3300000907: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM1_M1

Overview

Basic Information

• IMG/M Taxon OID: 3300000907
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0071004 | Gp0053808 | Ga0002398
• Sample Name: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM1_M1
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 23670115
• Sequencing Scaffolds: 23
• Novel Protein Genes: 24
• Associated Families: 24

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	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter → Anaeromyxobacter dehalogenans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Pleomorphomonadaceae	1
Not Available	9
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Alicycliphilus → Alicycliphilus denitrificans	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	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?
F000428	Metagenome / Metatranscriptome	1150	Y
F003776	Metagenome / Metatranscriptome	469	Y
F003981	Metagenome / Metatranscriptome	459	Y
F005285	Metagenome / Metatranscriptome	406	Y
F008734	Metagenome / Metatranscriptome	329	Y
F012254	Metagenome / Metatranscriptome	282	Y
F012266	Metagenome / Metatranscriptome	282	Y
F018965	Metagenome / Metatranscriptome	232	N
F022515	Metagenome / Metatranscriptome	214	Y
F029122	Metagenome / Metatranscriptome	189	N
F029833	Metagenome / Metatranscriptome	187	N
F034135	Metagenome / Metatranscriptome	175	Y
F037137	Metagenome / Metatranscriptome	168	Y
F037213	Metagenome / Metatranscriptome	168	Y
F037666	Metagenome	167	N
F040785	Metagenome / Metatranscriptome	161	Y
F042751	Metagenome / Metatranscriptome	157	N
F051371	Metagenome / Metatranscriptome	144	Y
F052907	Metagenome	142	Y
F053353	Metagenome / Metatranscriptome	141	N
F064046	Metagenome / Metatranscriptome	129	Y
F069409	Metagenome	124	Y
F075150	Metagenome / Metatranscriptome	119	N
F105938	Metagenome / Metatranscriptome	100	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI11871J12876_100132	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1798
JGI11871J12876_100647	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1120
JGI11871J12876_100660	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Myxococcales → Cystobacterineae → Anaeromyxobacteraceae → Anaeromyxobacter → Anaeromyxobacter dehalogenans	1115
JGI11871J12876_101360	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	828
JGI11871J12876_101377	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Pleomorphomonadaceae	825
JGI11871J12876_102152	Not Available	698
JGI11871J12876_102198	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	692
JGI11871J12876_102417	All Organisms → cellular organisms → Bacteria	672
JGI11871J12876_102576	All Organisms → cellular organisms → Bacteria	656
JGI11871J12876_102948	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	626
JGI11871J12876_103038	Not Available	619
JGI11871J12876_103659	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Alicycliphilus → Alicycliphilus denitrificans	583
JGI11871J12876_103721	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	580
JGI11871J12876_103813	All Organisms → cellular organisms → Bacteria	576
JGI11871J12876_104083	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	564
JGI11871J12876_104332	Not Available	554
JGI11871J12876_104433	Not Available	550
JGI11871J12876_104613	Not Available	543
JGI11871J12876_104770	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	538
JGI11871J12876_104887	Not Available	533
JGI11871J12876_105368	Not Available	517
JGI11871J12876_105396	Not Available	517
JGI11871J12876_105496	Not Available	514

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI11871J12876_100132	JGI11871J12876_1001321	F029122	MLIRPAIGDTDPIRYRRPTPDGQFSGNIIDEAMRPSTVRQI
JGI11871J12876_100647	JGI11871J12876_1006473	F052907	YGGAVRQAIAGWSPHLTWLAPAGAPGGTSADRFKAMSLALATARQSLDKLGTEISKAQAQDGDGPPRRKR*
JGI11871J12876_100660	JGI11871J12876_1006602	F037666	MADHDFDRFPGTARDEASGTPSEIFDVLWGALVELLGSPATATLLRRSARRQRGDFPELVELAITRKDFEYTYVVPAAWKYANERSNAALQALVQDLCSLLLELTGPVVLRRLKTSSQLAKCLQSLAEDK*
JGI11871J12876_101077	JGI11871J12876_1010771	F037213	MVRVLGPTGYKVVARLIAPERGLPSDRHPDRTKRAVVLEAVKVWPGNGGACRKGLVRRPTLTVSV
JGI11871J12876_101360	JGI11871J12876_1013601	F042751	MSAAIILRSFAAVLVCVLGVVPARAETPWIAALTQQALSAGYQATLPPNVSLVLGLAADGKSVPVKQLVTRAEQKVRTFNVSVAHHRDLVIFSVDEATQATVAYLLAPGGKLRKAVSYQIGAVPRQL
JGI11871J12876_101377	JGI11871J12876_1013771	F069409	LGAMLRAIGRGFGNGTFGMAQASAATADNTTASARLVAKAVDRNAAAREDGGTAFLRGESFNRSIPRSI*
JGI11871J12876_102152	JGI11871J12876_1021522	F051371	AVESLRQVRSALADYATAQRGAYPREFEALGEPVRTAAQFAQSVNYQIQYTPGPVEPDGSIRSYALQARAGNYGFLSFYTDNTGAVHATRENRAATAQDSPY*
JGI11871J12876_102198	JGI11871J12876_1021982	F000428	MRLDDHFGSSSTLQRNERVKLAASFWNNVGAGMVIGGIAGAFFLDKPPGAWTKVGIAVAGLVLGWICYSIASNILTYLHTAPDERR*
JGI11871J12876_102417	JGI11871J12876_1024171	F053353	RQILRKVARSTELSRGDIATEAKLAVGYYVYTISVAGVVRYIGKGKGLRLYSHMKEVRSRLKRDFRVQSIGSILQRNLTKAFLSEAQVTEQVLIDDLTEKAAYKLEYDKLREYVFAGKGDQLWNVIPASIQTPQEIQAYTERLQRNLNSRDRWVRTLSAMTLEALRGGQHQHRTET*
JGI11871J12876_102576	JGI11871J12876_1025762	F005285	GMARRWSEMNQGSRTGKGTAFMAARGPEELSPGGDRAFVVARKRGNARGAKGGRKVEA*
JGI11871J12876_102948	JGI11871J12876_1029482	F012254	PRMRDGSWRRLTDIANHYDLGFEVVLWARSFDLLEWTEALKDGAFDVLDAMCEQPKAVESTKRALWAAYLKGAGPDQRAANPQRAA*
JGI11871J12876_103038	JGI11871J12876_1030381	F003776	MKQSELDSMSLDELFMLHELLTATLEARITAERKALEDR
JGI11871J12876_103659	JGI11871J12876_1036591	F029833	MKVACFVNPLVQARGPCFNFGWVEALAKLLQPLRRDARCECMLIAGGWFRDWARQNQKGPLLAGLRTVWLDELALYRQLRALGELPTALDQTAYQADDAEHPALGVIADAMAREINGFEPDIIIGFAGQANYLAKLWPAALRLHIERGHFGRDPYPFSMYFDHVGTHGRSAVGSVGGLNL
JGI11871J12876_103721	JGI11871J12876_1037212	F012266	RLVLALQLPFFEVMALSFRLVGSAPERPCDDVCGLNPLLSESDGDAADFLD*
JGI11871J12876_103813	JGI11871J12876_1038131	F003981	MDHSPTVTAEDIDWLRKLRNARAANQPSPDIPTSVVRKLTQIACAELKSPKERSTRLRERDELERRKQSG*
JGI11871J12876_104083	JGI11871J12876_1040832	F008734	QGHQAGDGPSNLGQEDCHHRIDRVEERSVLRRPTSETTNSLSVFDRVRSISGYFSSGGRRVLETLWFESESQLIS*
JGI11871J12876_104332	JGI11871J12876_1043321	F022515	PRRAIQAFFLRTHGFVLRSDARSHSDYNLPMARARKLFPIYGSALANNMFTALGRGRVVDRFVAAYVAEYNRAAILGGASRDRELAETIGREAMLAMIHEVPQVLPRFFGKKQHATLKEEEKTAMDAFFLELMAALGRVWGWNAQDRRQFGHDLDLYSECAARPVKVAKGRKRGKVREEDPPFI
JGI11871J12876_104433	JGI11871J12876_1044332	F064046	RKPPMKETAGGVARWRVRRYGDLTAVVTECEYNFCDMARTLRMGENTFRRPCNFKELRVVKRAHITTFALCA*
JGI11871J12876_104613	JGI11871J12876_1046132	F037137	MDELTPDQEKAVAATVGAIQRIAMAIVAFPKEQRATHYALVRRNFEAAIKEFSIEGEMAQTWLDKTMIGIQSLVTEIEVG
JGI11871J12876_104770	JGI11871J12876_1047702	F040785	RLGTALREAFAEAMHDPQLIAEGAKMDLELGFVSGVDVQALVERLYKSPPEVIARAQAIVATN*
JGI11871J12876_104887	JGI11871J12876_1048872	F075150	LKAATNLNVVQPKLFQASRQDDRRFSDCTVSVIQILDDADAAFRILGAGLRTVLSVTTMFADKPHHLNGRTSAQR
JGI11871J12876_105368	JGI11871J12876_1053682	F105938	MKTTVMKLAFAKFAIALALAGGVALGAVAVSLTGATASFAQQCIPHYDS
JGI11871J12876_105396	JGI11871J12876_1053961	F018965	IRNDERIQASDRALRLFGPIRNFLSRFNEALGAFGKIEVAGPYPVGKYQHATATITAPNGRVVSWEFVLSEGGVSYQRSPYQLSEYGRLESQLKSDVVAFLEKV*
JGI11871J12876_105496	JGI11871J12876_1054962	F034135	MDIRDLTHALAYGDTFAQTASMLFRDLVEVRQKARELGLTEHPGKRVKVDP*