3300005954: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_21-May-14

Overview

Basic Information

• IMG/M Taxon OID: 3300005954
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114663 | Gp0115674 | Ga0073925
• Sample Name: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_21-May-14
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 176351269
• Sequencing Scaffolds: 21
• Novel Protein Genes: 27
• Associated Families: 27

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	2
Not Available	6
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Nostocales → Aphanizomenonaceae → Aphanizomenon → Aphanizomenon flos-aquae → Aphanizomenon flos-aquae WA102	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	2
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Skeletonemataceae → Skeletonema → Skeletonema marinoi-dohrnii complex → Skeletonema marinoi	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → unclassified Opitutae → Opitutae bacterium Tous-C10FEB	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Groundwater Microbial Communities From The Columbia River, Washington, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Sand → Unclassified → Sand → Groundwater Microbial Communities From The Columbia River, Washington, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): freshwater river biome → microcosm → sand
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Subsurface (non-saline)

Location Information

• Location: USA: Columbia River, Washington
• Coordinates
  • Lat. (^o): 46.372
  • Long. (^o): -119.272
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001055	Metagenome / Metatranscriptome	791	Y
F001068	Metagenome / Metatranscriptome	787	Y
F001286	Metagenome	731	Y
F001338	Metagenome / Metatranscriptome	719	Y
F001923	Metagenome / Metatranscriptome	617	Y
F007203	Metagenome / Metatranscriptome	356	Y
F009468	Metagenome / Metatranscriptome	317	Y
F012219	Metagenome / Metatranscriptome	282	Y
F019449	Metagenome / Metatranscriptome	229	Y
F026012	Metagenome / Metatranscriptome	199	Y
F027186	Metagenome / Metatranscriptome	195	Y
F027760	Metagenome / Metatranscriptome	193	Y
F032099	Metagenome / Metatranscriptome	181	Y
F053289	Metagenome	141	Y
F053809	Metagenome / Metatranscriptome	140	N
F054132	Metagenome	140	Y
F061552	Metagenome / Metatranscriptome	131	N
F067432	Metagenome / Metatranscriptome	125	Y
F073124	Metagenome / Metatranscriptome	120	Y
F082162	Metagenome	113	N
F082672	Metagenome / Metatranscriptome	113	N
F082695	Metagenome / Metatranscriptome	113	N
F092033	Metagenome / Metatranscriptome	107	N
F092936	Metagenome / Metatranscriptome	107	N
F097376	Metagenome / Metatranscriptome	104	Y
F100053	Metagenome / Metatranscriptome	103	N
F104469	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0073925_1001655	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	2908
Ga0073925_1003050	Not Available	1914
Ga0073925_1003066	All Organisms → Viruses → Predicted Viral	1907
Ga0073925_1004397	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	1503
Ga0073925_1007456	All Organisms → cellular organisms → Bacteria	1106
Ga0073925_1009432	Not Available	979
Ga0073925_1012029	Not Available	869
Ga0073925_1013180	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	832
Ga0073925_1016320	Not Available	754
Ga0073925_1018672	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Nostocales → Aphanizomenonaceae → Aphanizomenon → Aphanizomenon flos-aquae → Aphanizomenon flos-aquae WA102	712
Ga0073925_1019878	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	693
Ga0073925_1025256	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	628
Ga0073925_1026428	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	617
Ga0073925_1026522	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	616
Ga0073925_1031882	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	572
Ga0073925_1034938	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Skeletonemataceae → Skeletonema → Skeletonema marinoi-dohrnii complex → Skeletonema marinoi	552
Ga0073925_1036214	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → unclassified Opitutae → Opitutae bacterium Tous-C10FEB	544
Ga0073925_1040504	Not Available	521
Ga0073925_1041793	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	515
Ga0073925_1044430	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	503
Ga0073925_1044711	Not Available	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0073925_1001655	Ga0073925_10016552	F082695	LFVQFTFFSYESETGDETDVAKWAHKLMNRSVANRTITKQEAMCELGGLPMVICSESIETISITGSTKCATDTNTSTILSQYRNRPDAQQHLSLHQFYHIKKNKKLASTPSYREFIPHYVGGKGQPVYPITRSYARSELLKHLPWGRKNPMPNDCDLITMFKQFLENPKCPVGVRLGFERAKLRKELKEKGIQEAFQPDIEHSSNTDDVDDDEVGEVIALTESLGYTEDELEKLENNGFFLGKDYDWGKRIYTVSNPTIHHTRFGIILNY*
Ga0073925_1003050	Ga0073925_10030502	F053809	MMVTMLRQEIYTHYLFHKSNQYNSIMRPYTYTPKSHIRPYIRNTLLLIHDQLPLLHLHVNYLSQLQLINRRRLHDFDVLSGKRHTRGAGAIRVAEIGAAYAEDRIRAHLGALIVDNNDLLAEWFRLKTYTDGHTPLICSNRPALQMNTMPFDTDGVCTIQGNGIPHPADMRSTIQIIERILLPHHAQSAARCCTITDYRNHNAAYMCVKGFVREIKRSLDDVRGRLYYLQYDEIDLWRSVQNFEYNIEDSSTIIRELFANTQPTQPFPQVVTPTTNDVANPQIISPDNTVNHSEQVFTTTNGVAC*
Ga0073925_1003066	Ga0073925_10030664	F012219	MNLQNFRIEKQPAPSTDWLVYGDILTDDDILVATFGEDGTSVNEWWVRQDEFFQMNTVQSFAVTMAQQIMSGDAE*
Ga0073925_1004397	Ga0073925_10043971	F061552	HRRDFSVDPSSSSDTATCRYIATVKALTKMKDEEEMKRGVHITGTITMEATHHHPTCLHLLTTLVNEKITGFDCPILDISDSKMGRVGLAILVDMETTMVGNRIKKLVRKNMKCWTQPSIYAWPIVNSGLKIIDGVGLLILNDLAKSVYNFITTVQSEGNGTGSANRS*
Ga0073925_1007456	Ga0073925_10074563	F027186	MTSNFDFNFKNTPNLTLELPFSEHIEELRQRIIHIFCIILVLS
Ga0073925_1009432	Ga0073925_10094321	F073124	IGSGNKGKDGDMLRTSMEKMATYIGTKYGDEAAQEWISGKKIIPTEPTYSQAIRDRHAARVRATRDRIELKLRGLRVEKDAIQVEIDDTEGSDRALLKEMREVDDQIAKGEIELADEVEMKLTEDEKISHSNAWRSHRETTESLKKSRGKVYSLLLGQCTQVLIDKMKQDTDWVTISESFDPTLLFKLIEKFVLKQSDNQYATAVLISEQLSILSFRQDDHLGNAAYYDRFTTRVEVARQAGVCYYSPALLEEKATQLKLGAYDDLASDAKKKVVDQVEQEYLAYLFLNNSNAKLHSQLKKDVANDYSKGNTEAYPTDIHKALTLM
Ga0073925_1010754	Ga0073925_10107541	F104469	VDSFSENKFVDTTKAPAGDSDYACFTTSQKCITSLMYLLDDMECPDYAFQCIMDWARNCFEAGFDFNPKSKTRLGNLKWMYDSLHNAKQMLPNVMLIQLPDPLPDTKSMDVICYDFVPQLLSILQNKEMMSANNLVLDPNNPLAMYKPQNCRLGKALSGSVYQDMYQRLVSNPTKQLLCPLICYTDGTQIDALSRFSVESFLFMPAVLSHVTRCKAEAWRPFGYVQHVRSTQTKLNGAAKARNYHAQLQAMLQGLQRVQTGVDSRLQNVEIYCFGKCLRVDVLCPILFIAADTPAADKLCAHFSS
Ga0073925_1012029	Ga0073925_10120291	F092936	VLHDSELYEIPPVPQSKSQHGFILSGVDITLLNIQVTNINCGGAMCDGLNMYQNSVTADRCPCYNVLDREGKVCLVLSLKVSDTKNNLQFCVHNHTSKSLTQLFMKRIPKGAVAATITGNQKHMGNLSAKVMDMLALGNDYNGFIISGWIKRGTIADSGVVQPPTGSKWDKPQQVDSGGLTYHLTKIAYATPPSDRILGEYQFNAGSLV*
Ga0073925_1013180	Ga0073925_10131801	F032099	MAFEKGNKLSKGRPKKAEEEKVNNIFLKALGQLYNKETEEETKIEFVKTTLMDSQRGQLFIAEHIFGKPKEIIEATHNVNDFNIKDNFKVGNSNKSEI*
Ga0073925_1015833	Ga0073925_10158332	F092033	PGTRDFEGKCPGLFYVFLSRATDIGSPGDRSTSAIFFEGPDMTNDRITDLTHSLTTKREYIKVTKRRIWTNHLQNNLINIEISKQQKSSLINWCERTKISERDVQRVIQDPRWRKSDMLNH*
Ga0073925_1016320	Ga0073925_10163201	F082162	MLPFFTSFEVNKDKHTLKPYMAPVNHNIIDETTWLKIVHTLMGNFCQDDDDVKGTVAMEDMGNDACVLVGYHQNVSNRLKGETCLNVV*
Ga0073925_1018672	Ga0073925_10186722	F001338	MTTENNDRPPLTSISTNGTYRLKLIKPKFEKVKVWEDGTCSARLFFVDDKGFCLSKNFSTKYGKALAMLVGKYSGKFTNEIRLDATPAEYLQYIDGACGQTILVGVECEANGEYNGKPQYKYKLTYPKGSQKPTVANDLPNPEDVPY*
Ga0073925_1019878	Ga0073925_10198781	F001923	MSPPPPIDPESFPKELKDGVIASILGGLAMTARLLLSQEPVSVGWVVRRVLAAAITAALVGYAITDHIESPGFKMGVVGASGYAAPECLDYLIRYIKSKGDAEVGPAKKPHGKSKAPGKAKRKR*
Ga0073925_1019878	Ga0073925_10198782	F019449	MTTETFTTIVVPGIASVAYASAGIACFFAHRPALAIMWLCYSIANICLLSTVLRK*
Ga0073925_1025256	Ga0073925_10252561	F054132	QSRKPVDLARVQAIEFLDAALGADRRQLIKQYVENHDSAPKLAERIWQAIYDLSQGFIYAYQTALEEAMRQNGNARWKPLTPLLFARLVHYYGTDAKLRVFRYERWIPGKWMELHRVYMRASELGFDRVPVVMPSAGPNATPWTIEQEYLYVLLVHQLNTGNMSPPQLDWAMSQLRAWSRRLQMDSVPRSPEGFFVDIAGKTGLARRTG
Ga0073925_1026428	Ga0073925_10264282	F001068	MPDPAGSSLFDELRVQYETARTSPHQHEDVEGYQQIDARLRKAYGWLEKAMAYLDELKPAIQHRYDLGHGMVLQNPRFNRGYVGQHTQRIVGYPVIDEINIWYEIGTAEALTLEVSPGGEALAEKALDEAGLQYSARRIVDHAGVVTKCVL
Ga0073925_1026522	Ga0073925_10265221	F009468	TVEHAAKRTPQRLEAIFSVDAQCTNLRKNLTAQYIEHSSRSSKIEHQLWSALFDLTQAFLVTYNAFALEVSKHMQSAKWQQLLPELVGRQIMHMGLDAKVRLYRYEQWIPAKWAELHAHFTLACSRQIERQQVVFGPNGHATTIEHEYLFTLLLQLMNAGNMTARHLEWVAGELDEWAAPLRLSLESSSVTSFFVDLASREGLRR
Ga0073925_1031882	Ga0073925_10318821	F001286	VLEPLTNWFRALSDPLSSANNAARWIAHLPANDAAALQKEALELVAGFPGARKEAGPAQVEALLRIDGRLEPVLAQLTQQYTINYQKSTGVESRLWHSVFDLVKAFTAAYQLALKAGYPRADNKRWRAILPWVIVRLAYYRGLDGKYRLYRYSQWIPAQWRDFHELYEFA
Ga0073925_1034938	Ga0073925_10349381	F027760	QLDLTPNDHKIERKKIKSKLDDLNNKLAKEMTGRKFKLEPEQFSPEVTVKHYQTSSKKVAFRCKMKQIPANSNDATTGHKLQGMSKDAIIVSSWPTGGLAAMFKNWEYVVLSRVRTLSGLYLVKPIDMDKSFQPSPQLASYMDKIRKFEKDMLEKRKQAISKTFL*
Ga0073925_1036214	Ga0073925_10362141	F001055	ESTVATYLSTQTGLTTVTFLTGDSAATQTLPKAVVLCEAARAPSDLPEGEGNFSCSVRITLFSNADDTTLADHRARCAALSGNMRDLVSIKAAFTATGDASCYDVTMQSEDEGIDERSWATSFTFDILTVFPA*
Ga0073925_1036428	Ga0073925_10364281	F100053	SVPRLKGSTVRESGHRKPQSLVKVPRELLKLQQKVSIAIDIFFVNGHIFFMTYSRKICFTTVTHLVNRKVNEVWAAMHKIYQMYMLRGFHIVEIAGDGEFVWIADQVASLPTNPTLDLAAANEHVGLIERNIRFLKEKARSLRHSLPFERIPALMLIRMVLHTVPFMNSFPRKGGLQHYP
Ga0073925_1038822	Ga0073925_10388222	F026012	IVISLQNNLSINFFDMWIYEIYINKVSTHNKFMSQKSQNLEPSEYITIKLAYGSSVSQEKK*
Ga0073925_1040504	Ga0073925_10405041	F082672	EFLEKYNTSSKKPKYYEDNPGAENNVDLDRHFFKLHMDAAGIQYVYIPVRQVKRCIRIEILYVTSGDIFYLRLILLNRKAHSDRDVLTYNPVRGGGEPLVCTSYQQSAIAHGYVDSVDDVRATFIDMCSNGTGAQCRSYFVVLSLNGYATHAIFDDHNKRRFMFMDYITYQGV
Ga0073925_1041793	Ga0073925_10417931	F053289	MVSNTGTAMGDSTGYEVTLSAIEAEAPFILQGSVVTTLGI*
Ga0073925_1042987	Ga0073925_10429872	F067432	HTSCAEPKNAICDVKCEKPECEIKCPDKGCEMFDCPKCVTVCKQPHCVTHCQAPKPECEAVCEEPRCDWKCHKPNCPKPKCELVCENPNCVPKVECCPCAMGAPRVAQPFPFFKEAENNKECCSCKR*
Ga0073925_1044430	Ga0073925_10444302	F007203	EMDCLMYVQMQGVNLAPKVKELEKRIEMLENVVNELKLDKPRMGRPPKDKHGTERTEVNTTGRD*
Ga0073925_1044711	Ga0073925_10447111	F097376	MKKAVSPKKNKTAADVVAQKKQAKTGPVELDLAELKKVSGGLPKGGWIK*