3300003559: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_43 (Metagenome Metatranscriptome, Counting Only)

Overview

Basic Information

• IMG/M Taxon OID: 3300003559
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110148 | Gp0072767 | Ga0007427
• Sample Name: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_43 (Metagenome Metatranscriptome, Counting Only)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 24052023
• Sequencing Scaffolds: 37
• Novel Protein Genes: 41
• Associated Families: 29

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
Not Available	20
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	4
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Frankiales → Frankiaceae → Frankia → unclassified Frankia → Frankia sp. EUN1f	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Lactobacillales → Lactobacillaceae → Lactobacillus → Lactobacillus delbrueckii	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Methylobacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Bacillales → Paenibacillaceae → Paenibacillus → Paenibacillus alvei	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Joostella → Joostella marina	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Microvirga → Microvirga lotononidis	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Thermomicrobia → Sphaerobacteridae → Sphaerobacterales → Sphaerobacterineae → Sphaerobacteraceae → Sphaerobacter → Sphaerobacter thermophilus	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Afifellaceae → Afifella → Afifella pfennigii	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Phycisphaerae → Phycisphaerales → unclassified Phycisphaerales → Phycisphaerales bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Solirubrobacterales → Solirubrobacteraceae → Solirubrobacter → Solirubrobacter soli	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Unclassified → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): grassland biome → rhizosphere → soil
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Hopland, California, USA
• Coordinates
  • Lat. (^o): 38.972988
  • Long. (^o): -123.116539
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000203	Metagenome / Metatranscriptome	1619	Y
F001418	Metagenome / Metatranscriptome	698	Y
F001895	Metagenome / Metatranscriptome	620	Y
F003158	Metagenome / Metatranscriptome	504	Y
F005048	Metagenome / Metatranscriptome	413	Y
F005082	Metagenome / Metatranscriptome	412	Y
F014312	Metagenome / Metatranscriptome	264	Y
F016792	Metagenome / Metatranscriptome	244	Y
F018301	Metagenome / Metatranscriptome	235	Y
F018876	Metagenome / Metatranscriptome	232	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0007427J51700_100007	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	516
Ga0007427J51700_100092	Not Available	610
Ga0007427J51700_100492	Not Available	567
Ga0007427J51700_101706	Not Available	1097
Ga0007427J51700_101861	Not Available	570
Ga0007427J51700_103085	Not Available	598
Ga0007427J51700_103203	Not Available	563
Ga0007427J51700_103489	Not Available	1119
Ga0007427J51700_104323	Not Available	630
Ga0007427J51700_104584	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	2659

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0007427J51700_100007	Ga0007427J51700_1000071	F014312	RRLRLLRPTKGTANGVVRLWERVKAERFALAMTPLVEAERLARKTERFSERPDKNG*
Ga0007427J51700_100092	Ga0007427J51700_1000921	F001418	GSKGLKAEAEFTSSSGSVRALSVNAKKGLRDEERLETVPNSVK*
Ga0007427J51700_100492	Ga0007427J51700_1004921	F032547	QLSFLPACTVEAVQSRSSCVLPLVLPAPYFRSARIKAPGHASRLTPDRNPYLGTAFHSLDKTARFRTTLPKSMLLAYPFGSSLSLPRTRSIRPLVHAAWLAPNCANSTRQTRCPVPSQRPRPLFRPTLPFRAFGPFPIKALTSIPIERFTESTRPIALRSPLPAVLIEPATDQCSRLATSRSAYCLTNL
Ga0007427J51700_101706	Ga0007427J51700_1017062	F024042	MIEPVTRAHENGLVPGSSLSAEGKLRRAETALWGTSFRDEGKHGEPHDRQQGATPLHGRGGETVEVVRNHGDGTRGGLAAHPRRETRRRGSRASDSSASYDGGAIFGQPQERKSDRQVGPHGSGRDGKVGVKVRRVARVHGFVITRARS*
Ga0007427J51700_101861	Ga0007427J51700_1018611	F065302	VQGSRYDSATRLHADVRFAARCSG*IACHSPSPLFSM*RVTVASALNGHNTLPEPESRYGLSLAHNDAFATIARSTFLACTFVSPSDTFANPFDSRLLRSVRFRGRTGALSMPGTRFPRRSPTFPIDPRSPLPFRSSCENLPDQSVQPVPFQEARLA*RSIASYSPPLPLSIPLQINV*NSLRPARLSFR
Ga0007427J51700_103085	Ga0007427J51700_1030851	F062739	WFQVI*FPARSLPACTALSIAIQSAGRFACLLPYERFRRPQDRCFQARRLLPLSRDRVARNGLLLARDGCRLSAASIPGSKFRTCYFATLPDRLPCPFGLSAPPPCPGLLRLRPLQRLRPVAFLPSGSADRAYRLHSP*GQLRPSGSKRSTVLAACRSAWRTRPISLRSPQPIPLSSCWLRITVPGSLRFRRLAVPQTS
Ga0007427J51700_103203	Ga0007427J51700_1032031	F018301	MGMSLKVHQSDGTDNDDQGLSARDRKQLDRLGKLWKSDAERGLKTRHLMGKVLNEQVGPPARRKAHGKRVLELYGAELGIAPSDLNRMGWFSSLFPDFSDFRTQHPEIDSWTRFKTELPNLKPAKGGKARQPVANPSNPALGGVARSFANLTSKLNGLDIRPVGAERQKLVDALRELA
Ga0007427J51700_103489	Ga0007427J51700_1034891	F038031	MFTDPFSVTYNSVALSLPRTEVAKDYNRYRTADGEFEIIISNNLRQARDGIANASIKLVRRLPDPTPSNVFDNYRDIRNVFGFSYSFDAQTRAEASVDIPRLRTALLALVDSTLQGRIIAGEK*
Ga0007427J51700_104323	Ga0007427J51700_1043231	F018876	VPSARLSFGLPASFGSFVPTLDAWTKSPLSVECRLSSQAGEVTLRFRSAVLSSTEAVDAFAPLPLPVTSPVELRLASSFVRISFFGLAGDRSPFPLNAVAPAQPATKLLLLPNFASPALPGMDLPISLESSVPRLAPRSESPGSFGPSSSCKQEMFF
Ga0007427J51700_104584	Ga0007427J51700_1045841	F005082	TSKMTADPFRPAENVQVSMSNYLVFDLPKAGFTPAEANAVWQGFKTLIITSSDLMIVKLLGGES*
Ga0007427J51700_105933	Ga0007427J51700_1059331	F005082	PDPFRPTENVKVSMSVYMVFDLPPAGYTAVEGLAVYAGFKNQLAAGTDLLPTKLLGGES*
Ga0007427J51700_106241	Ga0007427J51700_1062411	F005082	ADPFKPSENVKVSMGYYLVFDLPPAGYTAAEALAVYTGFAALYSATSNAMITKLLGGES*
Ga0007427J51700_106702	Ga0007427J51700_1067021	F018301	RGLKTRHLMGKVLNEQVGPPARRKAHGKRVLELYGAELEIAPSDLNRMGWFSSLFPDFSDFRTQHPEIDSWTRFKTELPNLKPAKGGKARQPVVNPSNPALGGVARSFANLTSKLNGLDIRPVGAERQKLVDALRELAEAASRRLKIRVEVAVGVKESKQVVTKRSDRVARA*
Ga0007427J51700_106859	Ga0007427J51700_1068591	F005048	EQVDILLHLPHRAPLALSAQVRRRDSLSMGLKFEHTTPKAEDSIQDFVVETFASATTDNGRVALVVEPRHAERQALVRTLRELGRRAIGVATALDAVQMLVEEGAHVDTVFIEAVSESLPSLELVEFLSHNHPRIRRVLIGEQHEIAASWVAQATGEVHALLETPCDPEAVHRVLHRLQFTPNDAALS*
Ga0007427J51700_107789	Ga0007427J51700_1077891	F045561	RLGRPPERDLEPDFRKEDGGSGQKARAGRQPESRQAHPGNGETPGTSREGFFAVKAEGGGDVKAFPRCAGRAPGGAEAHEGSGSVEA*
Ga0007427J51700_108615	Ga0007427J51700_1086152	F024042	MIVAVTRTHGDGLVPPPSLSAEGKLRRAATALWGTSFRDEGKHGEPHDRQQGATPLHGRGGESVEVVRNHADGTRGGLAAHPRRETRRRVSRASDSSAPDDGGAIFGQPQERKSDRQVGPHGSGRDGKVGVKVRRVAR
Ga0007427J51700_109933	Ga0007427J51700_1099331	F039900	SLRNGSSWFRPDEGSQSKDRGPLLGQTHYSSTEKRGGVSGMEQFLSEKDQEVWKYVLSDYRTESERDSEADIPVPDRLLPKRRSQELVRMLKLSQMIGLLLWLNRSELITLGGRERLLYLQAKASFEAIEAGLRFARRLSQEEKLRSDFRHQMRELNRRPQSKHFRQSEARRIGVGYRDKGMLPGSSTGARTRAQKDAYIPSHLVPKILRDALQLVTPACLTADEEWVDLSMVAGSFGTQADIGARPLLPPL*
Ga0007427J51700_112783	Ga0007427J51700_1127832	F000203	GVRQALFPVLALGAPQGRAASFPTLFSTASGVFGLVAGPFSASQRLNFE*
Ga0007427J51700_113854	Ga0007427J51700_1138541	F019767	GINIGDPPMDTSAAVIGSGGDQRTITREEFLRRLGHLAEKWQAHHGAGLEIRHETGKLLNERFGPPTAKQKRGEGVLKEVVERLQVAESELSRMRRFAFHFESVKALKEKYPEATTWTAVKDLLPRLNKPKKGSAKGAASRAKRKQAKPVQFGRVKQSLEALTSKLRKAREGLTDAERKELLAQFRELVEAVAHCLKMPLSVSQVSEEPAPPAAPKE*
Ga0007427J51700_114302	Ga0007427J51700_1143021	F016792	GSVRPEGCRGPHHPVDPQGSMREYPVREPCPPKCCYPDMRRSNPTCEASGTTATIWEHQSGGGLAEDEWLNASERPWLRSVIENRPKVLIGRSQNGMRVGSSNGTLDDGGTVTRRTIGRSLPIRFSPLDNRVSPTRPVAARRRYPDRKAGDGGGGRGAAEQAKAAL*
Ga0007427J51700_114372	Ga0007427J51700_1143721	F083540	YLSTTSAFTAVNMFSPKKMFSPRAYRKNLNKHQMLLDEEHHSDLVELHSESFSLFQNSPVQKSLDQLQYRVDFKGSAFKDCAYMRDIHDNKILKAKTATWSMDHKFKVTNLQQHDVWGTASCKLGLDACKYLIYFRDIEKAWFRKTMCKNRQYFYEVEFMDFRPNKWTIEAPALHRMVIKRDEGVVATLNRGSFEIHEFLDTEDTFVVQCIVLLFAQAYADGVCLP*
Ga0007427J51700_115087	Ga0007427J51700_1150871	F100491	VPSDPQAACSPTGMHDQNVASGTGET*ALCSPPLVLANRGSVRRCASAFNPGRSPLLDATFRSTASRTGLATDPRNCVNVPGLHLRNDPQI*FGPFGAALLPPLSLLLASRGAIYARNPLLDPISGLMTRLRIPAPLWDLSTPRDQSSQPGFEP*SLPLQVARSSFAPRSAATIVSHHSSATDHRSRSATPCQARCP
Ga0007427J51700_115872	Ga0007427J51700_1158721	F044743	MIRRVLLGSVLAASLGVVAMANHPATFVLRSGERVSGELSYKGGTSYTLNGKDYPSNDIAIIEFVPGAPSAAELNQIPTMDNNPSEHERHVFVTRDGQVIFGKIYHISADGNTITFDRREGGRQDLSADNLARVYVNPAGARSVYASVLGNATPGAVATSGTTIQVPAN
Ga0007427J51700_116453	Ga0007427J51700_1164531	F101199	GAIGFDRMAAVAVACPGRTVGLDNHLCKTLTANTSDVAGRVGFNAPLALAA*
Ga0007427J51700_116453	Ga0007427J51700_1164532	F101199	MAAVAVACPGRTVGLDNHLCKTLTANTSDVAGRVGFNAPLALAA*
Ga0007427J51700_117499	Ga0007427J51700_1174992	F027072	LLKQGQVKSLMSLWSMLAEESADRCCTSAIRDINTVACRVEHEGLSFLTITLPELGKSAQSWLDQGKAGIHPAFQ*
Ga0007427J51700_118564	Ga0007427J51700_1185643	F027072	VKSLTSLWSELAEESASWCRTSATQDINTVLRRVEHEGLSFLTITLPDYGKAIQKWLDQGHVGIHSAFR
Ga0007427J51700_119282	Ga0007427J51700_1192821	F048058	DRSIEGDPMNSELPLVVELAEPKLIAGDVDIQLSSRTNTRQQSVSFSALGVLSDIAADVAVDDVIA*
Ga0007427J51700_119875	Ga0007427J51700_1198751	F038031	EVEKDYNRYNTADREFEVVISNNLRKPQNGIATVSIKLIRRLPDPTPVDVFDNYREIRNSFGFSYSFDAQTRAETSVDVPRLRTALDALVNTGFQTRLISGER*
Ga0007427J51700_120465	Ga0007427J51700_1204651	F079443	AIPLQVREMMDVREENAEGDVASAVPLSERERICKMRRMRLAWISSAVLALGLMATASWAQEPNPNAPGNEELPGVAIAGVSEEFAPVWGGPFSGSATLTINGQSYPVAVTSNSLDLAPLPDNFGRMVGTTVHVFDFGDGNLLMTSDEVRLTPTQPGWFSVQATLTITSGTGIFSNAAG
Ga0007427J51700_121734	Ga0007427J51700_1217341	F077592	GHLGWFPGTSPIGIRIDGDYTGFGARDLDCPNCSSTKLTQLSGSLEWRIPLDRKSKVNPVIYFLGGGGIDWFSDFAPYRKQDDNTIVTAGSNTITNFPGFGNVVSTDDSGTFYHWSVGGGVQFGGLFIESQYKSINTNGASSMHVPVLVGWNWNF*
Ga0007427J51700_122315	Ga0007427J51700_1223151	F005082	VVSMANYIVFDIPPAGYTNAEALAVWVGFKTLLTATSDAFVTKLLGGES*
Ga0007427J51700_122356	Ga0007427J51700_1223561	F005048	VDILLHLPHRAALALSAQVRRSDSLSMGLKFEHTTPKAEDSIQDFVVETFACATADDGRVALVVEPRHAERQTLVRTLRELGRRAIGVATALDAVRLLVEEGEHVDTVFVEVESESLPSLELVEFLSHNHPRIRRVLIGEPNQLAASWVAQATGEVHALLETPCDPEAVHSVLHRLQFTPNDAALS*
Ga0007427J51700_123154	Ga0007427J51700_1231541	F071030	MSAANSLVVAVFDDSTVAESAINDLRNTGFSNDEILYSSSQKRGGFFENLKSWMTGEETASIGDVAKNLKDMGLPDEAANYYARERDAGHPIVAVSSPGHEQSARSVLSRHGGHSHDVTPGGTTAGMGPGATPSTAGMGPGAMPSTAYDQSPQTAGYQPTGQPDQPISQRDRALEDQEARIPLREE
Ga0007427J51700_124190	Ga0007427J51700_1241901	F024042	MVAPVTRPHGNGLAPDPSLSAEGKLRRAGTAPWGTSFRDEEKHGEPQDRQHGATTVHGRGGESVEVVQNHGDGTRGGLAAHPRRETRRRGSRASDSSTSDDGGAIFGQPQERKSDRQVGPQGIGTRRESRRQGQ
Ga0007427J51700_125071	Ga0007427J51700_1250711	F003158	MANQAHSLRKAIENLINAKLHDALAKPGGLDRLIAHRVTGVASWEIRNAEKQLDQALSDVLEQHE
Ga0007427J51700_125467	Ga0007427J51700_1254671	F018301	MGSSQLVHPVNGTKDKDQGLSDSDRKLLDQLVRLWRSDAERGLKTRHTTGQALNRRLGPPTKRKAHGRRVLEVYGKELKIAPSDLHRMGWFSHLFPDFSDFRKQHPEIDSWTKFKTALPSLKPVKGGKARKPVANPSRPAFVGVTKAIANATSKVKGLDTRPRDAERRKLVAVVRELAEAVSRRLKIRVVVSVGVKDSKPVATKKMDRVA*
Ga0007427J51700_131758	Ga0007427J51700_1317581	F001895	LNNMRPTYAGPQSSTSTYKATHDSGKFAAAGRGGAYRGAMTNAVGPQSAHVETRATEDTGKYVGASKTATNGYRVAGDVAGPTSAHQEFRTTEDIGKYVGASATATDGYRVAGDVAGPTSAHQEFRTTEDIGKYVGASATATNGYRIAGDVAGPTSAHQEFRTTEDI
Ga0007427J51700_134748	Ga0007427J51700_1347481	F062239	ENPMKRELPLVVELAEPKLIAGEVDIQLSSQTSSGGKSNTFNVIGVLSDLVNDVTVDDVIA*
Ga0007427J51700_142224	Ga0007427J51700_1422242	F027072	VKSLMSLWSRLAEESASQCSTSAREDINTVFARVEHEGLSFLTITLPDYGKAIRKWLDQGQVTIHSS
Ga0007427J51700_143687	Ga0007427J51700_1436871	F055530	MKGVFKTSLMSALLLAIVSLGMAEAKADPVTFSTSGVFTCAGCAGSGSNSVTFLGGMGNALMITFTGLGSTSLNTPTGSSFGNFQTFVSGNG