3300017655: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C BE-Lig BY (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017655
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191743 | Ga0182739
• Sample Name: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 5th pass 30_C BE-Lig BY (version 2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 774665585
• Sequencing Scaffolds: 15
• Novel Protein Genes: 16
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Gemmatales → Gemmataceae → Limnoglobus → Limnoglobus roseus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
Not Available	3
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia 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
F004649	Metagenome / Metatranscriptome	429	Y
F005470	Metagenome / Metatranscriptome	399	Y
F008211	Metagenome / Metatranscriptome	337	Y
F015908	Metagenome / Metatranscriptome	251	Y
F020088	Metagenome / Metatranscriptome	226	Y
F025080	Metagenome	203	Y
F028375	Metagenome / Metatranscriptome	191	Y
F030705	Metagenome / Metatranscriptome	184	Y
F036409	Metagenome / Metatranscriptome	170	N
F037930	Metagenome / Metatranscriptome	167	Y
F047414	Metagenome / Metatranscriptome	149	Y
F057501	Metagenome / Metatranscriptome	136	Y
F073619	Metagenome / Metatranscriptome	120	Y
F087411	Metagenome / Metatranscriptome	110	Y
F092682	Metagenome / Metatranscriptome	107	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0182739_1009146	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	7012
Ga0182739_1016431	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	4521
Ga0182739_1016844	All Organisms → cellular organisms → Eukaryota → Sar → Alveolata → Ciliophora → Intramacronucleata → Oligohymenophorea	4429
Ga0182739_1022925	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Gemmatales → Gemmataceae → Limnoglobus → Limnoglobus roseus	3506
Ga0182739_1030366	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	2852
Ga0182739_1064467	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1681
Ga0182739_1078129	All Organisms → cellular organisms → Bacteria → Proteobacteria	1478
Ga0182739_1133536	Not Available	1033
Ga0182739_1181163	Not Available	845
Ga0182739_1200285	Not Available	790
Ga0182739_1206348	All Organisms → cellular organisms → Bacteria	775
Ga0182739_1207392	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	773
Ga0182739_1253806	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Dehalococcoidia → unclassified Dehalococcoidia → Dehalococcoidia bacterium	677
Ga0182739_1293298	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	616
Ga0182739_1352942	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	545

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0182739_1009146	Ga0182739_10091469	F003289	MXGNIVTEVALQTNFGVGFNNTKSDVLIHLTQXQYXWXFWFSFLWAFYYLVILRIVRFRTLKFRPRLATTFRPHGKXGDLIICLIPVSXCANIITNSTLILRMIEXQAETGLLTVRIRGKQXYXIYKFELKTFTDVLTVPKNIGNNKWWISTPGDLQVSDDYLHILQLRSQNKXV
Ga0182739_1016431	Ga0182739_10164313	F037930	MFGGMSVSITKGGKPKRSIASIRVERRYRNVIRLFLSGELPEFTHQRHVHVANILKHIPYGRELMHLGLQVMAYRNFVPDKYNVEITDRHWSQLDGTLPAVELFDDLPGGACGEREVGV
Ga0182739_1016844	Ga0182739_10168445	F047414	MHRDSLILSPLFSSNNHNGGFFGNFTPRYFSNVPHMPDNNKGFGPDDFLMRPSPTHMDIDVNSRFDKAVDNLKMELRNNPAPLMNDHHGMDQQGLNLDIDLIDDSYLHAPLTKSPHIQFPGSQPTSKCSFKKFGEWTLSPNASFLPRKKF
Ga0182739_1022925	Ga0182739_10229253	F020088	MESQNDKKKGRFRIEKLEERIAPSITLENPAGNTPQSESANNGQAIEAVNPAGHAPPGQN
Ga0182739_1022925	Ga0182739_10229254	F004649	MQFRNNERKVRFRIEKLEERIAPSNANFPPGQFPSGNPAQAPGQSNPNEVPATNPSND
Ga0182739_1030366	Ga0182739_10303664	F057501	AATVAAAKAAGAKMEGDVATVPIGGTPIKIAMLVDPDGNALEIMELPKDLTHLPH
Ga0182739_1064467	Ga0182739_10644671	F025080	MISFATDFRALWIALMTMLAGATSVAAQSAPIGCPPPRTIYTFTDSSSIQALPGAPAPFCRFANVNGGQQVDLFLGAFSAASPIVQANIDVLTTLLPLQVGKAVHLVRAGTGDKGWQANVSVEKHESVEVPVGRLNCFVLLWTEPSGQGRWERRWWYCPSLEYAAKYSAKFEVVSPGGRILSSSPTRWKLAGIRVP
Ga0182739_1078129	Ga0182739_10781294	F015908	MRYVTIAEVLGMLATQAQAESRTYRTQLIPKKSVQACSGWGQTYTVDVSNGVLTLGVNYARRLFSEPAESDGKITRSYRNPSGGILKFIGHGDGEYE
Ga0182739_1133536	Ga0182739_11335361	F028375	MDTSVACEQWLSSYPKFNWRSTFNFLQAPEVIKAVEFCDNGIACFVKGLQHELQDKDYQEAFNCYENGAMQLDSLCLFRLHEIYLGDTNFNVEYNERQAMCHLIYSALVSQFETFDHKVTFWGKLESFWKKDAANKDYILDLLMNPPTDYFQATGPLFAKLFTFYNNKETFIDILPELKSLSIDVTKNKFFSILNAIFDFMAYSYNSSFSKTDLEKYVETILDMLTNDILFDNFFQSYVAHLRIIRAKKKFAF
Ga0182739_1181163	Ga0182739_11811631	F092682	MHRTRHYLAALSARQSAAWRVCACIIDRSFVVIRLKHPAA
Ga0182739_1200285	Ga0182739_12002851	F005470	MSIKLRKEGQLITEFPNDMVPRSRLLTKLVEEFNSTEVDLEPAPGKDFSPATINKVKEFLQKFDKGLNKMPKKPLLIFVTYNDWLDNNFDEKLREWLEEFLKPKSFYDLVELFNAAFYLQIDDLREICAARIAHSIILERKAPEDFLRDFGIVTQYQDFFTPEEEAKFIEKEFINKNDFEGVAAEDEEELNKE
Ga0182739_1206348	Ga0182739_12063481	F036409	GKFHTLLFVHYDPETKKWKGPVVEAPFNDWNIDGGCPNFDAAGNIMIWSAGYDRGPDVITGGESGAGGVYDLYWLPTSEVIDYYKKAAGIG
Ga0182739_1207392	Ga0182739_12073923	F008211	MIILDGESSILRARGEPIIFRSQEETMEYAKLHDIQRWMIYGDRDGWWPIYTQDGPISAPPPPKERVDISLH
Ga0182739_1253806	Ga0182739_12538061	F087411	KTYVSQEATKLCADLFALGGGRHYRRNDIAARLLADSFAGTALRPPLALGLDGLLAQFED
Ga0182739_1293298	Ga0182739_12932982	F030705	QHRRRPRPPEVEAERLRLVRRLQLIQRMQAEGTSDDDFSTRLKSFVDAPREARLVDGDNPFLEALLKTWDAAQLPQAATLAAGAQPPAPSATVEFRW
Ga0182739_1352942	Ga0182739_13529421	F073619	RLELAPSVRATLTAWMRLYGDANALPGLATGPIETRFARLREHGGADTLDLWSTPARWAAGEGLSLRMPAIRLEFVCELDDGHLTATKVAQVPEDARLPDRETGAVGVHLVVERMELPPDRIEGEATDPGVKLLEGHFARLADRRWGGFVEPLRQALEAEASDDEDRTQRLTVRFTGASM