIPFVIPQPQKTGSYKITFWGEDQDHYPYDITGTLSLVQECSSDAQCPPNSYCKDGPGQSPPFSCQNS*
Ga0075489_1204417	Ga0075489_12044172	F020183	KENLIGYKGPLATVSVKDDIRLSRVAPKATSLFSGVGRANAKLTRTLTLTGAKTPTGDSIFEINASVPVGAAGADVDIICNDLGSYVSSAVFKTLVKNLLITY*
Ga0075489_1208663	Ga0075489_12086631	F000237	KSGTYISFYDGMLKEFQDAFVLFVFIYFIEHHFNASTVNYFFFERNISELDEIRFYGVAPHYFRPLMGLLVVSPSHYEGLMMGLFVLLAVLPIIYNFYNANQSQLPVIPMQSSLLQTSCFIIFMLSMYCTASMLPCGRYYYDPEGGYVGNPVKFSYQYSYLYLA*IIHHLDLIEHSSYQYTQSYLRKSQTQYLTCHRVVSRSSS
Ga0075489_1241103	Ga0075489_12411031	F017318	AVSPIKFQRTVTGAYDITTNGIAANTGMINFTLSDLPSSGEFTALFDLYKIERVEIEWTPEYTELTDAAPVSNAVNVYFNTAIDPAGTVPASVDDILQYRTLHSTPITKMHKRDFKPAFLLDNIIPASCYISCASPNSNLFGIAYGIPATGVAMTFRSRATFHLSMAQAK*
Ga0075489_1247142	Ga0075489_12471423	F024119	MAYILGGSNDEGFGFEKAIANFAIRAVHESTGLVNLTTVVTPTQGNVFEIPTFAPITYQDYNPAGSGGNVSGNASEQNPALGQ
Ga0075489_1250353	Ga0075489_12503534	F054064	MKIPTIPKVNNMATSMDGIKGLIGRKMTKTVKFMAEDIKISKLSVSEVIEIQERAKAIEKDEAEGFNVLKTVIRASVEGAKDLSDEDFSNFPLDELSKLSNEIMKFSGIGQDSGK*
Ga0075489_1250353	Ga0075489_12503535	F020197	DNSQKPFSMGYVLRTTAKHMRKSIDISIRKTFERVPEFANEQEKSQEVFKTLAFLHTMRKQLDDFQAQHSVNFKGE*
Ga0075489_1251191	Ga0075489_12511911	F022658	KNNPQGQLISAFNPSQLMKNDQTLKRLDVFGAVMVLYQSLVTDVSNLNDVDMANYKFAQERCETEWAKARELSNFYDLANNAPNGPATKLEENWLADVDYFNGDRRFF*
Ga0075489_1262709	Ga0075489_12627091	F000075	AAALLATVSANRYESMNEDELLVNLESTLSSALSSEARGDADAAVAKTAAIKNIQKALTARILKRLDDGQPLVEVARKMKAIEGMQPQINDMERRLGIMQSVEPVLENAIKTLQKVVDVRGMGKK*
Ga0075489_1268891	Ga0075489_12688911	F015606	NKMADMLTTDPFFALTNQVAGVREKVSDSIFENYKLQVAQTNDINNRAMQVALHDASALADLKQATSDGTLQTMLAAARTDAALGQTAAATMRAVMEQGELTRNLINGLNTQNLNTALINTNVAFTGLNGQYGGLGLAYGGAVSAYQNASSVNAVNALQSAISSQGLVNTGTMTGTTQTSTP
Ga0075489_1283500	Ga0075489_12835003	F015606	MADMLTTDPFFALTNQVAGVREKVSDSVFENYKLQVAQTNDINNRAMQVALHDASELASIKQEVSNGTLQAMLAAARTDAQIGATASVTQRTIFEQGELTRRLVQDLNTQNLNTALINTNTALTGLGVQYGGLGLAYGGAVSAYQSANSVSAVNALGSALASNGIINTGTLSGTTQTATPTTIR*
Ga0075489_1285266	Ga0075489_12852661	F044534	GIYHQFLWPESCPVSSHTNQELCREARSETALNGVRPTGRFDPCADAVTPEGFGCYCADQNAVAISGGTTPPEGLARSTSGARKEITTAGRERT*
Ga0075489_1285269	Ga0075489_12852691	F020793	MTLRPNFIPRGCYKEIRSYQMCKSKASEDACFADKISIMEVCPDHVLDALREKKKWYLRAEMIDNDTYKRAMSVSDFNKDRSVSDLKLKTWDYGKTANMRSDSLWQDDRWLPTKHSHPHRYDNVNFAEQEYMDFFGGTKGTAETEEYARNKIGVLSDTSQAIR*
Ga0075489_1285986	Ga0075489_12859861	F006508	VALANAPSKAVADQCQTVKTRKRNYRCVLTWFASRWRNHQPKRAEKPHSK
Ga0075489_1293889	Ga0075489_12938891	F021791	CVDYRIKPHIPPFEQIPANSVKFQSCDYTIQVECSCVNL*
Ga0075489_1293946	Ga0075489_12939461	F017318	CHYSADSRPGGYFSLHGGQAPSCRARNLLTKSQTKRGAKRRVSRNKSPQNIGNPTSVTPIKFERTVEGLFDIANTGLAPSVGVFNFSLNDLPNYTEFTALFDLYKIERIEIEWTPEYTELTDASLASNSVNVYFNTAIDPAGNTPAAVDDVLQYRTLHSTMITKRHKRDFIPAYLMDGIVPASCYISTASPSSNLWGVVYGIPAAGVAMTFRSRAKFHLSMAQSK*
Ga0075489_1294876	Ga0075489_12948764	F093948	MAVEFPTKVTAILSPLGGISQMDDLMLLGIHSTK*
Ga0075489_1298141	Ga0075489_12981412	F004323	MPPSGLRRSEGRATPAVAILSPVTRDHPSRALNGVFQAVALRLF
Ga0075489_1298187	Ga0075489_12981871	F006508	VALANAPSKAVADQRQAVKTRKRSRRRVLTWFAGRWRNHQPKRAEKPHSK
Ga0075489_1300042	Ga0075489_13000421	F082737	MPGLSPSHPARRTSLRFAPRLRNFSVGASLLSGTPASLPVRSQNLEADFHSPPTTSLSPDCRGGVRVPALPLQLCGTISVGPVRLDLHPRPVSRTAWGLLQSKPVAFRSCATPACLVESSLPFRVSTLPDQSTRSRWPTGNLLPGTPDLPSLPTGGRIRYQHQRIIVPAPLR
Ga0075489_1301573	Ga0075489_13015732	F000734	LHWEGHGVWAGPVKTFRNVGDVKNGTADLWTKGNLRVKRRDPWLWANALSKAVADPELAGEDAEMKT*
Ga0075489_1302396	Ga0075489_13023962	F017318	MRSPTAASPLKFQRTVEGAFDINCDGINPSVGVFNFSLNDLPSYTEFTALFDLYKVERIEIEWLPEYTELSDAGLTSNAINVQFNSAIDPAGNTPSVYTDVLQYRTLHSTGISKRHKRDFIPAYLLDGIVPAACYISTASPSSNLWGVVYGIPATGTAMVFRSRAKFYLSMAQSK*
Ga0075489_1303292	Ga0075489_13032921	F070166	MNLNNYIVQIHRRTKRITLQRFLVSKIAYGKDFSLIELAALFHNQLWLQVKCETDVHFKEKFGVSLEEIAKILKECNFSRGLQPGTISRMKAKVLALEGDFLIPQRNLPNLEAQLRNSITTKWRKQEGVEINKLPPKSFIGKGYRDHGTAPSPEIDGSPSWQEVGSEFSNLEREHTEAFLFLLKVIDNDPNVSIQERLQGLKRAIEVAEKIKRIHPNWRNSQITEASKGRIIDAKKVKKVIP*
Ga0075489_1303887	Ga0075489_13038871	F014854	LRWTAVDERKSLVVSRMIPGNWGKVESGWLARPLLDRIARFGGGGRIHQFLWSRSHAVSYAKRNLAARGDKKPLRVGSSSSGRFRAWANRSYPEGKWLLLCIGTGRVTLADSINRLKPPNESH*
Ga0075489_1305408	Ga0075489_13054081	F070166	MNLDNYVVQIHKRTKRITLQRFLISKIAYGEDFSLIELAALFHNQLWLQTKCQVDPHFREKFGMTLEVIATFLKECNFSRGLKPANISRMKAKALTLEGDFLIPKRNLPNLEVQLRNSISTKWRKPEGVEVSKLPPKQHVGKGYRDHGTAQKPEIDGSPSWQEVGSEFGNLERENTELALKIMKIIEGKSNDSILESLKTIQRFSTNCEAIERIHPNWRNPEIAKASKGKIRHEV*

Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300006372: 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_RNA1 (Metagenome Metatranscriptome)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences