3300006003: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_2-Sept-14

Overview

Basic Information

• IMG/M Taxon OID: 3300006003
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114663 | Gp0115673 | Ga0073912
• Sample Name: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_2-Sept-14
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 98989268
• Sequencing Scaffolds: 23
• Novel Protein Genes: 29
• Associated Families: 29

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → Viruses → Predicted Viral	2
Not Available	13
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	3
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Kyanoviridae → unclassified Kyanoviridae → Synechococcus phage S-SRM01	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → unclassified Caudoviricetes → Caudoviricetes sp.	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?
F000919	Metagenome / Metatranscriptome	834	Y
F000973	Metagenome / Metatranscriptome	817	Y
F001968	Metagenome / Metatranscriptome	610	Y
F003495	Metagenome / Metatranscriptome	483	Y
F011078	Metagenome / Metatranscriptome	295	N
F014573	Metagenome / Metatranscriptome	262	N
F018713	Metagenome	233	N
F019965	Metagenome	226	N
F021301	Metagenome / Metatranscriptome	219	N
F022403	Metagenome / Metatranscriptome	214	Y
F022817	Metagenome / Metatranscriptome	212	Y
F024100	Metagenome / Metatranscriptome	207	Y
F025502	Metagenome / Metatranscriptome	201	N
F026270	Metagenome	198	N
F036108	Metagenome	170	Y
F039047	Metagenome / Metatranscriptome	164	N
F041196	Metagenome	160	Y
F043897	Metagenome / Metatranscriptome	155	N
F050335	Metagenome / Metatranscriptome	145	N
F053242	Metagenome	141	N
F058796	Metagenome / Metatranscriptome	134	N
F062696	Metagenome	130	N
F063698	Metagenome / Metatranscriptome	129	N
F066500	Metagenome / Metatranscriptome	126	N
F068747	Metagenome	124	Y
F072345	Metagenome / Metatranscriptome	121	N
F086620	Metagenome	110	N
F100723	Metagenome / Metatranscriptome	102	N
F104469	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0073912_1004337	All Organisms → Viruses → Predicted Viral	1326
Ga0073912_1005032	All Organisms → Viruses → Predicted Viral	1215
Ga0073912_1005718	Not Available	1125
Ga0073912_1006144	Not Available	1074
Ga0073912_1006779	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Dinophyceae	1015
Ga0073912_1006879	Not Available	1008
Ga0073912_1007197	Not Available	981
Ga0073912_1009020	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	861
Ga0073912_1011073	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	766
Ga0073912_1011401	Not Available	754
Ga0073912_1011986	Not Available	735
Ga0073912_1013330	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	693
Ga0073912_1014467	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Kyanoviridae → unclassified Kyanoviridae → Synechococcus phage S-SRM01	663
Ga0073912_1014746	Not Available	657
Ga0073912_1015596	Not Available	638
Ga0073912_1016109	Not Available	628
Ga0073912_1018071	Not Available	593
Ga0073912_1019327	All Organisms → cellular organisms → Archaea → Euryarchaeota → unclassified Euryarchaeota → Euryarchaeota archaeon	572
Ga0073912_1020547	Not Available	555
Ga0073912_1021046	Not Available	549
Ga0073912_1021903	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → unclassified Caudoviricetes → Caudoviricetes sp.	538
Ga0073912_1024437	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	510
Ga0073912_1025478	Not Available	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0073912_1004337	Ga0073912_10043375	F022817	KASTHYLKNGKVHTGPVHKMNGQVHTGATHTASSKVLTHTKPKAKKK*
Ga0073912_1005032	Ga0073912_10050321	F086620	MLTKKQEQGLRILESIVQSQYPFVVSLSKSDKYRLDEYATTMGIILEIDPTTLSKFVGLPFAKKFKETPSIWDYYMRDRDLSFILHLFEDEHQHIMGWQFNKGMEEFITKVYSQLPTNMRVNIYSDSPDYDIPDWARRTLHSPRTLTIDRFFLAPDSKPPKFED*
Ga0073912_1005718	Ga0073912_10057182	F011078	VNKAEIIEELSRADWLTKATRNIAKNNELARELYQFYFLTILQKPDEQIEKIYNDGYIQFWTIRLLYLCINGNRHPFGESRIYDQYDVYDLHLSEEPDLLLEREEDERIEQKRINKINQVTESAYFYERELFKLWCSGMSARAIHRQTDISVREILRVVKLMKERCTTK*
Ga0073912_1006144	Ga0073912_10061441	F100723	NLRGAIFVPTSRRQRKNTFKKKSTLTVPCGTISKMTNKKWTPRSLRWTDSERQAKKIQSQNVRQIRWLFWRESQALREEIQKEISEKLIAKREAIE*
Ga0073912_1006779	Ga0073912_10067792	F003495	MKIKQDVTSKEVKVIPKDIAALDKRSVLAKVNSQGSGR*
Ga0073912_1006879	Ga0073912_10068792	F041196	MNLQENIQRIKSMMGLLVEEQQDKSIVLLDGTSSAGKSHTLNHLNAVPYYEANNPNQWVIIATDDFSGTGELGADGEERRLKLDHPNIRQWAKENADAGIVSGNYRKDGKEVPENPYEDEYIQNTDPRLWYVAQEIKTGPFKKIAIDDIGKEILQYLPGVKLKYILLHAPLYILLDNVKWRNDRAKKDPNFKYDGRDVKMVLGQYSKKYEATQSKPDINEGDPTTVLTKGGITDLLQKNGMSDEHIDEFLNSINLTEDGD
Ga0073912_1007197	Ga0073912_10071972	F001968	MFDELWSEIADAPGEIFDLPELRDLEEGKFDVNEYLNSN
Ga0073912_1009020	Ga0073912_10090201	F068747	EDIKQSLYEWFVSHPRKLTEWEGFSKKSAQNLLYRSLRNQALDYCQYWKAKSLGYETSDLFFYDADIVEALLPAVLRGDITEAPVLNLGMPGKPSAPAEGGNMMAMMAEIKAAYLKLSTEDRHILYHKYAGSLSYGDIAIELALPSDDAARMRHNRAIKKLITRLGGFRSYLDKDETSEVGNDEPNQNEDAEQGQETD*
Ga0073912_1011073	Ga0073912_10110732	F019965	MNDLEVMMQTVQIYIYQKKGVKVRIYLRDIRDINMLKQAYDYIQKNEHNKNTNN*
Ga0073912_1011401	Ga0073912_10114011	F050335	VQLTIIKCKDELHLKNECIWNATTYPLFFIVALSITQQPDSYHPAFNDTNFVITESSGGIYTSSNFKFIANVKVAATSVAKLKAPIYFGSVNKGVFNIGRIMESYVSNNWSFTDTSPSGCVDSFSDYEVEFGYEYSPSATGTITEYLDLTSATGTVWNAALNPFDLVTYAQAQYLATSASAKFLTNVRTRYIHRTQKDWLYALKGDATSVVITY
Ga0073912_1011986	Ga0073912_10119861	F026270	LLFEGGDEGYDGAVDQSPIVWLEIVDKIVKGDRTKWDFILQMPLIEFLNAMAFYKAKTKERQKRLEDAAGKGFNPYIVACLNEML*
Ga0073912_1011986	Ga0073912_10119862	F021301	RQMNILAIALNLSMDEVESMTLDKLTSEFEKLSFLNDLPKAPIQFMFKLRGRYFKLAKTPNEMCGHHFIELQQVFNGDVIESLNKIVALLSVEVDFFGRNKKVVDAQAHYEDKCGLMMGLPVPLPYTYALFFLEVYPELLKNILCSLKEEMKDMTEQLTKVQ*
Ga0073912_1013330	Ga0073912_10133303	F014573	MHIQDEQLRKELKKILAFKKRNSIVKEIQSNGSKFHFFQLTNFLQGKDVSLSTLKK
Ga0073912_1013822	Ga0073912_10138221	F072345	MISYQSIVDKITTFYDNHLQVKKVGSDFKEQMVNFATKDEKYPLVYVVPTGVTPYENVTVFNIELYCFDIIQMDRANITTILSDTQQILQDLYLEFTFSDDYDFDIDGQP
Ga0073912_1014467	Ga0073912_10144673	F000919	VEFRWSKLNNKYELVKWQECEGKEYCYVIAFFDKDKECYNMRTIGDRFFEDKDAWVVGKYALEFLNAIFQIEQDEEELK*
Ga0073912_1014746	Ga0073912_10147463	F063698	ILAGGDGFKYHGTGTVTSVGYAALVVQEDTVFTSFSVDGTNVLSARGLSAITLQQGAYLPSGGASKITGFIISSGSVIGY*
Ga0073912_1015596	Ga0073912_10155961	F043897	MTNEFAKISAESNMSDMITLSMEEITEANAWFDMVSAQFDEVEAAWDRLVEYVDNI*
Ga0073912_1016109	Ga0073912_10161092	F062696	MNYGTFRIYCLCLVGVCFSACSPQSTLSRLLKNHPYLYENFRHDSIRIENVLVQDSVFFFTKEKDTITFNNATIYREFDTLRLVQSCPPCTTYVSKTILQPTQKLLKETRYKRSLREKLEDSIFPLIIGLLLGLIITRRG*
Ga0073912_1017110	Ga0073912_10171101	F025502	EAILAIVQPVIDEQINALIAMIADLRNHMEEVMSEGEEVVEVEATKLSHHDKFSMVSKFLNNN*
Ga0073912_1018071	Ga0073912_10180712	F018713	MTPDPNLWAEIPQEVKDAAILLGNYFKKQGLDSWTLYDVSSRQNFNGAYNQGLDTAISLVSEGSDMETIICGLENSKKQFSNEGGDGIDYTKSF*
Ga0073912_1018732	Ga0073912_10187321	F104469	GSVAAVDSFSENKFVDTTKAPAGDSDYACFTTSQKCITSLMYLLDDMECPDYAFQSIMDWARNCFEAGFDFNPKSKTRLGNLKWMYDSLHNAKQMLPNVVSIQLPDPLPDTKSMDVICYDFVPQLLSILQNKEMMLANNLVLDPNNPLAMYKPQNSRLGEALSGSVYQDMYQRLVSNPTKQLLCPLICYTDGT
Ga0073912_1019327	Ga0073912_10193272	F000973	AWELKGIRNILGSMWHSRYQDGETDVLNPEAFADEYISTEECGRRLSVSDQTLRNWMAMGRKNPEKGWVEGIHYVNASPDPNRKAIIRVPWNHLIRSFAKNRDLDAQDYRKKSSPMYVSTGFDRLE*
Ga0073912_1020218	Ga0073912_10202182	F058796	DATHEVEGGLLVTTVGGMVTEIVEPEIEVEVEAEEFATVSAFNEVVAKMETAIAELTAKVATLTASNNTHKEAMSKAIDLIEKVADLPSEEPTKTPVSNKKNDQFEALKRLKNSLNK*
Ga0073912_1020547	Ga0073912_10205471	F022403	MPLRHGQKFYCQLLLDRHRYLLVDEMAKQQGKRTTALLREMVYSALEKALPLSEYRAAEAADNAAWADSVKRRVQGRQRSRQDGSDTAQDS*
Ga0073912_1021046	Ga0073912_10210462	F066500	QERFTKTWADNFNKLSEKETWLKDQSTPEYKRTVELLQRIPILTTLPNGLAHAVELMKLQDTAGRFQSVEAENKSLKEQLNKLQQKTAIGKSVPAGQLKAEEKDFSKLSQKEQRDALMRATREFDRESNQ*
Ga0073912_1021128	Ga0073912_10211282	F039047	MKMKIEVDINDLVALKVALGNSARRIDELMNDKPDWRNLYEFDKNSVEK
Ga0073912_1021903	Ga0073912_10219032	F024100	MADNSADIAKRIILGCVAEGMTIEAACASAGKSIKTYE
Ga0073912_1024437	Ga0073912_10244371	F053242	GEWKKPNENMATGQQLLLKAFAQVPKFTVLVIIGNTDNEQTEVGDVFQVVLGKCVKIGEGLDFLKDFYILWYEFANSKG*
Ga0073912_1025478	Ga0073912_10254783	F036108	LAITAINHYVDFLSSEIDFYEKEELLEDTDYQEHKSQLPEVYALLNWIKLEYFKHEN*