3300031491: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_R3 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300031491
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0132857 | Gp0330686 | Ga0314824
• Sample Name: Metatranscriptome of soil surface biofilm microbial communities from soil inoculated with nitrogen-fixing consortium DG1, State College, Pennsylvania, United States - MICR_R3 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 13333482
• Sequencing Scaffolds: 8
• Novel Protein Genes: 9
• Associated Families: 6

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	1
Not Available	2

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Freshwater → Groundwater → Unclassified → Soil → Soil Surface Biofilm Microbial Communities From Soil Inoculated With Nitrogen-fixing Consortium Dg1, State College, Pennsylvania, United States

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → land → biofilm material
• Earth Microbiome Project Ontology (EMPO): Unclassified

Location Information

• Location: USA: Pennsylvania
• Coordinates
  • Lat. (^o): 40.7997
  • Long. (^o): -77.8629
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000344	Metagenome / Metatranscriptome	1257	Y
F001633	Metagenome / Metatranscriptome	660	Y
F044880	Metagenome / Metatranscriptome	153	Y
F053640	Metagenome / Metatranscriptome	141	Y
F059886	Metagenome / Metatranscriptome	133	Y
F080014	Metagenome / Metatranscriptome	115	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314824_103121	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae	824
Ga0314824_103206	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Enterobacter → Enterobacter cloacae complex → Enterobacter hormaechei	810
Ga0314824_103270	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	802
Ga0314824_103413	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae → Escherichia	783
Ga0314824_103661	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Enterobacterales → Enterobacteriaceae	752
Ga0314824_104096	Not Available	706
Ga0314824_105856	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Opitutae → Opitutales → Opitutaceae → Lacunisphaera → Lacunisphaera limnophila	584
Ga0314824_107376	Not Available	523

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314824_103121	Ga0314824_1031211	F001633	GQLVGVGVRHTLFPGGTRLDTLAFAGVVLPDATLCGMQMFRSHGGTVLTVAGRDLSSEASAPGSDAPCRERRAGRGADTPATFIVARRHPYHGDGTGFWPIVGPALRV
Ga0314824_103206	Ga0314824_1032061	F001633	FVTRSFPAAHAWTRSLFAGGDLPDATLRGMRMFRSHGGTVLTVAGRELSSEASAPGSDAPCRERRAGRGVDTPATFIFRVGTFYRGVGISLWLIVGPALRV
Ga0314824_103270	Ga0314824_1032701	F000344	MRPKHLHAAESGVGKHTARESERVQACAAGKERVTN
Ga0314824_103413	Ga0314824_1034131	F053640	TVAAQRSEMVAESTTGIIPGDRGKAGGNWCRPPLMPAKAVMRHISPVPLAGVVSGQSTHELGTEPQGAIRNRVEWSQATQGVSTCASTQLPQRLRLLLRRPERHRVSRRDDPAKRPHSPHEWGAQGTYGGGERTDLGKVREPPHRGGVKHTSPSCKRQRSLRGKRSDP
Ga0314824_103661	Ga0314824_1036611	F059886	VIYASRLAFAVLRGGRHQLSPTFPRSPGIIPVVFSV
Ga0314824_103661	Ga0314824_1036612	F001633	GTRLDALAFAGGVLPDATLRGMRMFRSHGGTVLIVSDRDLSSEAFAPGSDTPCRERRAGRGADTPATFFVARRHLYHGDGTGFWPVVGPALRV
Ga0314824_104096	Ga0314824_1040961	F080014	FDVVGSPAELQAEVPGRPRKTTGTNASAKNELALAA
Ga0314824_105856	Ga0314824_1058561	F059886	VIYASHLALAIGRGGRHQLSPAFPRSPGIIPAVLSATFFRPLRFD
Ga0314824_107376	Ga0314824_1073761	F044880	MTASVKILFVSMMVAVALLTTTGTLTTAPSAEAQTPYCQVNPTACTPQFCAIYPQLCNLPVVNPVYPVYPVYPINQCGYVNCVAPINCAPVPYSPIYGQIYRPANCGVYPYGYGYNNLCTFNAPCNAPYVGGAPARLNLAVSPAIATCGSTPVTVQAHITDAYGVAVAN