3300021322: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.298 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300021322
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114516 | Gp0225714 | Ga0210330
• Sample Name: Metatranscriptome of estuarine sediment microbial communities from the Columbia River estuary, Washington, United States ? S.298 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 142286757
• Sequencing Scaffolds: 25
• Novel Protein Genes: 27
• Associated Families: 27

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	2
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Desulfobia → Candidatus Desulfobia pelagia	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria 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): 46.286
  • Long. (^o): -124.052
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001314	Metagenome / Metatranscriptome	725	Y
F006082	Metagenome / Metatranscriptome	382	Y
F016165	Metagenome / Metatranscriptome	249	Y
F016664	Metagenome / Metatranscriptome	245	Y
F020930	Metagenome / Metatranscriptome	221	Y
F033058	Metagenome / Metatranscriptome	178	Y
F049002	Metagenome / Metatranscriptome	147	Y
F052020	Metagenome / Metatranscriptome	143	Y
F053923	Metagenome / Metatranscriptome	140	Y
F054044	Metagenome / Metatranscriptome	140	Y
F055829	Metagenome / Metatranscriptome	138	Y
F058634	Metagenome / Metatranscriptome	134	Y
F059103	Metagenome / Metatranscriptome	134	Y
F059980	Metagenome / Metatranscriptome	133	Y
F065171	Metagenome / Metatranscriptome	128	Y
F069124	Metagenome / Metatranscriptome	124	Y
F070130	Metagenome / Metatranscriptome	123	Y
F072362	Metagenome / Metatranscriptome	121	Y
F074834	Metagenome / Metatranscriptome	119	Y
F074892	Metagenome / Metatranscriptome	119	Y
F077315	Metagenome / Metatranscriptome	117	Y
F077370	Metatranscriptome	117	Y
F079376	Metagenome / Metatranscriptome	116	Y
F088148	Metagenome / Metatranscriptome	109	Y
F090573	Metagenome / Metatranscriptome	108	Y
F095879	Metagenome / Metatranscriptome	105	Y
F102756	Metagenome / Metatranscriptome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0210330_1008403	Not Available	629
Ga0210330_1010167	Not Available	521
Ga0210330_1023925	Not Available	915
Ga0210330_1041037	Not Available	583
Ga0210330_1083134	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	678
Ga0210330_1094721	All Organisms → cellular organisms → Bacteria	2339
Ga0210330_1107435	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	811
Ga0210330_1118722	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	1272
Ga0210330_1131167	All Organisms → cellular organisms → Bacteria	505
Ga0210330_1155126	All Organisms → cellular organisms → Bacteria	603
Ga0210330_1159566	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	964
Ga0210330_1167914	Not Available	720
Ga0210330_1182491	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobulbaceae → Candidatus Desulfobia → Candidatus Desulfobia pelagia	890
Ga0210330_1186486	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Xanthomonadales → unclassified Xanthomonadales → Xanthomonadales bacterium	574
Ga0210330_1187516	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	790
Ga0210330_1197039	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	663
Ga0210330_1240444	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	600
Ga0210330_1251368	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	786
Ga0210330_1256478	Not Available	522
Ga0210330_1257083	Not Available	510
Ga0210330_1264003	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria	660
Ga0210330_1274247	All Organisms → cellular organisms → Bacteria → Terrabacteria group	698
Ga0210330_1284191	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium	572
Ga0210330_1288895	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	754
Ga0210330_1327546	All Organisms → cellular organisms → Bacteria	567

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0210330_1008403	Ga0210330_10084031	F053923	GDPPHASSVVNVLARAGQATLTGRSIKRTLQLRYAAHTIWNRGTCGCRAGADSAKAEPARKTLLCALAGATGVRATAWGEGTGRVNWGPSAVGGLDPQPDGIIHKPFGGRQRRRCGHSKRRSGRTTQPAGEPRATGLAVLVRSSRCRLVARPTTDKTPGMEIRTVAAYKRAGGRPRRWPRGQAGLKPYWGKPTVRNFRGGGGNEVQGLM
Ga0210330_1010167	Ga0210330_10101672	F072362	EYEMHRLFAIGFLVYLVGDPSLSMLASFSETRELIIASALALIAVPWVVSQIDN
Ga0210330_1023925	Ga0210330_10239252	F095879	PHYHPGTTVLGVVSGSFGWTLKAGKAHVVRGAGAGATGPVEDVTEPGTDVVLNAGDAIYYESDVVHTARGAGDTEAVILGSLVLKTGAPLLIRVDM
Ga0210330_1041037	Ga0210330_10410371	F077370	GKTNDRAIDILVNIFAVNSLGTPFYSFSTSAGSPQLSSNLTDLMILQFTEYSELAQIYGLVKLKKIQLGFTRSSNFIGGGTTILQNTPSIFLQASTIPYSTGSVVLQRAIAQSDNSIELDLQTYDPKSYEIFLPPHIVSNNRANNQTFAFGSQTWISTRLNNVQNLPDLFLNLGSLATPTFDPSTTSGNSVLI
Ga0210330_1083134	Ga0210330_10831341	F058634	MRHLSAVTATLILALGLSGCSSDQTQGVEGVGNVGMEVTLATPPAGPNEQIDTVDVSFYCDGIDPVLGVPRPPQSSPEEFTINTSTSQGPEPKNTIGLFEKQGLPAGNCYFSFTAASNTGNTQCTGELTVAVVTNETTEGTVVLACIHTPRYGGVRGDGTFNQCAEYRQIL
Ga0210330_1094721	Ga0210330_10947212	F069124	MGGWRFMEKWFCGSGFVAARDARRCSGFARTAIADSAIAVRLAAEKPGGGNTVLPTGGIRGVRKAGSIIGTGNVLTVSATRQPA
Ga0210330_1107435	Ga0210330_11074351	F059980	DFDIKSLHLMEEACSIGFSGGCEQGKPETALPELRRVIPVNEKRVNPQNKFCCS
Ga0210330_1118722	Ga0210330_11187221	F102756	LTPPASPAPPLHRLHDEEVERLLASGEHRRELIALFGEAGYRELSGLARRAAAVRRRGVAVYVLPGLMGSRIGARGRLVDDVI
Ga0210330_1131167	Ga0210330_11311672	F074834	VDDNRRALDDAALNAIRDQVRSTAAALREVHIEPGSPRAQALFGG
Ga0210330_1155126	Ga0210330_11551262	F088148	DAAHTTKANARQLTQGNGADYLLILKANQPTAWAKAQQLLPGAIPPSGPDDRQGPRAG
Ga0210330_1159566	Ga0210330_11595662	F049002	MAKTDLDEAQTELTRAIQKDAPCTFDEPIPVLVTLDNGVKYEGVAFEVQPKSTNFPRGLVMVRTGNTDIGVPVNYIRGR
Ga0210330_1167914	Ga0210330_11679141	F033058	MNRRRVLIWFAGRWRNHQSKRAEKPHSKSSSGDALDGPATRPETPLAVENSVGKPAAPEAPNAGTGKREW
Ga0210330_1178541	Ga0210330_11785411	F006082	NACRHGGGRVYAADGTEITWAIEAEYDRKVRRVQFRSK
Ga0210330_1182491	Ga0210330_11824911	F079376	MFDIVSTRQPGRPCVSFEVSRVCWTTEEGGRQMRYRESDSLVVPEKAGNAAGGKEATHGSVV
Ga0210330_1186486	Ga0210330_11864861	F016165	MLLKILSGVLGVAGLCWLALLFSSRAILVGERVEAAALHQQLVCTYFTGSGTMRKEYWYSKSDRFGRAACPRWESVREPE
Ga0210330_1187516	Ga0210330_11875162	F016664	MDQVVYEMPTLNEAKNAVEIVVHISESLEDRQRNNLVVALEKEDGIVSAEFCPLRYHLMLVRYDRDQYSSQDVLSAVGAQKLQARLIGPI
Ga0210330_1197039	Ga0210330_11970391	F054044	MISKYYSNSDIFSVPADRLGISHTVGILVLVIALTALILLFVDSSFRSAADQEECLQLVRALGLNSLSLAPSGRPLRNPGAIDPSIDLRFGPKFGRLPIDGADLF
Ga0210330_1240444	Ga0210330_12404441	F065171	PRSTEGFYVDLASKRGLVRRTGGEAGPTMHFLDTTPLADQLERAIHALRQADIGEPGAAAALSQQRIGVLEKVRPVVAPNLYGDLRRAPRTPVTMAAKVRIGLARICAELSPKAVVEPANDPDAGNEQIEVYAVADRPRNRPHVPDEHDSLSASIAPVADPAWQIKDRSVAGLRISAAGGIGQSLVLGALVAVRQSDAID
Ga0210330_1251368	Ga0210330_12513682	F059103	MSAPDPRDFVLRFAPLDARTAAWMLDFCGHLQQEIWRAYGDQIEAHWAATDPEQPIY
Ga0210330_1256478	Ga0210330_12564781	F077315	VICKASILFQSRFACCQVWVLLLLGLLVPAQAAEALKPDALPQAQATLERLEQQLATARTATAQQLKTLKKAIATVRSSAQDCIQQAQPKIEILDSELAIFQPAKSKDTQKKTAGETQPAEQPEAPFSPAIARQLQDLQSRKASLEGRIAICKLMLLRSNDLASDVDDYLSSLQ
Ga0210330_1257083	Ga0210330_12570832	F090573	MRVIRHSDPDTFLAAAAPMAERGQASASFFIGWAHAMKRTPPVAG
Ga0210330_1264003	Ga0210330_12640032	F020930	ELDTGSARYLIRFTQTLERQPGWAWTLFSAVRKLTP
Ga0210330_1274247	Ga0210330_12742471	F001314	MWILFTAPCPTPDGQTAEDLYRKRLPWITPEMQTSAREHGCRFHRAWYAEDGSAFYALANWDSREGASEFFRLWDIEDEPGEIAITLLGDVGLVPDP
Ga0210330_1284191	Ga0210330_12841912	F070130	LSRREHVYVRQMPDTPASQPDFFVGWWEIVFRSRDDEQTDVTGILEHVDAAGNFTVFRDGERIGAGHHVEFTVDPDGFTNLQEVAGAHKQIGRELAVYRFSGDVLEVCKASEHTGRPTSFASPRGSGWTHVAIRRISDDDPRIRAQR
Ga0210330_1288895	Ga0210330_12888951	F074892	MIPKYASIVLLGLLLSGCAEKGENVYKSWVGPDRSNMAIVTLRLGDDVRDITVRERVLPRSEYGTLLLVPGQYTLYEDDGASIGITIRPVLMNTEKARANGELILGHTYTLRAGKSQDGGERALWIEDARSGEIFIDTR
Ga0210330_1293276	Ga0210330_12932761	F055829	GTRLPLSILYTTEGDLMGAKPAFAEAALRITQHELNSCGIPATAKAGIILGEHGFPPGNEEDDVIDLNMERVRQNMRLVYERNLPKLRDGVTEFCFGMNEFNNHPDSWHLSSMECMVDYLHRGFDVIIFQPYYFINESIDLFEHLRHWAYEVEGIDEHEFHGGHEIAHNYRSDFN
Ga0210330_1327546	Ga0210330_13275462	F052020	EIRDRESGRLQILTYAALLWQLFRALIEGALDGLVRELNRKVVKKVLAAIDQTVEGFLNEALQISPQQVSVQLKAEELGYL