3300001120: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM3_M3

Overview

Basic Information

• IMG/M Taxon OID: 3300001120
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0071004 | Gp0054541 | Ga0002410
• Sample Name: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM3_M3
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 16435888
• Sequencing Scaffolds: 11
• Novel Protein Genes: 11
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp.	1
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
Not Available	4
All Organisms → cellular organisms → Bacteria → Proteobacteria	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Forest Soil Microbial Communities From Multiple Locations In Canada And Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Loam → Forest Soil → Forest Soil → Forest Soil Microbial Communities From Multiple Locations In Canada And Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): forest biome → solid layer → forest soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: El Dorado National Forest, Georgetown, California, USA
• Coordinates
  • Lat. (^o): 38.88
  • Long. (^o): -120.64
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000262	Metagenome / Metatranscriptome	1428	Y
F003794	Metagenome / Metatranscriptome	468	Y
F009926	Metagenome / Metatranscriptome	311	Y
F011976	Metagenome / Metatranscriptome	285	Y
F012266	Metagenome / Metatranscriptome	282	Y
F019179	Metagenome / Metatranscriptome	231	N
F029122	Metagenome / Metatranscriptome	189	N
F035891	Metagenome / Metatranscriptome	171	Y
F064046	Metagenome / Metatranscriptome	129	Y
F076660	Metagenome / Metatranscriptome	118	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12137J13328_100163	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1784
JGI12137J13328_100346	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp.	1497
JGI12137J13328_101592	All Organisms → cellular organisms → Bacteria	834
JGI12137J13328_101717	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	800
JGI12137J13328_102137	All Organisms → cellular organisms → Bacteria	717
JGI12137J13328_102704	Not Available	640
JGI12137J13328_103056	Not Available	608
JGI12137J13328_104192	Not Available	531
JGI12137J13328_104502	All Organisms → cellular organisms → Bacteria	518
JGI12137J13328_104665	All Organisms → cellular organisms → Bacteria → Proteobacteria	510
JGI12137J13328_104911	Not Available	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12137J13328_100163	JGI12137J13328_1001632	F029122	MLIRPAIGDTDPIRYRRPTPDGQFSGNIIDEAMRPSTAR
JGI12137J13328_100346	JGI12137J13328_1003463	F012266	GRTLALQLSFFEVSALSGSLVSSAPERPCDDVCGLNALLSESGGDAADFLD*
JGI12137J13328_101592	JGI12137J13328_1015922	F009926	MLGSLRVGRWGATSKIGFDHVGEDDARLGDVEGSDGRVHLVETLAAAQKFGIDRADLVEHLAQFAEVGEELADFGVSRIRHVTDARALAGSTDCGKISLGAMPSSVDTVAVGPPAAFVGLDQRAAQYLFDRRQAARKLVATLAKSCR*
JGI12137J13328_101717	JGI12137J13328_1017171	F000262	MSDKLKRLEQIYLTWMTILVALATVSCSGQDFGFLQPTPEDLCKCMPLEPDIADYRHAAKHVPIPNIVAQEVSVEIILTWSQDVFIPPDAPRTGRELEVFHIANAFLQNASVNALDCDVSMEISQTADKSSARMIVETPVDSEYCGARQNMQAQLKQHGFRLDSQHGGELPHALPVDVVGMAFEDFEHDRGHVATLWELHPAIVTLH*
JGI12137J13328_102137	JGI12137J13328_1021371	F076660	MDAQKTYVLWLNRNTEEQALSGRRARARQVAAHLS
JGI12137J13328_102704	JGI12137J13328_1027041	F019179	VCAPTPTQLRRNSSSGLIASAVLALMLSAQTAAFAQTNTPPANTQVIAPKQVGAWTVIGWSQGYCAAERPLPGAAGGGATLQFVLARFQAGYRLALGSQEWELKPQTTFPIELIAHPVLRSDASAIVVGPKLVVIELGADGQFVHKLA
JGI12137J13328_103056	JGI12137J13328_1030562	F003794	RSEMSLPDDTKTDDKEQCDNVIRLGTETLFAIAEQLRQMYDLDLRTKPSEKLERLMRRIERGDEPC*
JGI12137J13328_104192	JGI12137J13328_1041921	F064046	CEGFRMTAIRDDAACTGAVVRKPPMKETAGGVARWRVRRYGDLTAVVTECEYNFCDMARTLRMGENTFRRPCNFKELRVVKRAHITTFALCA*
JGI12137J13328_104502	JGI12137J13328_1045022	F011976	MIKINLLETAKGKNKRGSGGGGPVMPSMEMGDMGSPKLKVLVVLVLAGLFNLAYWYRLDHQSKAIAAQMKVAE
JGI12137J13328_104665	JGI12137J13328_1046651	F035891	MNRRTIVKGALGGILGLTLPPLARSAFSQEGPAVVPVREGFVML
JGI12137J13328_104911	JGI12137J13328_1049111	F064046	PHDGGAAHTGAGVRKPPMEETAGGVVKWRVRRYRDLTAVVPECEHNFCDMARTLRMGENTFRRPCNFKELRVVKRAHITTCALCA*