2084038016: Soil microbial communities from Hopland, California, USA, that is PCE polluted - amended with lactate

Overview

Basic Information

• IMG/M Taxon OID: 2084038016
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0046478 | Gp0051957 | Ga0010979
• Sample Name: Soil microbial communities from Hopland, California, USA, that is PCE polluted - amended with lactate
• Sequencing Status: Permanent Draft
• Sequencing Center: GATC-Biotech AG, Konstanz, Germany
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 6851318
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Soil Microbial Community From Hopland, California, Usa, That Is Pce Polluted
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Contaminated → Soil → Soil Microbial Community From Hopland, California, Usa, That Is Pce Polluted

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → land → contaminated soil
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: Hopland, California, USA
• Coordinates
  • Lat. (^o): 38.9727
  • Long. (^o): -123.1145
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000870	Metagenome / Metatranscriptome	851	Y
F022275	Metagenome / Metatranscriptome	215	Y
F023474	Metagenome / Metatranscriptome	210	Y
F023547	Metagenome / Metatranscriptome	209	Y
F030846	Metagenome / Metatranscriptome	184	Y
F031939	Metagenome / Metatranscriptome	181	Y
F039746	Metagenome / Metatranscriptome	163	Y
F061608	Metagenome / Metatranscriptome	131	Y
F069405	Metagenome / Metatranscriptome	124	N
F090794	Metagenome	108	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
SPCE_L_FRKAKSJ03BRFT1	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	513
SPCE_L_FSFSAB201A7FLO	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	519
SPCE_L_FSFSAB201B991S	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	503
SPCE_L_FSFSAB201DSVZS	All Organisms → cellular organisms → Bacteria → Acidobacteria	512
SPCE_L_FSFSAB201EO9FY	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	500
SPCE_L_FSPRUNR02G0A9U	Not Available	521
SPCE_L_FSPRUNR02GSSLW	Not Available	513
SPCE_L_FSPRUNR02HNOOX	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	510
SPCE_L_FSPRUNR02I7L28	Not Available	526
SPCE_L_FTC1UFH01DFJDF	All Organisms → cellular organisms → Bacteria	510

Sequences

Scaffold ID	Protein ID	Family	Sequence
SPCE_L_FRKAKSJ03BRFT1	SPCE_L_00116770	F090794	HSSGPLIPARRALEHRDDSLRRATGGGHASAADGNAFAIAADGNILEHHFATTTARRNATINCSRATAERDAAEFLVK
SPCE_L_FSFSAB201A7FLO	SPCE_L_00120950	F061608	RILTTYAINPGGSFVFDSDSKATFRPQRQGVAVKVVLACVQR
SPCE_L_FSFSAB201B991S	SPCE_L_00002910	F039746	PLWLFIGRLDAQAGGGHFTLHMTNGNQRALRLMLGQGLDQTFAYDAHTVFVLWQNGVPSVIQPQQMVVGDRISVRIRAPRGYSLRQVEAVPANHVGDHEPSTPGTT
SPCE_L_FSFSAB201DSVZS	SPCE_L_00015960	F022275	SGWTVRLSPGFGLNDNSHQLLLRWGLSYEFVGFGERVRRIWESR
SPCE_L_FSFSAB201EO9FY	SPCE_L_00031370	F030846	MSVITVRRTVIKGTPRETSIKRKVINGTAKKASPIRGSFRDLTRRYFAGENRLEFVIEALFFAIIVAISAWPILAAAGALQEFSN
SPCE_L_FSPRUNR02G0A9U	SPCE_L_00147830	F023474	LVGILHPEVANDRLEINTLAGNDTVDPSGLAAGAIQLFVDGVLVP
SPCE_L_FSPRUNR02GSSLW	SPCE_L_00000490	F023547	MRRKHKAFEKKPVAPHEAAERVMEAASQPVSTEAPDQLPDRRMRGIDETAPERSEFERTMKDYYAQTDVEGQGGIPKEPPDEDPMPLQHLEKPKHPPAHN
SPCE_L_FSPRUNR02HNOOX	SPCE_L_00086610	F031939	EPGNRKRGWNKSFNHPYRKPNDPAIGYWYLFAAEAELELGHDRAALDWALRADAFMPRSPLVQAWLASIYATIGDKSNAAKYVAALTKMAPGRTRLFMNRPSEDNNNVDGRSGPRIFDGLRLALGASLG
SPCE_L_FSPRUNR02I7L28	SPCE_L_00040460	F069405	RPGHEPEGEQVRIRQIATAVVIVATVAIATPAQANVGTSCSAWKTTKTGGHQSACYVRSADWQVAAKGRGYYDGSTKLVQMNISVSLQSSIDGITWSTLVSRSCGFTAVPSSSPGGSCLTAAEWVDAGALYRARTFLVLFEANGTVRTTNPSYSPITS
SPCE_L_FTC1UFH01DFJDF	SPCE_L_00112200	F000870	VCLMDQRSTEHRSLQEKTDREIIWTSHRNFQGWTCSQCEWNYPLPTLLNDPEARTAYDRLGAAKFREHKCAEHLSRLGGPDRESFTPRIRKLVTQGFKPKDAVELFLQEVALEYRNQPKTLEQARADGEDFLRRVKAGLI