3300021314: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.671 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021314
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225754 | Ga0210370
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.671 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 97391025
• Sequencing Scaffolds: 16
• Novel Protein Genes: 19
• Associated Families: 19

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	6
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	1
All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia	1
All Organisms → cellular organisms → Eukaryota → Sar	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Intertidal Zone → Estuary → Estuarine → Estuarine Microbial Communities From The Columbia River Estuary, To Analyze Effect Of Nutrient Fluxes, A Time Series

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): estuarine biome → estuary → sediment
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: Washington
• Coordinates
  • Lat. (^o): 46.27
  • Long. (^o): -123.946
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000344	Metagenome / Metatranscriptome	1257	Y
F001488	Metagenome / Metatranscriptome	686	Y
F001506	Metagenome / Metatranscriptome	681	Y
F001633	Metagenome / Metatranscriptome	660	Y
F001679	Metagenome / Metatranscriptome	653	Y
F001926	Metagenome / Metatranscriptome	616	Y
F011154	Metagenome / Metatranscriptome	294	Y
F014821	Metagenome / Metatranscriptome	259	Y
F017072	Metagenome / Metatranscriptome	243	Y
F017082	Metagenome / Metatranscriptome	242	Y
F023254	Metagenome / Metatranscriptome	210	Y
F024806	Metagenome / Metatranscriptome	204	Y
F044534	Metagenome / Metatranscriptome	154	Y
F044586	Metagenome / Metatranscriptome	154	Y
F060086	Metagenome / Metatranscriptome	133	Y
F064269	Metagenome / Metatranscriptome	128	Y
F067276	Metagenome / Metatranscriptome	125	Y
F076133	Metagenome / Metatranscriptome	118	Y
F089930	Metagenome / Metatranscriptome	108	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210370_1033997	Not Available	638
Ga0210370_1060133	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta	905
Ga0210370_1061313	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	2270
Ga0210370_1074195	Not Available	720
Ga0210370_1081086	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae	625
Ga0210370_1086864	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	960
Ga0210370_1086937	All Organisms → cellular organisms → Eukaryota → Sar → Stramenopiles → Ochrophyta → Bacillariophyta → Bacillariophyceae → Bacillariophycidae → Naviculales → Naviculaceae → Fistulifera → Fistulifera solaris	587
Ga0210370_1098544	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	619
Ga0210370_1108763	Not Available	738
Ga0210370_1166784	Not Available	711
Ga0210370_1168397	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	683
Ga0210370_1171404	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia	673
Ga0210370_1172390	All Organisms → cellular organisms → Eukaryota → Sar	674
Ga0210370_1178640	Not Available	755
Ga0210370_1188975	Not Available	611
Ga0210370_1191513	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	567

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210370_1033997	Ga0210370_10339971	F017072	MRMRDLAVGSDEKPLRTESSSPETFRFRMNRSHPEGEQLLLCISTVCAALAGSNQIEAAQRKTPKGGQKERGHREEHGNSAGSVKNFQAPAMLKTTPLDCEIKCNLREKRRDPWFRANASSKAMADPGLVVKTRTRDPQACLDLVRKPVAQPPAEAS
Ga0210370_1060133	Ga0210370_10601331	F089930	VDAVLWQLNCGAPDMSGGEVSEEFALKASHVTFKLHRRGDLFVQAVLTFMLRGGYLSKAIGRNRNVDKTALEPLSLHDILEVRAGCSGFDHTELPTASGKTKKKKDSKGENKQASLFMTIKATPTPLASSRSYIFRFKSRSARNDVMNGLRCILADMQIHEGVSISNLHTEKDAFDEREREEIMVPLSAVHEVINREREAYDRILLMLLQGNEDLKEKEDELLRLRNKLESVVDESKEKDRVQANDSKLIMQLSKKLETLLMDNEDLRDQNDRLNTRLVSVESEKMNLLARKS
Ga0210370_1061313	Ga0210370_10613134	F001488	MARLELTLNFPKSFQIKTFNVKSEKNLSPLAKLILQSVQFKHFYYVRDDISYLLKSNPIERDFLLQALYSIVISLQNNLSINFFDMWIYEIYINKVSTHNKFMSQKFQNLEPSEYITIKLAYGSNVSQEKK
Ga0210370_1074195	Ga0210370_10741951	F067276	QELKISEVATGSILTASRYEAHLDGGSQASTTNDKTVLWGFKWYTNKNPCRIRLICADGKTPIVPEGYGTVRIPADNAEGYVPIKCYYTPDIPNFILSPNSFKALLGKHYNGYKLECDDDKKNFRFSLNHKMRKSGSVLLRGTTRGGLCYTRPAVPPMPTTEGTAEMSLDMADKAAISMVEDHPQNSYRHEMKLHALSAKAERLLWHQRLAHCGDEQLCRAHMFSDGIPEITRGKDSAL
Ga0210370_1081086	Ga0210370_10810862	F044534	SHTNQELCGEARLETVPNRVRLTGSFDPCADAVTPEGFGCCCADQNAVAVPGGPTPPKGLVHSTNETRKGTGTAGRERIWQSP
Ga0210370_1086864	Ga0210370_10868642	F001506	MNRILYENRCKCNEEFSIIKKRKIKTRSEGKPLQYPKSSEITSKTFQMKYQTRLSTTAKCLLNNFQNKYIYYAIDDILYLLKTKPVERDNLLAVLYSPILSLQNNFSVDFFEIWIREVFIDEISKTNKFLKNDSKTLKQSNYITIKFFYKIPVKKKESLWEF
Ga0210370_1086937	Ga0210370_10869371	F014821	DPVVLAAIHRLLDPDADLDELRVNALQSEAISPEERALPRFSRRALKGLPTWDLWHKNEIEQLDQMKALGMFGAPIKLPEGGILMRFHWQYRIKVNGKRRSRLCCDGSPRAAPEVHSTTNTYASCLEHPIFRLFIALCAADGLTIFGGDAKDAFAHSPGPSMPTFMKIDDAFRDWYQERTGVLLDKDLVLPVLRA
Ga0210370_1087688	Ga0210370_10876882	F064269	MFMIPVLLAVCMVFACVPKILYLIFGIDTKRSTSRKLKSLIPTTLVNVKRYLGSTLHYFLSSTYNVVNTLLLPTQEQRVRRSSKRKALDRMFFMFLLMNHGRVSAKSARRGLIRLRPVTKSEIPQAIPQDLSAEMLAPWDNIPQGWSQRLLNGNELKQFDPDNV
Ga0210370_1098544	Ga0210370_10985441	F076133	GEARLETVPNRVRLTGSFDPCADAVTPEGFGCYCADQNAVTVPGGPTPPKGLVRRTNEARKGTGTAGRERIWQSP
Ga0210370_1098544	Ga0210370_10985442	F000344	MRPIHPHAAESGVGKHTARESESAKACAIGKERVANAHP
Ga0210370_1108763	Ga0210370_11087631	F060086	PFELDSNLLLSSGRHGEDRKRQYLYDHETPLLDDLADLLYLALPLLLLFK
Ga0210370_1137850	Ga0210370_11378501	F017082	DTKQYRKKCQLGSDGQLSFEMTGCIANGQEHKVDETFEDGTNFFICKSDGAALKIVNQGCVDGGKRVNKKDTVAKADALYSCEETVNGGSKLVQAGCIKDGKQYKAGESFEVGKYWFNCVRTGREKVVVKAAGCIANGKRINDGDRYFENDVVYECTVDGDKTDVRATGCVQNDGGNILERRLGCTW
Ga0210370_1166784	Ga0210370_11667841	F023254	FFHEDDVTVKVVRNSDLYGFELREDDCMKRVYISDFKRDGKGVKSRCSCNTICSTERATRRKYRGAYITAIDDKEIVTLEQAKEKLKELRNKKVDTFTMILAREPRPSKSMTRRAYDELELPDFDLDENLGEDYFETEGDLEGNSSMTNSHETNAFGTDYVPKIGTKIYKDFGTKGFFAGTITSGPHTRTKDGDDVTTWKVQYADGDREDMTASEIAYWKAPTEEVHTSTTEAKSK
Ga0210370_1168397	Ga0210370_11683971	F001633	LAFAGGVLPDATLRGMRMSRSHGGTVLTVAGRDLSSEASAPGSVASCRKRHAGRGADTPATFIFSRRHRYHGDGTSFWLVVGPALRV
Ga0210370_1171404	Ga0210370_11714042	F001679	MWGMPWRQEAKKGVEDCEKPGGLVKRELIPGYPNERDVNT
Ga0210370_1172390	Ga0210370_11723901	F001926	VRHEDIPETNNPKIRNPVLEADKLMKEVLNGGYNVHPVPPPNSEIKERIRRRYERKRIKKEKLLTLGYTTSGDP
Ga0210370_1178640	Ga0210370_11786402	F024806	MATNSNFNFTNNTAIILELPFSEHIEELRQRIFLVFGIILLLTCVAFIEVKSLV
Ga0210370_1188975	Ga0210370_11889751	F011154	MRSDEKPLRIESSRPGRFRAWANRSYPEGIRLLLCISTGGRLWRPPEGGLPNERRRKAGQSERPNREGHAASAGPVKTFQAVGDVKNDTADLWTKGNLRVKRRDPWHRANALSKAAADPALSGEDAEIKTQTCLGLVRRPV
Ga0210370_1191513	Ga0210370_11915131	F044586	MQTRRTLLQQAGSAALLATTSPWWMVPRSAHAARDKKLVVWHLAAL