3300003557: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Bulk_48 (Metagenome Metatranscriptome, Counting Only)

Overview

Basic Information

• IMG/M Taxon OID: 3300003557
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110148 | Gp0072772 | Ga0007432
• Sample Name: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Bulk_48 (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: 23425698
• Sequencing Scaffolds: 38
• Novel Protein Genes: 43
• Associated Families: 35

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa	1
Not Available	17
All Organisms → cellular organisms → Eukaryota → Opisthokonta → Fungi → Dikarya → Basidiomycota → Agaricomycotina → Agaricomycetes → Agaricomycetes incertae sedis → Polyporales → Fibroporiaceae → Fibroporia → Fibroporia radiculosa	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Aminicenantes → unclassified Aminicenantes → Aminicenantes bacterium SCGC AAA252-N07	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Micrococcaceae → Arthrobacter → unclassified Arthrobacter → Arthrobacter sp. H20	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.	4
All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Salinispira → Salinispira pacifica	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Pseudomonadales → Pseudomonadaceae → Pseudomonas → Pseudomonas fluorescens group → Pseudomonas fluorescens	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Methylobacteriaceae → Methylobacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Firmicutes → Bacilli → Lactobacillales → Lactobacillaceae → Lactobacillus → Lactobacillus delbrueckii	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Frankiales → unclassified Frankiales → Frankiales bacterium	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → Pirellulaceae → Candidatus Laterigemmans → Candidatus Laterigemmans baculatus	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 → grassland area → bulk 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?
F001380	Metagenome / Metatranscriptome	709	Y
F004796	Metagenome / Metatranscriptome	423	Y
F005082	Metagenome / Metatranscriptome	412	Y
F007777	Metagenome / Metatranscriptome	345	Y
F008193	Metagenome / Metatranscriptome	337	Y
F016792	Metagenome / Metatranscriptome	244	Y
F016972	Metagenome / Metatranscriptome	243	Y
F018301	Metagenome / Metatranscriptome	235	Y
F018726	Metagenome / Metatranscriptome	233	Y
F019767	Metagenome / Metatranscriptome	227	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0007432J51704_100570	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa	969
Ga0007432J51704_100764	Not Available	586
Ga0007432J51704_100996	Not Available	580
Ga0007432J51704_101514	Not Available	520
Ga0007432J51704_101690	All Organisms → cellular organisms → Eukaryota → Opisthokonta → Fungi → Dikarya → Basidiomycota → Agaricomycotina → Agaricomycetes → Agaricomycetes incertae sedis → Polyporales → Fibroporiaceae → Fibroporia → Fibroporia radiculosa	1878
Ga0007432J51704_101891	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Aminicenantes → unclassified Aminicenantes → Aminicenantes bacterium SCGC AAA252-N07	536
Ga0007432J51704_102274	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	812
Ga0007432J51704_102409	Not Available	575
Ga0007432J51704_102803	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Micrococcaceae → Arthrobacter → unclassified Arthrobacter → Arthrobacter sp. H20	793
Ga0007432J51704_103056	Not Available	714

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0007432J51704_100570	Ga0007432J51704_1005701	F034588	LPRWRLHPPASPLIRTSGCPSFRISGFTGDRSSSRLDSLSFGGAGCESSRSPLRFASPVSPTISFWVAPDPHPPVPADFRSESPRSSVPSGRPLRISGLLRLFASGFVVRSFPKSPWFLLAQRRRFRPSRVTPKLPSSADPYLLSQVAPASASTAGSMITPWLNRTLHPRLAPRMNLRYQSGTSIPDLISSALLIPIHRSQSADHEL*
Ga0007432J51704_100764	Ga0007432J51704_1007641	F076940	VPSDRFPALLSAGMHRTEQRNRKCRAFRLLAPRLAFSPPAGSMPPGTPRAAFDQDRSLVTAFRSPVTVAPSRSHHPGVNASSLLLRVQPLVCTARSDLPLHHRYRFAPASGDFVASIPLQRLRAARVAAPAISTPLQDYYFLPDQSVQSRWPPLGPPSEFARFPLAPWCRLLLGLAPDHRSWFATFPAACCSSNL
Ga0007432J51704_100996	Ga0007432J51704_1009961	F007777	LTQLRGSVARPILGVVERKAASRSGLLPVMEADAHLRTDPQLAKTSSGEQRAHVSPDPDATFRPRMPVGEQT
Ga0007432J51704_101188	Ga0007432J51704_1011881	F100491	KTVPSDRQAACSPTGMHGPNVASGTGET*ALCFPLKVLANRGSLRRCASALHSDRSPLLDATFRSTAPRTGLATDPRNCVNVPGLHLRNDPQIRSGPFGYVLPHPLCLLWLGGRDLHTNPLPNPT*RLIARLRTSAPLRELSLPRDQSSQPDFELQSLPLQVARSSFAPRSAATVLWIAQRFGSSFQIRYFLPGSLSLKP
Ga0007432J51704_101514	Ga0007432J51704_1015141	F004796	NSKDDTVNSTSLPLPLQLTKPVLLAGDLDTQVREGLSDAYDSKAQLCSHTQSSAQSKTLNVLGIQVDVNADIVVDDVIA*
Ga0007432J51704_101690	Ga0007432J51704_1016903	F016972	VRLTPLTDAIPVFNLYLKIYGNDRFPFGAKTSRYGPYELGYRRATKTFTK*
Ga0007432J51704_101891	Ga0007432J51704_1018911	F092500	RGPGILIGGVILVVVGVIVVALSINSLTSLSISMPDDISTKSLIKSALNINQTAVKETAKTVGISLGLAFSGMLVAAILIVNGIIALIGGTVVSFADRRHKKVNKAQQHLGSPIG*
Ga0007432J51704_102274	Ga0007432J51704_1022741	F033437	GLGVRHALFPGRTRLGALAFAGCVLPDATLRGRRMFRSHGGTVLTVAGRDLLSEASAPSSVTPCREWHAGRGADTSAILLRVGTVTAGTAPAFGRSLAPRYGSDLLTLRLLSLLQCGGVVFTLPH*
Ga0007432J51704_102409	Ga0007432J51704_1024091	F095010	RGCMSTNAFVQSILVGTRPTAAGSVRVAKGGCNSLRPDPGGRDAQTPETRGTIGSVLTKLVSPGSASSRTGPNGGRMSRNPIERRAPPQAVWSFDSHTSFVASPGGQRQGRIGEVLIRYFGRDAQGIITSRPRKCRTPTERWPPRTESETVSRFFPESGHPIGSRSGLRLLPSGRRGRLVVGLPPSLGTTE
Ga0007432J51704_102803	Ga0007432J51704_1028031	F031726	MIAVRHLPWPIAVLLATVILLLAAGLTAGGVGLPGADLPTLAPLAPGWVPEPGTAPRPRTWSEPGNNRLEVWEKIERDAALVIFGEEMTDAERGRCIKALALALAMNDLELSRQCTDPLLAELRQELTRQLGAEAREVLADLDERAIVRALYAARMGRHAPLMIGSFRAEVGFATYRHWKTTITEGRDDSEQRQTMPDTHQPFIRLLVILE*
Ga0007432J51704_102832	Ga0007432J51704_1028321	F031726	GTAPRPRTWSEPGNNRLEVWEKIERDAALVIFGEEMTDAERGRCIKALALALAMNDLELSRSYTDPLLAELRQELTRQLGAEAREVLADLDERAIVRALYAARMGRHTPLMIGSFRAEVGFATYRHWKTTITEGREDSEERQTMPDTHQPFIRLLVILE*
Ga0007432J51704_103056	Ga0007432J51704_1030561	F024042	MIEPVTRAHEDGLVPDSSLSAEGKLRRAESALWGTSFRDEGKHGEPHDRQQGATPLHGRGGETVEVVRNHGDGTRGGLAAHPRRETRRRGSRASDSSASYDGGAIFGQPQERKSDRQVGPHGSGRDGRVGVKVR
Ga0007432J51704_103249	Ga0007432J51704_1032491	F053640	EQSKRSGLKNSTESTAGIIPGDRGMAGDNWCRPPLLKAKADERHISPVPLAGVVSGQSTHEVGTEPQSAIRNRVERSQAHGEFRPVNRRSYPRGFRLLLRRPERSRGSRRDDPAKRPSSPHESGAQRNHDGGERTDLGKVRQPPQMGRRAKPRHPAAKAKAT*
Ga0007432J51704_103377	Ga0007432J51704_1033771	F024042	MIEPVTRAHENGLVPGSSLSAEGKLRRAETAPWGTSFRDEGKHGEPHDRQQGATPLHGRGGESVEVVRNHGDGTRGGLAAHPRRETRRRGSWASDSSAPYDGGAIFGQPQERKSDRQVGPHGSGRDGKVGVKVRRVARVHGFVITRARS*
Ga0007432J51704_103542	Ga0007432J51704_1035421	F001380	PGFTVRFSDPPACRRSLRGNVLRMIRLPLAIAAFQPATGHCNLRPQRTHTLPEPESRYGLSLAHNDAFATIARSMFLACTFVSTSETFANPFDSRLLRSVRFRGRTGALSMPGTRFPRRSPTLLNLLRFPLPFGSSFENPPDQSVQPVTVSGNPSRLTPDRFWFPEKLASSGLTHRS
Ga0007432J51704_103631	Ga0007432J51704_1036311	F024042	MVEPVTRAHVDGLVPDTSLSAEGKLRRAGTALWGTSFRDEGKHGEPQDRQQGANLCSGRGGETVEVVRNHEDGTRGGLAAHPRREPRKRGARASDSSASYDGGAIFGQPQERKSDRQVGRHGS
Ga0007432J51704_103885	Ga0007432J51704_1038851	F018301	MGMSLKVHQSDGTDNDDQGLSARDRKQLDRLGKLWKSDAERGLKTRHLMGKVLNEQVGPPARRKAHGKRVLELYGAELGIAPSDLNRMGWFSSLFPDFSDFRTQHPEIDSWTRFKTELPNLKPAKGGKARQPVVNPSNPALGGVARSFANLTSKLNGLDIRPVGAERQKLVD
Ga0007432J51704_105634	Ga0007432J51704_1056341	F079670	LKKGLKVLEMVKRERNKIIIIDNSLKLIQFLYIFLKKYINLS*
Ga0007432J51704_106394	Ga0007432J51704_1063941	F019936	RISVMQDESIYQSGDGLIQVQASHDSGKRYRHLLRVNHSKLAPDPFRPTENVKVSMSHYIVFDVPVAGYTTTEQIAVYTGFKTMYTAATDALITKLLGGES*
Ga0007432J51704_107077	Ga0007432J51704_1070771	F082288	RFRPNNKTKNMMSFLVLSSILGIAIVSTNAILTAQTVNAQFVVKLGGPDTDQVNSRIVGTLLKPGFTNKYNLTVNGKTIPIDYSVLDGSLVGILSDPSRKSLDLAVNPQANGAALEVNVPRHVIDSKNAAGKDAPFIVKVDGNRISGEPSGICVGTCPNILNSFKETYNTNTDRVLTVLVGPESRFIEIIGNHTSA*
Ga0007432J51704_107500	Ga0007432J51704_1075001	F016792	ASSATSPSTRSMDCSRAGPGLASGAACSIGCVRPEGHRGPHHLGDPQGSMMECPVREPCPPKCCYPDMRRSNPTCEAPGTTALLWKHQSGRGPAENGRLNVSERPWLRSVIENRPKVLTGRGQNGMRVGSSIVAVDDGGTVTRRTTGRSLPIRVSTLDNRVSPTRPAARRYPDRKEGG*
Ga0007432J51704_107532	Ga0007432J51704_1075321	F034588	CPSFRISGFTGDRSSSRLDSLSFGGAGCESSRSPLRFASPVSPTISFWVAPDAHPPVPADFRSESPRSSVPSGCPHRISGLLRRLALSFVARPFPKSPWFLLAQRRRFRPPRVASKPSSSADPYLLPQVAPASASTAGSMITPWLNRTLHPWLAPWMNLRYQSGTSIPDLTSSAFSISIHCPQSADHEHKTKTVTCAFHQAGAAVPISYK
Ga0007432J51704_108258	Ga0007432J51704_1082581	F018301	MGMSLKVHPANGTDHVDRALSAPDRKLLDRLVRLWKSDAERGLKTRHATGKVLNRRLGPPTQRKAHGQRVLEVYGERLDISPSDLSRMGWFSHLFPDFSDFRKQHPEIDSWAKFKTALPSLKPAKGGKARKPVKDASRPATRGVVKAIASLTAKLNRLDTPPVGAERAQLVAVVQELAKAATRRLKIRVEVSVGVKDSKPVATKKTNR
Ga0007432J51704_109017	Ga0007432J51704_1090171	F054493	TNQGPRKGIAASKEEATSDGEGNSGAPRARDFGREHXKRKRGGAQASIADGRQAPRKETPAGDQRTS*
Ga0007432J51704_111358	Ga0007432J51704_1113581	F027763	AITIGGTTTPLPRTFSEGNEAAYTSADGLLKLSLNHNLIKQGRTRHLLRFDHAKIAANPLEAGENVRVNMAVYTVFDTPPAGFYTAAEILAVYTGFKTLCSASSDAVIIKLIGGES*
Ga0007432J51704_111698	Ga0007432J51704_1116981	F005082	IDHSKITADPFIPTQNAKVSMSCYMVFDVPPAGYTNTQQLDVYTGFKTLFSATSDAAITKLLGGES*
Ga0007432J51704_111751	Ga0007432J51704_1117512	F066797	MFEHLSNNPSADLGGSSNYSKEKAKFDTIFLATLKTEVAKVFMTTEIAHELVDPNPKDYEIIEVDKSFWIVVKE*
Ga0007432J51704_112011	Ga0007432J51704_1120111	F016792	MREYPVREPCPPKCCYPDMRRSNPTCEASGTTATIWEHQSGGGLAEDEWLNASERPWLRSVIENRPKVLIGRSQNGMRVGSSNGTLDDGGTVTRRTIGRSLPIRFSPLDNRVSPTRPVAARRRYPDRKAGDGGGGRGAAEQAKAAL*
Ga0007432J51704_112109	Ga0007432J51704_1121091	F054493	TTNQRPRKGIAASKEEATSDGEADSGAHRTRDFGRGHDERKRGGAQASIADGRQAPKEETQAGGQRTS*
Ga0007432J51704_112325	Ga0007432J51704_1123251	F074932	PGRSMLEGQTVVGSDDHKLGTVVAERDNCVIIESGHVFKSKHAIPREFLHDTGGELRATVTKEVVDGSPKIDLNKWDCSEVRLAYGLDGPFEVDPDPNGLETAETDAARAGMKPAPAQRVDTLEGNDPNAVPVIRDRQANAADPSGVTANLSNENRTGGGDR*
Ga0007432J51704_112675	Ga0007432J51704_1126752	F084972	MAFTDPQSITISGTPISLPRVSSGDNESKYSSSDGLVDLSASHTYGRRTRRVLRVDHSKVAADPFIPAQNREVSMSNYMVFDIPNVGYTNADVQ
Ga0007432J51704_113977	Ga0007432J51704_1139771	F099956	VEKPFDTPGRGSRPGPGSTFTLAPGVRLEPLGDGSAVLFSKALDQSLSLNHTAALLCSFA
Ga0007432J51704_113977	Ga0007432J51704_1139772	F038822	MNINSLSDRRVFLKRTIQGAGIAFAAPAILSSLSTRALQAQASGAGTGAVAGNPYGTNDGRGL*
Ga0007432J51704_114654	Ga0007432J51704_1146543	F096396	MKSLISLWSRTANELAVRCRTSATRDIKTIASRTENEGLWFLAVTLASFGKATEKWLNQGFVDPTDVPSFKRTNGHPTGRPAFLQGFLDRVFCSDSGALMDEPDIEAIYAIRQ
Ga0007432J51704_115385	Ga0007432J51704_1153851	F038502	MDTATQVRPAKVTKTNDRAALAKDLKLVDRLVSLWRDNADRDLGTRYQTGKLLNERLGSPTERQSHGRRVLKTAAERLGIAESDLNRMRWFAHLADATALRQVHPEIDSWTKFKEGLPDLKAEYGFETRKPAENPSRPALRGVVRSCTNLASMLDGLDLQPGDAERKDFLDALQKLAEAASRRLKISVMVAVE*
Ga0007432J51704_121181	Ga0007432J51704_1211811	F019767	AVIGSGGDQRTITREEFLRRLGQLAEKWQAHHGAGLEIRHETGKLLNERFGPPTAKQKRGEGVLKEVVERLQVAESELSRMRRFAFHFESVKALKEKYPEATTWTAVKDLLPRLNKPKKGSAKGAASRAKRKQAKPVQFGRVKQSLEALTSKLRKAREGLTDAERKELLAQFRELVEAVAHCLKMPLSVSQVSEEPAPPAAPKE*
Ga0007432J51704_124875	Ga0007432J51704_1248751	F043998	GVQMKTKSISVMCIALVLAFASIASAQARVQAGSDEDKALRKIKTQDANPDAQIPMLLDFEKQYPKSQALSEVYAMLVDIYMTKQDNAKIIEYGEKAIKADDKNVSALVAVSRAYAMKRENLEVAVSYAQKAVDNVNKMKTQPAPSNYSPAEWEQLIKDNEDAAKGQLSYAKAVKQ*
Ga0007432J51704_129059	Ga0007432J51704_1290592	F075517	MFTDPITLTPGASFDAGAVSLPRVSQQGAISVYQAGPLTVNAGSLLRVSASHQYGKRTRRVLRCDYSDNAGSTLISGTTAPRSMSCYVVFDIPSAGQFSATD
Ga0007432J51704_129325	Ga0007432J51704_1293252	F096396	MKSLTSLWSCTAQEMAVRCCTSAARDIKTVERRFKHEGLSFLAITLADFGKAIQKWLDQGFVVPSDAPSFARGSGRLIGLPVFLQGFLGRVFEPCSGALLENPDIEA
Ga0007432J51704_129975	Ga0007432J51704_1299751	F018726	RLMLPDPVTITAASPTPQLVFAVVKQDGYGSERKDTGGNGYTVITNHSYQKGGGDKHYVQMTQTLNATDPYSGLTKKQTASVSITIVRPAFGFTDAAMIALAKALTDYRDDSEVTTAKLLQFQS*
Ga0007432J51704_130807	Ga0007432J51704_1308071	F008193	MRTRLFLVTLAAALLAVPAALANNGHLVRYSFLGQLTATPGNGGVSITVQGGNKIALRAMLGAPVTQTFAYGSTTEFLKWSKGVPAIVQATDLAAGDFVWVHVRAPRGASLADIEHNAAGIVGDHGTQLFKPSKPLYLFRGKLTAVNGNTVTVDVAGGNHH
Ga0007432J51704_132580	Ga0007432J51704_1325801	F102266	VTGGTANGQIELQGYSQNHYGTANFTNDPTPIDRTVTAGSDGSATISDLRPASNTRIRARVKGCAFGTNALGSVINVRTQLTLAAKRTGTRTVVISGGSIPARPGGLIVGIYRDGVLIGQARADQTSGQYSVTLHFPASDQGKRINLNARTGQDAQNAPGQSNTRSLLIT*
Ga0007432J51704_133058	Ga0007432J51704_1330582	F031471	MRLTGFDAIEYAEKEGLALHKAAGRIDDGADNLSVAEAEAIADDDPDAIWLDVPDDEYYG