3300026106: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_A_D1_MG (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300026106
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0114514 | Gp0125953 | Ga0209927
• Sample Name: Salt pond soil microbial communities from South San Francisco under conditions of wetland restoration - Salt Pond MetaG SF2_A_D1_MG (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 116748770
• Sequencing Scaffolds: 30
• Novel Protein Genes: 31
• Associated Families: 28

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	5
All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Alkalispirochaeta → Alkalispirochaeta odontotermitis	1
Not Available	11
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria → Synechococcales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → Desulfobacteraceae → unclassified Desulfobacteraceae → Desulfobacteraceae bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Cellvibrionales → Halieaceae → unclassified Halieaceae → gamma proteobacterium HIMB55	1
All Organisms → cellular organisms → Archaea → Euryarchaeota → Stenosarchaea group → Halobacteria → unclassified Halobacteria → Halobacteria archaeon	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius algarvensis Delta 1 endosymbiont	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Cyanobacteria/Melainabacteria group → Cyanobacteria	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): 37.4971
  • Long. (^o): -122.129
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001488	Metagenome / Metatranscriptome	686	Y
F004052	Metagenome / Metatranscriptome	455	Y
F005815	Metagenome / Metatranscriptome	389	Y
F010065	Metagenome	309	Y
F012678	Metagenome / Metatranscriptome	278	Y
F012874	Metagenome / Metatranscriptome	276	Y
F037736	Metagenome / Metatranscriptome	167	Y
F041201	Metagenome / Metatranscriptome	160	Y
F042016	Metagenome / Metatranscriptome	159	Y
F044506	Metagenome / Metatranscriptome	154	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209927_1002205	All Organisms → cellular organisms → Bacteria	2832
Ga0209927_1004146	All Organisms → cellular organisms → Bacteria	2131
Ga0209927_1006197	All Organisms → cellular organisms → Bacteria → Spirochaetes → Spirochaetia → Spirochaetales → Spirochaetaceae → Alkalispirochaeta → Alkalispirochaeta odontotermitis	1750
Ga0209927_1009503	Not Available	1401
Ga0209927_1010604	Not Available	1326
Ga0209927_1011141	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → unclassified Deltaproteobacteria → Olavius sp. associated proteobacterium Delta 1	1292
Ga0209927_1011341	All Organisms → cellular organisms → Bacteria → Proteobacteria	1280
Ga0209927_1012415	All Organisms → cellular organisms → Bacteria	1221
Ga0209927_1015427	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Desulfobacterales → unclassified Desulfobacterales → Desulfobacterales bacterium	1087
Ga0209927_1016347	Not Available	1053

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209927_1002205	Ga0209927_10022053	F084253	IKAAQEFAVRRTSVRRSRKPAENAEQDKKGHLWMETN
Ga0209927_1004146	Ga0209927_10041463	F088916	MPSTTLDNVKGSELPKTWADKINIIPDKTYTVIIQPQDERQTLQKIMSRISHTAKTRGMTPDILENILGEKIKHVL
Ga0209927_1006197	Ga0209927_10061973	F044506	GMMKQWNSGIVGSGMMQCWINGPATGGIEDKIKMVNILLKTNNPSFHPSIIPFPGKIRRPQKTSIFSVGCRNSETLNHMVIPIRAKLLVLMHWRIF
Ga0209927_1009503	Ga0209927_10095031	F037736	VPYRVQLDGLQILWLLANPLRTHGIGESGSKTITGWLLMSAADANHIWWLNTNPFTGLLLHLNSYRILHLPCGFLNMLCFLLLCHRQRNDNY
Ga0209927_1010604	Ga0209927_10106041	F058158	MDQVMKEKQKSHKTHFTKTEKDDTDIWNLPVKEREHILTQIAKARRTNRARTWIELIFMLSFIYYMLYDIYKDGDLDTIIKFLKI
Ga0209927_1011141	Ga0209927_10111411	F044506	MMEQWNSGIMGSGMVQCWINGPATSGIDDKIKMVNILLKTNIPSFHPSIIPFPGQIRKSQKTSIFSVGCRNSETYNYT
Ga0209927_1011341	Ga0209927_10113413	F054047	IFCWVSFLYPTYTPAIFVLSAKPDKMAEDRIIPKIIKM
Ga0209927_1012415	Ga0209927_10124151	F012874	KVRNSVMPAKAGIQNYLKTLDSRLRGNDVKGRFKTFYETINFEILN
Ga0209927_1015427	Ga0209927_10154271	F070127	MQKLNFSITINLSLTLKEDKASINIKNVDLIPAVVSLPVRLNSGDSIPQPKPQKKKTVHDIILQTAKNCVVDAGQNKFTGAKLFHLALLNHPGLKRNTFAAQVIAAAPNHSSHRHYPNQKDYFTYLGNGYYKLNQRYLKIREDQMLRPSDWVRDHVKRKYIDPAKKDGK
Ga0209927_1016347	Ga0209927_10163472	F092076	MFSHKIDKLQGIILIRASGTPTTITMIDHIQSVLNDPDYDPKYNSIIVLEENTHIAGVPTEKIELIRRVLDGYAQQRKGRHWAVVAPNERQEAFLKLNLELISPVKLNIRIFKSEEDALNWIKGR
Ga0209927_1020134	Ga0209927_10201343	F001488	MARLELTLNFPKSFQIKTFNVKSEKTLSPLAKLILQSVQFKHFYYVRDDISYLLKSNPVERDFLLQALYSTVISLQNNLSINFFDMWVYEIYINKVSTHNKFMNQKSQNLE
Ga0209927_1022786	Ga0209927_10227862	F081352	KISTITLACLLVLNLTAGAAVVVEHCPPLLGSSSPMDIDHCDGMLNFAFPMQGCCGECNDIFCDLIKNPLQDANAVNASPFQGSCYPFFLGTVDPIAESGTWVASSAPRYLFFAALAWSQIPLYIENLALII
Ga0209927_1026707	Ga0209927_10267071	F059980	CKMGFSGGFEQGKPETALPELRRFIPVNMKWVNPQNKFCYG
Ga0209927_1030024	Ga0209927_10300241	F099322	SVRMVLDGVSLIRYSDGAWCRVAPPSAHDLKDNWYRSSPSLLIRWLDAVGKVRPVKSNE
Ga0209927_1030134	Ga0209927_10301341	F070131	MIGKMLTKIIIVGVLAFCFLLQVDLAGGDNGINNQKKTKINVPMEIEIFFSSTPMLNEYTVLNIEIRALIDTPNTLIEIEIPRDGFEIISGSTQFNEDLSSGSTATYQLEVLPTAQGQYTIAASAKSEETDYIFGKREELYVNIGEEFSELSKSSFIPEIADTRSGAVKIEDFSEPPIQVLPDQKPQEDQEVLYFAAPGTGQIQVRGYW
Ga0209927_1032625	Ga0209927_10326251	F005815	MTMNTTRLTMYCTTGEAATVIDFIDTLRDALWETYGEQITRMHHEEHDDRIRDSNQCEFEFNDEIPF
Ga0209927_1034777	Ga0209927_10347771	F072360	LRSGMNLKPNILKSFSRRTLWIFFILFVSVSFSTSGVIANSCQGGADCLNCAAAAHPHLPGMDVEMVNQGCQSTEQNRSCGFEAGHSADDFDRIATTVTSGTHSYSGIFSIASDESDQAHLHLEFLTQFQYPDRGELTPIFLLNQSLLC
Ga0209927_1035133	Ga0209927_10351332	F087210	MRFLIAALAFAGAETALAHTPDTGFLSNFGHQLTSLHHSPAAMLLGVLVLVLMLVAVRKLTTR
Ga0209927_1035604	Ga0209927_10356041	F070125	VTTAEQRRQWIEALHAYRDDSERLFGLVASLANLLDRKLIIETMESVLGIAAVHDGDCIIFDDLAIRFGSDDRVKSVFRTIDGL
Ga0209927_1036790	Ga0209927_10367902	F054047	IGQGLFVGWVEHPGIFCWVSFLNPTYVPTIFLLSAKPNKMAEDRTVPDNFKRWEWN
Ga0209927_1038061	Ga0209927_10380611	F042016	MAPERKLYQKIKKHFNEFSLIRLENLSLSGTPDLLVY
Ga0209927_1042786	Ga0209927_10427861	F044506	MQCWINGSATGGSDDNIKMVNILLKTNIPSFHPSIIPFPGEISKSQKTSIFSVGCRNSETFNYLLFSVV
Ga0209927_1043086	Ga0209927_10430861	F050381	MKKILVIIAIILIPTIAFANFSIQLDNNTGKKMFYLLYWVDHTYDWPHPFNLAGGELKSSESIDLRSDYRNGKYYVVWSDNGDWQNKVMLDVYDDVKSVIVTPIKSSMTK
Ga0209927_1043259	Ga0209927_10432592	F004052	IRLEHLSMRTPTTIAYVTLAVLLASCDQRHPASDIDPELGLACFESHRASLPPGTQYEGIEKLDGTRLTIRIMNGVEVVTMDCTLNPDGTLK
Ga0209927_1047553	Ga0209927_10475531	F103280	MLTTMKKLVAFLTISSIWLLPVILPEIQAQQTAAPPSTTASSPAITIEELKSRRMAIESMTDIDATVKTDSLKYIDQAISHAELALSTNHKANEFLQLIQTAPERLKILQAELKKSFMAPEKVEARAQQMSTLKLEQRLRQKKAE
Ga0209927_1051600	Ga0209927_10516001	F010065	MRGESGISFTGLYICGAISLIMLVLKLSVIDTWSWWRVLLPLGLFVGFNVTNIVVAFIYLSFAHIPERPDGDEADILEPHTINVHYVAAMLFFVVFGDNMVRWIEGSETSHWFWLFSGKDEALAVFGSLSVLALFSYWSRLGRVLKAAG
Ga0209927_1054634	Ga0209927_10546342	F057781	MKLPDLQMLAHWLDPALVATLETRRRKKKEWHRRRKLATLQTLWLMLA
Ga0209927_1055684	Ga0209927_10556841	F105202	QLIQSDLHLDIQQRAHLYLASLYFSPMNPNRDYKLALKHLETYAIFDPDFVNGVDPRLLLAAIIELERLSAIADAQSKAIQALNQEVEILKIQASASRGSKYDTQEANRMLKKRIGRLQNKIRNLEASNAQLNKTIEMLSKLDSSLEEKRSNFIKMDSGKVE
Ga0209927_1058458	Ga0209927_10584583	F012678	MLNQHSIEEIADIHNLLRDIKEEYNEGIKPILIKNSPKLFKNPHTVPK
Ga0209927_1059441	Ga0209927_10594411	F061862	KGKLNMQDDETMWYENDAPVREYLDRELPRKTAGAEKDPKTVRFSWFKIMKKSFHIK
Ga0209927_1060378	Ga0209927_10603782	F041201	RILVQDRGGSEFQTGGILLYVEDLKRGTNKDIGPKDIFEMGSSYLF