3300017560: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 30_C BE-Lig BY (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300017560
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191731 | Ga0182747
• Sample Name: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd 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: 714019368
• Sequencing Scaffolds: 15
• Novel Protein Genes: 18
• Associated Families: 17

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	2
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Sphaerobacteridae → Sphaerobacterales → Sphaerobacterineae → Sphaerobacteraceae → Sphaerobacter → Sphaerobacter thermophilus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Rhodopseudomonas → Rhodopseudomonas palustris	1
Not Available	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	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?
F006745	Metagenome	365	Y
F007999	Metagenome	341	Y
F011177	Metagenome / Metatranscriptome	294	Y
F011188	Metagenome / Metatranscriptome	294	Y
F012659	Metagenome / Metatranscriptome	278	Y
F014308	Metagenome / Metatranscriptome	264	Y
F017764	Metagenome / Metatranscriptome	239	Y
F025080	Metagenome	203	Y
F033108	Metagenome / Metatranscriptome	178	Y
F035663	Metagenome / Metatranscriptome	171	Y
F038355	Metagenome / Metatranscriptome	166	Y
F046720	Metagenome / Metatranscriptome	151	Y
F052417	Metagenome / Metatranscriptome	142	Y
F057525	Metagenome / Metatranscriptome	136	Y
F072045	Metagenome / Metatranscriptome	121	Y
F089956	Metagenome / Metatranscriptome	108	Y
F099198	Metagenome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0182747_1000660	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	30986
Ga0182747_1001465	All Organisms → cellular organisms → Bacteria	18317
Ga0182747_1003016	All Organisms → cellular organisms → Bacteria	11560
Ga0182747_1003251	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	10983
Ga0182747_1003270	All Organisms → cellular organisms → Bacteria	10957
Ga0182747_1006596	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Sphaerobacteridae → Sphaerobacterales → Sphaerobacterineae → Sphaerobacteraceae → Sphaerobacter → Sphaerobacter thermophilus	7254
Ga0182747_1029133	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Rhodopseudomonas → Rhodopseudomonas palustris	2856
Ga0182747_1159079	Not Available	918
Ga0182747_1184887	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia	831
Ga0182747_1194065	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	804
Ga0182747_1197203	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	795
Ga0182747_1244093	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	689
Ga0182747_1316491	All Organisms → cellular organisms → Bacteria	581
Ga0182747_1320696	All Organisms → cellular organisms → Bacteria → Proteobacteria	576
Ga0182747_1370211	All Organisms → cellular organisms → Bacteria	524

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0182747_1000660	Ga0182747_100066022	F011177	MSEYLEDGTEILRPAEAAGRLGVRTRVVIEAMYYRRLPRVRLSDGLLGIPAPALEGFEAEPVQ
Ga0182747_1000660	Ga0182747_100066023	F033108	VSEFDDPVPPAILLDLDEVFRVLEALEGSLVVILDHGLAPGLLDELRTVIAMLHHRLGFDQGGWNV
Ga0182747_1001465	Ga0182747_10014656	F007999	MINQQHARQTHERAAKARQNLVNALRECGELADAVETFEGNELMEVLDYLDSLRFVMAESGQILQGVVRGSR
Ga0182747_1003016	Ga0182747_100301611	F035663	VNTQELTEIHQALAAVHDAVGTLTFPGCDRDDMFELMERVEAELDAAHPNTQVIGTFLNSIARSLRNQPEAREACLRIEDVMERTGLPSTWQTGL
Ga0182747_1003251	Ga0182747_100325113	F052417	MARRASELPTDPVIVVTNPDEDCSPERLREFLDELLSTEPELETVHGAEAVRALRDENG
Ga0182747_1003270	Ga0182747_100327013	F006745	MRTSEHATRATSAVVIYVVILVAFQVFLLTVAVEAFASDDEPLAWATAAVSVSLATGSAVLLRYLRP
Ga0182747_1006596	Ga0182747_10065963	F011188	VETYNIYMDELPTGEEFDGDEMVEVEFRVVPGSDDDGDPENNAVIAGLDLVDLINMRDALQQEIDNYALTALEVEASNLVEE
Ga0182747_1029133	Ga0182747_10291334	F012659	MQNDDSTLEVLLQIRNWIRAAAHDPVKKNLERALPDAKSRAAYQMLDGTASMDSVRIACKMSPNALVALASRCEQLGLMELNHEKKRIRLFDLSHFGLQANGQSASE
Ga0182747_1034228	Ga0182747_10342282	F046720	MSVLETDLIDYVYLDDGDETPVLVVSDPLSWRPPEDETHLDVLREKLNAQIAFVETGQIKSVWPPYSGGLVRVEVVARHALNQAAEEFYGMARKVMRKANMRLDFRLCDA
Ga0182747_1159079	Ga0182747_11590792	F072045	LPVLHVRKPNEAPPPSRSSRAVREQQQKYDDFVRKIDTNDVGDLELEPNENLRSVKVRLRRASSRLGLDIDIWDANGHVYFQRVTRRSRRRQS
Ga0182747_1180448	Ga0182747_11804482	F057525	LGFRKTGRFDSPVEIAVLTCDVGERDIGHSDGRRPWPHLRLTRHPNTGALDDQ
Ga0182747_1184887	Ga0182747_11848872	F038355	MYTLTLTPDERRAFDWVGDRYTAGAVADLLRDCIPEESPEWEEDGDITFNLLEHIAWQVRDLAEEEGNAWPCFAPDLAEKLNDLCWSIV
Ga0182747_1194065	Ga0182747_11940651	F025080	MISFATDFRALWIALMAMLAGATSVAAQSAPIGCPPPRTIYTFTDSSSIQALPGAPAPFCRFANVNGGQQVDLFLGAFSAASPIVQANIDVLTTLLPLQVGKAVHLVRAGTGDKGWQANVSVEKHESVEVPVGRLNCFVLLWTEPSGQGRWERRWWYCPSLEYAAKYSAKFEVVSPGGRILSSSPTSWELAGIRVP
Ga0182747_1197203	Ga0182747_11972032	F099198	MADAITALIGAIIMVGYIVLVAAKLATPPLWIICVIGLALMLWAFWGDDWKPLFKRSNGK
Ga0182747_1244093	Ga0182747_12440931	F017764	MTATLTLNLDSKVLKWAEQEALSHHTTLPEVLGRQLQVMAGNWRDSQQGKTPVTDALRGAVKLPANFDAKTLLTEELKKKHG
Ga0182747_1316491	Ga0182747_13164911	F014308	MSANSIGIQVIMPKTGTSTQQQPQQQADARGDDVHAPRQAPPPPGMGKLVDKLV
Ga0182747_1320696	Ga0182747_13206962	F035663	QELTEIHQALAAVHDAVGTLTFPGCDRDDMFELMDRVESELSAAHPNTQVIGTFLNSIARSLRNQPEARDACLRLEGLMERTGLPSTWQTGI
Ga0182747_1370211	Ga0182747_13702112	F089956	MATHELELDAFAQTGEQGRSVSGDDRLDQELVLVDQSEIRQRQGECHATHPKALARLLLEPLNRGAQVASHQLGVLIDPAQRARHDVLVRPIDGLGER