3300006006: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_12-Aug-14

Overview

Basic Information

• IMG/M Taxon OID: 3300006006
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114663 | Gp0115671 | Ga0073916
• Sample Name: Groundwater microbial communities from the Columbia River, Washington, USA, for microbe roles in carbon and contaminant biogeochemistry - GW-RW metaG T4_12-Aug-14
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 131149379
• Sequencing Scaffolds: 31
• Novel Protein Genes: 36
• Associated Families: 35

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → Viruses → Predicted Viral	3
Not Available	16
All Organisms → Viruses	2
All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	3
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	2
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Nitrospirae	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Caudovirales → Myoviridae → unclassified Myoviridae → Synechococcus phage S-CRM01	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → Acinetobacter → Acinetobacter baylyi	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Epsilonproteobacteria → Campylobacterales → Campylobacteraceae → Campylobacter → Campylobacter ureolyticus	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?
F000166	Metagenome / Metatranscriptome	1810	Y
F001165	Metagenome / Metatranscriptome	760	Y
F001190	Metagenome / Metatranscriptome	753	Y
F002909	Metagenome	521	Y
F003111	Metagenome / Metatranscriptome	506	Y
F003299	Metagenome / Metatranscriptome	495	N
F003537	Metagenome / Metatranscriptome	480	Y
F003690	Metagenome / Metatranscriptome	473	Y
F003784	Metagenome	468	Y
F004723	Metagenome / Metatranscriptome	426	Y
F004953	Metagenome / Metatranscriptome	417	Y
F006111	Metagenome / Metatranscriptome	381	N
F007203	Metagenome / Metatranscriptome	356	Y
F007919	Metagenome / Metatranscriptome	342	Y
F008161	Metagenome / Metatranscriptome	338	Y
F008490	Metagenome / Metatranscriptome	332	Y
F009204	Metagenome	321	Y
F011078	Metagenome / Metatranscriptome	295	N
F011485	Metagenome / Metatranscriptome	290	N
F015867	Metagenome / Metatranscriptome	251	N
F025096	Metagenome / Metatranscriptome	203	Y
F026270	Metagenome	198	N
F033033	Metagenome	178	N
F038081	Metagenome	166	N
F040531	Metagenome / Metatranscriptome	161	Y
F051707	Metagenome	143	N
F052464	Metagenome	142	N
F052965	Metagenome / Metatranscriptome	142	Y
F057379	Metagenome	136	N
F064517	Metagenome / Metatranscriptome	128	N
F075465	Metagenome / Metatranscriptome	119	Y
F082169	Metagenome	113	N
F083917	Metagenome	112	Y
F089902	Metagenome / Metatranscriptome	108	Y
F099283	Metagenome	103	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0073916_1002611	All Organisms → Viruses → Predicted Viral	1593
Ga0073916_1003145	All Organisms → Viruses → Predicted Viral	1458
Ga0073916_1003854	Not Available	1332
Ga0073916_1004787	All Organisms → Viruses → Predicted Viral	1201
Ga0073916_1007105	Not Available	997
Ga0073916_1008515	All Organisms → Viruses	918
Ga0073916_1009229	All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	885
Ga0073916_1009872	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	857
Ga0073916_1011035	Not Available	813
Ga0073916_1011385	Not Available	802
Ga0073916_1011668	Not Available	793
Ga0073916_1011790	All Organisms → cellular organisms → Bacteria	789
Ga0073916_1012214	All Organisms → Viruses	777
Ga0073916_1013022	All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	754
Ga0073916_1013255	All Organisms → cellular organisms → Bacteria → Nitrospirae	748
Ga0073916_1014157	All Organisms → cellular organisms → Archaea → unclassified Archaea → archaeon	727
Ga0073916_1014656	Not Available	715
Ga0073916_1015439	Not Available	699
Ga0073916_1016501	Not Available	678
Ga0073916_1016852	Not Available	673
Ga0073916_1017477	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → Caudovirales → Myoviridae → unclassified Myoviridae → Synechococcus phage S-CRM01	662
Ga0073916_1018906	Not Available	638
Ga0073916_1018942	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Moraxellales → Moraxellaceae → Acinetobacter → Acinetobacter baylyi	638
Ga0073916_1019062	Not Available	636
Ga0073916_1019425	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Caudovirales phage	632
Ga0073916_1021663	Not Available	602
Ga0073916_1022354	Not Available	594
Ga0073916_1022869	Not Available	588
Ga0073916_1024675	Not Available	568
Ga0073916_1026150	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Epsilonproteobacteria → Campylobacterales → Campylobacteraceae → Campylobacter → Campylobacter ureolyticus	554
Ga0073916_1027661	Not Available	541

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0073916_1002611	Ga0073916_10026114	F002909	GSLLQQIIVEWWNKKVIPPIWANLDANGTNASSKLRQSFIPGTITKSPTSINTILLAEDYWEFVEYGRKPTRGGHIEGTPYLWQSLKTWISQKGIKPAEDQTYDSLAKAIAKKIHRSGTKAQPFLEKAFTESIQMELVNELNARFGDLIFSEDIKI*
Ga0073916_1003145	Ga0073916_10031452	F007203	MYVQMQGVNLAPKVKELEKRIEMLENVVNELKLDKPRMGRPPKDKHGTERLEVNTTGRD*
Ga0073916_1003854	Ga0073916_10038545	F011078	EELSKAEWLTKATKNIAKGNELARELYQFYFLTILQKPDEQIEKIYNDGYIQFWTIRLLYLCINGNRHPFGESRIYDQYDVYDLHLSEEPDLLLEREEDEQMEQKRFNKINQVTESAYFYERELFKLWCSGMSARAIHRQTDISVREILRVVKLMKERCTTK*
Ga0073916_1004787	Ga0073916_10047871	F026270	DDRAVDQSPIVWLEIVDKIVKGDRTKWDFILDMPLIEFLNAMAFYKAKTKERQKRLEDAAGKGFNPYIVACLNEML*
Ga0073916_1004787	Ga0073916_10047872	F099283	VALSITQQPDSYHPAFNDTNFVITESSGGIYTSSNFKFIANVKVAATSVAKLKAPIYFGSVNKGVFNIGRIMESYVSNNWSFTDTSPSGCVDSFSDYEVEFGYEYSPSATGTITEYLDLTSATGTVWNAALNPFDLVTYAQAQYLATSSSAKFLTNVRTRYIHRTQKDWLYALKGDATSVVITYSDASTQTFTLPSSKVVRIPVGSQLTIPGGATYFDVVLKLGGTAKSE
Ga0073916_1007105	Ga0073916_10071052	F004953	MNKSMMLVQATWQESQTFRMIPTSTDCPYVECIFDPTSNVFVVISNIKKTTLHMLPKLDEYGQPLTGSKGMKQERHKLEVFQEFYVEDKKATEELIKAFAVNAESFDYKKFMKEAKKA*
Ga0073916_1008515	Ga0073916_10085154	F089902	MMTERAQKLMDAIYQERNTWADTEQKLVAAIIRKTMEHVKSMTAQKLNNLTVLDRGDMMTLSKEVENL*
Ga0073916_1009229	Ga0073916_10092292	F011485	KLFVASVLVSVAVFAADTEPTVNASINAGYNNHYIVNGLAKTSGSAFAGFDIGKTYFGVDGYVGGVILPDSNSIDESHWKLGVGKALKISEKFSLRGDLQVLRHQSSILGGRNSTEIAPKIALVNPYLTPYIRGSHDFNLGQSGYIVGAERPTDVFGWFTLTPTVEYGKFTDYDVVAVKIGVSRTFFNHLQPYAEVGYYDNNFQSSKYKFASQEFSGDVVAVAGVRWNF*
Ga0073916_1009872	Ga0073916_10098721	F052464	MDTQVQPKEIDDWLKQSVALVAGSIAGLGTNQRKVRYFAFEGQNDEVTK*
Ga0073916_1011035	Ga0073916_10110352	F057379	MGKYIKGDVNLSMLYLKEIPEILNGIDIDGSLILSGNGLTTLNNFPKLVTENIDLMRNPLISLKGIKQNFITTLKVGGKFPDFEGCPPNVTRLTCVGNIRLTSLKHMPTNISEIKIMAGSLKSLEHLTQNQRCTYNLMDCRIKSLVGLPNRCRALNVAFNDFEDFTGAPEIVDGTFNCGHNPIVSLKGFPKQADIVVIHNFM
Ga0073916_1011385	Ga0073916_10113853	F008490	MMNTSENSMMNDMGMEEDVMPYPAPDKQYPNASKYSSYDSIQTGAMGKAAK*
Ga0073916_1011668	Ga0073916_10116682	F009204	MKTTIKYYTQNIYGVRREKFIDKNQERVFFQLTGRRTLDSVSRELIRDLSGSSIEFEQSLPPE*C*
Ga0073916_1011790	Ga0073916_10117901	F038081	MILNKQEIKNILSMLLSEDKENAIIAFSCLNNYANKKHLGELLVLYQFGRTSAEVWEKECKKVFKLIKNVLKLDSTDYRLPSSTVFSALINNKCSEQSIELYLELFTNQLSNNLYNMGYPTDKLEINVKLKDND*
Ga0073916_1012214	Ga0073916_10122143	F001165	NDAPKPRIPDSVDAQRLEAMQLVARMKESADKFGVGFVGGFIAPNGEKFMMSNMDEADTQALLPEDLK*
Ga0073916_1013022	Ga0073916_10130223	F033033	PEDQKEFEIANQSADMYAVICHLEERLRSYRKHGNDFENVNEALDAIHTILYDELNARRINIHD*
Ga0073916_1013146	Ga0073916_10131462	F000166	MPNIPTPEHAELFAQSVRKWQQVLSLGDWRIEKGIKPAKAAMASVEFTPNARLAVYRLGDFGAEKITPESIDMTCLHELLHVFLHDLMTVAQDPKSSQDEIEMQEHRVINLLEKLLSKDSNG*
Ga0073916_1013255	Ga0073916_10132552	F008161	MESSQKDALIGTITWWGFHALLMWMGAWHFLSRETADGSILASDLFAGGLIGATVLSLLRLSVGCHLLRFIALIGILLVVFHVWQGKAAWGSLTDVAIWAYTFYSFGPSSWRYSLYSPLGVFGKVKA*
Ga0073916_1014157	Ga0073916_10141571	F033033	MKAILEFNLPEDQKEFEIANQSADMHAVICHLEERLRSYRKHGNDFENVNEALDAIHTVLYDELNARRINIHD*
Ga0073916_1014656	Ga0073916_10146561	F003690	MTISGFELVVSNEYGIEFDSFLGAIYLPWHTIILTALAVVAYKVYKRKRAK*
Ga0073916_1015439	Ga0073916_10154392	F004723	MKKGDKFIHTDIVGRKYEVTYTGTRREVKGCEFEFFVDDKGDSCFFTDTEVKKMKKI*
Ga0073916_1015439	Ga0073916_10154393	F015867	MKYKVNYYDYDSDSYLEKDLYWMASYRGSFDFVPVDDGPKENWKGFHIDGSGVNVFYNDKGMNITVDGFQLMKSGGYGKTTTFIQSAI*
Ga0073916_1016501	Ga0073916_10165012	F001190	MTSTPTGQSTSDDYFDINKFEELLARLESSKGRQQRQKSLEGRRDIFAGGLASMMGNF*
Ga0073916_1016852	Ga0073916_10168521	F003537	LLKIEIQFLLNKLSLLWPIDSKLGVWVAYIKRQLEIATQMSVIKVNVTVAKNRNSVSA*
Ga0073916_1017477	Ga0073916_10174773	F007919	MNKVKFTHITRTICPKTRIHYLDGIDEYGNHWMAQMEHTTEKWLCFSEIWYLDAQQPVQL
Ga0073916_1018906	Ga0073916_10189061	F083917	MIKVRIKKLPQAKTGYQVQGALVNDVSAMGGADYNAYIGKPKLIASKYITAVPRDEANLEAEGGETVYGDIN
Ga0073916_1018942	Ga0073916_10189422	F003784	MYDDDRERVGHNVTDFAAYGLSHLAAGQADTVDTHTPTTNPLVDHVAVSSYRGQGVTTEDLTSFIESFASLRAHRVKGVGHEQYSHAKGQKFESFTTSDTIRELIEELADASNYIDFLAIKLLNIQ
Ga0073916_1019062	Ga0073916_10190621	F003111	KNRQTLSLPEFWREAQVEALNYAKARGLGEVPLSYVIVKRRNASIDQAWVIQDLAQWLKEKQ*
Ga0073916_1019062	Ga0073916_10190624	F040531	MPAQDWSRVRKAGRYKGAIDANTIPIGPIVQHFGG
Ga0073916_1019425	Ga0073916_10194252	F003299	MCQLKTMTMKIYKVVFKTFDYWNGPVKLVTRIIEAYDADHVKQLIQKNDDLIMLIEEI*
Ga0073916_1021663	Ga0073916_10216632	F051707	MNLQENIQRIRSMMNLSESDKNKIWLLRRLETQDIKEYLNEQIDSLTDQISPCGYSTSEDYKDVIFEVASSNFINHFSDELYVKHEMSEIEEIIWYLLTKKYGNYLINKFDGRICDDEY*
Ga0073916_1022354	Ga0073916_10223541	F064517	MARTTTENIYYGRSQQITADGCFAISFFRPSTSNPVNVAGIPLEAGQTLSIKQNVGDEDWSTYEIVFGTGTATN
Ga0073916_1022869	Ga0073916_10228691	F082169	MKFNLKTILAWGGAFVAYRLYKLYELGENVIYKPVGVSFTRGKSINDFVVRVKMELLNPTKTTLQMRGIDGKLKIKDQVIGTFASAPFTIKAGISYFFLDFKVLPNTTGVQIITAIIAKKVPVFIVEMNKRLPYFSITEVFAINP
Ga0073916_1024675	Ga0073916_10246752	F025096	QWVVQAWVKTEAATLYAKSINLEGIIEHVTWDKDGAPSPGVQHFSGDVRTIPFAWMNAKERLLITEPVSIHFYTLLKEESSAPTPMDHYLGVVTTESIGKGSVITWRVYFDTTGWSPMASIMSSQLKRLLEKGIQSWIDEYGGALIPVEVKE*
Ga0073916_1026150	Ga0073916_10261501	F006111	MISYQSIVDKITTFYDNHLQVKKVGSDFKEQMVNFATADEKYPLVYVVPTGVTPYENVSIFNLELYCFDIIQMDRANITTILSDTQQILQDLYLEFTFSDDYDFDIDGQPTFIPLNNDLLDYAAGWQMNLSVVIPSWTNCQIPEQNA*
Ga0073916_1027661	Ga0073916_10276612	F052965	MDKPGLIEVAFHDWWLGSYKRPPTAQATMTHVAFAKHMITMLELTQDVQTP*
Ga0073916_1027902	Ga0073916_10279021	F075465	ESEKTQYSNDWRSYRERTTQLTKHRGQAFSLILGQCTQLLQDKMKQDTDWNVVSTSYDPLSLYRLIERTILAQTDDQYPFATIYDQELAFYSFRQESLSNPQWYERFNTKVDVGEAIGVTRQHRVLLDYVAMELHTQAFATLGAAEQEAVRTDAEERYLSYAFLRQSGIQHGNLKTDLQ