3300003157: Avena fatua rhizosphere microbial communities - H3_Bulk_Litter_17 (Metagenome Metatranscriptome, Counting Only)

Overview

Basic Information

• IMG/M Taxon OID: 3300003157
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110115 | Gp0061289 | Ga0006774
• Sample Name: Avena fatua rhizosphere microbial communities - H3_Bulk_Litter_17 (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: 654573
• Sequencing Scaffolds: 7
• Novel Protein Genes: 11
• Associated Families: 11

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
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Chlorophyta → core chlorophytes → Chlorophyceae → CS clade → Chlamydomonadales → Volvocaceae → Volvox → Volvox carteri	1
Not Available	4

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizosphere → Soil → Unclassified → Avena Fatua Rhizosphere → Avena Fatua Rhizosphere Microbial Communities From Hopland, California, Usa, For Root-Enhanced Decomposition Of Organic Matter Studies

Alternative Ecosystem Assignments

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

Location Information

• Location: Hopland, California, USA
• Coordinates
  • Lat. (^o): 38.97364
  • Long. (^o): -123.117453
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000203	Metagenome / Metatranscriptome	1619	Y
F001024	Metagenome / Metatranscriptome	803	Y
F001633	Metagenome / Metatranscriptome	660	Y
F026580	Metagenome / Metatranscriptome	197	Y
F027071	Metagenome / Metatranscriptome	195	Y
F030647	Metagenome / Metatranscriptome	184	N
F034588	Metagenome / Metatranscriptome	174	N
F056192	Metagenome / Metatranscriptome	138	Y
F065302	Metagenome / Metatranscriptome	127	Y
F076133	Metagenome / Metatranscriptome	118	Y
F100491	Metatranscriptome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0006774J45829_10005	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Oscillatoriophycideae → Chroococcales → Microcystaceae → Microcystis → Microcystis aeruginosa	664
Ga0006774J45829_10032	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	534
Ga0006774J45829_10115	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Chlorophyta → core chlorophytes → Chlorophyceae → CS clade → Chlamydomonadales → Volvocaceae → Volvox → Volvox carteri	648
Ga0006774J45829_10204	Not Available	530
Ga0006774J45829_10309	Not Available	827
Ga0006774J45829_10537	Not Available	580
Ga0006774J45829_10620	Not Available	527

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0006774J45829_10005	Ga0006774J45829_100051	F034588	ASPLIRTSGCPSFRISGFTGDRSSSRLDSLSFGGAGCESSRSPLRFASPVSPTISFWVAPDPHPPVPADFRSESPRSSVPSGRPLRISGLLRLFALGFVAQPFPKSPWFLLAQRRRFRLSRVAPKLPSSADPYLLPQVAPASASTAGSMITPWLNRTLHPRLAPWMNLRYQSGTSIPDLTSSALLISIHCPQSADHEL*
Ga0006774J45829_10032	Ga0006774J45829_100321	F076133	DPCADAVTPEGFGCYCADQNAVEIPGGTTPPKGPVRRTNGARKGVTTAGRERT*
Ga0006774J45829_10032	Ga0006774J45829_100322	F001633	TRLDALAFAGGVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDASCRKRRAGRGADTPATFTFSRRHPYHGDGASFWPAVGPALRV*
Ga0006774J45829_10104	Ga0006774J45829_101041	F000203	ALFPALTFGAFLAEAASFPTLFSTASGVFGLVAGPSSALRSLNFE*
Ga0006774J45829_10115	Ga0006774J45829_101151	F026580	SSVMRKGTARGGTIRNRSESSRVVQESFEPERIAVTQRVNGCYCVSARANGSGGFRKEVSQRKDAERRDKVSVRTGEDTGSRQDP*
Ga0006774J45829_10116	Ga0006774J45829_101161	F056192	SKRFEGQRAKREVAELER*SAARWYVKTIATRRGVKADRATRYGKFLRLKSGRAL*SGRDRKVLKGSGSPNTSGELWERKLATGDSR*SSPAGRKKPGEAGSGKPNGSIEILRQL*RCRPGASTRPRGFAARQTFAAGE*KAASRSKLLPERRADEHQSYDPRLNKTGRGERRAHVTSDPDAKLRPCMPVGERAIHRVTWN
Ga0006774J45829_10204	Ga0006774J45829_102041	F065302	TRLHADVRFAARCSG*IACHSPSPLFSM*RVTVASALNGHNTLPEPESRYGLSLAHNDAFATIARSTFLACTFVSPSDTFANPFDSRLLRSVRFRGRTGALSMPGTRFPRRSPTFPIDPRSPLPFRSSCENPPDQSVQPVPFQEARLA*RSIASYSPPLPLSIPLQINV*NSLRPA
Ga0006774J45829_10252	Ga0006774J45829_102521	F100491	TVPSDRQAACSPTGMHGPNVASGTGET*ALCFPLKVLANRGSLRRCASALHSDRSPLLDATFRSTAPRTGLATDPRNCVNVPGLHLRNDPQIRSGPFGYVLPHPLCLLWLGGRDLHTNPLPNPT*RLIARLRTSAPLRELSLPRDQSSQPDFELQSLPLQVARSSFAPRSAATVLWIAQRFGSSFQIRYFLPGSLSLKP
Ga0006774J45829_10309	Ga0006774J45829_103091	F001024	MRPKTPLAVENGVGKLAAKERLMPAWERECGELPSPNLSLSD
Ga0006774J45829_10537	Ga0006774J45829_105372	F030647	LGANFLLYLRTPKIRPEIETRLGYPVLNSDHVHLSDMTVFIASSSVHLLFVIQHGGKIKPKIGPKVIHILLALEKLFLL*
Ga0006774J45829_10620	Ga0006774J45829_106201	F027071	ATTPLRKQLPLFVQRRHRPSTPLAPALANLRSKHKRQHGNAPSGQRINFLRNHFTGKRFAPSLPLHQLSLTLRIKIIGHFNKAKLNSTDTSLLAKLCISSANALANILAIGNFTLLANHQTAVPEEISFDLLGPSNRRYCYPRSAAISASCPTNTSTPNRQGNSCKYCYLAEVIR