3300026127: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_C_D1_MG (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026127
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125948 | Ga0209956
• Sample Name: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_C_D1_MG (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 226995202
• Sequencing Scaffolds: 11
• Novel Protein Genes: 12
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium	1
Not Available	4
All Organisms → cellular organisms → Archaea	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	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): 37.4965
  • Long. (^o): -122.1329
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003187	Metagenome / Metatranscriptome	502	Y
F007188	Metagenome / Metatranscriptome	356	Y
F025809	Metagenome	200	Y
F027211	Metagenome / Metatranscriptome	195	Y
F047069	Metagenome / Metatranscriptome	150	Y
F069017	Metagenome / Metatranscriptome	124	Y
F074459	Metagenome / Metatranscriptome	119	Y
F084079	Metagenome / Metatranscriptome	112	Y
F099485	Metagenome / Metatranscriptome	103	Y
F105625	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209956_1001472	All Organisms → cellular organisms → Bacteria	5041
Ga0209956_1009152	All Organisms → cellular organisms → Bacteria	2012
Ga0209956_1024486	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Planctomycetales → Planctomycetaceae → unclassified Planctomycetaceae → Planctomycetaceae bacterium	1201
Ga0209956_1041506	Not Available	906
Ga0209956_1065662	All Organisms → cellular organisms → Archaea	704
Ga0209956_1070319	Not Available	678
Ga0209956_1075414	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → unclassified Actinomycetia → Actinomycetia bacterium	653
Ga0209956_1084829	Not Available	613
Ga0209956_1107905	Not Available	538
Ga0209956_1112534	All Organisms → cellular organisms → Bacteria	526
Ga0209956_1122269	All Organisms → cellular organisms → Bacteria	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209956_1001472	Ga0209956_10014728	F047069	PPVKRASLLLGSGTTASCDGSFSQDLNALWCPVCPKPNHNPGAGVVVQAQLWYRDPLNTSNQTTSLSDAIEFSVGP
Ga0209956_1009152	Ga0209956_10091522	F027211	MVRTYWLVPVFYEASGNLDLRPFARTDQIEACRPRAMWLPIVRGQVG
Ga0209956_1024486	Ga0209956_10244861	F047069	NGRQANPWGNGTSLQCVAPPVQRAGLLSASGTAGLCNGQFTQDLNARWTAKPNQNPGAGALVQAQFWYRDPANTGNQTTSLSDALEFNVCP
Ga0209956_1041506	Ga0209956_10415062	F074459	MVGVGTAGVCNGTFSQDLNARWQFKPNQNPGAGAVVQAQLWYRDPLNTSNQTTSLSDAVEFTVGP
Ga0209956_1065662	Ga0209956_10656622	F099485	MKQKIMQNWQHSPSKTQVAIKPVKAVSKSLRQTKSPILTNEDLMGISWILFEEKD
Ga0209956_1070319	Ga0209956_10703192	F003187	MGGVIMKKILVIVCSAILAIGVAGCAGKAPVGKGKAPVVHTKG
Ga0209956_1075414	Ga0209956_10754142	F025809	VDVDFRSGPGLGVLFRASVDEAGRMSGYSFDIDPIYDGGGYLVRQWQADRELWNPIARVGAVDPSSMYGMLTVRLVVVDDRLVALVNGVEVLQVDNLKQTSTDQGREAATGDRVGIQAWSSSDLVIDTLRVAGF
Ga0209956_1084829	Ga0209956_10848291	F069017	PRIKSGAGCAAILAGQLDDVGGQPLFIVTAVRDLTLCRAMLAERHTGAALGDGQYPSNMLDTGAATRGA
Ga0209956_1100912	Ga0209956_11009121	F084079	MPKTYDTVYGYDGSGYTVGDRVELHPATDLGMRGVRYGTVTRLSLTPNDRVHVELDKRPGRTFAGSADTFRRVEG
Ga0209956_1107905	Ga0209956_11079051	F074459	PLSSGFCLLGTCGGSFTLDLNARWCATCPKPAHNPGAGAVGQAQLWYRDPTNTSNQTSSMSDAVEFVVEP
Ga0209956_1112534	Ga0209956_11125342	F007188	IHVLLPCLQSALHSLGDSPARSLSALAQKLGVSEADAARMATLPPEVPEPVANPPGAATPISPLLPMTVLSDASCAPKTLLNRPIVIAARKKTTR
Ga0209956_1122269	Ga0209956_11222691	F105625	MSDVGTTHEDLEQFLAEHHLVGAGLRREGVAPLREGNTSAYWDWEGI