3300020598: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 37_C Kraft BY (version 2)

Overview

Basic Information

• IMG/M Taxon OID: 3300020598
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127392 | Gp0191728 | Ga0180218
• Sample Name: Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 37_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: 304073422
• Sequencing Scaffolds: 10
• Novel Protein Genes: 12
• Associated Families: 12

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	1
All Organisms → cellular organisms → Archaea → TACK group → Crenarchaeota → Thermoprotei → Acidilobales → Caldisphaeraceae → Caldisphaera → Caldisphaera lagunensis	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Rivibacter → Rivibacter subsaxonicus	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?
F000135	Metagenome / Metatranscriptome	1961	Y
F011188	Metagenome / Metatranscriptome	294	Y
F016724	Metagenome / Metatranscriptome	245	Y
F017885	Metagenome / Metatranscriptome	238	Y
F019412	Metagenome / Metatranscriptome	230	Y
F036958	Metagenome	169	Y
F061594	Metagenome / Metatranscriptome	131	Y
F064527	Metagenome / Metatranscriptome	128	Y
F090842	Metagenome / Metatranscriptome	108	Y
F094284	Metagenome	106	N
F099198	Metagenome	103	Y
F104871	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0180218_1000458	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	38506
Ga0180218_1004843	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	5875
Ga0180218_1012030	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi	2975
Ga0180218_1013538	All Organisms → cellular organisms → Bacteria	2721
Ga0180218_1035061	All Organisms → cellular organisms → Bacteria	1324
Ga0180218_1039452	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1210
Ga0180218_1041145	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1173
Ga0180218_1077328	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → unclassified Pseudolabrys → Pseudolabrys sp. Root1462	723
Ga0180218_1077540	All Organisms → cellular organisms → Archaea → TACK group → Crenarchaeota → Thermoprotei → Acidilobales → Caldisphaeraceae → Caldisphaera → Caldisphaera lagunensis	722
Ga0180218_1116614	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Rivibacter → Rivibacter subsaxonicus	519

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0180218_1000458	Ga0180218_100045815	F036958	MSVILIFAGFVLVGDTLAVGISYLVEQVSNSISLMVFLALYILVFWISWKLAVQVTERYVIHEH
Ga0180218_1004843	Ga0180218_10048435	F104871	MPDREAHLRTLAERLMFSVEQTGDRFTFTRTADVSRPVREAGLTIDQAEELLETWKLRGPHGG
Ga0180218_1012030	Ga0180218_10120303	F090842	MLKRFFGSSEEPLIPVCPDHDVEMRLRGKMGKPTRFSDQSASEYTLIYFCPVPGCNNTATRERQRLQIPAPGVAPERPIFSRLDDGR
Ga0180218_1013538	Ga0180218_10135382	F011188	VDTYNIYMDELPAGEEIDGEEIVEVEFRVVPGSSDENDPESNAVIAGLDLVDLINLRDALQQEIDNYALTALEASASRIADIEV
Ga0180218_1035061	Ga0180218_10350613	F019412	MQILVLVLCTKGRSLRQAIADDARLESFGLQVTKETQPGRAPGWLKLHGTDRTRGALNIEWDSESSLLRARVITRGTRKPSPIVGEFVNYLLARFSSRIVSITTAFR
Ga0180218_1039452	Ga0180218_10394523	F064527	LLLRADNLLKNEGDPEDRERRAREALEEARAVAAGGGVDERVVALIDRRLAALEAGGPR
Ga0180218_1041145	Ga0180218_10411453	F017885	MNEICFQCPSCGHDLKQSIGRLKQSQHMTCPGCGIGINIDTNRLAQVSEEIQKAIDKVPPEITIKFYRPIEQD
Ga0180218_1076224	Ga0180218_10762243	F000135	MDAQATLVMWFQLRSPECAEEFERLMAEDRDIVHGSLETVAEWRLTAPADVPGQSIGEADYVLIAEIVELDRFQEQASERVQQLADDLQHLVAHRGMLVVRHIL
Ga0180218_1077328	Ga0180218_10773282	F099198	MADAITALIGAIIMIGYILLIAGKLAALPLWICSLIGLALMVWAFWGDDWKPLFARTRKSTAR
Ga0180218_1077540	Ga0180218_10775401	F094284	PSVPTRRDMHRQYPASRAAAGADEGQTKESQVSKVREFMTGWESPDRHQMIPLVWSDRTKEGLRGTAKGKRFTPKLRPFDMLSEPNQRLKIFESADVRIGVESVTGTAPWFRRNSDFDEILFQFCGTSHVESEFGKFDLGAGEVLVIPGGVSYRSIGAGDCLRMWIDLHEPIFKVLDEAEHTSETQYTVRRLNGPNWTVPAAAQQANSRVIEKLFIWDEDPEDATIIERDYSDLVGVSSV
Ga0180218_1114352	Ga0180218_11143521	F016724	MRAKKSILGLVDTGREVRRPPLVGMQFLHQPAMGAADFVPPRASLQA
Ga0180218_1116614	Ga0180218_11166142	F061594	VGPKLQAFYDSLDARQKRAFDTGGRVGGIFDWWGKK