3300026883: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_10-June-14 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026883
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114663 | Gp0115670 | Ga0209895
• 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 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 61414965
• Sequencing Scaffolds: 9
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1
All Organisms → Viruses → Predicted Viral	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	1
Not Available	4

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?
F005780	Metagenome / Metatranscriptome	390	Y
F024650	Metagenome / Metatranscriptome	205	Y
F044595	Metagenome	154	Y
F050934	Metagenome	144	N
F052686	Metagenome / Metatranscriptome	142	Y
F053809	Metagenome / Metatranscriptome	140	N
F068469	Metagenome / Metatranscriptome	124	Y
F076893	Metagenome / Metatranscriptome	117	Y
F076944	Metagenome / Metatranscriptome	117	Y
F092936	Metagenome / Metatranscriptome	107	N
F104469	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209895_1000412	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	4542
Ga0209895_1007010	All Organisms → Viruses → Predicted Viral	1043
Ga0209895_1007603	All Organisms → cellular organisms → Bacteria → Proteobacteria	988
Ga0209895_1008787	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Coscinodiscophyceae → Thalassiosirophycidae → Thalassiosirales → Thalassiosiraceae → Thalassiosira → Thalassiosira oceanica	899
Ga0209895_1010293	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	813
Ga0209895_1011872	Not Available	741
Ga0209895_1011974	Not Available	736
Ga0209895_1014986	Not Available	638
Ga0209895_1021091	Not Available	515

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209895_1000412	Ga0209895_10004121	F044595	VKSAHIVTANRPMNGLVAFVRAAAAMESFRGCASALHLTLPASFQLDRNEDRMHP
Ga0209895_1007010	Ga0209895_10070101	F092936	LVIIAAIKIQSRIPLAPGAFFTVENPAIVQKWMANGTLPLIFTAQSIKSVTHDKFRLYEIPPVPQSKSQHGFILSGVDITLLNIQVTNINCGGAMCDGLNMYQNSVTADRCPCYSVLDREGKVCLVLSLKVSDPKNNLQFCVHNHTSKSLTQLFMKRIPKGAVAATITGNQKHMGNLSAKVMDMLALGNDYNGFIISGWIKRGTIADSGVVQPPTGSKWDKPQQVDSGGLTYHLTKIAYASPPSDRLLGEYQFNAGSLV
Ga0209895_1007603	Ga0209895_10076031	F052686	MADKPGSKPTSSAPKPVAPKGSEAGTMGLDDRGNVTWEWKDQGDLLADDTLGAAERVRALVDPRLKVTDDDDPGNPIKSNPKGLKSGYNPYNSGALGKQSWKKKRNL
Ga0209895_1008787	Ga0209895_10087871	F050934	IQAAIFQKHIQATHPNVTSNEMPPEHTLIIEGDITSSRSNTTRQRIDRHLRHRIITTCGDANVMMGSKHIDPALCIYIGAYLICIDNKHLTDKVPRGNGTLCRVLGMKLNENAQSYKCKNYYGKKVWTVNAADVEWVECEHVNKTSFLTQLESQIKELKCQLDLTPNDHKIERKKIKSKLDDLNNKLAKEMTGRKFKLEPEQFSPEVTVKHYQTSSKKVAFRCKMKQIPANSNDATTGHKLQGMSKDAIIVSSWPTGGLSAMFKNWEYVVLSRVRTLSGLYLVKPIDMDKSFQPSPQLA
Ga0209895_1010293	Ga0209895_10102931	F005780	MAQETVSIAWCDNGMVDGKFMQGVTDVMLKSGINFTTTLRSQGNQIARQREKIIRYWYENNTSEWLLWVDSDVVISPEKFRLLWDNKDVKERPIVTGVYFTTDTPEEPLMIPMPTIFNFAEAQDGVVGIKRVHPMP
Ga0209895_1011872	Ga0209895_10118721	F053809	KSHIRPYIRNTLLLINDQLPLLHLHVNYLSQLQLINRRRLHDFDVLSGKRHTRGAGAIRVAEIGAAYAEDRIRAHLGALIVDNNDLLAEWFRLKTYTDGHTPLICSNRPALQMNTMPFDTDGVCTIQGDGIPHPADMRSTIQIIERILLPHAQSAARCCTITDYRNHNAAYMCVKGFVRETKRSLDDVRGRLYYLQYDEIDLWRSVQNFEYNIEDCSTIIRELFANTQPTQPFPQVVTPTTNDVAH
Ga0209895_1011974	Ga0209895_10119742	F024650	TFSLAQNNNNTYMAASWACRTLVSKFARMVTTQLDGALSADYSDLMMHYQQLADTLEYQGKTSGAALGVLAGGLTKSSVEAVRADTNRIEGSFRRDQFKNPPSYNTPEYE
Ga0209895_1013391	Ga0209895_10133911	F104469	FVDTTKAPAGDSDYACFTTSQKCITSLMYLLDDMECPDYAFQSIMDWARNCFEAGFDFNPKSKTRLGNLKWMYDSLHNAKQMLPNVVSIQLPDPLPDTKSMDVICYDFVPQLLSILQNKEMMSANNLVLDPNNPLAMYKPHDSRLGEALSGSVCRDMYHRLVSNPSKQLLCPLICYTDGTQVDSLSRFSVEPFLFTPAVLSHAARCKADAWRPFGYVQHSKSNLRSD
Ga0209895_1014986	Ga0209895_10149861	F076893	GYKYPVWYSKKAITNIICLKNLIKCYRVTYDSEVDTTFVVHCSASGLPDLLFEMHPCGLHVCYPKKMGQFGFVQTVQDNMKLFSKRQLAGAQRARELYERLLYPSTSDFRAIVCAGGVPGSDVTLDDVKAAEVIWGRSVLKMKGNMTRKNGKRMTQSIVKVPTELIKLHKNVELAIDCFFVNKHIFFTTISTKICFTTITHLTKRNKEDVWV
Ga0209895_1021091	Ga0209895_10210911	F068469	VKGNDKPAILAALISSNDKVWGEFYMHPLKTNMRLATAAAAQARGGILSQEEQAQLQYADMLIDVSK
Ga0209895_1021091	Ga0209895_10210912	F076944	VEDDNDVDDQDLATCDFKKERCDYLHEVSVIFWDEFISNDRILMEAVLEEFKTRWELPRYYIFVCAGDFAQVCI