3300007757: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_B_D1_MG

Overview

Basic Information

• IMG/M Taxon OID: 3300007757
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125946 | Ga0102949
• Sample Name: Soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG R2A_B_D1_MG
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 360035414
• Sequencing Scaffolds: 20
• Novel Protein Genes: 20
• Associated Families: 18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Thermoleophilales → Thermoleophilaceae → Thermoleophilum → Thermoleophilum album	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Archaea	2
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → Lacipirellulaceae → Pirellulimonas → Pirellulimonas nuda	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → unclassified Rhizobium → Rhizobium sp.	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales	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): 37.496
  • Long. (^o): -122.1329
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000532	Metagenome / Metatranscriptome	1046	Y
F002483	Metagenome / Metatranscriptome	555	Y
F003627	Metagenome / Metatranscriptome	476	Y
F005789	Metagenome / Metatranscriptome	390	Y
F009170	Metagenome / Metatranscriptome	322	Y
F019205	Metagenome / Metatranscriptome	231	Y
F028464	Metagenome / Metatranscriptome	191	Y
F039119	Metagenome / Metatranscriptome	164	Y
F049640	Metagenome / Metatranscriptome	146	Y
F049899	Metagenome	146	N
F054877	Metagenome / Metatranscriptome	139	Y
F065013	Metagenome / Metatranscriptome	128	Y
F070130	Metagenome / Metatranscriptome	123	Y
F074892	Metagenome / Metatranscriptome	119	Y
F077325	Metagenome	117	Y
F082716	Metagenome	113	Y
F088283	Metagenome / Metatranscriptome	109	Y
F094435	Metagenome / Metatranscriptome	106	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0102949_1002687	All Organisms → cellular organisms → Bacteria	3303
Ga0102949_1005407	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Thermoleophilia → Thermoleophilales → Thermoleophilaceae → Thermoleophilum → Thermoleophilum album	2476
Ga0102949_1005764	All Organisms → cellular organisms → Bacteria	2418
Ga0102949_1009974	All Organisms → cellular organisms → Bacteria	1947
Ga0102949_1023509	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae	1371
Ga0102949_1028044	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Corynebacteriales	1275
Ga0102949_1052570	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	982
Ga0102949_1086141	All Organisms → cellular organisms → Archaea	802
Ga0102949_1097491	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Planctomycetia → Pirellulales → Lacipirellulaceae → Pirellulimonas → Pirellulimonas nuda	762
Ga0102949_1097884	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales → unclassified Rhodospirillales → Rhodospirillales bacterium	760
Ga0102949_1102709	Not Available	745
Ga0102949_1109414	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Deltaproteobacteria bacterium	726
Ga0102949_1121116	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	697
Ga0102949_1127695	All Organisms → cellular organisms → Archaea	682
Ga0102949_1141233	Not Available	655
Ga0102949_1145378	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → Nitrosopumilaceae → unclassified Nitrosopumilaceae → Nitrosopumilaceae archaeon	647
Ga0102949_1168282	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Rhizobiaceae → Rhizobium/Agrobacterium group → Rhizobium → unclassified Rhizobium → Rhizobium sp.	610
Ga0102949_1212799	Not Available	557
Ga0102949_1233941	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Acidimicrobiia → Acidimicrobiales → unclassified Acidimicrobiales → Acidimicrobiales bacterium	537
Ga0102949_1242242	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Chromatiales	530

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0102949_1002687	Ga0102949_10026873	F005789	MKAGKTRTRDGALSALRTPTNPPVPTMLVPLDASPLNVVRSMRGAIVDARIAYPEVLHVEIKDSDGELWRLATQDAEWSPSDPAELVGRSVADADIDAETGELRCKLSDGAVLDVKPAEREADDDPSNWELIAPGGVALEFGPGVRWQIGSADSPAS*
Ga0102949_1005407	Ga0102949_10054074	F003627	VDRETSKREMAAGLQAGAFAAAVFALCFVAAMLYIAS*
Ga0102949_1005764	Ga0102949_10057643	F019205	MASEGSRKFELMFDSRKTYRDKALDAADLVIDFATLGEYGLESVDTAPRACEGRRRLANQRSTGTWNAAIDRFAAQS*
Ga0102949_1009974	Ga0102949_10099743	F000532	VALIKERLGIEAETKAGGTGEFEVIADGETIAERGGNWLTRGFGAGYPDLDGVVDELEARTR*
Ga0102949_1023509	Ga0102949_10235093	F082716	IIAPVVLISLVYIVFITSNDMIEEKEFIVSLSCPELREYTQSQIIDSKLYFGHEVFLSYAEERYDTSC*
Ga0102949_1028044	Ga0102949_10280443	F002483	LDRELERLRGLPVFAGSALATRRPQLKVRRASKRPNKLGFAVPAEFRLQVTAYPGIGVGDILETLLHELTHLHVGRAAEAHAWHGRTFKAALAQAMREAYGVEVPPPAHTRHGVYAAAITATL*
Ga0102949_1052570	Ga0102949_10525702	F094435	MNFNWALLPAACLLLFPITQIAAQEQAVLGQGNVSCDAWLIDRRENNAQASGRIAWILGYVTAFNQYGSKPAGDVSAGMDTDEIMVWID
Ga0102949_1086141	Ga0102949_10861412	F077325	LSKKGNWTEKDEATIKAIIVNMINQKQMFRNLGEKGELPSSFNVQNSREFVLGIFTGIVINLFANYWVGEHEAGLLPEDLDFLYHKIALSNELIFVGLFE*
Ga0102949_1097491	Ga0102949_10974911	F049640	GGAATCGGVAPRPSTEKLRMARHPAIKLELLPHERAALLKWNYTPEVRAQLEACASSDNIETITITSVDANWLASDLTHAIVKRGCRDQDVIDLSERLEYVDQSGDGSLDGWYY*
Ga0102949_1097884	Ga0102949_10978841	F009170	MVRIADACYCRRTTAQTQAQELKQNLSKVMRSFGRSCRGQGKVFVKLVRQTEQQLLDVGETISTLARQAQASLEQTTTLSETQRAWFNEHLTTAMRHHEQIRQQSKQLTQGKKLAHFKVVNAYDPTIAPIIKGKSNCPAQFGRKAGIMSEPASGYIFANLTPKGNPSDESYVLPLIDKVEQAIGRAQQGPKRSIHSLAGDLGVNDPVLRQALHERGILSVGIPKTVEPINAHPSAQ
Ga0102949_1102709	Ga0102949_11027092	F039119	MFHLPEPASAEWQSRQLVVTPEQLGLHSVGDCQQRAEKLGLTPMPPLPYRQEFWRLDVLLKWSKRNGFEQLPMLGRGLGHRR*
Ga0102949_1109414	Ga0102949_11094141	F028464	MPWVGLGTDRKNPTFRHVDGSVMNGRLYIDDRIIVHEQGMLDRSFLHDPEVLEAAAEYGDPYQVLAPVSHEAHGSGTLL*
Ga0102949_1121116	Ga0102949_11211162	F065013	MEMGSTVSSQLVGWTRTALLPGDVVTLYVWPAKTGEPVGRFNKVEFDDGTVLRDSQRGADDGGRSDTGLRQ*
Ga0102949_1127695	Ga0102949_11276952	F077325	MSGKGNWTEKDEATIMAIIVNMINQKEMLKDLGGKSEMQNSFKIENPKEYVLGLFSGIVINLFANYWVGEHEAGLRPEGLSYLYHKISESSDLITKGLFE*
Ga0102949_1141233	Ga0102949_11412331	F074892	MRQRYAVIALLGLLLSACAERGENVYRTWVGPDRSNMAIVTLRLGEDVKDVTVRERVLPRSEYGTVLLAPGAYTLYEEDGASIGINIRPAIVSLERARANGELILGHTYVLRAGKSKQTGERALWIEDARSGDVFVDRR*
Ga0102949_1145378	Ga0102949_11453782	F082716	MISKDDIKLMPFTFIVAPILLISLTFVVVITYEDMIDEKELIVSLSCPELREYTENQIIESKLYYGSEVYLSY
Ga0102949_1168282	Ga0102949_11682822	F049899	MGLPPTTTAATVAAVVVGGNPIGGGLRGSVTATIVGALFLTYLGQLVLAVGFETSAQNIVQAIIIIASVGIVEAGRRIRFEWIRFKFWITSPDVEFRIRTTFTRTMSRLGLSKLLDVAPQVRWRWRTAYLRLKKRLEITE*
Ga0102949_1212799	Ga0102949_12127991	F054877	VKKYRNLRVLARFRPMNTDDLDSELINLVGEEAEFRYHKFVDEDDTPYSNQWVLTAEDQRFGDYWFPEYDLEIRREKLSH*
Ga0102949_1233941	Ga0102949_12339411	F070130	QMPATPASQPDSFVGWWEIVFHIKDGEQTDVTDIIEHVDAAGNFTVLRDGERIGAGHHVDFTVDPDGFTNVPVAADPDLQIARELAIYRFSRDVLEVCKASEHQGRPTSFASPRGSGWTHVAIRRISDDDPRVRTQR*
Ga0102949_1242242	Ga0102949_12422421	F088283	GSLACVAGCATNDHVTGTYAPSCVAFEGNTIELADSRFTWDKFTDEVRVDDAGNTIDPFPGFPVRGTYTVVDDVVRLVTDVGDLAAELHLVRRPGQVYLLTDSEFDAWQSNGTVPNCALLLGAGE*