3300026144: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_A_D2_MG (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026144
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125945 | Ga0209954
• Sample Name: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_A_D2_MG (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 218009731
• Sequencing Scaffolds: 12
• Novel Protein Genes: 15
• Associated Families: 13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	3
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1
Not Available	4
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Nitrosopumilus adriaticus	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Wetlands → Unclassified → Soil → Salt Pond Water, Soil And Salt Crust Microbial Communities From South San Francisco Under Conditions Of Wetland Restoration.

Alternative Ecosystem Assignments

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

Location Information

• Location: South San Francisco, USA
• Coordinates
  • Lat. (^o): 37.4962
  • Long. (^o): -122.1329
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001127	Metagenome / Metatranscriptome	769	Y
F003470	Metagenome / Metatranscriptome	485	Y
F031688	Metagenome / Metatranscriptome	182	Y
F035704	Metagenome	171	N
F037805	Metagenome / Metatranscriptome	167	Y
F043464	Metagenome / Metatranscriptome	156	Y
F055778	Metagenome / Metatranscriptome	138	Y
F071971	Metagenome	121	N
F077325	Metagenome	117	Y
F082716	Metagenome	113	Y
F093463	Metagenome	106	Y
F093897	Metagenome	106	Y
F105217	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209954_1001358	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	4713
Ga0209954_1001725	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Candidatus Nitrosopumilus sediminis	4223
Ga0209954_1002552	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	3438
Ga0209954_1002816	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus	3281
Ga0209954_1009062	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → unclassified Planctomycetota → Planctomycetota bacterium	1749
Ga0209954_1012461	Not Available	1486
Ga0209954_1013028	All Organisms → cellular organisms → Bacteria	1453
Ga0209954_1014272	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1384
Ga0209954_1035082	Not Available	883
Ga0209954_1035247	Not Available	881
Ga0209954_1046286	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → Nitrosopumilus → Nitrosopumilus adriaticus	773
Ga0209954_1100521	Not Available	535

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209954_1001358	Ga0209954_10013584	F105217	VDTIKEKNELVDSIQFRLFYAEINLDKIPVAIPLDIFPKDKISSEIAMDGFLFYANGALDLIFTEINKKLDLGLALNQINPSDIVQALEKKNSDETKKIIEVFQKNFQKPVHEEKIITDKEFNDGLNRYGYDVIGFHAEYENRDQVKYQHFWNRASSRLWEIRNQENLESYDSLLKNAGQKGTDKPRNHLRVKLASDDRPAVYWDSAHYENPKRYFTNILFLVKKFIDKILEILKPLYLPDSKTP
Ga0209954_1001725	Ga0209954_10017253	F082716	LISKKDIKHMPVTFIIAPVVLISLVYIVFITSNDMIEEKEFIVSLSCPELREYTQSQIIDSKLYFGHEVFLSYAEERYDTSC
Ga0209954_1002552	Ga0209954_10025524	F077325	LSKKGNWTEKDEATIKAIIVNMINQKQMFRNLGEKGELPSSFNVQNSREFVLGIFTGIVINLFANYWVGEHEAGLLPEDLDFLYHKIALSNELILVGLFE
Ga0209954_1002816	Ga0209954_10028164	F055778	MLSNVDFPEPELPTIRTISPFSIENDTSSRALTLLSPSP
Ga0209954_1009062	Ga0209954_10090622	F003470	MVRIADACYCRRTTAQTQAQELKQNLSKVMRSFGRSCRGQGKVFVKLVRQTEQQLLDVGETISTLARQAQASLEQTTTLSETQRAWFNEHLTTAMRHHEQIRQQSKQLTQGKKLAHFKVVNAYDPTIAPIIKGKSNCPAQFGRKPGIMSEPASGYIFANLTPKGNPSDESYVLPLIDKVEQAIGRAQQGPKRSIHSLAGDLGVNDPVLRQALHERGILSVGIPKTVEPINAHPSAQEVLDILNEADLNRKRTPHQVHLACASGFSRPVVESHIAALLSRGAGSVRYKGMEGAVVQQGMTVMSYNGAVLVRIRQQKLTKRAQKFRRLLGLKPPKVNEINQEKN
Ga0209954_1012461	Ga0209954_10124614	F031688	MKTYIIYVKGYEKGVIKAASHNAAEKKAWKKFSDYPREQISVAYTEV
Ga0209954_1013028	Ga0209954_10130281	F043464	IAATRTATDAELPLYGLTNGALVHTEARIPGTDVRVVFSEFTLAAGSQQSANPFQWRIQDVGAPQFQLQVAGLDALLDRTRQAGYRFLSVDGRPIPRPFGRFVFAIDPDGVLVEYVEPQTSR
Ga0209954_1014272	Ga0209954_10142723	F093897	MKLGFYISIGVAIGALVVGFVLLNDIQQEKDAKTVWIQKIPTQCNDVWNAEYSEYYEINPEMKEISGEESKAILETIIKNHYENQGISILDLNLEVDYYDGVRCEACSCLGWDRLSIQISQNDLDGIPVSEGWEVLN
Ga0209954_1035082	Ga0209954_10350822	F001127	MGHDHIEQYAAEEGGVTLHTWTDVQGAKKENFYITGMPGAPVPTWFRTVLRKKDLADIANFPNHPS
Ga0209954_1035247	Ga0209954_10352472	F001127	MDHPHIEQYQARDGGVTLHTWTDMQGDKKENFYITGMPGAPVPAWFRTVLRKKHLADIANFPNHLS
Ga0209954_1046286	Ga0209954_10462861	F071971	MRITVFYNAESTIKAINNTAKYGLENLNKVHDAFSMGLTITQIDNAIINAPDAIAVHRYTLPTISSPFSVVMKNGAIENNTITTVDPAMAR
Ga0209954_1049969	Ga0209954_10499691	F037805	MRHLLLPAQAWWDAQRFDQPTWQVASWRDQKARHIHLHVAKALGKVVQMLDEAAPLTSNTALQGRVRDEALPDIAIYRSQLINLLPDGCALPASLSATTPGGNLQAEANWRHAALSLSRASAELAGYLEPQEHGAASPASHLMQAIEHLQASAAAL
Ga0209954_1100521	Ga0209954_11005211	F001127	MDSYLEQYETKAESVTLHTWTEEQGAKKDHFYITGMPGTPIPGWFRKVLSQKRLADIANFPHTPSCFYD
Ga0209954_1105802	Ga0209954_11058022	F035704	MALRINDSEYYAIDSHSHLGKRKTPLGHGVASFLG
Ga0209954_1114416	Ga0209954_11144161	F093463	VGTEEPRGAVHWIDHFVVGTNDMVAWSNWGVNAIGLDRQPIVGLTTAQRK