3300000732: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM3_M2

Overview

Basic Information

• IMG/M Taxon OID: 3300000732
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0071004 | Gp0054785 | Ga0002414
• Sample Name: Forest soil microbial communities from El Dorado National Forest, California, USA - Mediterranean Blodgett CA OM3_M2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 40831740
• Sequencing Scaffolds: 61
• Novel Protein Genes: 65
• Associated Families: 62

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	7
All Organisms → Viruses → Predicted Viral	1
Not Available	19
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	10
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. URHD0069	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Pleomorphomonadaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Nitrobacter	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Reyranellaceae → Reyranella → unclassified Reyranella → Reyranella sp.	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. 195	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → unclassified Chloroflexi → Chloroflexi bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium erythrophlei	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → unclassified Gammaproteobacteria → Gammaproteobacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	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
F001281	Metagenome / Metatranscriptome	732	Y
F001868	Metagenome / Metatranscriptome	624	Y
F002350	Metagenome / Metatranscriptome	568	Y
F003104	Metagenome / Metatranscriptome	507	Y
F003794	Metagenome / Metatranscriptome	468	Y
F004310	Metagenome / Metatranscriptome	444	Y
F005285	Metagenome / Metatranscriptome	406	Y
F005599	Metagenome / Metatranscriptome	395	Y
F006963	Metagenome / Metatranscriptome	361	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI12023J11887_1000313	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2438
JGI12023J11887_1000511	All Organisms → Viruses → Predicted Viral	2043
JGI12023J11887_1000657	Not Available	1871
JGI12023J11887_1000777	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1760
JGI12023J11887_1001587	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1298
JGI12023J11887_1001755	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → unclassified Bradyrhizobium → Bradyrhizobium sp. URHD0069	1245
JGI12023J11887_1001979	All Organisms → cellular organisms → Bacteria → Proteobacteria	1174
JGI12023J11887_1002055	Not Available	1157
JGI12023J11887_1002333	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1083
JGI12023J11887_1002634	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1020

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI12023J11887_1000313	JGI12023J11887_10003133	F069298	LHDAARFRARSTSHSVAALGGCTNIPLAAVGAQEDETILESGFLGHAKVRFVHLDPPGLFKSWKI*
JGI12023J11887_1000511	JGI12023J11887_10005115	F038265	HCVARTRGDPFGVAETLRGIAAGKHAVTNYRGLPAVSYRQMSDTKT*
JGI12023J11887_1000657	JGI12023J11887_10006571	F005285	MHGVSGDGMARRWSEMNQGSRTGKGTAFMAARGPEELSPGGDRAFVVARKRGNARGAKGGRKVEA*
JGI12023J11887_1000777	JGI12023J11887_10007771	F005599	MPTLLPFGEGRVSGEAIDTRTRSIRRGSGHGTLERWFG*
JGI12023J11887_1001587	JGI12023J11887_10015872	F027923	MKRTRHKRTPSVRRRALEFIAAHPGCTEALLAAENIPADVLVELVQSGLVIARIERLDDEDGAVEVTCAWITXTGERVLAARG*
JGI12023J11887_1001755	JGI12023J11887_10017553	F101712	MDVSSSASSIANSLNTVSTSREIPHEFRYHAKVLNDHLADVLRSGLFDDIDHFFKMLELHVRNRRAR*
JGI12023J11887_1001979	JGI12023J11887_10019792	F075150	LKAATNLNVVQPKLFQASRQDDRHFSDCTVSVIQILDDADGAFRILGAELRTVLSATTMYADKPHRL*
JGI12023J11887_1002055	JGI12023J11887_10020552	F037137	MDELTPDQEKAVAATVGAIQRIAMAIVAFPKEQRATHYALVRRNFEAAIKEFSIEGEMAQTWLDKTMIGIQSLVTEIEVGGGAAGGKA*
JGI12023J11887_1002055	JGI12023J11887_10020553	F061299	MSDNVPDPDVKKRAEFISEVLTTVLEEGGYDSAVAQARRFLANNTPAQMEQMKPHFSSLALEFRILAGFFKD*
JGI12023J11887_1002333	JGI12023J11887_10023333	F083953	MLRRIRLKDAVDAQVASSEFSAFLKGAAATNLSQEQREELFREFLQWQKNQRNGTQR*
JGI12023J11887_1002634	JGI12023J11887_10026341	F014173	MVKHGALSKSHVHQMLASKDARVRRAAYTLLEASNPALRRNSELFLEIIRFIWEANPSYDVYREFNKRHLIVPYKVHELISARLK
JGI12023J11887_1002743	JGI12023J11887_10027431	F069409	GFGNGTFGMAQASAATADNTTASARLVAKAVDRNAAAREDGGTAFLRGESFNRSIPRSI*
JGI12023J11887_1002910	JGI12023J11887_10029103	F041458	MLLRAEDQAKFQGRIDDKGATVWASYRIEGRVEGKPVVQSDKRMFASEQEARTWLLGEAEQRGFNDFEPEVHAGA*
JGI12023J11887_1003497	JGI12023J11887_10034971	F025123	MTKLDNRCAHCGGKFGLVSHHHRGLRFCREACKENFLAKTAKDYARMRKWFGLSCRTRNQEPG*
JGI12023J11887_1003658	JGI12023J11887_10036582	F061050	MPDEVTPDYVRARWAYSELLSWGHGHLYQGPGVQDLKEKLALGVPFDELGKAEHYLLIDQFDRVRGNHFNRYIIGIPNFKPVLWSRDELAAVHVIPYFVRDVSSLEHLKVTFKQWIEADPVR
JGI12023J11887_1003740	JGI12023J11887_10037402	F067945	MNVIGSPANTVILHWNECGTSWAQLPWRDWVRFRGFDDGGLSLLVGAEAGEHYFLVCVLDDRGELANVIPHRYVLSTDGRLVHGFDGLRQAEREEYCRIQLLHLPTIEDSERYNELDARGFAVNL
JGI12023J11887_1003789	JGI12023J11887_10037891	F028295	MSWTAHYFDRRLNSDGVSRAFASKEDALVAACDLMRRNCVVNFVQGPNDEKIDATTITAWCKRRPKRKDGPAAS*
JGI12023J11887_1003931	JGI12023J11887_10039311	F046730	MGLENVFLSVRPIVESLARSTMWSSTTLFSNNRRVQRERPLGGLEQA
JGI12023J11887_1004036	JGI12023J11887_10040363	F054174	MAWTDLISGCFGFGTAPFASNRPDEDIAKEAIAAAQAEGATRADFAQLIALYPRRYIKSDQVLRERIREDAGRLDRLWKVAPSTDGPETSPSS*
JGI12023J11887_1004122	JGI12023J11887_10041222	F006963	MYARHRREVQTVRCAMTFLLFTTLLCALGATQASAQNALSQQLLELDDDERNAAFTLMLRDGHRKCDQVVRTLFKGTILGVDEWEAMCRNRISYSFTVLAKPNETMIMFVSCRELLATSRMLLHRAGSKTKATGCKIK*
JGI12023J11887_1004404	JGI12023J11887_10044041	F000262	MSDKLKRLEQIYLTWMTILVALATVSCSGQDFGFLQPTPEDLCKCMPLEPDIADYRHAAKHVPIPNIVAQEVSVEIILTWSQDVFIPPDAPRTGRELEVFHIANAFLQNASVNALDCDVSMEXSQTADKSSARMIVETPVDSEYCGARQNMQAQLKQHGFRLDSQHGGELPHALPVDVVGMAFEDFEHDRGHVATLWELHPAIVTLH*
JGI12023J11887_1004504	JGI12023J11887_10045042	F010656	MEVLIGFFALRPIFTFWGLKVVWYTYLLNILIQAYIAVSGIFQVLAQRGISWEAWSPNFLPLILTIVVQLALVRLLLEVAAIILSTARHSREQPRAPAL*
JGI12023J11887_1004894	JGI12023J11887_10048941	F018466	MANSLRNAVIGFGLAGTLVVAAVAPSFAQGVYANPYFYTAPQGYAGYSGYAYAPGYGARSWDYPAGYDTSGMPYSYRELGWQPGPYGTRCYPTLRAQNRC*
JGI12023J11887_1005234	JGI12023J11887_10052342	F105319	VDSLNRSLSEDMLGEYIARLESEVGVTINQNTLNQVVSGGAVDSAN*
JGI12023J11887_1005329	JGI12023J11887_10053291	F045203	MNARARSFWREEIALVALLFAFFAGIVCFALPLPFDARLFPLVIGGAGILLTLAIAAVE
JGI12023J11887_1005341	JGI12023J11887_10053411	F009926	GSDGRVHLVETLAAAQKFGIDRADLVEHLAQFAEVGEELADFGVSRIRHVTDARALAGSTDCGKISLGAMPSSVDTVAVGPPAAFVGLDQRAAQYLFDRRQAARKLVATLAKSCR*
JGI12023J11887_1005437	JGI12023J11887_10054372	F027566	MKTRVIKYLGALGLGAALVLTAATSSFAQRHDPNCIPQYDTSGAQTAPYC*
JGI12023J11887_1005788	JGI12023J11887_10057881	F020387	MTYIEQAIKEAVDHGYQPNVERYPEMEGISPLQIAIAMQADVFIDPAFWKALGKKRGWTTDDDFKYWQKSVAEWEDKYWKKFWHRFIDHLAEDKDAESFFKALDSPPRQRPDSHH*
JGI12023J11887_1005788	JGI12023J11887_10057882	F058290	VEHTFESLPRVDKDNKISITLRGEVERTRDALKLIFTKYCLPKSG*
JGI12023J11887_1005870	JGI12023J11887_10058701	F037615	MNTLTTARTIVLVFSLIALAAPSQAAQRTNARDHGPSLEQKCHELVGKEEREGEGRGHIGHLQVQRFSDCMMGMPN*
JGI12023J11887_1006232	JGI12023J11887_10062322	F057343	AVEEFTANLNMKLGNLPVAPPAKDVLEPRFVDAALKQLGPYQKK*
JGI12023J11887_1006382	JGI12023J11887_10063821	F005599	PEQASKVTMRMPTLLPFGEGRVSGEAIDKSTRSIRRGSGHGTSERWFG*
JGI12023J11887_1006452	JGI12023J11887_10064522	F031228	MDHREIAVRVPVMNEVQFLFPFEPCKPLKSRSLYVVFLVEKDVRVERRRTCDCLNHEEVDWQYEVCTRSYQKHRNEEKGCIVAFVTEVGR*
JGI12023J11887_1006591	JGI12023J11887_10065911	F079254	MQTVARWGEPGRMLQVDPWSKAAECDRAIEFIADPERRIVLESLRSFWVALCNELSLLDQEDRVGPLSTINQIHTELMAVCRRAMH*
JGI12023J11887_1006911	JGI12023J11887_10069112	F069796	MKSITIVSILTALSVPFTATRATADDDYKKICRVNENLRVLDDDADANSCRAIAVDSQAQEYQIGCRDSENKGPIIVTAPFNINDKAATVTSSKLAANTQNTTTPGQFAKCAKVWGRR*
JGI12023J11887_1007086	JGI12023J11887_10070861	F065946	EPDVRTARTMAWACAGIAACNAVPACAAEPFHGRWAPDAQACIGEGVIASPVVVNSLSLQWREAACVVRTSYRVRDAWHIGARCWGEGAISNVPITLRMRGEQLLLGWAGAPAEELRRCP
JGI12023J11887_1007763	JGI12023J11887_10077632	F044758	NPAGGKEDDYGWVVQAMADCDVQAKHKLDTLYFLIIPVTTTGVSLPGWSPTTIGAVGDAVSLLHSSDTVIGLRNRALALYQKPLTFAVSDPRTKTVYKWKPAVGVTTLTTQDTDQPALTLGFEAPDLGKEIEWGPTINLTKGTCYWINPLILAAARSG*
JGI12023J11887_1008026	JGI12023J11887_10080262	F027285	MPEPLVTFRGAVRCARAPGPLGVTLIGETPERPGESTALAFSAAAPAGFPESLDNAVVERLGADQYRIYSPPREWVIAAAAVHLHREIAVQFYRAIPPRPVPLPKRWFWRVVLGLAASRAGLAALRALRR*
JGI12023J11887_1008048	JGI12023J11887_10080481	F008140	MVAGAVLGAIASAGATGANAQGVYLQGPGFGVEIGRPAYRDRYYRSYHDYDSPRFYSERRYQRGPYAYERRWRGRDWD*
JGI12023J11887_1008058	JGI12023J11887_10080581	F064046	XCEGFRMTAIRDDAACTGAVVRKPPMKETAGGVARWRVRRYGDLTAVVTECEYNFCDMARTLRMGENTFRRPCNFKELRVVKRAHITTFALCA*
JGI12023J11887_1008304	JGI12023J11887_10083042	F001868	GMATEFYFTPELHLKDGRIIRDLNDAASFAREQEVRPGVDQRDEVLHKTERAASKEDAHAAAHSFVRWLEELDVLE*
JGI12023J11887_1008366	JGI12023J11887_10083661	F002350	ISKEMEAHLLILVQLRNNAADCIRLAEAARTSAHKSLFIEMAERWLTLAERAEKTRG*
JGI12023J11887_1008504	JGI12023J11887_10085042	F094490	VHIALVVDQSVKFRLLVQPRTKPIGTYTYVITRTDDPDWGETTAEYFFTREAALAAGRAALDRILKRQTS*
JGI12023J11887_1008883	JGI12023J11887_10088831	F003794	MSLPDDTKTDDKEQCDNVIRLGTETLFAIAEQLRQMYDLDLRTKPSEKLERLMRRIERGDEPC*
JGI12023J11887_1009125	JGI12023J11887_10091253	F028604	MGACTIGDVSQDFRPVLELNPVYAVGERLHHDPLHE*
JGI12023J11887_1009138	JGI12023J11887_10091382	F004310	MLDRSLEAEFESYRKTLSTDEARRAFDELIERLLSQHGVDYVRGYVXALKDASF*
JGI12023J11887_1009407	JGI12023J11887_10094071	F013562	CFYARRHGRRLYMGYEETPETSPDITRDVARRTLAEGKRVFPALDVLGERDIRSAWCGRVFYTLDDYPFVERRHGGRVITFAAPSDHGNSLALRIGQLVGNAVAPSTLQPRSDDDIRQRRRNGQQLRLFESLPKGLRLRPGKRYQEAAYREPEAAVAEYARQTSDPDLP*
JGI12023J11887_1009881	JGI12023J11887_10098812	F024969	THPRAGRGDRLMDPALLQSAFRLGFVILALSLLVLPFEDRSSAEFVATVLAALIGLLFIGIVTVLARSSLPPPPRSQPRTMVDKAIGKGYNEPDSHSGGK*
JGI12023J11887_1009971	JGI12023J11887_10099712	F057531	MADTHALNNDRTRAADSDVDILGKLDYWRALLHERGLHTEAMVMGRAASEIRILREQVSEKLTKRRA*
JGI12023J11887_1010014	JGI12023J11887_10100141	F005599	MPTLLPFGEGRASGEAIDTRTRSIRRGSGHGTLERWFG*
JGI12023J11887_1010158	JGI12023J11887_10101581	F029882	MAGYTDKSRRYLRWAAANERRAASAHGGEFKTMLLWVAAQYRDLAEQTDNPERWRAKRAAAGARRE*
JGI12023J11887_1010433	JGI12023J11887_10104332	F036786	MIWRQREPTLKEILSDSIVTALMEADGVDPHELEAMLKKIGRMSESVQRVRPW
JGI12023J11887_1010709	JGI12023J11887_10107091	F052030	MPVDLRPAIPTLPARQGALNAHRESLVAKLATCITVLIATIAVLIVA
JGI12023J11887_1010795	JGI12023J11887_10107951	F055459	MGIFGRKVDDEFDALIHAIGRLLHGKGHDLQRAVLTDLVSRWIMGHHPSQRRQALAMHVQAVRDLIELNEDALATRNRGEPEDW*
JGI12023J11887_1010978	JGI12023J11887_10109782	F083042	DLERELTVGDADRADLTLHLLKSLQPAPITDRPHSWDY*
JGI12023J11887_1011322	JGI12023J11887_10113222	F099613	MAEIIILAERRKARQERRATNVMAMPFXLMAAYMACGAATYAAIVEASTAGLRRPQ*
JGI12023J11887_1011324	JGI12023J11887_10113241	F042436	MKLQQWRQRSLLLSDCCEQAVFCVLLLARAMNNENEKGREHDLRQGIVSLIRANEQALKKPITDEEVQKLKAAAGRLDQMLKAAVDTDGQVLRSAAARLDQLLEDIATGKDVTY
JGI12023J11887_1011399	JGI12023J11887_10113991	F001281	MGRILASLVLAASLLSVASSEASAWVCRAVGVGSGGWGRSASIVDAKLQALRRCEHRSPVPVCTILWCR
JGI12023J11887_1011666	JGI12023J11887_10116661	F099698	FDIDQNGTEGILSESQTLSNGNVLAAVETFDQTTGKILNVLVKTTTQDDFVTLGVVGNSVGLVEREHVISLFHVQRTFRLLNPLSANKFTGLWTPPIDTKHLLEEVSRNQGTTNVAVFASGFNANPVVFSSNVAANTFGPLVQLTDPAFTFGVPPVLALNTKTNQAVLAQDFGSP
JGI12023J11887_1011787	JGI12023J11887_10117871	F029482	SLCVVATSSVAAKHKSSAAAKHRSVTAKQRSVTPTPKQRPVVATDQTPTNKNDCLTVSQILYGRAEALSKGAKQAIPREFTRVASNLDESCGEEDFEKARISIDWMNTCLTNYTKDYSLGFCTRNKGYFCTINPRSDACLQSQ*
JGI12023J11887_1012464	JGI12023J11887_10124642	F026312	MTTFWLAFSDPDAPSDKRFLGVAIFDMDESGGELSVPEIVRRAHDLGINPGGQVLVQEVEAIPDEYKNRLITDDALLLKLGSRGRSITH*
JGI12023J11887_1012519	JGI12023J11887_10125191	F003104	MTLAGTERRRRQLVTAGLGTALTLVMGAVLIMGFRLATHMRANISALQTASMLQTYPVEISHQLNSLRDRLEVRAYSGQALADLQGTVKRFSQKLTELSVSGELDLPQLHRALLLWHQYAPVLDPVVSFSGQPYVDSDTAGSSLSREGHQHYAEVKRAQLFASDS
JGI12023J11887_1012708	JGI12023J11887_10127082	F045814	MRQFNVGEVVTFIPDWILRSAAPGDYKIVSSMPDRDGDHMYRIKSPLEEHERVV
JGI12023J11887_1012710	JGI12023J11887_10127102	F006963	MTRPLFMTLLCVLGTAQAFAQNRVSQQLLELDDDERNAAFTLMLKDSDRRCDQVVRTLFKGTILGVDEWEALCKDRNAYSISVLAELDEAIITSLTCRELLATS
JGI12023J11887_1012828	JGI12023J11887_10128281	F060961	MPDAVPPPTRDIVVVHSSDLHLDHDYTARLHGGDGTAGL