3300017565: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 30_C Kraft BY (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017565
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191734 | Ga0182745
• Sample Name: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 30_C Kraft BY (version 2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 919071438
• Sequencing Scaffolds: 19
• Novel Protein Genes: 20
• Associated Families: 20

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria	1
Not Available	4
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Saprospiria → Saprospirales → Saprospiraceae → unclassified Saprospiraceae → Saprospiraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 200	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Unclassified → Soil → Lignin-Adapted Enriched Soil Microbial Communities From Emeryville, California, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: USA: Emeryville, California
• Coordinates
  • Lat. (^o): 37.83
  • Long. (^o): -122.29
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003289	Metagenome / Metatranscriptome	495	Y
F006009	Metagenome / Metatranscriptome	384	Y
F007768	Metagenome / Metatranscriptome	345	Y
F011188	Metagenome / Metatranscriptome	294	Y
F014051	Metagenome	266	Y
F017764	Metagenome / Metatranscriptome	239	Y
F018299	Metagenome / Metatranscriptome	235	Y
F025080	Metagenome	203	Y
F030787	Metagenome / Metatranscriptome	184	Y
F035602	Metagenome / Metatranscriptome	171	Y
F035663	Metagenome / Metatranscriptome	171	Y
F037930	Metagenome / Metatranscriptome	167	Y
F039184	Metagenome / Metatranscriptome	164	Y
F046720	Metagenome / Metatranscriptome	151	Y
F053454	Metagenome	141	Y
F055568	Metagenome / Metatranscriptome	138	Y
F081030	Metagenome	114	Y
F091556	Metagenome / Metatranscriptome	107	Y
F097539	Metagenome / Metatranscriptome	104	Y
F105308	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0182745_1000099	All Organisms → cellular organisms → Bacteria → Proteobacteria	122058
Ga0182745_1005111	All Organisms → cellular organisms → Bacteria → Proteobacteria	10786
Ga0182745_1007255	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	8705
Ga0182745_1010083	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	7116
Ga0182745_1025403	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3914
Ga0182745_1047672	All Organisms → cellular organisms → Bacteria	2525
Ga0182745_1055284	Not Available	2269
Ga0182745_1061050	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	2113
Ga0182745_1081983	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → unclassified Chloroflexia → Chloroflexia bacterium	1705
Ga0182745_1152552	Not Available	1096
Ga0182745_1163817	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Saprospiria → Saprospirales → Saprospiraceae → unclassified Saprospiraceae → Saprospiraceae bacterium	1044
Ga0182745_1163981	All Organisms → cellular organisms → Bacteria → Acidobacteria	1043
Ga0182745_1197760	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	916
Ga0182745_1229564	Not Available	827
Ga0182745_1248218	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	784
Ga0182745_1285750	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	713
Ga0182745_1328933	Not Available	649
Ga0182745_1370508	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 200	600
Ga0182745_1493292	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0182745_1000099	Ga0182745_100009972	F035663	MRIAPPHRALQCGGVNTQDLSEIHQTLSAVHDAVGTLTFPGCDRDDMFELMDRVESELSAAHPNTQVIGTFLNSIARSLRNQPEARDACLRLEGLMERTGLPSTWQTGI
Ga0182745_1005111	Ga0182745_100511112	F014051	KEFLAIDFWATKDDGLPQKKIEAVAALMKKIGAIKEDKQPVKFVDFVDQSIWKDANAKVK
Ga0182745_1007255	Ga0182745_100725512	F097539	MTQRPWTHLVDQPAARHLVAVRHAPKAADEPAALLTTLIEGLCPNGDFALLTRCEEEGAVTLCAFATPRDAEQLASAVGAEETEDYPEWASQRCFTLDEPTAQAITDAIEASGIALGVLQHHAPSGVQYANH
Ga0182745_1010083	Ga0182745_10100838	F039184	MTEDWGFVRAADMARTIDERFELGWIASIEAAWQAADLDHGTFGFVLAMADGRRLYWLYTSDDAEAGRPEDFDAVELAAGETPSAPDDARWYDPARLNERLAVMRRFG
Ga0182745_1025403	Ga0182745_10254035	F025080	MISFATDFRALWIALMTMLAGATSVAAQSAPIGCPPPRTIYTFTDSSSIQALPGAPAPFCRFANVNGGQQVDLFLGAFSAASPIVQANIDVLTTLLPLQVGKAVHLVRAGTGDKGWQANVSVEKHESVEVPVGRLNCFVLLWTEPSGQGRWERRWWYCPSLEYAAKYSAKFEVVSPGGRILSSSPTSWELAGIRVP
Ga0182745_1047672	Ga0182745_10476723	F053454	GAVDQQTGVFYSTAGPYISATDDRGRTFNTVYPGRGTAAAAFGRVVATRTVNELAGYTCPCLVFSVTSDRGANWDEQVIAQGPEYSNVGTIRYPITAASPVNEGHYAVAVYQPDHRTVKVYYTRDGGNTWRMALPGPTPANVPVTNANQVGLNYTNDGNLLVTWRGFRNPGAFNTFVALLQGDRFGPTIKVSPELSVYPTLTYSGNYGQGNGGGDFTTWVTGTATTAFVAFPYAPRGEVLDTYVARVPMSLLRPSAR
Ga0182745_1055284	Ga0182745_10552841	F035602	MSVSNEIKNWLETYPRLNWRLTFDFLLAPENSKAVEFSDYGVACFVKGFQKEFIDRDYNEALNWYETGAMQYDSLCLFKLHEIYIGDTHFKVPYNERQALCHLIYSALLSQFEIFDTKVSFWQKFEAFWKKESSKTAYIQELLISPSADYFVATGGLFSKLFTFYATKNNFPDILPELQNLSIDILKTKFFSIINAMFDFLAYTYNSGFSKVDLQKYVDTILDMLTNDILFDNFFQNYITHIKLLRAKKKFAHVFQRRLETDCFWVWSFSFLVSMKNYYLGILQTYDETFCDGSLVLKWKNTASWVNNFVGFCCEKGIGTTKDPKKALEAYDRDMREMPRVLFSRFRHILIRKQALSKGQQPFQEEVDPELEAEVTELKGMIEGRFEDQ
Ga0182745_1061050	Ga0182745_10610501	F003289	MXGNIVTEVALQTNFGVGFNNMQSDVLIHLTQXQYXWXFXFSFLXAFYYLVILRIIRFRTLKFRPRLATTYRPHGKXGDLIICLIPISXCINIITNSSFILRMIEXQAETGLLTVRIRGKQWYWIYKFELKTFTDILTVPKNIGRNKXQISTPGDLQVADDYLHILQLRSQNKXVKKYXNDLSQKFYRNKNFHLISPQEQLKFNFYQNLTNYEFLKNSKNLKINNFLNINVSDKNNFLVLNN
Ga0182745_1081983	Ga0182745_10819832	F037930	MSVSITKGGKPKRSIASIRVERRYRNVIRLFLSGELPEFTHQRHVHVANILKHIPYGRELMHLGLQVMAYRNFVPDKYNVEITDRHWSQLDGTLPAVELFDDLPGGACGEREVGV
Ga0182745_1152552	Ga0182745_11525522	F091556	MELISLFIGWHPDDVFLRQVSVEMAELIIVFGTIAATLGVLVVFGNWWSR
Ga0182745_1163817	Ga0182745_11638172	F017764	LNRESIFLYIKGMTATLTLNLDSKVLKWAEQEALSHHTTLPEVLGRQLQVMAGNWRDSQQGKTPVTDALRGAVKLPANFDAKTLLTEELKKKHG
Ga0182745_1163981	Ga0182745_11639812	F055568	MMITIDPKLEARIRAKAQAEGLTVDAYVERLVSADQAAEEELETLALEGLQSGAPVEAGLQYWEEKHRRLDERLKHTGTC
Ga0182745_1197760	Ga0182745_11977601	F011188	MDTYNIYMDELPTGEEFDGEEMVEVEFRVVPDSEDDGDAKANAVIAGLDLVDLINLRDALQQEIDNYALTALESAASAAVEQG
Ga0182745_1229564	Ga0182745_12295641	F018299	DNDLLSTRELVFTSSESFNGVGNVLFNESDGVKDLVDFNSSNFTCGFTESTSHTGLKSISTGAGKHFVDSDNVEWMNSASQMEAFLTASFDQILVGSNTAGFQSFRTDLFLFKRDQMNTEGEFLNLSLLFTSIVDSDSWVGDTSVVTRLGEWFSVPVSITSSRSSSHYSINV
Ga0182745_1248218	Ga0182745_12482181	F105308	MTEFMPLVEPDDLPADLRAQWDATEREGLRDFLRLMAHAPEQFRTFNAAYASARFDNRLGVRLTE
Ga0182745_1285750	Ga0182745_12857501	F007768	AGAGVLTIFIDGDERAVNLPNRGEAGRKAWTEAVAARKGAIKTDDFNGVNIDVPVDTLTKVGHFSVFFSQTGGYSPQAGNTSPDPHPTGIFVGTTGTGGGANAETIQGLELRYDTRGPVTTRLELRFDPPIRAWAADVYSVDGVGFGEGNRPDSNDHTTLHVLKHSIDLTEVLPYAGSGYMSFFGIVSDEPFDTISFTAENDGDRFRLDNVSIAE
Ga0182745_1328933	Ga0182745_13289331	F006009	MTGGEQKMLWRGVAAGTLIGIAIGGMIALFIATRPQLLSGLIQ
Ga0182745_1370508	Ga0182745_13705081	F081030	MAEEAGWLTAVVALLATGLLAAWTARACLQAQQRDSSPSDVLVWSALAAVFVGYSQLKLVRGLGWLTGFGGWLRSLARQHGLYADRRAFQIIATVAVALGVIVLFVYGLMWIWHYIKRYRLAIGFASLAVGFGLIRFISLHEVDAWTAANPWARPLIELVACAGASTLALVRLHQLGELPRLFQRFRA
Ga0182745_1416963	Ga0182745_14169631	F046720	MSVLETDLIDYVYLDDGDETPVLVVSDPLSWRPPEDETHLDVLREKLNAQIAFVETGQIKSVWPPYSGGLVRVEVVARHALNQAAEEFYGM
Ga0182745_1493292	Ga0182745_14932921	F030787	QRLVLEVDMSDPEFFTQPFPRATNEYAPSNLTIEPFNCSPEGVTGTLRR