3300003288: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_44 (Metagenome Metatranscriptome, Counting Only)

Overview

Basic Information

• IMG/M Taxon OID: 3300003288
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110148 | Gp0072768 | Ga0007428
• Sample Name: Grassland soil microbial communities from Hopland, California, USA - Sample H4_Rhizo_44 (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: 5529794
• Sequencing Scaffolds: 12
• Novel Protein Genes: 15
• Associated Families: 15

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
Not Available	7
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.	2

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?
F001633	Metagenome / Metatranscriptome	660	Y
F004796	Metagenome / Metatranscriptome	423	Y
F005082	Metagenome / Metatranscriptome	412	Y
F022652	Metagenome / Metatranscriptome	213	Y
F033437	Metagenome / Metatranscriptome	177	Y
F034588	Metagenome / Metatranscriptome	174	N
F039900	Metagenome / Metatranscriptome	162	Y
F048143	Metagenome / Metatranscriptome	148	N
F079670	Metagenome / Metatranscriptome	115	N
F081897	Metagenome / Metatranscriptome	114	Y
F082288	Metagenome / Metatranscriptome	113	N
F096396	Metagenome / Metatranscriptome	104	Y
F100491	Metatranscriptome	102	Y
F102642	Metagenome / Metatranscriptome	101	Y
F102643	Metagenome / Metatranscriptome	101	N

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0007428J48920_100035	Not Available	599
Ga0007428J48920_100221	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa	770
Ga0007428J48920_100226	Not Available	818
Ga0007428J48920_100471	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	603
Ga0007428J48920_100972	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	801
Ga0007428J48920_101650	Not Available	776
Ga0007428J48920_103326	Not Available	587
Ga0007428J48920_103467	Not Available	534
Ga0007428J48920_103591	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.	1769
Ga0007428J48920_106113	Not Available	779
Ga0007428J48920_106754	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Leviviricetes → Norzivirales → Fiersviridae → unclassified Fiersviridae → Leviviridae sp.	559
Ga0007428J48920_107847	Not Available	583

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0007428J48920_100035	Ga0007428J48920_1000351	F079670	LKKGLKVLEMVKRERNKIIIIDNSLKLSTTLYFSFKKKYNLS*
Ga0007428J48920_100221	Ga0007428J48920_1002211	F034588	LPRWLLHPPASPLIRTSGCPSFRISGFTGDRSSSRLDSLSFGGAGCESSRSPLRFASPVSPTISFWVAPDPHPPVPADFRSESPRSSVPSGRPLRISGLLRLFVLGFVAQTFPKSPWFLLAQRRRFRLSRVAPKLPSSADPYLPPQVAPASASTAGSMITP
Ga0007428J48920_100226	Ga0007428J48920_1002262	F081897	GLNGGWEFAMLSFPCRHLAPYLGMAAGFPTLFSTASGVFGLVAGPSSTLRLLNFE*
Ga0007428J48920_100471	Ga0007428J48920_1004711	F033437	TRLGALAFAGCVLPDATLRGKRMFRSHGGTVLTVAGRDLLSEVFAPSSVAPCRERHAGRGADTSAILLRVGTVTAGTAPAFGWSLALRYGSDLLPLRLLSLLQCGGVVFTLPH*
Ga0007428J48920_100859	Ga0007428J48920_1008591	F100491	VPSDRQAACSPTGMHGPNVASGTGET*ALCFPLKVLANRGSLRRCASALHSDRSPLLDATFRSTAPRTGLATDPRNCVNVPGLHLRNDPQIRSGPFGYVLPHPLCLLWLGGRDLHTNPLPNPT*RLIARLRTSAPLRELSLPRDQSSQPDFELQSLPLQVARSSFAPRSAATVLWIAQRFGSSFQIRY
Ga0007428J48920_100972	Ga0007428J48920_1009721	F001633	GGTRLDALAFAGGVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDTPCRERRAGRGADTPATFVSSRRHPYHGDGASFWPAVGPALRV*
Ga0007428J48920_101650	Ga0007428J48920_1016503	F004796	MTATNLPLPLRLTEPVLLAGDLDTQVREGLSDAYDGKAQLCSGTHSSTQSKTLNLLGIQVDVNADAVVDDVIA
Ga0007428J48920_103326	Ga0007428J48920_1033261	F022652	RLLPSKSRVHGTIERTTRMLSVRSAAKCALSSVCCSPLLPFSLPRVNTANAVFGYRTLPEPVSRCGLSLTRNDTFAPFRGQCSRPAPSIPRRTPSRIRSIQNSIAPFGFEADPGRYPCPKPVFRADFRRSRGFSQPPLPFRPFRALRIKAFSRLPPHEARPARPRFPFAPLAVSFDSTPDQRLRFSASCPTNRSV
Ga0007428J48920_103467	Ga0007428J48920_1034671	F048143	EQPSADMIDERLAAWQAGDYPEGWSVYDALGWSRDEYMIWLADPSRVPERPLSALPDPEIYAPVERHEERVESA*
Ga0007428J48920_103591	Ga0007428J48920_1035911	F005082	RVNHSKLAPDPFRPTENVKVSMSHYIVFDVPVAGYTTTEQIAVYTGFKTMYTAATDALITKLLGGES*
Ga0007428J48920_104778	Ga0007428J48920_1047781	F102642	MTLACFLNETLLSERRRKAGQREHSTREGHDVWAGRVKTFRNAGDVEKGAAGP*
Ga0007428J48920_105074	Ga0007428J48920_1050741	F102643	GGRSHPKLNILGRPIAKKYSDGKVKRTLKRRSKVLETVKRETDGASNYPMGIQIIHFYSASQLVNKSTECLVGWLLGYYVRYLVCMFVNIKCERGIFHGGR*
Ga0007428J48920_106113	Ga0007428J48920_1061131	F039900	VNHSLAEQDRETWNYVLSDYRTESERDSEADIPVPDRLLPKRRSQELVRMLKLGQMIGILLWLNREELITLGGRERLLYLQAKASFEALEAGLRFARRLSLEEKLRSDFRHQMRELNRRPQSRHFRQVEARRIGVGYRDKGMLPGSSSGARTTAQRDAFVPSHLLPDLLLGAIRSVYPEFLTADEEWVDLSMVAGSFGTQASIGARPLLPPL*
Ga0007428J48920_106754	Ga0007428J48920_1067542	F096396	MKSLISLWSRTANELAVRCRTSATRDIKTITSRTENEGLWFLAVTLASFGKATEKWLNQGFVDPTDVPSFKRTNGHPTGRPAFLQGFLDRVFCSDSGALMDEPDIE
Ga0007428J48920_107847	Ga0007428J48920_1078471	F082288	NKTKNMISFLVLSSILGIAIVSTNAILTAQTVNAQFVVKLGGPDTDQVNSRIVGTLLKPGFTNKYNLTVNGKTIPIDYSVLDGSLVGILSDPSRKSLDLAVNPQANGAALEVNVPRHVIDSKNAAGKDAPFIVKVDGNRISGEPSGICVGTCPNILNSFKETYNTNTDRVLTVLVGPESRFIEIIGNHTSA*