3300005991: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_10-June-14

Overview

Basic Information

• IMG/M Taxon OID: 3300005991
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114663 | Gp0115670 | Ga0073923
• Sample Name: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_10-June-14
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 194459428
• Sequencing Scaffolds: 20
• Novel Protein Genes: 21
• Associated Families: 21

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	1
Not Available	12
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → unclassified Opitutae → Opitutae bacterium Tous-C10FEB	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	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
F001733	Metagenome / Metatranscriptome	644	Y
F005780	Metagenome / Metatranscriptome	390	Y
F012202	Metagenome	282	Y
F013630	Metagenome / Metatranscriptome	269	N
F024650	Metagenome / Metatranscriptome	205	Y
F028490	Metagenome / Metatranscriptome	191	Y
F033471	Metagenome	177	Y
F035633	Metagenome / Metatranscriptome	171	Y
F038918	Metagenome	165	N
F044025	Metagenome / Metatranscriptome	155	Y
F044498	Metagenome	154	N
F044595	Metagenome	154	Y
F050934	Metagenome	144	N
F053267	Metagenome / Metatranscriptome	141	Y
F053809	Metagenome / Metatranscriptome	140	N
F069706	Metagenome / Metatranscriptome	123	Y
F070593	Metagenome / Metatranscriptome	123	Y
F072817	Metagenome / Metatranscriptome	121	Y
F078934	Metagenome / Metatranscriptome	116	Y
F104469	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0073923_1004073	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1817
Ga0073923_1008492	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	1185
Ga0073923_1009018	Not Available	1144
Ga0073923_1011152	Not Available	1013
Ga0073923_1012645	Not Available	945
Ga0073923_1014508	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	881
Ga0073923_1020896	Not Available	736
Ga0073923_1021415	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	729
Ga0073923_1023941	Not Available	693
Ga0073923_1024749	Not Available	683
Ga0073923_1025961	Not Available	669
Ga0073923_1025997	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → unclassified Opitutae → Opitutae bacterium Tous-C10FEB	668
Ga0073923_1031249	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes	617
Ga0073923_1033927	All Organisms → cellular organisms → Bacteria	596
Ga0073923_1036587	Not Available	577
Ga0073923_1040927	Not Available	552
Ga0073923_1042823	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	542
Ga0073923_1043369	Not Available	539
Ga0073923_1045245	Not Available	531
Ga0073923_1045267	Not Available	530

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0073923_1004073	Ga0073923_10040731	F044595	MNGLVAFVRAAAAMESFRGCASALHLTLPASFQLDRNEDQL
Ga0073923_1008492	Ga0073923_10084921	F050934	IQAAIFQKHIQATHPNVTSNEMPPEHTLIIEGDITSSRSNTTRQRIDRHLRHRIITTCGDANVMMGSKHIDPALCIYIGAYLICIDNKHLTDKVPRGNGTLCRVLGMKLNENAQSYKCKNYYGKKVWTVNAADVEWVECEHVNKTSFLTQLESQIKELKCQLDLTPNDHKIERKKIKSKLDDLNNKLAKEMTGRKFKLEPEQFSPEVTVKHYQTSSKKVAFRCKMKQIPANSNDATTGHKLQGMSKDAIIVSSWPTGGLAAMFKNWEYVVLSRVRTLSGLYLVKPIDMDKSFQPSPQLASYMDKIRKFEKDMLEKRKQAISKTFL*
Ga0073923_1009018	Ga0073923_10090182	F044498	MQTDLNTFSSVANNERVLLLSRYSTNCSLTELLELQSPMAEIQSETVSILSFLNGAIQRPLSYEQHIMNQKLTCAKKKFEKSCLLAYREFCDMELEHNLLVMQCCNDEMVLCSKAYDHHCYPCCKPSNEKSTSDFNDKKTCETNIVFDGLQDEGIMAPDYYPD
Ga0073923_1011152	Ga0073923_10111523	F044025	MIKKYKIVFVLFFVAMSAMSCQKNFYSGKAKSTDCGCPNKKGMVGY*
Ga0073923_1012645	Ga0073923_10126451	F053809	KSHIRPYIRNTLLLINDQLPLLHLHVNYLSQLQLINRRRLHDFDVLSGKRHTRGAGAIRVAEIGAAYAEDRIRAHLGALIVDNNDLLAEWFRLKTYTDGHTPLICSNRPALQMNTMPFDTDGVCTIQGDGIPHPADMRSTIQIIERILLPHAQSAARCCTITDYRNHNAAYMCVKGFVRETKRSLDDVRGRLYYLQYDEIDLWRSVQNFEYNIEDCSTIIRELFANTQPTQPFPQVVTPTTNDVAHNARKSPNYLTR*
Ga0073923_1014508	Ga0073923_10145081	F005780	MAQETVSIAWCDNGMVDGKFMQGVTDVMLKSGINFTTTLRSQGNQIARQREKIIRYWYENNTSEWLLWVDSDVVISPEKFRLLWDNKDVKERPIVTGVYFTTDTPEEPLMIPMPTIFNFAEAQDGVVGIKRVHPMPENQLIKVEAAGMGFVLMHRDVID
Ga0073923_1020896	Ga0073923_10208962	F024650	TFSLAQNNNNTYMAASWACRTLVSKFARMVTTQLDGALSADYSDLMMHYQQLADTLEYQGKTSGAALGVLAGGLTKSSVEAVRADTNRIEGSFRRDQFKNPPSYNTPEYE*
Ga0073923_1021415	Ga0073923_10214151	F053267	MNNYRDIDKDQLIKLADAYCDYCIESTKEVVSGSGKLVEQKERHLPTVSYFLYHWLRRQHFDFYKRTNFYDAMKNKEHPLSDTIKSIDNQFNALATDIVANEGKGIFYAKNKLGMTDKQQVDGSMTFKADFGTE*
Ga0073923_1023941	Ga0073923_10239411	F038918	MDDYYRNKISLCPKYIEWTRLSDNSEMFYCKTTYRKPDDETKLLAHIKRTIVTNDRAAQKRKKPKSESLTYDELLEKVRNNDVYKEFMKLEPGKMKFYDCRNYENGNADDEIKLMKRISNRMNCNKRRTSGVDVEIGKRGTVVADSVGVDVEIETKDAAVALLSLNNPRGGDATSP
Ga0073923_1024749	Ga0073923_10247491	F069706	GGPVPRSAGQAPSPQGTLGRIPSHLSLAVSAASASVLPTSGYFGSQKRQAVEINARRVICPKHARGAHGSRDYARHQEAATKAIPYPFASAKHFHAKNADGEASNKYANLQSEYAGNLAKIKTLKRRMDAWDMISPFVIPDFIDPYALSVEDRWGDRKLTGVNLLKNWGKVTLKQCRNWQRDSFDYACTEDLTSMEWAKSLMMNSCDVLLVDRIDEKFDELDLYEQG
Ga0073923_1025961	Ga0073923_10259611	F078934	MCMTSQSLSFTPQTQPIGQLLRGSPVLSGEGVRLIVRSYFVSSG
Ga0073923_1025997	Ga0073923_10259972	F001055	MGTRSIRHVVEATLATYLSTQTGLTTVQFLTGDSNVTQTLPKAVVLCDSASPPADLPEGLGNFSCSVRITLFSNADDTTLADHRARCAALSGNMNDVDSIQAAFAATGDATCYDVTPRSEDEGIDERSWATSFAYDVLTVLPPA*
Ga0073923_1031249	Ga0073923_10312491	F012202	QAYIIARLKEITMPELLDALAEAHAGKPIDIYEHLQPDLIDRTTDTIWEFIQAIKNIRE*
Ga0073923_1033599	Ga0073923_10335991	F104469	VTSLMYLLDDMECPDYAFQSIMEWARNCFEAGFDFNPRSRTRLANLKWMYNSLHNSEQLLPSVVTIQLPDPLPTVKSMDVICYDFVPQLLSILQNKKMMSGNNLVLDPMNPLSMYKPSDNRLGESLSGSVYQSMYQRLVTNPSKQFLCPLICYTDGTQVDALSRFSVEPFLFTPAVLSHAARCKAEAWRPFGYVQHLRC
Ga0073923_1033927	Ga0073923_10339271	F070593	METGWESFGMAGLGSWLIMAGWTIGLAILAWWFYMPNPMDR
Ga0073923_1036587	Ga0073923_10365872	F001733	FGGDHTKMNGISISRLVVVVLIAFVASFSTVFGDGVRTAEAKDIAELGAVLALYGSKAVAAGVTAAMSAALGFLTMPFKGVQANSLKVGK*
Ga0073923_1040927	Ga0073923_10409271	F013630	KIGGASHPLLFNMNSLRNIMEVAGMETFNDLSLQKDLGKSMDFALNCAFYAILEAAENDGKPTPFATVQKLGASIKKFQELTPAIEGFTAAITEFFAPVEESTGE*
Ga0073923_1042823	Ga0073923_10428231	F072817	RVDCELAAVAFGGPATALAKVPTGTVLRCKGFLARRYRTGITVALHVNEFETLDHALEGN
Ga0073923_1043369	Ga0073923_10433691	F028490	GQSGNYTGFAYGQNQAVNQQRVEGNQAVASTQAPAPSGNPYDGIDMPQLGTLFDPTTRPNEPITAGVDFGAGPGSEALPKNLTNDSRMDENAKIAQEYLPDLAFAAQSPNAPDSFKRFVNYLIENARGFNNNG*
Ga0073923_1045245	Ga0073923_10452451	F035633	QTVQDNMKLFSKRQLAGAQRARELYERLLYPSTSDFRAIVSAGGVPGSDVTLDDVKAAEVIWGRSVLKMKGNMTRKNGKRMTQSIVKVPTELIKLHKNVELAIDCFFVNKHIFFTTISTKICFTTITHLTKRNKEDVWVALLATYKMYLMRGFRIVVVKGDQEFASISDLVAGLPTM
Ga0073923_1045267	Ga0073923_10452671	F033471	MDAFNGKYYLQSGEEQPATILLMKDKISIGLRDEHGNPRMVYWPYDQIIRDEFWKRGQSIVRCGSYPVQTIEIEAKEFADK