3300000901: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA Ref_M2

Overview

Basic Information

• IMG/M Taxon OID: 3300000901
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0071004 | Gp0054728 | Ga0002400
• Sample Name: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA Ref_M2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 12638430
• Sequencing Scaffolds: 10
• Novel Protein Genes: 11
• Associated Families: 11

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Acidiferrobacterales → Acidiferrobacteraceae → Acidiferrobacter → Acidiferrobacter thiooxydans	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Microvirga → Microvirga lotononidis	1
Not Available	2
All Organisms → cellular organisms → Bacteria	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?
F001749	Metagenome / Metatranscriptome	642	Y
F005917	Metagenome / Metatranscriptome	386	Y
F029122	Metagenome / Metatranscriptome	189	N
F030264	Metagenome / Metatranscriptome	186	Y
F037348	Metagenome / Metatranscriptome	168	Y
F039262	Metagenome / Metatranscriptome	164	Y
F048591	Metagenome / Metatranscriptome	148	Y
F075150	Metagenome / Metatranscriptome	119	N
F081571	Metagenome / Metatranscriptome	114	Y
F098996	Metagenome / Metatranscriptome	103	Y
F104848	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12192J12874_100115	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1772
JGI12192J12874_100396	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Acidiferrobacterales → Acidiferrobacteraceae → Acidiferrobacter → Acidiferrobacter thiooxydans	1161
JGI12192J12874_100567	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	980
JGI12192J12874_100601	All Organisms → cellular organisms → Bacteria → Acidobacteria	955
JGI12192J12874_100724	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Microvirga → Microvirga lotononidis	867
JGI12192J12874_100753	Not Available	849
JGI12192J12874_101666	All Organisms → cellular organisms → Bacteria	596
JGI12192J12874_102315	Not Available	526
JGI12192J12874_102352	All Organisms → cellular organisms → Bacteria → Acidobacteria	523
JGI12192J12874_102609	All Organisms → cellular organisms → Bacteria → Acidobacteria	503

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12192J12874_100115	JGI12192J12874_1001152	F029122	MLIRPAIGDTDPIRYRRPTPDGQFSGNIIDEAMRPF
JGI12192J12874_100396	JGI12192J12874_1003961	F081571	KGVFVESSGRLWGLMLEKAVHCLGILHYGWAWNLASKMDGTSSEAKPTALGYVFVPWFSTGTNSARDFR*
JGI12192J12874_100567	JGI12192J12874_1005671	F098996	MHEFHYAKEHVIARTFHKAFRLIKKYLLLGLLVAIALK
JGI12192J12874_100601	JGI12192J12874_1006011	F037348	MGHESQIELWSPNLTTFCFVGFGTDRLRREPAMKTADRENPIHGATWARNRAHGAAGQNRTRSIEWAEKQEKFRPKEMCFFLTSPFIELTSSYPNSQQNI
JGI12192J12874_100724	JGI12192J12874_1007243	F048591	MDPAVAGLDFAKAGIVLANMIESYLAGGAPPSNPEGAVHDKPQDCRSTSVTAS
JGI12192J12874_100753	JGI12192J12874_1007532	F075150	LEHHSAIQFLKAATNLNVVQPKLFQASRQDDHRFSDCTVSVIQILDDADAAFRILGAELRTVLSATTMFADKPHSL*
JGI12192J12874_101666	JGI12192J12874_1016661	F001749	MSDERFVETRTESPAWTLPAIIVLGLIAIGGLAFGWNASSKLDSTQQSVAAQLKTTQQAVQQDMSSLKDRLAQDEKANTDLQGDLKVVTGKLKITQGQLKKARDEAAKLNYATTEKLTALDTSVHSE
JGI12192J12874_102315	JGI12192J12874_1023151	F030264	MAQGDEPKGEPKYMSEFQESANTNTTGTPRWVGLAVAVLGGISLLGLGVGLSALNQARSVEQSTQ
JGI12192J12874_102338	JGI12192J12874_1023382	F104848	MRVRSLLVLGIVLLFGTAAFAQDYAKIEVPLNYSYMRFNPENSHIISGL
JGI12192J12874_102352	JGI12192J12874_1023521	F039262	CAKPHVEDRVSTRAFQKSSALAEAEIVPYLRRAELARSLSELFGCRIRENKKGSGLYAMPSEAQRSICGCETQNLRFELCANELRASLVLPSGEVLRDLPVVDHDWRNFVDAALALNRGANRLPRLERFLNSHFHYKIMSCPHHFIRLGLTRPYHDLCWLMLDTLFPLPRQEW
JGI12192J12874_102609	JGI12192J12874_1026092	F005917	MQVRPHLPGYRRLQVFRNAAIRTGVYVGVCLTLVFTAWLVIANHAPFLERFALERNIAAAAILCFLAAVPIFRFLRLPGHLLASGLLGWLIFSLSYRTLCLIFHGLSNRLSTFHVFMLGAVVYMI